From 391aabe280bbd2b13fd3bd82b850ba5656b6d572 Mon Sep 17 00:00:00 2001
From: Jenny Medina <medina.stsci@gmail.com>
Date: Thu, 31 Oct 2024 14:30:32 -0400
Subject: [PATCH 01/47] .

---
 poetry.lock    | 1214 ++++++++++++++++++++++++------------------------
 pyproject.toml |    2 +-
 2 files changed, 618 insertions(+), 598 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 0b87e58a1..4fcc24a14 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -35,13 +35,13 @@ dev = ["black", "docutils", "flake8", "ipython", "m2r", "mistune (<2.0.0)", "pyt
 
 [[package]]
 name = "anyio"
-version = "4.5.0"
+version = "4.6.2.post1"
 description = "High level compatibility layer for multiple asynchronous event loop implementations"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "anyio-4.5.0-py3-none-any.whl", hash = "sha256:fdeb095b7cc5a5563175eedd926ec4ae55413bb4be5770c424af0ba46ccb4a78"},
-    {file = "anyio-4.5.0.tar.gz", hash = "sha256:c5a275fe5ca0afd788001f58fca1e69e29ce706d746e317d660e21f70c530ef9"},
+    {file = "anyio-4.6.2.post1-py3-none-any.whl", hash = "sha256:6d170c36fba3bdd840c73d3868c1e777e33676a69c3a72cf0a0d5d6d8009b61d"},
+    {file = "anyio-4.6.2.post1.tar.gz", hash = "sha256:4c8bc31ccdb51c7f7bd251f51c609e038d63e34219b44aa86e47576389880b4c"},
 ]
 
 [package.dependencies]
@@ -52,7 +52,7 @@ typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""}
 
 [package.extras]
 doc = ["Sphinx (>=7.4,<8.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
-test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.21.0b1)"]
+test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "truststore (>=0.9.1)", "uvloop (>=0.21.0b1)"]
 trio = ["trio (>=0.26.1)"]
 
 [[package]]
@@ -319,21 +319,20 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "bleach"
-version = "6.1.0"
+version = "6.2.0"
 description = "An easy safelist-based HTML-sanitizing tool."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "bleach-6.1.0-py3-none-any.whl", hash = "sha256:3225f354cfc436b9789c66c4ee030194bee0568fbf9cbdad3bc8b5c26c5f12b6"},
-    {file = "bleach-6.1.0.tar.gz", hash = "sha256:0a31f1837963c41d46bbf1331b8778e1308ea0791db03cc4e7357b97cf42a8fe"},
+    {file = "bleach-6.2.0-py3-none-any.whl", hash = "sha256:117d9c6097a7c3d22fd578fcd8d35ff1e125df6736f554da4e432fdd63f31e5e"},
+    {file = "bleach-6.2.0.tar.gz", hash = "sha256:123e894118b8a599fd80d3ec1a6d4cc7ce4e5882b1317a7e1ba69b56e95f991f"},
 ]
 
 [package.dependencies]
-six = ">=1.9.0"
 webencodings = "*"
 
 [package.extras]
-css = ["tinycss2 (>=1.1.0,<1.3)"]
+css = ["tinycss2 (>=1.1.0,<1.5)"]
 
 [[package]]
 name = "cachetools"
@@ -449,101 +448,116 @@ files = [
 
 [[package]]
 name = "charset-normalizer"
-version = "3.3.2"
+version = "3.4.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
 python-versions = ">=3.7.0"
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 [[package]]
@@ -888,13 +896,13 @@ dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"]
 
 [[package]]
 name = "dill"
-version = "0.3.8"
+version = "0.3.9"
 description = "serialize all of Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.extras]
@@ -903,13 +911,13 @@ profile = ["gprof2dot (>=2022.7.29)"]
 
 [[package]]
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-version = "0.3.8"
+version = "0.3.9"
 description = "Distribution utilities"
 optional = false
 python-versions = "*"
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 [[package]]
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 description = "An implementation of lxml.xmlfile for the standard library"
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 [[package]]
@@ -1083,13 +1091,13 @@ files = [
 
 [[package]]
 name = "google-api-core"
-version = "2.20.0"
+version = "2.22.0"
 description = "Google API client core library"
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 [package.dependencies]
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 requests = ">=2.18.0,<3.0.0.dev0"
 
 [package.extras]
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 grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"]
@@ -1287,61 +1296,70 @@ vertica = ["sqlalchemy (>=1.3.18,<2.0.0)", "sqlalchemy-vertica-python (>=0.5.10)
 
 [[package]]
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-version = "1.66.1"
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 python-versions = ">=3.8"
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 [[package]]
 name = "marshmallow"
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+version = "3.23.0"
 description = "A lightweight library for converting complex datatypes to and from native Python datatypes."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
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 [package.dependencies]
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+dev = ["marshmallow[tests]", "pre-commit (>=3.5,<5.0)", "tox"]
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+tests = ["pytest", "simplejson"]
 
 [[package]]
 name = "matplotlib-inline"
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 description = "Optional static typing for Python"
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 ]
 
 [package.dependencies]
@@ -2198,6 +2222,7 @@ typing-extensions = ">=4.6.0"
 
 [package.extras]
 dmypy = ["psutil (>=4.0)"]
+faster-cache = ["orjson"]
 install-types = ["pip"]
 mypyc = ["setuptools (>=50)"]
 reports = ["lxml"]
@@ -2979,13 +3004,13 @@ twisted = ["twisted"]
 
 [[package]]
 name = "prompt-toolkit"
-version = "3.0.47"
+version = "3.0.48"
 description = "Library for building powerful interactive command lines in Python"
 optional = false
 python-versions = ">=3.7.0"
 files = [
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 ]
 
 [package.dependencies]
@@ -2993,13 +3018,13 @@ wcwidth = "*"
 
 [[package]]
 name = "proto-plus"
-version = "1.24.0"
+version = "1.25.0"
 description = "Beautiful, Pythonic protocol buffers."
 optional = false
 python-versions = ">=3.7"
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 ]
 
 [[package]]
@@ -4212,27 +4232,27 @@ files = [
 
 [[package]]
 name = "sphinx"
-version = "7.4.7"
+version = "7.3.7"
 description = "Python documentation generator"
 optional = false
 python-versions = ">=3.9"
 files = [
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+    {file = "sphinx-7.3.7-py3-none-any.whl", hash = "sha256:413f75440be4cacf328f580b4274ada4565fb2187d696a84970c23f77b64d8c3"},
+    {file = "sphinx-7.3.7.tar.gz", hash = "sha256:a4a7db75ed37531c05002d56ed6948d4c42f473a36f46e1382b0bd76ca9627bc"},
 ]
 
 [package.dependencies]
 alabaster = ">=0.7.14,<0.8.0"
-babel = ">=2.13"
-colorama = {version = ">=0.4.6", markers = "sys_platform == \"win32\""}
-docutils = ">=0.20,<0.22"
+babel = ">=2.9"
+colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
+docutils = ">=0.18.1,<0.22"
 imagesize = ">=1.3"
-importlib-metadata = {version = ">=6.0", markers = "python_version < \"3.10\""}
-Jinja2 = ">=3.1"
-packaging = ">=23.0"
-Pygments = ">=2.17"
-requests = ">=2.30.0"
-snowballstemmer = ">=2.2"
+importlib-metadata = {version = ">=4.8", markers = "python_version < \"3.10\""}
+Jinja2 = ">=3.0"
+packaging = ">=21.0"
+Pygments = ">=2.14"
+requests = ">=2.25.0"
+snowballstemmer = ">=2.0"
 sphinxcontrib-applehelp = "*"
 sphinxcontrib-devhelp = "*"
 sphinxcontrib-htmlhelp = ">=2.0.0"
@@ -4243,8 +4263,8 @@ tomli = {version = ">=2", markers = "python_version < \"3.11\""}
 
 [package.extras]
 docs = ["sphinxcontrib-websupport"]
-lint = ["flake8 (>=6.0)", "importlib-metadata (>=6.0)", "mypy (==1.10.1)", "pytest (>=6.0)", "ruff (==0.5.2)", "sphinx-lint (>=0.9)", "tomli (>=2)", "types-docutils (==0.21.0.20240711)", "types-requests (>=2.30.0)"]
-test = ["cython (>=3.0)", "defusedxml (>=0.7.1)", "pytest (>=8.0)", "setuptools (>=70.0)", "typing_extensions (>=4.9)"]
+lint = ["flake8 (>=3.5.0)", "importlib_metadata", "mypy (==1.9.0)", "pytest (>=6.0)", "ruff (==0.3.7)", "sphinx-lint", "tomli", "types-docutils", "types-requests"]
+test = ["cython (>=3.0)", "defusedxml (>=0.7.1)", "pytest (>=6.0)", "setuptools (>=67.0)"]
 
 [[package]]
 name = "sphinx-click"
@@ -4464,13 +4484,13 @@ typing = ["mypy (>=1.6,<2.0)", "traitlets (>=5.11.1)"]
 
 [[package]]
 name = "tinycss2"
-version = "1.3.0"
+version = "1.4.0"
 description = "A tiny CSS parser"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "tinycss2-1.3.0-py3-none-any.whl", hash = "sha256:54a8dbdffb334d536851be0226030e9505965bb2f30f21a4a82c55fb2a80fae7"},
-    {file = "tinycss2-1.3.0.tar.gz", hash = "sha256:152f9acabd296a8375fbca5b84c961ff95971fcfc32e79550c8df8e29118c54d"},
+    {file = "tinycss2-1.4.0-py3-none-any.whl", hash = "sha256:3a49cf47b7675da0b15d0c6e1df8df4ebd96e9394bb905a5775adb0d884c5289"},
+    {file = "tinycss2-1.4.0.tar.gz", hash = "sha256:10c0972f6fc0fbee87c3edb76549357415e94548c1ae10ebccdea16fb404a9b7"},
 ]
 
 [package.dependencies]
@@ -4493,13 +4513,13 @@ files = [
 
 [[package]]
 name = "tomli"
-version = "2.0.1"
+version = "2.0.2"
 description = "A lil' TOML parser"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
-    {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
+    {file = "tomli-2.0.2-py3-none-any.whl", hash = "sha256:2ebe24485c53d303f690b0ec092806a085f07af5a5aa1464f3931eec36caaa38"},
+    {file = "tomli-2.0.2.tar.gz", hash = "sha256:d46d457a85337051c36524bc5349dd91b1877838e2979ac5ced3e710ed8a60ed"},
 ]
 
 [[package]]
@@ -4515,13 +4535,13 @@ files = [
 
 [[package]]
 name = "toolz"
-version = "0.12.1"
+version = "1.0.0"
 description = "List processing tools and functional utilities"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "toolz-0.12.1-py3-none-any.whl", hash = "sha256:d22731364c07d72eea0a0ad45bafb2c2937ab6fd38a3507bf55eae8744aa7d85"},
-    {file = "toolz-0.12.1.tar.gz", hash = "sha256:ecca342664893f177a13dac0e6b41cbd8ac25a358e5f215316d43e2100224f4d"},
+    {file = "toolz-1.0.0-py3-none-any.whl", hash = "sha256:292c8f1c4e7516bf9086f8850935c799a874039c8bcf959d47b600e4c44a6236"},
+    {file = "toolz-1.0.0.tar.gz", hash = "sha256:2c86e3d9a04798ac556793bced838816296a2f085017664e4995cb40a1047a02"},
 ]
 
 [[package]]
@@ -4546,13 +4566,13 @@ files = [
 
 [[package]]
 name = "tqdm"
-version = "4.66.5"
+version = "4.66.6"
 description = "Fast, Extensible Progress Meter"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "tqdm-4.66.5-py3-none-any.whl", hash = "sha256:90279a3770753eafc9194a0364852159802111925aa30eb3f9d85b0e805ac7cd"},
-    {file = "tqdm-4.66.5.tar.gz", hash = "sha256:e1020aef2e5096702d8a025ac7d16b1577279c9d63f8375b63083e9a5f0fcbad"},
+    {file = "tqdm-4.66.6-py3-none-any.whl", hash = "sha256:223e8b5359c2efc4b30555531f09e9f2f3589bcd7fdd389271191031b49b7a63"},
+    {file = "tqdm-4.66.6.tar.gz", hash = "sha256:4bdd694238bef1485ce839d67967ab50af8f9272aab687c0d7702a01da0be090"},
 ]
 
 [package.dependencies]
@@ -4581,13 +4601,13 @@ test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,
 
 [[package]]
 name = "types-python-dateutil"
-version = "2.9.0.20240906"
+version = "2.9.0.20241003"
 description = "Typing stubs for python-dateutil"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "types-python-dateutil-2.9.0.20240906.tar.gz", hash = "sha256:9706c3b68284c25adffc47319ecc7947e5bb86b3773f843c73906fd598bc176e"},
-    {file = "types_python_dateutil-2.9.0.20240906-py3-none-any.whl", hash = "sha256:27c8cc2d058ccb14946eebcaaa503088f4f6dbc4fb6093d3d456a49aef2753f6"},
+    {file = "types-python-dateutil-2.9.0.20241003.tar.gz", hash = "sha256:58cb85449b2a56d6684e41aeefb4c4280631246a0da1a719bdbe6f3fb0317446"},
+    {file = "types_python_dateutil-2.9.0.20241003-py3-none-any.whl", hash = "sha256:250e1d8e80e7bbc3a6c99b907762711d1a1cdd00e978ad39cb5940f6f0a87f3d"},
 ]
 
 [[package]]
@@ -4618,13 +4638,13 @@ typing-extensions = ">=3.7.4"
 
 [[package]]
 name = "tzdata"
-version = "2024.1"
+version = "2024.2"
 description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
 files = [
-    {file = "tzdata-2024.1-py2.py3-none-any.whl", hash = "sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252"},
-    {file = "tzdata-2024.1.tar.gz", hash = "sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd"},
+    {file = "tzdata-2024.2-py2.py3-none-any.whl", hash = "sha256:a48093786cdcde33cad18c2555e8532f34422074448fbc874186f0abd79565cd"},
+    {file = "tzdata-2024.2.tar.gz", hash = "sha256:7d85cc416e9382e69095b7bdf4afd9e3880418a2413feec7069d533d6b4e31cc"},
 ]
 
 [[package]]
@@ -4687,23 +4707,23 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
 [[package]]
 name = "uwsgi"
-version = "2.0.26"
+version = "2.0.28"
 description = "The uWSGI server"
 optional = true
 python-versions = "*"
 files = [
-    {file = "uwsgi-2.0.26.tar.gz", hash = "sha256:86e6bfcd4dc20529665f5b7777193cdc48622fb2c59f0a7f1e3dc32b3882e7f9"},
+    {file = "uwsgi-2.0.28.tar.gz", hash = "sha256:79ca1891ef2df14508ab0471ee8c0eb94bd2d51d03f32f90c4bbe557ab1e99d0"},
 ]
 
 [[package]]
 name = "virtualenv"
-version = "20.26.5"
+version = "20.27.1"
 description = "Virtual Python Environment builder"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "virtualenv-20.26.5-py3-none-any.whl", hash = "sha256:4f3ac17b81fba3ce3bd6f4ead2749a72da5929c01774948e243db9ba41df4ff6"},
-    {file = "virtualenv-20.26.5.tar.gz", hash = "sha256:ce489cac131aa58f4b25e321d6d186171f78e6cb13fafbf32a840cee67733ff4"},
+    {file = "virtualenv-20.27.1-py3-none-any.whl", hash = "sha256:f11f1b8a29525562925f745563bfd48b189450f61fb34c4f9cc79dd5aa32a1f4"},
+    {file = "virtualenv-20.27.1.tar.gz", hash = "sha256:142c6be10212543b32c6c45d3d3893dff89112cc588b7d0879ae5a1ec03a47ba"},
 ]
 
 [package.dependencies]
@@ -4901,4 +4921,4 @@ aws = ["uWSGI"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9.0,<3.11"
-content-hash = "e72a6816f0534115e5b8cd1c0e55e1e35778e4a059caebfc0b7c2bae96c65a59"
+content-hash = "778e34917bfa185db91ec0873f29e959466a52576d213cf59ebcc721c73f3751"
diff --git a/pyproject.toml b/pyproject.toml
index cccda5718..7cc316db1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -37,7 +37,7 @@ schematic = "schematic.__main__:main"
 
 [tool.poetry.dependencies]
 python = ">=3.9.0,<3.11"
-
+sphinx = "7.3.7"
 click = "^8.0.0"
 click-log = "^0.4.0"
 google-api-python-client = "^2.0.0"

From 3d1fecbfa8d57ca530ec7f53f1f5b75e0ec74334 Mon Sep 17 00:00:00 2001
From: Jenny Medina <medina.stsci@gmail.com>
Date: Thu, 31 Oct 2024 14:48:23 -0400
Subject: [PATCH 02/47] Also lock sphinx-click

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 7cc316db1..79755c50b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -58,7 +58,7 @@ synapseclient = "4.5.1"
 tenacity = "^8.0.1"
 toml = "^0.10.2"
 great-expectations = "^0.15.0"
-sphinx-click = "^4.0.0"
+sphinx-click = "4.4.0"
 itsdangerous = "^2.0.0"
 openpyxl = "^3.0.9"
 "backports.zoneinfo" = {markers = "python_version < \"3.9\"", version = "^0.2.1"}

From b8d6f6cb8995c7bf1e6a20d6a16012a2be8b0b21 Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Fri, 1 Nov 2024 10:31:13 -0700
Subject: [PATCH 03/47] Update README.md

---
 README.md | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 03cd5118e..6c1f9002f 100644
--- a/README.md
+++ b/README.md
@@ -486,10 +486,16 @@ docker run -v %cd%:/schematic \
 
 Main contributors and developers:
 
+- [Robert Allaway](https://github.com/allaway)
+- [Gianna Jordan](https://github.com/giajordan)
+- [Lingling Peng](https://github.com/linglp)
+- [Bryan Fauble](https://github.com/BryanFauble)
+
+
+## Alumni
 - [Milen Nikolov](https://github.com/milen-sage)
 - [Mialy DeFelice](https://github.com/mialy-defelice)
 - [Sujay Patil](https://github.com/sujaypatil96)
 - [Bruno Grande](https://github.com/BrunoGrandePhD)
-- [Robert Allaway](https://github.com/allaway)
-- [Gianna Jordan](https://github.com/giajordan)
-- [Lingling Peng](https://github.com/linglp)
+
+

From 97abaaab9d7918e8f2e09bc1207fae09b88fb055 Mon Sep 17 00:00:00 2001
From: Jenny Medina <medina.stsci@gmail.com>
Date: Fri, 1 Nov 2024 16:27:43 -0400
Subject: [PATCH 04/47] move documentation libraries to doc group. update
 README. write new lock file.

---
 README.md      |  9 +++++++--
 poetry.lock    | 10 +++++-----
 pyproject.toml | 10 +++++-----
 3 files changed, 17 insertions(+), 12 deletions(-)

diff --git a/README.md b/README.md
index 03cd5118e..0e608c358 100644
--- a/README.md
+++ b/README.md
@@ -270,12 +270,17 @@ poetry debug info
 
 Before you begin, make sure you are in the latest `develop` of the repository.
 
-The following command will install the dependencies based on what we specify in the `poetry.lock` file of this repository. If this step is taking a long time, try to go back to Step 2 and check your version of `poetry`. Alternatively, you can try deleting the lock file and regenerate it by doing `poetry install` (Please note this method should be used as a last resort because this would force other developers to change their development environment)
+The following command will install the dependencies based on what we specify in the `poetry.lock` file of this repository (which is generated from the libraries listed in the `pyproject.toml` file). If this step is taking a long time, try to go back to Step 2 and check your version of `poetry`. Alternatively, you can try deleting the lock file and regenerate it by doing `poetry lock` (Please note this method should be used as a last resort because this would force other developers to change their development environment).
 
 ```
-poetry install --all-extras
+poetry install --dev,doc
 ```
 
+This command will install:
+* The main dependencies required for running the package.
+* Development dependencies for testing, linting, and code formatting.
+* Documentation dependencies such as `sphinx` for building and maintaining documentation.
+
 ### 5. Set up configuration files
 
 The following section will walk through setting up your configuration files with your credentials to allow for communication between `schematic` and the Synapse API.
diff --git a/poetry.lock b/poetry.lock
index 4fcc24a14..ef1518720 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2121,13 +2121,13 @@ files = [
 
 [[package]]
 name = "marshmallow"
-version = "3.23.0"
+version = "3.23.1"
 description = "A lightweight library for converting complex datatypes to and from native Python datatypes."
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "marshmallow-3.23.0-py3-none-any.whl", hash = "sha256:82f20a2397834fe6d9611b241f2f7e7b680ed89c49f84728a1ad937be6b4bdf4"},
-    {file = "marshmallow-3.23.0.tar.gz", hash = "sha256:98d8827a9f10c03d44ead298d2e99c6aea8197df18ccfad360dae7f89a50da2e"},
+    {file = "marshmallow-3.23.1-py3-none-any.whl", hash = "sha256:fece2eb2c941180ea1b7fcbd4a83c51bfdd50093fdd3ad2585ee5e1df2508491"},
+    {file = "marshmallow-3.23.1.tar.gz", hash = "sha256:3a8dfda6edd8dcdbf216c0ede1d1e78d230a6dc9c5a088f58c4083b974a0d468"},
 ]
 
 [package.dependencies]
@@ -2135,7 +2135,7 @@ packaging = ">=17.0"
 
 [package.extras]
 dev = ["marshmallow[tests]", "pre-commit (>=3.5,<5.0)", "tox"]
-docs = ["alabaster (==1.0.0)", "autodocsumm (==0.2.13)", "sphinx (==8.1.3)", "sphinx-issues (==5.0.0)", "sphinx-version-warning (==1.1.2)"]
+docs = ["alabaster (==1.0.0)", "autodocsumm (==0.2.14)", "sphinx (==8.1.3)", "sphinx-issues (==5.0.0)", "sphinx-version-warning (==1.1.2)"]
 tests = ["pytest", "simplejson"]
 
 [[package]]
@@ -4921,4 +4921,4 @@ aws = ["uWSGI"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9.0,<3.11"
-content-hash = "778e34917bfa185db91ec0873f29e959466a52576d213cf59ebcc721c73f3751"
+content-hash = "efc1087459d60c13452c8cb50661294face689bafabb84cb83604441337828f2"
diff --git a/pyproject.toml b/pyproject.toml
index 79755c50b..5dcb7afa8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -34,10 +34,8 @@ packages = [
 [tool.poetry.scripts]
 schematic = "schematic.__main__:main"
 
-
 [tool.poetry.dependencies]
 python = ">=3.9.0,<3.11"
-sphinx = "7.3.7"
 click = "^8.0.0"
 click-log = "^0.4.0"
 google-api-python-client = "^2.0.0"
@@ -58,11 +56,9 @@ synapseclient = "4.5.1"
 tenacity = "^8.0.1"
 toml = "^0.10.2"
 great-expectations = "^0.15.0"
-sphinx-click = "4.4.0"
 itsdangerous = "^2.0.0"
 openpyxl = "^3.0.9"
 "backports.zoneinfo" = {markers = "python_version < \"3.9\"", version = "^0.2.1"}
-pdoc = "^14.0.0"
 dateparser = "^1.1.4"
 pandarallel = "^1.6.4"
 pyopenssl = {version = "^23.0.0", optional = true}
@@ -84,7 +80,6 @@ opentelemetry-instrumentation-flask = {version=">=0.48b0 ", optional = true}
 api = ["connexion", "Flask", "Flask-Cors", "Jinja2", "pyopenssl", "opentelemetry-api", "opentelemetry-sdk", "opentelemetry-exporter-otlp-proto-grpc", "opentelemetry-instrumentation-flask"]
 aws = ["uWSGI"]
 
-
 [tool.poetry.group.dev.dependencies]
 pytest = "^8.0.0"
 pytest-cov = "^4.0.0"
@@ -99,6 +94,11 @@ pylint = "^2.16.1"
 pytest-xdist = "^3.5.0"
 pre-commit = "^3.6.2"
 
+[tool.poetry.group.doc.dependencies]
+pdoc = "^14.0.0"
+sphinx = "7.3.7"
+sphinx-click = "4.4.0"
+
 [tool.black]
 line-length = 88
 include = '\.pyi?$'

From e5cfa79c2e02b9660497c6fbbaf31bf3cbc2010d Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Fri, 1 Nov 2024 20:03:13 -0700
Subject: [PATCH 05/47] Update copyright

---
 LICENSE   |  2 +-
 README.md | 15 ++++++++++-----
 2 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/LICENSE b/LICENSE
index 32686c9a9..b41205876 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021 Sage Bionetworks
+Copyright (c) 2024 Sage Bionetworks
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
diff --git a/README.md b/README.md
index 6c1f9002f..a40eeea52 100644
--- a/README.md
+++ b/README.md
@@ -484,18 +484,23 @@ docker run -v %cd%:/schematic \
 
 # Contributors
 
-Main contributors and developers:
 
-- [Robert Allaway](https://github.com/allaway)
+Sage main contributors and developers:
+
 - [Gianna Jordan](https://github.com/giajordan)
 - [Lingling Peng](https://github.com/linglp)
 - [Bryan Fauble](https://github.com/BryanFauble)
-
+- [Andrew Lamb](https://github.com/andrewelamb)
+- [Brad Macdonald](https://github.com/BWMac)
+- [Milen Nikolov](https://github.com/milen-sage)
 
 ## Alumni
-- [Milen Nikolov](https://github.com/milen-sage)
 - [Mialy DeFelice](https://github.com/mialy-defelice)
 - [Sujay Patil](https://github.com/sujaypatil96)
 - [Bruno Grande](https://github.com/BrunoGrandePhD)
+- [Jason Hwee](https://github.com/hweej)
+- [Xengie Doan](https://github.com/xdoan)
+- [James Eddy](https://github.com/jaeddy)
+- [Yooree Chae](https://github.com/ychae)
 
-
+See all [contributors](https://github.com/Sage-Bionetworks/schematic/graphs/contributors)

From 7e83244607cd3cd6af619658b5f1dc54f68f94d6 Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Fri, 1 Nov 2024 20:09:52 -0700
Subject: [PATCH 06/47] update version and copyright

---
 docs/source/conf.py | 2 +-
 pyproject.toml      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 1cd10df3d..3c6728a93 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -25,7 +25,7 @@
 
 toml_metadata = _parse_toml(toml_file_path)
 project = toml_metadata["name"]
-copyright = "2022, Sage Bionetworks"
+copyright = "2024, Sage Bionetworks"
 
 author = toml_metadata["authors"]
 
diff --git a/pyproject.toml b/pyproject.toml
index 5dcb7afa8..d415c661c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "schematicpy"
-version = "23.11.1"
+version = "24.11.1"
 description = "Package for biomedical data model and metadata ingress management"
 authors = [
     "Milen Nikolov <milen.nikolov@sagebase.org>",

From de14646ee64140fc0691f095278cffc46828c001 Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Fri, 1 Nov 2024 21:01:37 -0700
Subject: [PATCH 07/47] Add in documentation

---
 docs/source/asset_store.rst   |   2 +
 docs/source/cli_reference.rst |  32 ++++
 docs/source/conf.py           |  14 +-
 docs/source/generate.rst      |   4 +
 docs/source/index.rst         |  60 ++++++-
 docs/source/installation.rst  | 319 ++++++++++++++++++++++++++++++++++
 docs/source/submit.rst        |  12 ++
 docs/source/validate.rst      |  10 ++
 8 files changed, 449 insertions(+), 4 deletions(-)
 create mode 100644 docs/source/asset_store.rst
 create mode 100644 docs/source/generate.rst
 create mode 100644 docs/source/installation.rst
 create mode 100644 docs/source/submit.rst
 create mode 100644 docs/source/validate.rst

diff --git a/docs/source/asset_store.rst b/docs/source/asset_store.rst
new file mode 100644
index 000000000..0b6535e79
--- /dev/null
+++ b/docs/source/asset_store.rst
@@ -0,0 +1,2 @@
+Setting up your asset store
+===========================
diff --git a/docs/source/cli_reference.rst b/docs/source/cli_reference.rst
index a2bd78cd2..0acb08627 100644
--- a/docs/source/cli_reference.rst
+++ b/docs/source/cli_reference.rst
@@ -2,6 +2,38 @@
 CLI Reference
 =============
 
+
+1. Generate a new manifest as a Google Sheet
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. code-block:: shell
+
+   schematic manifest -c /path/to/config.yml get -dt <your data type> -s
+
+2. Grab an existing manifest from Synapse
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. code-block:: shell
+
+   schematic manifest -c /path/to/config.yml get -dt <your data type> -d <your synapse dataset folder id> -s
+
+3. Validate a manifest
+~~~~~~~~~~~~~~~~~~~~~~
+
+.. code-block:: shell
+
+   schematic model -c /path/to/config.yml validate -dt <your data type> -mp <your csv manifest path>
+
+4. Submit a manifest as a file
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. code-block:: shell
+
+   schematic model -c /path/to/config.yml submit -mp <your csv manifest path> -d <your synapse dataset folder id> -vc <your data type> -mrt file_only
+
+
+
+
 .. click:: schematic.__main__:main
   :prog: schematic
   :nested: full
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 3c6728a93..1ca33992d 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -12,6 +12,9 @@
 #
 import os
 import sys
+
+import sphinx_rtd_theme
+
 file_dir = os.path.dirname(__file__) 
 sys.path.append(file_dir)
 from utils import _parse_toml
@@ -33,12 +36,13 @@
 release = toml_metadata["version"]
 
 
+
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ["sphinx_click"]
+extensions = ["sphinx_click", "sphinx_rtd_theme"]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
@@ -55,15 +59,21 @@
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = []
 
+# The master toctree document.
+master_doc = "index"
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = "alabaster"
+html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
+
+html_theme_options = {
+    'collapse_navigation': False,
+}
diff --git a/docs/source/generate.rst b/docs/source/generate.rst
new file mode 100644
index 000000000..91a9cb7f6
--- /dev/null
+++ b/docs/source/generate.rst
@@ -0,0 +1,4 @@
+Generate
+========
+
+Provides a manifest template for users for a particular project or data type. If a project with annotations already exists, a semi-filled-out template is provided to the user so that they do not start from scratch. If there are no existing annotations, an empty manifest template is provided.
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 444807c0f..ce360acd2 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -6,7 +6,63 @@
 Welcome to Schematic's documentation!
 =====================================
 
+**SCHEMATIC** is an acronym for *Schema Engine for Manifest Ingress and Curation*. The Python-based infrastructure provides a *novel* schema-based, metadata ingress ecosystem, which is meant to streamline the process of biomedical dataset annotation, metadata validation, and submission to a data repository for various data contributors.
+
+Schematic tackles these goals:
+
+- “Ensure the highest quality structured data or metadata be contributed to Synapse BEFORE it lands in Synapse”
+- “Add accountability to data contributors for the data they upload”
+- “Visualize data models and their relationships with each other”
+
+The usage of JSON-LD
+--------------------
+
+The usage of JSON-LD to capture our data models extends beyond the creation, validation, and submission of annotations/manifests into Synapse. It can create relationships between different data models and, in the future, drive transformation of data from one data model to another. Visualization of these data models and their relationships is also possible (see *Schema Visualization - Design & Platform*), which allows the community to see the depth of connections between all the data uploaded into Synapse. As with all products, we must start somewhere.
+
+
+The following are the three main endpoints that assist with the high-level goals outlined above, with additional goals to come.
+
+1. Manifest Generation
+----------------------
+
+Provides a manifest template for users for a particular project or data type. If a project with annotations already exists, a semi-filled-out template is provided to the user so that they do not start from scratch. If there are no existing annotations, an empty manifest template is provided.
+
+2. Validate Manifest
+--------------------
+
+Given a filled-out manifest:
+
+- The manifest is validated against the JSON-LD schema as it maps to GX rules.
+- A ``jsonschema`` is generated from the data model. The data model can be in CSV, JSON-LD format, as input formats are decoupled from the internal data model representation within Schematic.
+- A set of validation rules is defined in the data model. Some validation rules are implemented via GX; others are custom Python code. All validation rules have the same interface.
+- Certain GX rules require looping through all projects a user has access to, or a specified scope of projects, to find other projects with manifests.
+- Validation results are provided before the manifest file is uploaded into Synapse.
+
+3. Submit Manifest
+------------------
+
+- Validates the manifest. If errors are present, the manifest is not stored.
+- If valid:
+  - Stores the manifest in Synapse.
+  - Uploads the manifest to a view, updating file views with annotations as follows:
+
+      - **Store manifest only**
+      - **Store manifest and annotations** (to update a file view)
+      - **Store manifest and update a corresponding Synapse table**
+
+4. Visualize Data Models
+-------------------------
+
+This endpoint allows you to visulize your data models and their relationships with each other.
+
+
 .. toctree::
    :maxdepth: 1
-   
-   cli_reference
\ No newline at end of file
+   :hidden:
+
+   installation
+   asset_store
+   generate
+   validate
+   submit
+   cli_reference
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
new file mode 100644
index 000000000..d07414cae
--- /dev/null
+++ b/docs/source/installation.rst
@@ -0,0 +1,319 @@
+Installation
+============
+
+Installation Requirements
+-------------------------
+
+- Your installed python version must be 3.9.0 ≤ version < 3.11.0
+- You need to be a registered and certified user on `synapse.org <https://www.synapse.org/>`_
+
+.. note::
+   To create Google Sheets files from Schematic, please follow our credential policy for Google credentials. You can find a detailed tutorial `Google Credentials Guide <https://scribehow.com/shared/Get_Credentials_for_Google_Drive_and_Google_Sheets_APIs_to_use_with_schematicpy__yqfcJz_rQVeyTcg0KQCINA>`_.  
+   If you're using ``config.yml``, make sure to specify the path to ``schematic_service_account_creds.json`` (see the ``google_sheets > service_account_creds`` section for more information).
+
+Installation Guide For: Users
+-----------------------------
+
+The instructions below assume you have already installed `python <https://www.python.org/downloads/>`_, with the release version meeting the constraints set in the `Installation Requirements`_ section, and do not have a Python environment already active.
+
+1. Verify your python version
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Ensure your python version meets the requirements from the `Installation Requirements`_ section using the following command:
+
+.. code-block:: shell
+
+   python3 --version
+
+If your current Python version is not supported by Schematic, you can switch to the supported version using a tool like `pyenv <https://github.com/pyenv/pyenv?tab=readme-ov-file#switch-between-python-versions>`_. Follow the instructions in the pyenv documentation to install and switch between Python versions easily.
+
+.. note::
+   You can double-check the current supported python version by opening up the `pyproject.toml <https://github.com/Sage-Bionetworks/schematic/blob/main/pyproject.toml#L39>`_ file in this repository and finding the supported versions of python in the script.
+
+2. Set up your virtual environment
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Once you are working with a python version supported by `schematic`, you will need to activate a virtual environment within which you can install the package. Below we will show how to create your virtual environment either with ``venv`` or with ``conda``.
+
+2a. Set up your virtual environment with ``venv``
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Python 3 has built-in support for virtual environments with the ``venv`` module, so you no longer need to install ``virtualenv``:
+
+.. code-block:: shell
+
+   python3 -m venv .venv
+   source .venv/bin/activate
+
+2b. Set up your virtual environment with ``conda``
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+``conda`` is a powerful package and environment management tool that allows users to create isolated environments used particularly in data science and machine learning workflows. If you would like to manage your environments with ``conda``, continue reading:
+
+1. **Download your preferred ``conda`` installer**: Begin by `installing conda <https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html>`_. We personally recommend working with Miniconda, which is a lightweight installer for ``conda`` that includes only ``conda`` and its dependencies.
+2. **Execute the ``conda`` installer**: Once you have downloaded your preferred installer, execute it using ``bash`` or ``zsh``, depending on the shell configured for your terminal environment. For example:
+
+   .. code-block:: shell
+
+      bash Miniconda3-latest-MacOSX-arm64.sh
+
+3. **Verify your ``conda`` setup**: Follow the prompts to complete your setup. Then verify your setup by running the ``conda`` command.
+4. **Create your ``schematic`` environment**: Begin by creating a fresh ``conda`` environment for ``schematic`` like so:
+
+   .. code-block:: shell
+
+      conda create --name 'schematicpy' python=3.10
+
+5. **Activate the environment**: Once your environment is set up, you can now activate your new environment with ``conda``:
+
+   .. code-block:: shell
+
+      conda activate schematicpy
+
+3. Install ``schematic`` dependencies
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Install the package using `pip <https://pip.pypa.io/en/stable/quickstart/>`_:
+
+.. code-block:: shell
+
+   python3 -m pip install schematicpy
+
+If you run into ``ERROR: Failed building wheel for numpy``, the error might be able to resolve by upgrading pip. Please try to upgrade pip by:
+
+.. code-block:: shell
+
+   pip3 install --upgrade pip
+
+4. Get your data model as a ``JSON-LD`` schema file
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Now you need a schema file, e.g. ``model.jsonld``, to have a data model that schematic can work with. While you can download a super basic `example data model <https://raw.githubusercontent.com/Sage-Bionetworks/schematic/refs/heads/develop/tests/data/example.model.jsonld>`_, you’ll probably be working with a DCC-specific data model. For non-Sage employees/contributors using the CLI, you might care only about the minimum needed artifact, which is the  ``.jsonld``; locate and download only that from the right repo.
+
+Here are some example repos with schema files:
+
+- https://github.com/ncihtan/data-models/
+- https://github.com/nf-osi/nf-metadata-dictionary/
+
+5. Obtain Google credential files
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Any function that interacts with a Google sheet (such as ``schematic manifest get``) requires Google Cloud credentials.
+
+1. **Option 1**: `Step-by-step <https://scribehow.com/shared/Get_Credentials_for_Google_Drive_and_Google_Sheets_APIs_to_use_with_schematicpy__yqfcJz_rQVeyTcg0KQCINA?referrer=workspace>`_ guide on how to create these credentials in Google Cloud.
+   - Depending on your institution's policies, your institutional Google account may or may not have the required permissions to complete this. A possible workaround is to use a personal or temporary Google account.
+
+.. warning::
+   At the time of writing, Sage Bionetworks employees do not have the appropriate permissions to create projects with their Sage Bionetworks Google accounts. You would follow instructions using a personal Google account.
+
+2. **Option 2**: Ask your DCC/development team if they have credentials previously set up with a service account.
+
+Once you have obtained credentials, be sure that the json file generated is named in the same way as the ``service_acct_creds`` parameter in your ``config.yml`` file. You will find more context on the ``config.yml`` in section [6. Set up configuration files](#6-set-up-configuration-files).
+
+.. note::
+   Running ``schematic init`` is no longer supported due to security concerns. To obtain ``schematic_service_account_creds.json``, please follow the `instructions <https://scribehow.com/shared/Enable_Google_Drive_and_Google_Sheets_APIs_for_project__yqfcJz_rQVeyTcg0KQCINA>`_. Schematic uses Google’s API to generate Google sheet templates that users fill in to provide (meta)data. Most Google sheet functionality could be authenticated with service account. However, more complex Google sheet functionality requires token-based authentication. As browser support that requires the token-based authentication diminishes, we are hoping to deprecate token-based authentication and keep only service account authentication in the future.
+
+.. note::
+   Use the ``schematic_service_account_creds.json`` file for the service account mode of authentication (*for Google services/APIs*). Service accounts are special Google accounts that can be used by applications to access Google APIs programmatically via OAuth2.0, with the advantage being that they do not require human authorization.
+
+6. Set up configuration files
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The following section will walk through setting up your configuration files with your credentials to allow for communication between ``schematic`` and the Synapse API.
+
+There are two main configuration files that need to be created and modified:
+
+- ``.synapseConfig``
+- ``config.yml``
+
+**Create and modify the ``.synapseConfig``**
+
+The ``.synapseConfig`` file is what enables communication between ``schematic`` and the Synapse API using your credentials. You can automatically generate a ``.synapseConfig`` file by running the following in your command line and following the prompts.
+
+.. tip::
+   You can generate a new authentication token on the Synapse website by going to ``Account Settings`` > ``Personal Access Tokens``.
+
+.. code-block:: shell
+
+   synapse config
+
+After following the prompts, a new ``.synapseConfig`` file and ``.synapseCache`` folder will be created in your home directory. You can view these hidden assets in your home directory with the following command:
+
+.. code-block:: shell
+
+   ls -a ~
+
+The ``.synapseConfig`` is used to log into Synapse if you are not using an environment variable (i.e. ``SYNAPSE_ACCESS_TOKEN``) for authentication, and the ``.synapseCache`` is where your assets are stored if you are not working with the CLI and/or you have specified ``.synapseCache`` as the location in which to store your manifests, in your ``config.yml``.
+
+**Create and modify the ``config.yml``**
+
+In this repository there is a ``config_example.yml`` file with default configurations to various components that are required before running ``schematic``, such as the Synapse ID of the main file view containing all your project assets, the
+
+Installation Guide For: Contributors
+------------------------------------
+
+The instructions below assume you have already installed `python <https://www.python.org/downloads/>`_, with the release version meeting the constraints set in the `Installation Requirements`_ section, and do not have an environment already active (e.g., with ``pyenv``). For development, we recommend working with versions > python 3.9 to avoid issues with ``pre-commit``'s default hook configuration.
+
+When contributing to this repository, please first discuss the change you wish to make via the `service desk <https://sagebionetworks.jira.com/servicedesk/customer/portal/5/group/8>`_ so that we may track these changes.
+
+Once you have finished setting up your development environment using the instructions below, please follow the guidelines in `CONTRIBUTION.md <https://github.com/Sage-Bionetworks/schematic/blob/develop-fds-2218-update-readme/CONTRIBUTION.md>`_ during your development.
+
+Please note we have a `code of conduct <CODE_OF_CONDUCT.md>`_, please follow it in all your interactions with the project.
+
+1. Clone the ``schematic`` package repository
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+For development, you will be working with the latest version of ``schematic`` on the repository to ensure compatibility between its latest state and your changes. Ensure your current working directory is where you would like to store your local fork before running the following command:
+
+.. code-block:: shell
+
+   git clone https://github.com/Sage-Bionetworks/schematic.git
+
+2. Install ``poetry``
+~~~~~~~~~~~~~~~~~~~~~
+
+Install ``poetry`` (version 1.3.0 or later) using either the `official installer <https://python-poetry.org/docs/#installing-with-the-official-installer>`_ or ``pip``. If you have an older installation of Poetry, we recommend uninstalling it first.
+
+.. code-block:: shell
+
+   pip install poetry
+
+Check to make sure your version of poetry is > v1.3.0
+
+.. code-block:: shell
+
+   poetry --version
+
+3. Start the virtual environment
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Change directory (``cd``) into your cloned ``schematic`` repository, and initialize the virtual environment using the following command with ``poetry``:
+
+.. code-block:: shell
+
+   poetry shell
+
+To make sure your poetry version and python version are consistent with the versions you expect, you can run the following command:
+
+.. code-block:: shell
+
+   poetry debug info
+
+4. Install ``schematic`` dependencies
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Before you begin, make sure you are in the latest ``develop`` branch of the repository.
+
+The following command will install the dependencies based on what we specify in the ``poetry.lock`` file of this repository (which is generated from the libraries listed in the ``pyproject.toml`` file). If this step is taking a long time, try to go back to Step 2 and check your version of ``poetry``. Alternatively, you can try deleting the lock file and regenerate it by running ``poetry lock`` (Note: this method should be used as a last resort because it may force other developers to change their development environment).
+
+.. code-block:: shell
+
+   poetry install --dev,doc
+
+This command will install:
+- The main dependencies required for running the package.
+- Development dependencies for testing, linting, and code formatting.
+- Documentation dependencies such as ``sphinx`` for building and maintaining documentation.
+
+5. Set up configuration files
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The following section will walk through setting up your configuration files with your credentials to allow for communication between ``schematic`` and the Synapse API.
+
+There are two main configuration files that need to be created and modified:
+- ``.synapseConfig``
+- ``config.yml``
+
+**Create and modify the ``.synapseConfig``**
+
+The ``.synapseConfig`` file is what enables communication between ``schematic`` and the Synapse API using your credentials. You can automatically generate a ``.synapseConfig`` file by running the following in your command line and following the prompts.
+
+.. tip::
+   You can generate a new authentication token on the Synapse website by going to ``Account Settings`` > ``Personal Access Tokens``.
+
+.. code-block:: shell
+
+   synapse config
+
+After following the prompts, a new ``.synapseConfig`` file and ``.synapseCache`` folder will be created in your home directory. You can view these hidden assets in your home directory with the following command:
+
+.. code-block:: shell
+
+   ls -a ~
+
+The ``.synapseConfig`` is used to log into Synapse if you are not using an environment variable (i.e., ``SYNAPSE_ACCESS_TOKEN``) for authentication, and the ``.synapseCache`` is where your assets are stored if you are not working with the CLI and/or you have specified ``.synapseCache`` as the location to store your manifests in your ``config.yml``.
+
+.. important::
+   When developing on ``schematic``, keep your ``.synapseConfig`` in your current working directory to avoid authentication errors.
+
+**Create and modify the ``config.yml``**
+
+In this repository, there is a ``config_example.yml`` file with default configurations to various components required before running ``schematic``, such as the Synapse ID of the main file view containing all your project assets, the base name of your manifest files, etc.
+
+Copy the contents of the ``config_example.yml`` (located in the base directory of the cloned ``schematic`` repo) into a new file called ``config.yml``:
+
+.. code-block:: shell
+
+   cp config_example.yml config.yml
+
+Once you've copied the file, modify its contents according to your use case. For example, if you wanted to change the folder where manifests are downloaded, your config should look like:
+
+.. code-block:: text
+
+   manifest:
+     manifest_folder: "my_manifest_folder_path"
+
+.. important::
+   Be sure to update your ``config.yml`` with the location of your ``.synapseConfig`` created in the step above to avoid authentication errors. Paths can be specified relative to the ``config.yml`` file or as absolute paths.
+
+.. note::
+   ``config.yml`` is ignored by git.
+
+6. Obtain Google credential files
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Any function that interacts with a Google Sheet (such as ``schematic manifest get``) requires Google Cloud credentials.
+
+1. **Option 1**: Follow the step-by-step `guide <https://scribehow.com/shared/Get_Credentials_for_Google_Drive_and_Google_Sheets_APIs_to_use_with_schematicpy__yqfcJz_rQVeyTcg0KQCINA?referrer=workspace>`_ on how to create these credentials in Google Cloud.
+   - Depending on your institution's policies, your institutional Google account may or may not have the required permissions to complete this. A possible workaround is to use a personal or temporary Google account.
+
+.. warning::
+   At the time of writing, Sage Bionetworks employees do not have the appropriate permissions to create projects with their Sage Bionetworks Google accounts. You would follow instructions using a personal Google account.
+
+2. **Option 2**: Ask your DCC/development team if they have credentials previously set up with a service account.
+
+Once you have obtained credentials, ensure that the JSON file generated is named in the same way as the ``service_acct_creds`` parameter in your ``config.yml`` file.
+
+.. important::
+   For testing, ensure there is no environment variable ``SCHEMATIC_SERVICE_ACCOUNT_CREDS``. Check the file ``.env`` to ensure this is not set. Also, verify that config files used for testing, such as ``config_example.yml``, do not contain ``service_acct_creds_synapse_id``.
+
+.. note::
+   Running ``schematic init`` is no longer supported due to security concerns. To obtain  ``schematic_service_account_creds.json``, please follow the `instructions <https://scribehow.com/shared/Enable_Google_Drive_and_Google_Sheets_APIs_for_project__yqfcJz_rQVeyTcg0KQCINA>`_. Schematic uses Google’s API to generate Google Sheet templates that users fill in to provide (meta)data.
+   Most Google Sheet functionality could be authenticated with a service account. However, more complex Google Sheet functionality requires token-based authentication. As browser support that requires token-based authentication diminishes, we hope to deprecate token-based authentication and keep only service account authentication in the future.
+
+.. note::
+   Use the ``schematic_service_account_creds.json`` file for the service account mode of authentication (*for Google services/APIs*). Service accounts are special Google accounts that can be used by applications to access Google APIs programmatically via OAuth2.0, with the advantage being that they do not require human authorization.
+
+7. Set up pre-commit hooks
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This repository is configured to utilize pre-commit hooks as part of the development process. To enable these hooks, run the following command and look for the success message:
+
+.. code-block:: shell
+
+   pre-commit install
+
+   pre-commit installed at .git/hooks/pre-commit
+
+You can run ``pre-commit`` manually across the entire repository like so:
+
+.. code-block:: shell
+
+   pre-commit run --all-files
+
+After running this step, your setup is complete, and you can test it in a Python instance or by running a command based on the examples in the command line usage section.
+
+8. Verify your setup
+~~~~~~~~~~~~~~~~~~~~
+
+After running the steps above, your setup is complete, and you can test it in a ``python`` instance or by running a command based on the examples
diff --git a/docs/source/submit.rst b/docs/source/submit.rst
new file mode 100644
index 000000000..1afd9f408
--- /dev/null
+++ b/docs/source/submit.rst
@@ -0,0 +1,12 @@
+Submit
+======
+
+
+- Validates the manifest. If errors are present, the manifest is not stored.
+- If valid:
+  - Stores the manifest in Synapse.
+  - Uploads the manifest to a view, updating file views with annotations as follows:
+
+      - **Store manifest only**
+      - **Store manifest and annotations** (to update a file view)
+      - **Store manifest and update a corresponding Synapse table**
diff --git a/docs/source/validate.rst b/docs/source/validate.rst
new file mode 100644
index 000000000..c6f55321b
--- /dev/null
+++ b/docs/source/validate.rst
@@ -0,0 +1,10 @@
+Validate
+========
+
+Given a filled-out manifest:
+
+- The manifest is validated against the JSON-LD schema as it maps to GX rules.
+- A ``jsonschema`` is generated from the data model. The data model can be in CSV, JSON-LD format, as input formats are decoupled from the internal data model representation within Schematic.
+- A set of validation rules is defined in the data model. Some validation rules are implemented via GX; others are custom Python code. All validation rules have the same interface.
+- Certain GX rules require looping through all projects a user has access to, or a specified scope of projects, to find other projects with manifests.
+- Validation results are provided before the manifest file is uploaded into Synapse.

From e0d3e103a9329ca144e3ad946603d85ecac2fc0c Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Fri, 1 Nov 2024 21:32:16 -0700
Subject: [PATCH 08/47] Add to documentation

---
 docs/source/asset_store.rst | 68 +++++++++++++++++++++++++++++++++++++
 docs/source/validate.rst    |  2 ++
 2 files changed, 70 insertions(+)

diff --git a/docs/source/asset_store.rst b/docs/source/asset_store.rst
index 0b6535e79..abe3c9bf0 100644
--- a/docs/source/asset_store.rst
+++ b/docs/source/asset_store.rst
@@ -1,2 +1,70 @@
 Setting up your asset store
 ===========================
+
+
+This document covers the minimal recommended elements needed in Synapse to interface with the Data Curator App (DCA) and provides options for Synapse project layout.
+
+There are two options for setting up a DCC Synapse project:
+
+1. Each team of DCC contributors has its own Synapse project that stores the team's datasets.
+2. All DCC datasets are stored in the same Synapse project.
+
+Option 1: Distributed Synapse Projects
+--------------------------------------
+
+Pick **option 1** if you answer "yes" to one or more of the following questions:
+
+- Does the DCC have multiple contributing institutions/labs, each with different data governance and access controls?
+- Does the DCC have multiple institutions with limited cross-institutional sharing?
+- Will contributors submit more than 100 datasets per release or per month?
+- Are you not willing to annotate each DCC dataset folder with the annotation `contentType:dataset`?
+
+Option 2: Single Synapse Project
+--------------------------------
+
+Pick **option 2** if you don't select option 1 and you answer "yes" to any of these questions:
+
+- Does the DCC have a project with pre-existing datasets in a complex folder hierarchy?
+- Does the DCC envision collaboration on the same dataset collection across multiple teams with shared access controls?
+- Are you willing to set up local access control for each dataset folder and annotate each with `contentType:dataset`?
+
+If neither option fits, select option 1.
+
+Option 1: Access & Project Setup - Multiple Contributing Projects
+------------------------------------------------------------------
+
+1. Create a DCC Admin Team with admin permissions.
+2. Create a Team for each data contributing institution. Begin with a "Test Team" if all teams are not yet identified.
+3. Create a Synapse Project for each institution and grant the respective team **Edit** level access.
+   - E.g., for institutions A, B, and C, create Projects A, B, and C with Teams A, B, and C. Team A has **Edit** access to Project A, etc.
+4. Within each project, create top-level dataset folders in the **Files** tab for each dataset type.
+5. Create another Synapse Project (e.g., MyDCC) containing the main **Fileview** for all DCC projects.
+   - Ensure all teams have **Download** level access to this file view.
+   - Include both file and folder entities and add the columns `id`, `name`, `type`, `parentId`, and `projectId` to the Fileview schema.
+
+Option 2: Access & Project Setup - Single Contributing Project
+--------------------------------------------------------------
+
+1. Create a Team for each data contributing institution.
+2. Create a single Synapse Project (e.g., MyDCC).
+3. Within this project, create dataset folders for each contributor. Organize them as needed.
+   - Use `contentType:dataset` for each dataset folder, which should not nest inside other dataset folders and must have unique names.
+4. In MyDCC, create the main **DCC Fileview** with `MyDCC` as scope. Add column `contentType` to the schema and grant teams **Download** level access.
+   - Add both file and folder entities and ensure columns `id`, `name`, `type`, `parentId`, `projectId`, and `contentType` are included.
+
+External Cloud Buckets Setup
+-----------------------------
+
+If DCC contributors require external cloud buckets, select one of the following configurations:
+
+1. **Basic External Storage Bucket (Default)**:
+   - Create an S3 bucket for Synapse uploads via web or CLI. Contributors will upload data without needing AWS credentials.
+   - Provision an S3 bucket, attach it to the Synapse project, and create folders for specific assay types.
+
+2. **Custom Storage Location**:
+   - For large datasets or if contributors prefer cloud storage, enable uploads via AWS CLI or GCP CLI.
+   - Configure the custom storage location with an AWS Lambda or Google Cloud function for syncing.
+   - If using AWS, provision a bucket, set up Lambda sync, and assign IAM write access.
+   - For GCP, use Google Cloud function sync and obtain contributor emails for access.
+
+Finally, set up a `synapse-service-lambda` account for syncing external cloud buckets with Synapse, granting "Edit & Delete" permissions on the contributor's project.
diff --git a/docs/source/validate.rst b/docs/source/validate.rst
index c6f55321b..db31073d6 100644
--- a/docs/source/validate.rst
+++ b/docs/source/validate.rst
@@ -8,3 +8,5 @@ Given a filled-out manifest:
 - A set of validation rules is defined in the data model. Some validation rules are implemented via GX; others are custom Python code. All validation rules have the same interface.
 - Certain GX rules require looping through all projects a user has access to, or a specified scope of projects, to find other projects with manifests.
 - Validation results are provided before the manifest file is uploaded into Synapse.
+
+More validation documentation can be found here: https://sagebionetworks.jira.com/wiki/spaces/SCHEM/pages/3302785036/Schematic+Validation

From 070d58bb5ff4a5b7f752bb5c67e500eb2d608b6b Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Fri, 1 Nov 2024 21:36:27 -0700
Subject: [PATCH 09/47] Edit dependencies

---
 poetry.lock    | 318 +++++++++++++++++++++++++++++++++++++++++++++----
 pyproject.toml |   1 +
 2 files changed, 293 insertions(+), 26 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index ef1518720..6654f83dd 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,9 +1,10 @@
-# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
+# This file is automatically @generated by Poetry and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
 version = "0.7.16"
 description = "A light, configurable Sphinx theme"
+category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -15,6 +16,7 @@ files = [
 name = "altair"
 version = "4.2.0"
 description = "Altair: A declarative statistical visualization library for Python."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -37,6 +39,7 @@ dev = ["black", "docutils", "flake8", "ipython", "m2r", "mistune (<2.0.0)", "pyt
 name = "anyio"
 version = "4.6.2.post1"
 description = "High level compatibility layer for multiple asynchronous event loop implementations"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -59,6 +62,7 @@ trio = ["trio (>=0.26.1)"]
 name = "appnope"
 version = "0.1.4"
 description = "Disable App Nap on macOS >= 10.9"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -70,6 +74,7 @@ files = [
 name = "argon2-cffi"
 version = "23.1.0"
 description = "Argon2 for Python"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -90,6 +95,7 @@ typing = ["mypy"]
 name = "argon2-cffi-bindings"
 version = "21.2.0"
 description = "Low-level CFFI bindings for Argon2"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -127,6 +133,7 @@ tests = ["pytest"]
 name = "arrow"
 version = "1.3.0"
 description = "Better dates & times for Python"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -140,12 +147,13 @@ types-python-dateutil = ">=2.8.10"
 
 [package.extras]
 doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"]
-test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"]
+test = ["dateparser (>=1.0.0,<2.0.0)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (>=3.0.0,<4.0.0)"]
 
 [[package]]
 name = "astroid"
 version = "2.15.8"
 description = "An abstract syntax tree for Python with inference support."
+category = "dev"
 optional = false
 python-versions = ">=3.7.2"
 files = [
@@ -162,6 +170,7 @@ wrapt = {version = ">=1.11,<2", markers = "python_version < \"3.11\""}
 name = "asttokens"
 version = "2.4.1"
 description = "Annotate AST trees with source code positions"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -180,6 +189,7 @@ test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
 name = "async-lru"
 version = "2.0.4"
 description = "Simple LRU cache for asyncio"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -194,6 +204,7 @@ typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
 name = "asyncio"
 version = "3.4.3"
 description = "reference implementation of PEP 3156"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -207,6 +218,7 @@ files = [
 name = "asyncio-atexit"
 version = "1.0.1"
 description = "Like atexit, but for asyncio"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -221,6 +233,7 @@ test = ["pytest", "uvloop"]
 name = "attrs"
 version = "24.2.0"
 description = "Classes Without Boilerplate"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -240,6 +253,7 @@ tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
 name = "babel"
 version = "2.16.0"
 description = "Internationalization utilities"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -254,6 +268,7 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
 name = "beautifulsoup4"
 version = "4.12.3"
 description = "Screen-scraping library"
+category = "main"
 optional = false
 python-versions = ">=3.6.0"
 files = [
@@ -275,6 +290,7 @@ lxml = ["lxml"]
 name = "black"
 version = "23.12.1"
 description = "The uncompromising code formatter."
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -321,6 +337,7 @@ uvloop = ["uvloop (>=0.15.2)"]
 name = "bleach"
 version = "6.2.0"
 description = "An easy safelist-based HTML-sanitizing tool."
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -338,6 +355,7 @@ css = ["tinycss2 (>=1.1.0,<1.5)"]
 name = "cachetools"
 version = "5.5.0"
 description = "Extensible memoizing collections and decorators"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -349,6 +367,7 @@ files = [
 name = "certifi"
 version = "2024.8.30"
 description = "Python package for providing Mozilla's CA Bundle."
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -360,6 +379,7 @@ files = [
 name = "cffi"
 version = "1.17.1"
 description = "Foreign Function Interface for Python calling C code."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -439,6 +459,7 @@ pycparser = "*"
 name = "cfgv"
 version = "3.4.0"
 description = "Validate configuration and produce human readable error messages."
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -450,6 +471,7 @@ files = [
 name = "charset-normalizer"
 version = "3.4.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
+category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -564,6 +586,7 @@ files = [
 name = "click"
 version = "8.1.7"
 description = "Composable command line interface toolkit"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -578,6 +601,7 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 name = "click-log"
 version = "0.4.0"
 description = "Logging integration for Click"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -592,6 +616,7 @@ click = "*"
 name = "clickclick"
 version = "20.10.2"
 description = "Click utility functions"
+category = "main"
 optional = true
 python-versions = "*"
 files = [
@@ -607,6 +632,7 @@ PyYAML = ">=3.11"
 name = "colorama"
 version = "0.4.6"
 description = "Cross-platform colored terminal text."
+category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
@@ -618,6 +644,7 @@ files = [
 name = "comm"
 version = "0.2.2"
 description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -633,18 +660,19 @@ test = ["pytest"]
 
 [[package]]
 name = "connexion"
-version = "2.14.1"
+version = "2.14.2"
 description = "Connexion - API first applications with OpenAPI/Swagger and Flask"
+category = "main"
 optional = true
 python-versions = ">=3.6"
 files = [
-    {file = "connexion-2.14.1-py2.py3-none-any.whl", hash = "sha256:f343717241b4c4802a694c38fee66fb1693c897fe4ea5a957fa9b3b07caf6394"},
-    {file = "connexion-2.14.1.tar.gz", hash = "sha256:99aa5781e70a7b94f8ffae8cf89f309d49cdb811bbd65a8e2f2546f3b19a01e6"},
+    {file = "connexion-2.14.2-py2.py3-none-any.whl", hash = "sha256:a73b96a0e07b16979a42cde7c7e26afe8548099e352cf350f80c57185e0e0b36"},
+    {file = "connexion-2.14.2.tar.gz", hash = "sha256:dbc06f52ebeebcf045c9904d570f24377e8bbd5a6521caef15a06f634cf85646"},
 ]
 
 [package.dependencies]
 clickclick = ">=1.2,<21"
-flask = ">=1.0.4,<3"
+flask = ">=1.0.4,<2.3"
 inflection = ">=0.3.1,<0.6"
 itsdangerous = ">=0.24"
 jsonschema = ">=2.5.1,<5"
@@ -652,19 +680,20 @@ packaging = ">=20"
 PyYAML = ">=5.1,<7"
 requests = ">=2.9.1,<3"
 swagger-ui-bundle = {version = ">=0.0.2,<0.1", optional = true, markers = "extra == \"swagger-ui\""}
-werkzeug = ">=1.0,<3"
+werkzeug = ">=1.0,<2.3"
 
 [package.extras]
 aiohttp = ["MarkupSafe (>=0.23)", "aiohttp (>=2.3.10,<4)", "aiohttp-jinja2 (>=0.14.0,<2)"]
 docs = ["sphinx-autoapi (==1.8.1)"]
-flask = ["flask (>=1.0.4,<3)", "itsdangerous (>=0.24)"]
+flask = ["flask (>=1.0.4,<2.3)", "itsdangerous (>=0.24)"]
 swagger-ui = ["swagger-ui-bundle (>=0.0.2,<0.1)"]
-tests = ["MarkupSafe (>=0.23)", "aiohttp (>=2.3.10,<4)", "aiohttp-jinja2 (>=0.14.0,<2)", "aiohttp-remotes", "decorator (>=5,<6)", "flask (>=1.0.4,<3)", "itsdangerous (>=0.24)", "pytest (>=6,<7)", "pytest-aiohttp", "pytest-cov (>=2,<3)", "swagger-ui-bundle (>=0.0.2,<0.1)", "testfixtures (>=6,<7)"]
+tests = ["MarkupSafe (>=0.23)", "aiohttp (>=2.3.10,<4)", "aiohttp-jinja2 (>=0.14.0,<2)", "aiohttp-remotes", "decorator (>=5,<6)", "flask (>=1.0.4,<2.3)", "itsdangerous (>=0.24)", "pytest (>=6,<7)", "pytest-aiohttp", "pytest-cov (>=2,<3)", "swagger-ui-bundle (>=0.0.2,<0.1)", "testfixtures (>=6,<7)"]
 
 [[package]]
 name = "coverage"
 version = "7.6.4"
 description = "Code coverage measurement for Python"
+category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -742,6 +771,7 @@ toml = ["tomli"]
 name = "cryptography"
 version = "41.0.7"
 description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -787,6 +817,7 @@ test-randomorder = ["pytest-randomly"]
 name = "dataclasses-json"
 version = "0.6.7"
 description = "Easily serialize dataclasses to and from JSON."
+category = "main"
 optional = false
 python-versions = "<4.0,>=3.7"
 files = [
@@ -802,6 +833,7 @@ typing-inspect = ">=0.4.0,<1"
 name = "dateparser"
 version = "1.2.0"
 description = "Date parsing library designed to parse dates from HTML pages"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -824,6 +856,7 @@ langdetect = ["langdetect"]
 name = "debugpy"
 version = "1.8.7"
 description = "An implementation of the Debug Adapter Protocol for Python"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -859,6 +892,7 @@ files = [
 name = "decorator"
 version = "5.1.1"
 description = "Decorators for Humans"
+category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -870,6 +904,7 @@ files = [
 name = "defusedxml"
 version = "0.7.1"
 description = "XML bomb protection for Python stdlib modules"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -881,6 +916,7 @@ files = [
 name = "deprecated"
 version = "1.2.14"
 description = "Python @deprecated decorator to deprecate old python classes, functions or methods."
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -898,6 +934,7 @@ dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"]
 name = "dill"
 version = "0.3.9"
 description = "serialize all of Python"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -913,6 +950,7 @@ profile = ["gprof2dot (>=2022.7.29)"]
 name = "distlib"
 version = "0.3.9"
 description = "Distribution utilities"
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -924,6 +962,7 @@ files = [
 name = "docutils"
 version = "0.21.2"
 description = "Docutils -- Python Documentation Utilities"
+category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -935,6 +974,7 @@ files = [
 name = "entrypoints"
 version = "0.4"
 description = "Discover and load entry points from installed packages."
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -946,6 +986,7 @@ files = [
 name = "et-xmlfile"
 version = "2.0.0"
 description = "An implementation of lxml.xmlfile for the standard library"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -957,6 +998,7 @@ files = [
 name = "exceptiongroup"
 version = "1.2.2"
 description = "Backport of PEP 654 (exception groups)"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -971,6 +1013,7 @@ test = ["pytest (>=6)"]
 name = "execnet"
 version = "2.1.1"
 description = "execnet: rapid multi-Python deployment"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -985,6 +1028,7 @@ testing = ["hatch", "pre-commit", "pytest", "tox"]
 name = "executing"
 version = "2.1.0"
 description = "Get the currently executing AST node of a frame, and other information"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -999,6 +1043,7 @@ tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipyth
 name = "fastjsonschema"
 version = "2.20.0"
 description = "Fastest Python implementation of JSON schema"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1013,6 +1058,7 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc
 name = "filelock"
 version = "3.16.1"
 description = "A platform independent file lock."
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1029,6 +1075,7 @@ typing = ["typing-extensions (>=4.12.2)"]
 name = "flake8"
 version = "6.1.0"
 description = "the modular source code checker: pep8 pyflakes and co"
+category = "dev"
 optional = false
 python-versions = ">=3.8.1"
 files = [
@@ -1045,6 +1092,7 @@ pyflakes = ">=3.1.0,<3.2.0"
 name = "flask"
 version = "2.1.3"
 description = "A simple framework for building complex web applications."
+category = "main"
 optional = true
 python-versions = ">=3.7"
 files = [
@@ -1067,6 +1115,7 @@ dotenv = ["python-dotenv"]
 name = "flask-cors"
 version = "3.0.10"
 description = "A Flask extension adding a decorator for CORS support"
+category = "main"
 optional = true
 python-versions = "*"
 files = [
@@ -1082,6 +1131,7 @@ Six = "*"
 name = "fqdn"
 version = "1.5.1"
 description = "Validates fully-qualified domain names against RFC 1123, so that they are acceptable to modern bowsers"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4"
 files = [
@@ -1093,6 +1143,7 @@ files = [
 name = "google-api-core"
 version = "2.22.0"
 description = "Google API client core library"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1117,6 +1168,7 @@ grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"]
 name = "google-api-python-client"
 version = "2.123.0"
 description = "Google API Client Library for Python"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1125,7 +1177,7 @@ files = [
 ]
 
 [package.dependencies]
-google-api-core = ">=1.31.5,<2.0.dev0 || >2.3.0,<3.0.0.dev0"
+google-api-core = ">=1.31.5,<2.0.0 || >2.3.0,<3.0.0.dev0"
 google-auth = ">=1.19.0,<3.0.0.dev0"
 google-auth-httplib2 = ">=0.1.0"
 httplib2 = ">=0.15.0,<1.dev0"
@@ -1135,6 +1187,7 @@ uritemplate = ">=3.0.1,<5"
 name = "google-auth"
 version = "2.35.0"
 description = "Google Authentication Library"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1158,6 +1211,7 @@ requests = ["requests (>=2.20.0,<3.0.0.dev0)"]
 name = "google-auth-httplib2"
 version = "0.1.1"
 description = "Google Authentication Library: httplib2 transport"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1173,6 +1227,7 @@ httplib2 = ">=0.19.0"
 name = "google-auth-oauthlib"
 version = "0.8.0"
 description = "Google Authentication Library"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1191,6 +1246,7 @@ tool = ["click (>=6.0.0)"]
 name = "googleapis-common-protos"
 version = "1.65.0"
 description = "Common protobufs used in Google APIs"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1208,6 +1264,7 @@ grpc = ["grpcio (>=1.44.0,<2.0.0.dev0)"]
 name = "graphviz"
 version = "0.20.3"
 description = "Simple Python interface for Graphviz"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1224,6 +1281,7 @@ test = ["coverage", "pytest (>=7,<8.1)", "pytest-cov", "pytest-mock (>=3)"]
 name = "great-expectations"
 version = "0.15.50"
 description = "Always know what to expect from your data."
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1298,6 +1356,7 @@ vertica = ["sqlalchemy (>=1.3.18,<2.0.0)", "sqlalchemy-vertica-python (>=0.5.10)
 name = "grpcio"
 version = "1.67.1"
 description = "HTTP/2-based RPC framework"
+category = "main"
 optional = true
 python-versions = ">=3.8"
 files = [
@@ -1365,6 +1424,7 @@ protobuf = ["grpcio-tools (>=1.67.1)"]
 name = "h11"
 version = "0.14.0"
 description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1376,6 +1436,7 @@ files = [
 name = "httpcore"
 version = "1.0.6"
 description = "A minimal low-level HTTP client."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1390,13 +1451,14 @@ h11 = ">=0.13,<0.15"
 [package.extras]
 asyncio = ["anyio (>=4.0,<5.0)"]
 http2 = ["h2 (>=3,<5)"]
-socks = ["socksio (==1.*)"]
+socks = ["socksio (>=1.0.0,<2.0.0)"]
 trio = ["trio (>=0.22.0,<1.0)"]
 
 [[package]]
 name = "httplib2"
 version = "0.22.0"
 description = "A comprehensive HTTP client library."
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -1411,6 +1473,7 @@ pyparsing = {version = ">=2.4.2,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.0.2 || >3.0
 name = "httpx"
 version = "0.27.2"
 description = "The next generation HTTP client."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1421,21 +1484,22 @@ files = [
 [package.dependencies]
 anyio = "*"
 certifi = "*"
-httpcore = "==1.*"
+httpcore = ">=1.0.0,<2.0.0"
 idna = "*"
 sniffio = "*"
 
 [package.extras]
 brotli = ["brotli", "brotlicffi"]
-cli = ["click (==8.*)", "pygments (==2.*)", "rich (>=10,<14)"]
+cli = ["click (>=8.0.0,<9.0.0)", "pygments (>=2.0.0,<3.0.0)", "rich (>=10,<14)"]
 http2 = ["h2 (>=3,<5)"]
-socks = ["socksio (==1.*)"]
+socks = ["socksio (>=1.0.0,<2.0.0)"]
 zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "identify"
 version = "2.6.1"
 description = "File identification library for Python"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1450,6 +1514,7 @@ license = ["ukkonen"]
 name = "idna"
 version = "3.10"
 description = "Internationalized Domain Names in Applications (IDNA)"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1464,6 +1529,7 @@ all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2
 name = "imagesize"
 version = "1.4.1"
 description = "Getting image size from png/jpeg/jpeg2000/gif file"
+category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -1475,6 +1541,7 @@ files = [
 name = "importlib-metadata"
 version = "8.4.0"
 description = "Read metadata from Python packages"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1494,6 +1561,7 @@ test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "p
 name = "inflection"
 version = "0.5.1"
 description = "A port of Ruby on Rails inflector to Python"
+category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1505,6 +1573,7 @@ files = [
 name = "iniconfig"
 version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1516,6 +1585,7 @@ files = [
 name = "ipykernel"
 version = "6.29.5"
 description = "IPython Kernel for Jupyter"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1529,7 +1599,7 @@ comm = ">=0.1.1"
 debugpy = ">=1.6.5"
 ipython = ">=7.23.1"
 jupyter-client = ">=6.1.12"
-jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
+jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
 matplotlib-inline = ">=0.1"
 nest-asyncio = "*"
 packaging = "*"
@@ -1549,6 +1619,7 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio
 name = "ipython"
 version = "8.18.1"
 description = "IPython: Productive Interactive Computing"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1586,6 +1657,7 @@ test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.22)", "pa
 name = "ipywidgets"
 version = "8.1.5"
 description = "Jupyter interactive widgets"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1607,6 +1679,7 @@ test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"]
 name = "isodate"
 version = "0.6.1"
 description = "An ISO 8601 date/time/duration parser and formatter"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1621,6 +1694,7 @@ six = "*"
 name = "isoduration"
 version = "20.11.0"
 description = "Operations with ISO 8601 durations"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1635,6 +1709,7 @@ arrow = ">=0.15.0"
 name = "isort"
 version = "5.13.2"
 description = "A Python utility / library to sort Python imports."
+category = "dev"
 optional = false
 python-versions = ">=3.8.0"
 files = [
@@ -1649,6 +1724,7 @@ colors = ["colorama (>=0.4.6)"]
 name = "itsdangerous"
 version = "2.2.0"
 description = "Safely pass data to untrusted environments and back."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1660,6 +1736,7 @@ files = [
 name = "jedi"
 version = "0.19.1"
 description = "An autocompletion tool for Python that can be used for text editors."
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1679,6 +1756,7 @@ testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
 name = "jinja2"
 version = "3.1.4"
 description = "A very fast and expressive template engine."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1696,6 +1774,7 @@ i18n = ["Babel (>=2.7)"]
 name = "json5"
 version = "0.9.25"
 description = "A Python implementation of the JSON5 data format."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1707,6 +1786,7 @@ files = [
 name = "jsonpatch"
 version = "1.33"
 description = "Apply JSON-Patches (RFC 6902)"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
 files = [
@@ -1721,6 +1801,7 @@ jsonpointer = ">=1.9"
 name = "jsonpointer"
 version = "3.0.0"
 description = "Identify specific nodes in a JSON document (RFC 6901)"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1732,6 +1813,7 @@ files = [
 name = "jsonschema"
 version = "4.23.0"
 description = "An implementation of JSON Schema validation for Python"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1761,6 +1843,7 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 name = "jsonschema-specifications"
 version = "2024.10.1"
 description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1775,6 +1858,7 @@ referencing = ">=0.31.0"
 name = "jupyter-client"
 version = "8.6.3"
 description = "Jupyter protocol implementation and client libraries"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1784,7 +1868,7 @@ files = [
 
 [package.dependencies]
 importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""}
-jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
+jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
 python-dateutil = ">=2.8.2"
 pyzmq = ">=23.0"
 tornado = ">=6.2"
@@ -1798,6 +1882,7 @@ test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pyt
 name = "jupyter-core"
 version = "5.7.2"
 description = "Jupyter core package. A base package on which Jupyter projects rely."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1818,6 +1903,7 @@ test = ["ipykernel", "pre-commit", "pytest (<8)", "pytest-cov", "pytest-timeout"
 name = "jupyter-events"
 version = "0.10.0"
 description = "Jupyter Event System library"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1843,6 +1929,7 @@ test = ["click", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.19.0)", "p
 name = "jupyter-lsp"
 version = "2.2.5"
 description = "Multi-Language Server WebSocket proxy for Jupyter Notebook/Lab server"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1858,6 +1945,7 @@ jupyter-server = ">=1.1.2"
 name = "jupyter-server"
 version = "2.14.2"
 description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1870,7 +1958,7 @@ anyio = ">=3.1.0"
 argon2-cffi = ">=21.1"
 jinja2 = ">=3.0.3"
 jupyter-client = ">=7.4.4"
-jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
+jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
 jupyter-events = ">=0.9.0"
 jupyter-server-terminals = ">=0.4.4"
 nbconvert = ">=6.4.4"
@@ -1894,6 +1982,7 @@ test = ["flaky", "ipykernel", "pre-commit", "pytest (>=7.0,<9)", "pytest-console
 name = "jupyter-server-terminals"
 version = "0.5.3"
 description = "A Jupyter Server Extension Providing Terminals."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1913,6 +2002,7 @@ test = ["jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-jupyter[server] (>
 name = "jupyterlab"
 version = "4.2.5"
 description = "JupyterLab computational environment"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1948,6 +2038,7 @@ upgrade-extension = ["copier (>=9,<10)", "jinja2-time (<0.3)", "pydantic (<3.0)"
 name = "jupyterlab-pygments"
 version = "0.3.0"
 description = "Pygments theme using JupyterLab CSS variables"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1959,6 +2050,7 @@ files = [
 name = "jupyterlab-server"
 version = "2.27.3"
 description = "A set of server components for JupyterLab and JupyterLab like applications."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1985,6 +2077,7 @@ test = ["hatch", "ipykernel", "openapi-core (>=0.18.0,<0.19.0)", "openapi-spec-v
 name = "jupyterlab-widgets"
 version = "3.0.13"
 description = "Jupyter interactive widgets for JupyterLab"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1996,6 +2089,7 @@ files = [
 name = "lazy-object-proxy"
 version = "1.10.0"
 description = "A fast and thorough lazy object proxy."
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2042,6 +2136,7 @@ files = [
 name = "makefun"
 version = "1.15.6"
 description = "Small library to dynamically create python functions."
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2053,6 +2148,7 @@ files = [
 name = "markupsafe"
 version = "3.0.2"
 description = "Safely add untrusted strings to HTML/XML markup."
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2123,6 +2219,7 @@ files = [
 name = "marshmallow"
 version = "3.23.1"
 description = "A lightweight library for converting complex datatypes to and from native Python datatypes."
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2142,6 +2239,7 @@ tests = ["pytest", "simplejson"]
 name = "matplotlib-inline"
 version = "0.1.7"
 description = "Inline Matplotlib backend for Jupyter"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2156,6 +2254,7 @@ traitlets = "*"
 name = "mccabe"
 version = "0.7.0"
 description = "McCabe checker, plugin for flake8"
+category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2167,6 +2266,7 @@ files = [
 name = "mistune"
 version = "3.0.2"
 description = "A sane and fast Markdown parser with useful plugins and renderers"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2178,6 +2278,7 @@ files = [
 name = "mypy"
 version = "1.13.0"
 description = "Optional static typing for Python"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2231,6 +2332,7 @@ reports = ["lxml"]
 name = "mypy-extensions"
 version = "1.0.0"
 description = "Type system extensions for programs checked with the mypy type checker."
+category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -2242,6 +2344,7 @@ files = [
 name = "nbclient"
 version = "0.10.0"
 description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor."
+category = "main"
 optional = false
 python-versions = ">=3.8.0"
 files = [
@@ -2251,7 +2354,7 @@ files = [
 
 [package.dependencies]
 jupyter-client = ">=6.1.12"
-jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
+jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
 nbformat = ">=5.1"
 traitlets = ">=5.4"
 
@@ -2264,6 +2367,7 @@ test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=
 name = "nbconvert"
 version = "7.16.4"
 description = "Converting Jupyter Notebooks (.ipynb files) to other formats.  Output formats include asciidoc, html, latex, markdown, pdf, py, rst, script.  nbconvert can be used both as a Python library (`import nbconvert`) or as a command line tool (invoked as `jupyter nbconvert ...`)."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2302,6 +2406,7 @@ webpdf = ["playwright"]
 name = "nbformat"
 version = "5.10.4"
 description = "The Jupyter Notebook format"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2312,7 +2417,7 @@ files = [
 [package.dependencies]
 fastjsonschema = ">=2.15"
 jsonschema = ">=2.6"
-jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
+jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
 traitlets = ">=5.1"
 
 [package.extras]
@@ -2323,6 +2428,7 @@ test = ["pep440", "pre-commit", "pytest", "testpath"]
 name = "nest-asyncio"
 version = "1.6.0"
 description = "Patch asyncio to allow nested event loops"
+category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -2334,6 +2440,7 @@ files = [
 name = "networkx"
 version = "3.2.1"
 description = "Python package for creating and manipulating graphs and networks"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2352,6 +2459,7 @@ test = ["pytest (>=7.2)", "pytest-cov (>=4.0)"]
 name = "nodeenv"
 version = "1.9.1"
 description = "Node.js virtual environment builder"
+category = "dev"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
@@ -2363,6 +2471,7 @@ files = [
 name = "notebook"
 version = "7.2.2"
 description = "Jupyter Notebook - A web-based notebook environment for interactive computing"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2386,6 +2495,7 @@ test = ["importlib-resources (>=5.0)", "ipykernel", "jupyter-server[test] (>=2.4
 name = "notebook-shim"
 version = "0.2.4"
 description = "A shim layer for notebook traits and config"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2403,6 +2513,7 @@ test = ["pytest", "pytest-console-scripts", "pytest-jupyter", "pytest-tornasync"
 name = "numpy"
 version = "1.26.4"
 description = "Fundamental package for array computing in Python"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2448,6 +2559,7 @@ files = [
 name = "oauth2client"
 version = "4.1.3"
 description = "OAuth 2.0 client library"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2466,6 +2578,7 @@ six = ">=1.6.1"
 name = "oauthlib"
 version = "3.2.2"
 description = "A generic, spec-compliant, thorough implementation of the OAuth request-signing logic"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2482,6 +2595,7 @@ signedtoken = ["cryptography (>=3.0.0)", "pyjwt (>=2.0.0,<3)"]
 name = "openpyxl"
 version = "3.1.5"
 description = "A Python library to read/write Excel 2010 xlsx/xlsm files"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2496,6 +2610,7 @@ et-xmlfile = "*"
 name = "opentelemetry-api"
 version = "1.27.0"
 description = "OpenTelemetry Python API"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2511,6 +2626,7 @@ importlib-metadata = ">=6.0,<=8.4.0"
 name = "opentelemetry-exporter-otlp-proto-common"
 version = "1.27.0"
 description = "OpenTelemetry Protobuf encoding"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2525,6 +2641,7 @@ opentelemetry-proto = "1.27.0"
 name = "opentelemetry-exporter-otlp-proto-grpc"
 version = "1.27.0"
 description = "OpenTelemetry Collector Protobuf over gRPC Exporter"
+category = "main"
 optional = true
 python-versions = ">=3.8"
 files = [
@@ -2545,6 +2662,7 @@ opentelemetry-sdk = ">=1.27.0,<1.28.0"
 name = "opentelemetry-exporter-otlp-proto-http"
 version = "1.27.0"
 description = "OpenTelemetry Collector Protobuf over HTTP Exporter"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2565,6 +2683,7 @@ requests = ">=2.7,<3.0"
 name = "opentelemetry-instrumentation"
 version = "0.48b0"
 description = "Instrumentation Tools & Auto Instrumentation for OpenTelemetry Python"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2581,6 +2700,7 @@ wrapt = ">=1.0.0,<2.0.0"
 name = "opentelemetry-instrumentation-flask"
 version = "0.48b0"
 description = "Flask instrumentation for OpenTelemetry"
+category = "main"
 optional = true
 python-versions = ">=3.8"
 files = [
@@ -2604,6 +2724,7 @@ instruments = ["flask (>=1.0)"]
 name = "opentelemetry-instrumentation-httpx"
 version = "0.48b0"
 description = "OpenTelemetry HTTPX Instrumentation"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2624,6 +2745,7 @@ instruments = ["httpx (>=0.18.0)"]
 name = "opentelemetry-instrumentation-requests"
 version = "0.48b0"
 description = "OpenTelemetry requests instrumentation"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2644,6 +2766,7 @@ instruments = ["requests (>=2.0,<3.0)"]
 name = "opentelemetry-instrumentation-threading"
 version = "0.48b0"
 description = "Thread context propagation support for OpenTelemetry"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2660,6 +2783,7 @@ wrapt = ">=1.0.0,<2.0.0"
 name = "opentelemetry-instrumentation-urllib"
 version = "0.48b0"
 description = "OpenTelemetry urllib instrumentation"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2677,6 +2801,7 @@ opentelemetry-util-http = "0.48b0"
 name = "opentelemetry-instrumentation-wsgi"
 version = "0.48b0"
 description = "WSGI Middleware for OpenTelemetry"
+category = "main"
 optional = true
 python-versions = ">=3.8"
 files = [
@@ -2694,6 +2819,7 @@ opentelemetry-util-http = "0.48b0"
 name = "opentelemetry-proto"
 version = "1.27.0"
 description = "OpenTelemetry Python Proto"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2708,6 +2834,7 @@ protobuf = ">=3.19,<5.0"
 name = "opentelemetry-sdk"
 version = "1.27.0"
 description = "OpenTelemetry Python SDK"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2724,6 +2851,7 @@ typing-extensions = ">=3.7.4"
 name = "opentelemetry-semantic-conventions"
 version = "0.48b0"
 description = "OpenTelemetry Semantic Conventions"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2739,6 +2867,7 @@ opentelemetry-api = "1.27.0"
 name = "opentelemetry-util-http"
 version = "0.48b0"
 description = "Web util for OpenTelemetry"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2750,6 +2879,7 @@ files = [
 name = "overrides"
 version = "7.7.0"
 description = "A decorator to automatically detect mismatch when overriding a method."
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2761,6 +2891,7 @@ files = [
 name = "packaging"
 version = "24.1"
 description = "Core utilities for Python packages"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2772,6 +2903,7 @@ files = [
 name = "pandarallel"
 version = "1.6.5"
 description = "An easy to use library to speed up computation (by parallelizing on multi CPUs) with pandas."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2791,6 +2923,7 @@ doc = ["mkdocs-material"]
 name = "pandas"
 version = "2.2.3"
 description = "Powerful data structures for data analysis, time series, and statistics"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2873,6 +3006,7 @@ xml = ["lxml (>=4.9.2)"]
 name = "pandocfilters"
 version = "1.5.1"
 description = "Utilities for writing pandoc filters in python"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -2884,6 +3018,7 @@ files = [
 name = "parso"
 version = "0.8.4"
 description = "A Python Parser"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2899,6 +3034,7 @@ testing = ["docopt", "pytest"]
 name = "pathspec"
 version = "0.12.1"
 description = "Utility library for gitignore style pattern matching of file paths."
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2910,6 +3046,7 @@ files = [
 name = "pdoc"
 version = "14.7.0"
 description = "API Documentation for Python Projects"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2929,6 +3066,7 @@ dev = ["hypothesis", "mypy", "pdoc-pyo3-sample-library (==1.0.11)", "pygments (>
 name = "pexpect"
 version = "4.9.0"
 description = "Pexpect allows easy control of interactive console applications."
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2943,6 +3081,7 @@ ptyprocess = ">=0.5"
 name = "platformdirs"
 version = "4.3.6"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2959,6 +3098,7 @@ type = ["mypy (>=1.11.2)"]
 name = "pluggy"
 version = "1.5.0"
 description = "plugin and hook calling mechanisms for python"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2974,6 +3114,7 @@ testing = ["pytest", "pytest-benchmark"]
 name = "pre-commit"
 version = "3.8.0"
 description = "A framework for managing and maintaining multi-language pre-commit hooks."
+category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2992,6 +3133,7 @@ virtualenv = ">=20.10.0"
 name = "prometheus-client"
 version = "0.21.0"
 description = "Python client for the Prometheus monitoring system."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3006,6 +3148,7 @@ twisted = ["twisted"]
 name = "prompt-toolkit"
 version = "3.0.48"
 description = "Library for building powerful interactive command lines in Python"
+category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -3020,6 +3163,7 @@ wcwidth = "*"
 name = "proto-plus"
 version = "1.25.0"
 description = "Beautiful, Pythonic protocol buffers."
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3037,6 +3181,7 @@ testing = ["google-api-core (>=1.31.5)"]
 name = "protobuf"
 version = "4.25.5"
 description = ""
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3057,6 +3202,7 @@ files = [
 name = "psutil"
 version = "5.9.8"
 description = "Cross-platform lib for process and system monitoring in Python."
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
@@ -3085,6 +3231,7 @@ test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"]
 name = "ptyprocess"
 version = "0.7.0"
 description = "Run a subprocess in a pseudo terminal"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -3096,6 +3243,7 @@ files = [
 name = "pure-eval"
 version = "0.2.3"
 description = "Safely evaluate AST nodes without side effects"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -3110,6 +3258,7 @@ tests = ["pytest"]
 name = "pyasn1"
 version = "0.6.1"
 description = "Pure-Python implementation of ASN.1 types and DER/BER/CER codecs (X.208)"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3121,6 +3270,7 @@ files = [
 name = "pyasn1-modules"
 version = "0.4.1"
 description = "A collection of ASN.1-based protocols modules"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3135,6 +3285,7 @@ pyasn1 = ">=0.4.6,<0.7.0"
 name = "pycodestyle"
 version = "2.11.1"
 description = "Python style guide checker"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3146,6 +3297,7 @@ files = [
 name = "pycparser"
 version = "2.22"
 description = "C parser in Python"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3157,6 +3309,7 @@ files = [
 name = "pydantic"
 version = "1.10.18"
 description = "Data validation and settings management using python type hints"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3216,6 +3369,7 @@ email = ["email-validator (>=1.0.3)"]
 name = "pyflakes"
 version = "3.1.0"
 description = "passive checker of Python programs"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3227,6 +3381,7 @@ files = [
 name = "pygments"
 version = "2.18.0"
 description = "Pygments is a syntax highlighting package written in Python."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3241,6 +3396,7 @@ windows-terminal = ["colorama (>=0.4.6)"]
 name = "pygsheets"
 version = "2.0.6"
 description = "Google Spreadsheets Python API v4"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -3259,6 +3415,7 @@ pandas = ["pandas (>=0.14.0)"]
 name = "pyjwt"
 version = "2.9.0"
 description = "JSON Web Token implementation in Python"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3276,6 +3433,7 @@ tests = ["coverage[toml] (==5.0.4)", "pytest (>=6.0.0,<7.0.0)"]
 name = "pylint"
 version = "2.17.7"
 description = "python code static checker"
+category = "dev"
 optional = false
 python-versions = ">=3.7.2"
 files = [
@@ -3302,6 +3460,7 @@ testutils = ["gitpython (>3)"]
 name = "pyopenssl"
 version = "23.3.0"
 description = "Python wrapper module around the OpenSSL library"
+category = "main"
 optional = true
 python-versions = ">=3.7"
 files = [
@@ -3320,6 +3479,7 @@ test = ["flaky", "pretend", "pytest (>=3.0.1)"]
 name = "pyparsing"
 version = "3.2.0"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -3334,6 +3494,7 @@ diagrams = ["jinja2", "railroad-diagrams"]
 name = "pytest"
 version = "8.3.3"
 description = "pytest: simple powerful testing with Python"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3356,6 +3517,7 @@ dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments
 name = "pytest-asyncio"
 version = "0.24.0"
 description = "Pytest support for asyncio"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3374,6 +3536,7 @@ testing = ["coverage (>=6.2)", "hypothesis (>=5.7.1)"]
 name = "pytest-cov"
 version = "4.1.0"
 description = "Pytest plugin for measuring coverage."
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3392,6 +3555,7 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtuale
 name = "pytest-mock"
 version = "3.14.0"
 description = "Thin-wrapper around the mock package for easier use with pytest"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3409,6 +3573,7 @@ dev = ["pre-commit", "pytest-asyncio", "tox"]
 name = "pytest-rerunfailures"
 version = "12.0"
 description = "pytest plugin to re-run tests to eliminate flaky failures"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3424,6 +3589,7 @@ pytest = ">=6.2"
 name = "pytest-xdist"
 version = "3.6.1"
 description = "pytest xdist plugin for distributed testing, most importantly across multiple CPUs"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3444,6 +3610,7 @@ testing = ["filelock"]
 name = "python-dateutil"
 version = "2.9.0.post0"
 description = "Extensions to the standard Python datetime module"
+category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
@@ -3458,6 +3625,7 @@ six = ">=1.5"
 name = "python-dotenv"
 version = "0.21.1"
 description = "Read key-value pairs from a .env file and set them as environment variables"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3472,6 +3640,7 @@ cli = ["click (>=5.0)"]
 name = "python-json-logger"
 version = "2.0.7"
 description = "A python library adding a json log formatter"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -3483,6 +3652,7 @@ files = [
 name = "pytz"
 version = "2024.2"
 description = "World timezone definitions, modern and historical"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -3494,6 +3664,7 @@ files = [
 name = "pywin32"
 version = "308"
 description = "Python for Window Extensions"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -3521,6 +3692,7 @@ files = [
 name = "pywinpty"
 version = "2.0.14"
 description = "Pseudo terminal support for Windows from Python."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3536,6 +3708,7 @@ files = [
 name = "pyyaml"
 version = "6.0.2"
 description = "YAML parser and emitter for Python"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3598,6 +3771,7 @@ files = [
 name = "pyzmq"
 version = "26.2.0"
 description = "Python bindings for 0MQ"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3719,6 +3893,7 @@ cffi = {version = "*", markers = "implementation_name == \"pypy\""}
 name = "rdflib"
 version = "6.3.2"
 description = "RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information."
+category = "main"
 optional = false
 python-versions = ">=3.7,<4.0"
 files = [
@@ -3740,6 +3915,7 @@ networkx = ["networkx (>=2.0.0,<3.0.0)"]
 name = "referencing"
 version = "0.35.1"
 description = "JSON Referencing + Python"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3755,6 +3931,7 @@ rpds-py = ">=0.7.0"
 name = "regex"
 version = "2024.9.11"
 description = "Alternative regular expression module, to replace re."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3858,6 +4035,7 @@ files = [
 name = "requests"
 version = "2.32.3"
 description = "Python HTTP for Humans."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3879,6 +4057,7 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 name = "requests-oauthlib"
 version = "2.0.0"
 description = "OAuthlib authentication support for Requests."
+category = "main"
 optional = false
 python-versions = ">=3.4"
 files = [
@@ -3897,6 +4076,7 @@ rsa = ["oauthlib[signedtoken] (>=3.0.0)"]
 name = "rfc3339-validator"
 version = "0.1.4"
 description = "A pure python RFC3339 validator"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -3911,6 +4091,7 @@ six = "*"
 name = "rfc3986-validator"
 version = "0.1.1"
 description = "Pure python rfc3986 validator"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -3922,6 +4103,7 @@ files = [
 name = "rpds-py"
 version = "0.20.1"
 description = "Python bindings to Rust's persistent data structures (rpds)"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4034,6 +4216,7 @@ files = [
 name = "rsa"
 version = "4.9"
 description = "Pure-Python RSA implementation"
+category = "main"
 optional = false
 python-versions = ">=3.6,<4"
 files = [
@@ -4048,6 +4231,7 @@ pyasn1 = ">=0.1.3"
 name = "ruamel-yaml"
 version = "0.17.17"
 description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order"
+category = "main"
 optional = false
 python-versions = ">=3"
 files = [
@@ -4066,6 +4250,7 @@ jinja2 = ["ruamel.yaml.jinja2 (>=0.2)"]
 name = "ruamel-yaml-clib"
 version = "0.2.12"
 description = "C version of reader, parser and emitter for ruamel.yaml derived from libyaml"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -4116,6 +4301,7 @@ files = [
 name = "scipy"
 version = "1.13.1"
 description = "Fundamental algorithms for scientific computing in Python"
+category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -4158,6 +4344,7 @@ test = ["array-api-strict", "asv", "gmpy2", "hypothesis (>=6.30)", "mpmath", "po
 name = "send2trash"
 version = "1.8.3"
 description = "Send file to trash natively under Mac OS X, Windows and Linux"
+category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
 files = [
@@ -4174,6 +4361,7 @@ win32 = ["pywin32"]
 name = "setuptools"
 version = "66.1.1"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4190,6 +4378,7 @@ testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (
 name = "six"
 version = "1.16.0"
 description = "Python 2 and 3 compatibility utilities"
+category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
@@ -4201,6 +4390,7 @@ files = [
 name = "sniffio"
 version = "1.3.1"
 description = "Sniff out which async library your code is running under"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4212,6 +4402,7 @@ files = [
 name = "snowballstemmer"
 version = "2.2.0"
 description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
+category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -4223,6 +4414,7 @@ files = [
 name = "soupsieve"
 version = "2.6"
 description = "A modern CSS selector implementation for Beautiful Soup."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4234,6 +4426,7 @@ files = [
 name = "sphinx"
 version = "7.3.7"
 description = "Python documentation generator"
+category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -4270,6 +4463,7 @@ test = ["cython (>=3.0)", "defusedxml (>=0.7.1)", "pytest (>=6.0)", "setuptools
 name = "sphinx-click"
 version = "4.4.0"
 description = "Sphinx extension that automatically documents click applications"
+category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4282,10 +4476,31 @@ click = ">=7.0"
 docutils = "*"
 sphinx = ">=2.0"
 
+[[package]]
+name = "sphinx-rtd-theme"
+version = "3.0.1"
+description = "Read the Docs theme for Sphinx"
+category = "dev"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "sphinx_rtd_theme-3.0.1-py2.py3-none-any.whl", hash = "sha256:921c0ece75e90633ee876bd7b148cfaad136b481907ad154ac3669b6fc957916"},
+    {file = "sphinx_rtd_theme-3.0.1.tar.gz", hash = "sha256:a4c5745d1b06dfcb80b7704fe532eb765b44065a8fad9851e4258c8804140703"},
+]
+
+[package.dependencies]
+docutils = ">0.18,<0.22"
+sphinx = ">=6,<9"
+sphinxcontrib-jquery = ">=4,<5"
+
+[package.extras]
+dev = ["bump2version", "transifex-client", "twine", "wheel"]
+
 [[package]]
 name = "sphinxcontrib-applehelp"
 version = "2.0.0"
 description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
+category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -4302,6 +4517,7 @@ test = ["pytest"]
 name = "sphinxcontrib-devhelp"
 version = "2.0.0"
 description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
+category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -4318,6 +4534,7 @@ test = ["pytest"]
 name = "sphinxcontrib-htmlhelp"
 version = "2.1.0"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
+category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -4330,10 +4547,26 @@ lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
 standalone = ["Sphinx (>=5)"]
 test = ["html5lib", "pytest"]
 
+[[package]]
+name = "sphinxcontrib-jquery"
+version = "4.1"
+description = "Extension to include jQuery on newer Sphinx releases"
+category = "dev"
+optional = false
+python-versions = ">=2.7"
+files = [
+    {file = "sphinxcontrib-jquery-4.1.tar.gz", hash = "sha256:1620739f04e36a2c779f1a131a2dfd49b2fd07351bf1968ced074365933abc7a"},
+    {file = "sphinxcontrib_jquery-4.1-py2.py3-none-any.whl", hash = "sha256:f936030d7d0147dd026a4f2b5a57343d233f1fc7b363f68b3d4f1cb0993878ae"},
+]
+
+[package.dependencies]
+Sphinx = ">=1.8"
+
 [[package]]
 name = "sphinxcontrib-jsmath"
 version = "1.0.1"
 description = "A sphinx extension which renders display math in HTML via JavaScript"
+category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -4348,6 +4581,7 @@ test = ["flake8", "mypy", "pytest"]
 name = "sphinxcontrib-qthelp"
 version = "2.0.0"
 description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
+category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -4364,6 +4598,7 @@ test = ["defusedxml (>=0.7.1)", "pytest"]
 name = "sphinxcontrib-serializinghtml"
 version = "2.0.0"
 description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
+category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -4380,6 +4615,7 @@ test = ["pytest"]
 name = "stack-data"
 version = "0.6.3"
 description = "Extract data from python stack frames and tracebacks for informative displays"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -4399,6 +4635,7 @@ tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
 name = "swagger-ui-bundle"
 version = "0.0.9"
 description = "swagger_ui_bundle - swagger-ui files in a pip package"
+category = "main"
 optional = true
 python-versions = "*"
 files = [
@@ -4413,6 +4650,7 @@ Jinja2 = ">=2.0"
 name = "synapseclient"
 version = "4.5.1"
 description = "A client for Synapse, a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4450,6 +4688,7 @@ tests = ["flake8 (>=3.7.0,<4.0)", "func-timeout (>=4.3,<5.0)", "pandas (>=1.5,<3
 name = "tenacity"
 version = "8.5.0"
 description = "Retry code until it succeeds"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4465,6 +4704,7 @@ test = ["pytest", "tornado (>=4.5)", "typeguard"]
 name = "terminado"
 version = "0.18.1"
 description = "Tornado websocket backend for the Xterm.js Javascript terminal emulator library."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4486,6 +4726,7 @@ typing = ["mypy (>=1.6,<2.0)", "traitlets (>=5.11.1)"]
 name = "tinycss2"
 version = "1.4.0"
 description = "A tiny CSS parser"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4504,6 +4745,7 @@ test = ["pytest", "ruff"]
 name = "toml"
 version = "0.10.2"
 description = "Python Library for Tom's Obvious, Minimal Language"
+category = "main"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
@@ -4515,6 +4757,7 @@ files = [
 name = "tomli"
 version = "2.0.2"
 description = "A lil' TOML parser"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4526,6 +4769,7 @@ files = [
 name = "tomlkit"
 version = "0.13.2"
 description = "Style preserving TOML library"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4537,6 +4781,7 @@ files = [
 name = "toolz"
 version = "1.0.0"
 description = "List processing tools and functional utilities"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4548,6 +4793,7 @@ files = [
 name = "tornado"
 version = "6.4.1"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4568,6 +4814,7 @@ files = [
 name = "tqdm"
 version = "4.66.6"
 description = "Fast, Extensible Progress Meter"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4588,6 +4835,7 @@ telegram = ["requests"]
 name = "traitlets"
 version = "5.14.3"
 description = "Traitlets Python configuration system"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4603,6 +4851,7 @@ test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,
 name = "types-python-dateutil"
 version = "2.9.0.20241003"
 description = "Typing stubs for python-dateutil"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4614,6 +4863,7 @@ files = [
 name = "typing-extensions"
 version = "4.12.2"
 description = "Backported and Experimental Type Hints for Python 3.8+"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4625,6 +4875,7 @@ files = [
 name = "typing-inspect"
 version = "0.9.0"
 description = "Runtime inspection utilities for typing module."
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -4640,6 +4891,7 @@ typing-extensions = ">=3.7.4"
 name = "tzdata"
 version = "2024.2"
 description = "Provider of IANA time zone data"
+category = "main"
 optional = false
 python-versions = ">=2"
 files = [
@@ -4651,6 +4903,7 @@ files = [
 name = "tzlocal"
 version = "5.2"
 description = "tzinfo object for the local timezone"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4668,6 +4921,7 @@ devenv = ["check-manifest", "pytest (>=4.3)", "pytest-cov", "pytest-mock (>=3.3)
 name = "uri-template"
 version = "1.3.0"
 description = "RFC 6570 URI Template Processor"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4682,6 +4936,7 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake
 name = "uritemplate"
 version = "4.1.1"
 description = "Implementation of RFC 6570 URI Templates"
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -4693,6 +4948,7 @@ files = [
 name = "urllib3"
 version = "1.26.20"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
+category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
 files = [
@@ -4709,6 +4965,7 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 name = "uwsgi"
 version = "2.0.28"
 description = "The uWSGI server"
+category = "main"
 optional = true
 python-versions = "*"
 files = [
@@ -4719,6 +4976,7 @@ files = [
 name = "virtualenv"
 version = "20.27.1"
 description = "Virtual Python Environment builder"
+category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4739,6 +4997,7 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess
 name = "wcwidth"
 version = "0.2.13"
 description = "Measures the displayed width of unicode strings in a terminal"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -4750,6 +5009,7 @@ files = [
 name = "webcolors"
 version = "24.8.0"
 description = "A library for working with the color formats defined by HTML and CSS."
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4765,6 +5025,7 @@ tests = ["coverage[toml]"]
 name = "webencodings"
 version = "0.5.1"
 description = "Character encoding aliases for legacy web content"
+category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -4776,6 +5037,7 @@ files = [
 name = "websocket-client"
 version = "1.8.0"
 description = "WebSocket client for Python with low level API options"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4790,25 +5052,27 @@ test = ["websockets"]
 
 [[package]]
 name = "werkzeug"
-version = "2.3.8"
+version = "2.2.3"
 description = "The comprehensive WSGI web application library."
+category = "main"
 optional = true
-python-versions = ">=3.8"
+python-versions = ">=3.7"
 files = [
-    {file = "werkzeug-2.3.8-py3-none-any.whl", hash = "sha256:bba1f19f8ec89d4d607a3bd62f1904bd2e609472d93cd85e9d4e178f472c3748"},
-    {file = "werkzeug-2.3.8.tar.gz", hash = "sha256:554b257c74bbeb7a0d254160a4f8ffe185243f52a52035060b761ca62d977f03"},
+    {file = "Werkzeug-2.2.3-py3-none-any.whl", hash = "sha256:56433961bc1f12533306c624f3be5e744389ac61d722175d543e1751285da612"},
+    {file = "Werkzeug-2.2.3.tar.gz", hash = "sha256:2e1ccc9417d4da358b9de6f174e3ac094391ea1d4fbef2d667865d819dfd0afe"},
 ]
 
 [package.dependencies]
 MarkupSafe = ">=2.1.1"
 
 [package.extras]
-watchdog = ["watchdog (>=2.3)"]
+watchdog = ["watchdog"]
 
 [[package]]
 name = "widgetsnbextension"
 version = "4.0.13"
 description = "Jupyter interactive widgets for Jupyter Notebook"
+category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4820,6 +5084,7 @@ files = [
 name = "wrapt"
 version = "1.16.0"
 description = "Module for decorators, wrappers and monkey patching."
+category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -4899,6 +5164,7 @@ files = [
 name = "zipp"
 version = "3.20.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
+category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4915,10 +5181,10 @@ test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools",
 type = ["pytest-mypy"]
 
 [extras]
-api = ["Flask", "Flask-Cors", "Jinja2", "connexion", "opentelemetry-api", "opentelemetry-exporter-otlp-proto-grpc", "opentelemetry-instrumentation-flask", "opentelemetry-sdk", "pyopenssl"]
+api = ["connexion", "Flask", "Flask-Cors", "Jinja2", "pyopenssl", "opentelemetry-api", "opentelemetry-sdk", "opentelemetry-exporter-otlp-proto-grpc", "opentelemetry-instrumentation-flask"]
 aws = ["uWSGI"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9.0,<3.11"
-content-hash = "efc1087459d60c13452c8cb50661294face689bafabb84cb83604441337828f2"
+content-hash = "0cdcd5891f5028d89505bb36bb7b5d9c7ba17b2296574170eb575e12d4627b93"
diff --git a/pyproject.toml b/pyproject.toml
index d415c661c..339be5789 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -96,6 +96,7 @@ pre-commit = "^3.6.2"
 
 [tool.poetry.group.doc.dependencies]
 pdoc = "^14.0.0"
+sphinx-rtd-theme = "3.0.1"
 sphinx = "7.3.7"
 sphinx-click = "4.4.0"
 

From 028f6e800b230d61cadfb07d3e4c28667b90e59f Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Fri, 1 Nov 2024 21:41:28 -0700
Subject: [PATCH 10/47] Add to documentation

---
 docs/source/asset_store.rst | 40 ++++++++++++++++++++++---------------
 1 file changed, 24 insertions(+), 16 deletions(-)

diff --git a/docs/source/asset_store.rst b/docs/source/asset_store.rst
index abe3c9bf0..273210351 100644
--- a/docs/source/asset_store.rst
+++ b/docs/source/asset_store.rst
@@ -19,6 +19,19 @@ Pick **option 1** if you answer "yes" to one or more of the following questions:
 - Will contributors submit more than 100 datasets per release or per month?
 - Are you not willing to annotate each DCC dataset folder with the annotation `contentType:dataset`?
 
+Access & Project Setup - Multiple Contributing Projects
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+1. Create a DCC Admin Team with admin permissions.
+2. Create a Team for each data contributing institution. Begin with a "Test Team" if all teams are not yet identified.
+3. Create a Synapse Project for each institution and grant the respective team **Edit** level access.
+   - E.g., for institutions A, B, and C, create Projects A, B, and C with Teams A, B, and C. Team A has **Edit** access to Project A, etc.
+4. Within each project, create top-level dataset folders in the **Files** tab for each dataset type.
+5. Create another Synapse Project (e.g., MyDCC) containing the main **Fileview** for all DCC projects.
+   - Ensure all teams have **Download** level access to this file view.
+   - Include both file and folder entities and add the columns `id`, `name`, `type`, `parentId`, and `projectId` to the Fileview schema.
+
+
 Option 2: Single Synapse Project
 --------------------------------
 
@@ -30,20 +43,9 @@ Pick **option 2** if you don't select option 1 and you answer "yes" to any of th
 
 If neither option fits, select option 1.
 
-Option 1: Access & Project Setup - Multiple Contributing Projects
-------------------------------------------------------------------
 
-1. Create a DCC Admin Team with admin permissions.
-2. Create a Team for each data contributing institution. Begin with a "Test Team" if all teams are not yet identified.
-3. Create a Synapse Project for each institution and grant the respective team **Edit** level access.
-   - E.g., for institutions A, B, and C, create Projects A, B, and C with Teams A, B, and C. Team A has **Edit** access to Project A, etc.
-4. Within each project, create top-level dataset folders in the **Files** tab for each dataset type.
-5. Create another Synapse Project (e.g., MyDCC) containing the main **Fileview** for all DCC projects.
-   - Ensure all teams have **Download** level access to this file view.
-   - Include both file and folder entities and add the columns `id`, `name`, `type`, `parentId`, and `projectId` to the Fileview schema.
-
-Option 2: Access & Project Setup - Single Contributing Project
---------------------------------------------------------------
+Access & Project Setup - Single Contributing Project
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 1. Create a Team for each data contributing institution.
 2. Create a single Synapse Project (e.g., MyDCC).
@@ -52,16 +54,22 @@ Option 2: Access & Project Setup - Single Contributing Project
 4. In MyDCC, create the main **DCC Fileview** with `MyDCC` as scope. Add column `contentType` to the schema and grant teams **Download** level access.
    - Add both file and folder entities and ensure columns `id`, `name`, `type`, `parentId`, `projectId`, and `contentType` are included.
 
-External Cloud Buckets Setup
------------------------------
 
-If DCC contributors require external cloud buckets, select one of the following configurations:
+Synapse External Cloud Buckets Setup
+------------------------------------
+
+If DCC contributors require external cloud buckets, select one of the following configurations.  For more information on how to
+set this up on Synapse, view this documentation: https://help.synapse.org/docs/Custom-Storage-Locations.2048327803.html
 
 1. **Basic External Storage Bucket (Default)**:
    - Create an S3 bucket for Synapse uploads via web or CLI. Contributors will upload data without needing AWS credentials.
    - Provision an S3 bucket, attach it to the Synapse project, and create folders for specific assay types.
 
 2. **Custom Storage Location**:
+
+This is an advanced setup for users that do not want to upload files directly via the Synapse API, but rather
+create pointers to the data.
+
    - For large datasets or if contributors prefer cloud storage, enable uploads via AWS CLI or GCP CLI.
    - Configure the custom storage location with an AWS Lambda or Google Cloud function for syncing.
    - If using AWS, provision a bucket, set up Lambda sync, and assign IAM write access.

From 2ed9764e9f315d8fa25552d07315b84f00c46bf1 Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Fri, 1 Nov 2024 21:42:40 -0700
Subject: [PATCH 11/47] edit documentation

---
 docs/source/asset_store.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/source/asset_store.rst b/docs/source/asset_store.rst
index 273210351..a30c2032d 100644
--- a/docs/source/asset_store.rst
+++ b/docs/source/asset_store.rst
@@ -29,7 +29,7 @@ Access & Project Setup - Multiple Contributing Projects
 4. Within each project, create top-level dataset folders in the **Files** tab for each dataset type.
 5. Create another Synapse Project (e.g., MyDCC) containing the main **Fileview** for all DCC projects.
    - Ensure all teams have **Download** level access to this file view.
-   - Include both file and folder entities and add the columns `id`, `name`, `type`, `parentId`, and `projectId` to the Fileview schema.
+   - Include both file and folder entities and add ALL default columns.
 
 
 Option 2: Single Synapse Project
@@ -52,7 +52,7 @@ Access & Project Setup - Single Contributing Project
 3. Within this project, create dataset folders for each contributor. Organize them as needed.
    - Use `contentType:dataset` for each dataset folder, which should not nest inside other dataset folders and must have unique names.
 4. In MyDCC, create the main **DCC Fileview** with `MyDCC` as scope. Add column `contentType` to the schema and grant teams **Download** level access.
-   - Add both file and folder entities and ensure columns `id`, `name`, `type`, `parentId`, `projectId`, and `contentType` are included.
+   - Add both file and folder entities and add ALL default columns.
 
 
 Synapse External Cloud Buckets Setup

From 4ea312211c9f6249f648ec070068405bef502cba Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Fri, 1 Nov 2024 21:45:38 -0700
Subject: [PATCH 12/47] Add more details

---
 docs/source/asset_store.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/asset_store.rst b/docs/source/asset_store.rst
index a30c2032d..f98c02549 100644
--- a/docs/source/asset_store.rst
+++ b/docs/source/asset_store.rst
@@ -27,7 +27,7 @@ Access & Project Setup - Multiple Contributing Projects
 3. Create a Synapse Project for each institution and grant the respective team **Edit** level access.
    - E.g., for institutions A, B, and C, create Projects A, B, and C with Teams A, B, and C. Team A has **Edit** access to Project A, etc.
 4. Within each project, create top-level dataset folders in the **Files** tab for each dataset type.
-5. Create another Synapse Project (e.g., MyDCC) containing the main **Fileview** for all DCC projects.
+5. Create another Synapse Project (e.g., MyDCC) containing the main **Fileview** that includes in the scope all the DCC projects.
    - Ensure all teams have **Download** level access to this file view.
    - Include both file and folder entities and add ALL default columns.
 

From 356a72279cb3ecacbea109004eb348fd3ca536e7 Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Fri, 1 Nov 2024 21:50:00 -0700
Subject: [PATCH 13/47] Add in configuration

---
 docs/source/configuration.rst | 51 +++++++++++++++++++++++++++++++++++
 docs/source/generate.rst      |  4 ---
 docs/source/index.rst         |  6 ++---
 docs/source/submit.rst        | 12 ---------
 docs/source/validate.rst      | 12 ---------
 5 files changed, 54 insertions(+), 31 deletions(-)
 create mode 100644 docs/source/configuration.rst
 delete mode 100644 docs/source/generate.rst
 delete mode 100644 docs/source/submit.rst
 delete mode 100644 docs/source/validate.rst

diff --git a/docs/source/configuration.rst b/docs/source/configuration.rst
new file mode 100644
index 000000000..ce354319c
--- /dev/null
+++ b/docs/source/configuration.rst
@@ -0,0 +1,51 @@
+Configure Schematic
+===================
+
+Schematic takes a configuration file with the following structure:
+
+.. code-block:: yaml
+    # This is an example config for Schematic.
+    # All listed values are those that are the default if a config is not used.
+    # Save this as config.yml, this will be gitignored.
+    # Remove any fields in the config you don't want to change
+    # If you remove all fields from a section, the entire section should be removed including the header.
+    # Change the values of any fields you do want to change
+
+    # This describes where assets such as manifests are stored
+    asset_store:
+        # This is when assets are stored in a synapse project
+        synapse:
+            # Synapse ID of the file view listing all project data assets.
+            master_fileview_id: "syn23643253"
+            # Path to the synapse config file, either absolute or relative to this file
+            config: ".synapseConfig"
+            # Base name that manifest files will be saved as
+            manifest_basename: "synapse_storage_manifest"
+
+    # This describes information about manifests as it relates to generation and validation
+    manifest:
+        # Location where manifests will saved to
+        manifest_folder: "manifests"
+        # Title or title prefix given to generated manifest(s)
+        title: "example"
+        # Data types of manifests to be generated or data type (singular) to validate manifest against
+        data_type:
+            - "Biospecimen"
+            - "Patient"
+
+    # Describes the location of your schema
+    model:
+        # Location of your schema jsonld, it must be a path relative to this file or absolute
+        location: "tests/data/example.model.jsonld"
+
+    # This section is for using google sheets with Schematic
+    google_sheets:
+        # Path to the synapse config file, either absolute or relative to this file
+        service_acct_creds: "schematic_service_account_creds.json"
+        # When doing google sheet validation (regex match) with the validation rules.
+        #   true is alerting the user and not allowing entry of bad values.
+        #   false is warning but allowing the entry on to the sheet.
+        strict_validation: true
+
+
+This document will go into detail what each of these configurations mean.
diff --git a/docs/source/generate.rst b/docs/source/generate.rst
deleted file mode 100644
index 91a9cb7f6..000000000
--- a/docs/source/generate.rst
+++ /dev/null
@@ -1,4 +0,0 @@
-Generate
-========
-
-Provides a manifest template for users for a particular project or data type. If a project with annotations already exists, a semi-filled-out template is provided to the user so that they do not start from scratch. If there are no existing annotations, an empty manifest template is provided.
diff --git a/docs/source/index.rst b/docs/source/index.rst
index ce360acd2..1fefce585 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -50,6 +50,8 @@ Given a filled-out manifest:
       - **Store manifest and annotations** (to update a file view)
       - **Store manifest and update a corresponding Synapse table**
 
+More validation documentation can be found here: https://sagebionetworks.jira.com/wiki/spaces/SCHEM/pages/3302785036/Schematic+Validation
+
 4. Visualize Data Models
 -------------------------
 
@@ -62,7 +64,5 @@ This endpoint allows you to visulize your data models and their relationships wi
 
    installation
    asset_store
-   generate
-   validate
-   submit
+   configuration
    cli_reference
diff --git a/docs/source/submit.rst b/docs/source/submit.rst
deleted file mode 100644
index 1afd9f408..000000000
--- a/docs/source/submit.rst
+++ /dev/null
@@ -1,12 +0,0 @@
-Submit
-======
-
-
-- Validates the manifest. If errors are present, the manifest is not stored.
-- If valid:
-  - Stores the manifest in Synapse.
-  - Uploads the manifest to a view, updating file views with annotations as follows:
-
-      - **Store manifest only**
-      - **Store manifest and annotations** (to update a file view)
-      - **Store manifest and update a corresponding Synapse table**
diff --git a/docs/source/validate.rst b/docs/source/validate.rst
deleted file mode 100644
index db31073d6..000000000
--- a/docs/source/validate.rst
+++ /dev/null
@@ -1,12 +0,0 @@
-Validate
-========
-
-Given a filled-out manifest:
-
-- The manifest is validated against the JSON-LD schema as it maps to GX rules.
-- A ``jsonschema`` is generated from the data model. The data model can be in CSV, JSON-LD format, as input formats are decoupled from the internal data model representation within Schematic.
-- A set of validation rules is defined in the data model. Some validation rules are implemented via GX; others are custom Python code. All validation rules have the same interface.
-- Certain GX rules require looping through all projects a user has access to, or a specified scope of projects, to find other projects with manifests.
-- Validation results are provided before the manifest file is uploaded into Synapse.
-
-More validation documentation can be found here: https://sagebionetworks.jira.com/wiki/spaces/SCHEM/pages/3302785036/Schematic+Validation

From b1493b0961e15082ef8b748365aaab019024e457 Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Fri, 1 Nov 2024 21:59:21 -0700
Subject: [PATCH 14/47] Add in more terms

---
 docs/source/configuration.rst |  1 +
 docs/source/index.rst         | 34 +++++++++++++++++++++++++++++++---
 2 files changed, 32 insertions(+), 3 deletions(-)

diff --git a/docs/source/configuration.rst b/docs/source/configuration.rst
index ce354319c..f84fa49e9 100644
--- a/docs/source/configuration.rst
+++ b/docs/source/configuration.rst
@@ -4,6 +4,7 @@ Configure Schematic
 Schematic takes a configuration file with the following structure:
 
 .. code-block:: yaml
+
     # This is an example config for Schematic.
     # All listed values are those that are the default if a config is not used.
     # Save this as config.yml, this will be gitignored.
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 1fefce585..5579486bc 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -10,9 +10,37 @@ Welcome to Schematic's documentation!
 
 Schematic tackles these goals:
 
-- “Ensure the highest quality structured data or metadata be contributed to Synapse BEFORE it lands in Synapse”
-- “Add accountability to data contributors for the data they upload”
-- “Visualize data models and their relationships with each other”
+- Ensure the highest quality structured data or metadata be contributed to Synapse BEFORE it lands in Synapse
+- Add accountability to data contributors for the data they upload
+- Visualize data models and their relationships with each other
+
+Important Concepts
+------------------
+
+.. important::
+   Before moving reading more about schematic, this section covers essential Synapse concepts relevant for using the Schematic tool effectively.
+
+Synapse FileViews
+~~~~~~~~~~~~~~~~~
+Data managers and DCC owners are responsible for setting up a **FileView** that integrates with Schematic. Note that FileViews appear under the "Tables" tab in Synapse and can be named according to the project’s needs. For instance, a FileView for the **NF project** could have a different name than a FileView for the **AD project**.
+
+For more information on Synapse projects, visit:
+- `Synapse projects <https://help.synapse.org/docs/Uploading-and-Organizing-Data-Into-Projects,-Files,-and-Folders.2048327716.html>`_
+- `Synapse annotations <https://help.synapse.org/docs/Annotating-Data-With-Metadata.2667708522.html>`_
+
+Synapse Folders
+~~~~~~~~~~~~~~~
+
+Folders in Synapse allow users to organize data within projects. More details on uploading and organizing data can be found at `Synapse folders <https://help.synapse.org/docs/Uploading-and-Organizing-Data-Into-Projects,-Files,-and-Folders.2048327716.html>`_
+
+Datasets
+~~~~~~~~
+You will hear the term **dataset** used frequently at Sage. The term dataset refers to three different concepts:
+
+1. Dataset: This is the concept of a dataset which is a collection of files.
+2. Schematic Dataset: This refers to a folder containing files. These folders are annotated with `contentType:dataset`.
+3. Synapse Dataset Entity: This is an object in Synapse which appears under the "Dataset" tab and represents a user-defined collection of Synapse files and versions.
+
 
 The usage of JSON-LD
 --------------------

From 92c2db6c3783f708bb6912222d392ef3c5f5e5d6 Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Fri, 1 Nov 2024 22:00:29 -0700
Subject: [PATCH 15/47] Edit

---
 docs/source/index.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/index.rst b/docs/source/index.rst
index 5579486bc..f886e8057 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -48,7 +48,7 @@ The usage of JSON-LD
 The usage of JSON-LD to capture our data models extends beyond the creation, validation, and submission of annotations/manifests into Synapse. It can create relationships between different data models and, in the future, drive transformation of data from one data model to another. Visualization of these data models and their relationships is also possible (see *Schema Visualization - Design & Platform*), which allows the community to see the depth of connections between all the data uploaded into Synapse. As with all products, we must start somewhere.
 
 
-The following are the three main endpoints that assist with the high-level goals outlined above, with additional goals to come.
+The following are the four main endpoints that assist with the high-level goals outlined above, with additional goals to come.
 
 1. Manifest Generation
 ----------------------

From 99bc347ba9024cdb499195a78bd4230f6f83156e Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Fri, 1 Nov 2024 22:04:45 -0700
Subject: [PATCH 16/47] Add documentation

---
 docs/source/index.rst | 31 ++++++++++++++++++-------------
 1 file changed, 18 insertions(+), 13 deletions(-)

diff --git a/docs/source/index.rst b/docs/source/index.rst
index f886e8057..08d9953b9 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -14,6 +14,10 @@ Schematic tackles these goals:
 - Add accountability to data contributors for the data they upload
 - Visualize data models and their relationships with each other
 
+.. contents::
+   :depth: 2
+   :local:
+
 Important Concepts
 ------------------
 
@@ -41,22 +45,23 @@ You will hear the term **dataset** used frequently at Sage. The term dataset ref
 2. Schematic Dataset: This refers to a folder containing files. These folders are annotated with `contentType:dataset`.
 3. Synapse Dataset Entity: This is an object in Synapse which appears under the "Dataset" tab and represents a user-defined collection of Synapse files and versions.
 
+JSON-LD
+~~~~~~~
+JSON-LD is a lightweight Linked Data format. The usage of JSON-LD to capture our data models extends beyond the creation, validation, and submission of annotations/manifests into Synapse. It can create relationships between different data models and, in the future, drive transformation of data from one data model to another. Visualization of these data models and their relationships is also possible (see *Schema Visualization - Design & Platform*), which allows the community to see the depth of connections between all the data uploaded into Synapse. As with all products, we must start somewhere.
 
-The usage of JSON-LD
---------------------
-
-The usage of JSON-LD to capture our data models extends beyond the creation, validation, and submission of annotations/manifests into Synapse. It can create relationships between different data models and, in the future, drive transformation of data from one data model to another. Visualization of these data models and their relationships is also possible (see *Schema Visualization - Design & Platform*), which allows the community to see the depth of connections between all the data uploaded into Synapse. As with all products, we must start somewhere.
 
+Schematic services
+------------------
 
 The following are the four main endpoints that assist with the high-level goals outlined above, with additional goals to come.
 
-1. Manifest Generation
-----------------------
+Manifest Generation
+~~~~~~~~~~~~~~~~~~~
 
 Provides a manifest template for users for a particular project or data type. If a project with annotations already exists, a semi-filled-out template is provided to the user so that they do not start from scratch. If there are no existing annotations, an empty manifest template is provided.
 
-2. Validate Manifest
---------------------
+Manifest Validation
+~~~~~~~~~~~~~~~~~~~
 
 Given a filled-out manifest:
 
@@ -66,8 +71,8 @@ Given a filled-out manifest:
 - Certain GX rules require looping through all projects a user has access to, or a specified scope of projects, to find other projects with manifests.
 - Validation results are provided before the manifest file is uploaded into Synapse.
 
-3. Submit Manifest
-------------------
+Manifest Submission
+~~~~~~~~~~~~~~~~~~~
 
 - Validates the manifest. If errors are present, the manifest is not stored.
 - If valid:
@@ -80,10 +85,10 @@ Given a filled-out manifest:
 
 More validation documentation can be found here: https://sagebionetworks.jira.com/wiki/spaces/SCHEM/pages/3302785036/Schematic+Validation
 
-4. Visualize Data Models
--------------------------
+Data Model Visualization
+~~~~~~~~~~~~~~~~~~~~~~~~
 
-This endpoint allows you to visulize your data models and their relationships with each other.
+These endpoints allows you to visulize your data models and their relationships with each other.
 
 
 .. toctree::

From 5b99d89182507e395874a21f74ce6bdb489aefe8 Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Fri, 1 Nov 2024 22:13:54 -0700
Subject: [PATCH 17/47] Add documentation

---
 docs/source/index.rst | 26 ++++++++++++++++++++------
 1 file changed, 20 insertions(+), 6 deletions(-)

diff --git a/docs/source/index.rst b/docs/source/index.rst
index 08d9953b9..565dc2c78 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -10,8 +10,8 @@ Welcome to Schematic's documentation!
 
 Schematic tackles these goals:
 
-- Ensure the highest quality structured data or metadata be contributed to Synapse BEFORE it lands in Synapse
-- Add accountability to data contributors for the data they upload
+- Ensure the highest quality structured data or metadata be contributed to Synapse before it lands in Synapse
+- Provide excel templates that correspond to a data model that can be filled out by data contributors
 - Visualize data models and their relationships with each other
 
 .. contents::
@@ -22,11 +22,11 @@ Important Concepts
 ------------------
 
 .. important::
-   Before moving reading more about schematic, this section covers essential Synapse concepts relevant for using the Schematic tool effectively.
+   Before moving reading more about schematic, this section covers essential concepts relevant for using the Schematic tool effectively.
 
 Synapse FileViews
 ~~~~~~~~~~~~~~~~~
-Data managers and DCC owners are responsible for setting up a **FileView** that integrates with Schematic. Note that FileViews appear under the "Tables" tab in Synapse and can be named according to the project’s needs. For instance, a FileView for the **NF project** could have a different name than a FileView for the **AD project**.
+Users are responsible for setting up a **FileView** that integrates with Schematic. Note that FileViews appear under the "Tables" tab in Synapse and can be named according to the project's needs. For instance, a FileView for the **Project A** could have a different name than a FileView for the **Project B**.
 
 For more information on Synapse projects, visit:
 - `Synapse projects <https://help.synapse.org/docs/Uploading-and-Organizing-Data-Into-Projects,-Files,-and-Folders.2048327716.html>`_
@@ -39,9 +39,9 @@ Folders in Synapse allow users to organize data within projects. More details on
 
 Datasets
 ~~~~~~~~
-You will hear the term **dataset** used frequently at Sage. The term dataset refers to three different concepts:
+You will hear the term **dataset** used frequently. The term dataset refers to three different concepts:
 
-1. Dataset: This is the concept of a dataset which is a collection of files.
+1. Dataset: A collection of data that is organized and curated for analysis, processing, and/or sharing.
 2. Schematic Dataset: This refers to a folder containing files. These folders are annotated with `contentType:dataset`.
 3. Synapse Dataset Entity: This is an object in Synapse which appears under the "Dataset" tab and represents a user-defined collection of Synapse files and versions.
 
@@ -49,6 +49,20 @@ JSON-LD
 ~~~~~~~
 JSON-LD is a lightweight Linked Data format. The usage of JSON-LD to capture our data models extends beyond the creation, validation, and submission of annotations/manifests into Synapse. It can create relationships between different data models and, in the future, drive transformation of data from one data model to another. Visualization of these data models and their relationships is also possible (see *Schema Visualization - Design & Platform*), which allows the community to see the depth of connections between all the data uploaded into Synapse. As with all products, we must start somewhere.
 
+Manifest
+~~~~~~~~
+A manifest is a structured file that contains metadata about a dataset.
+It is a list of files and their associated metadata. The metadata includes information such as the file name,
+file type, and file size. The manifest is used to validate the metadata before it is uploaded to Synapse.
+The manifest can also used to create a view in Synapse that displays the metadata for each file in the dataset.
+
+Component/Data type
+~~~~~~~~~~~~~~~~~~~
+"component" and "data type" are used interchangeably. The component/data type is determined from the specified JSON-LD data model.
+If the string "component" exists in the depends on column, the "Attribute" value in that row is a data type.
+Examples of a data type is "Biospecimen", "Patient": https://github.com/Sage-Bionetworks/schematic/blob/develop/tests/data/example.model.csv#L3.
+Each data type/component should a manifest template that has different columns.
+
 
 Schematic services
 ------------------

From ceefd9e16660cb07f6670219a93b8c7945560670 Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Fri, 1 Nov 2024 22:25:57 -0700
Subject: [PATCH 18/47] Add --all-extras

---
 .readthedocs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index a9472a17d..0e179d326 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -14,7 +14,7 @@ build:
     post_install:
       - pip install poetry==1.3.0
       - poetry config virtualenvs.create false
-      - poetry install --with doc
+      - poetry install --all-extras
     #Poetry will install my dependencies into the virtualenv created by readthedocs if I set virtualenvs.create=false
     # You can also specify other tool versions:
     # nodejs: "16"

From 55498a96b2e2445fc0d40ca7ec8def5a5000fd4a Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Fri, 1 Nov 2024 22:37:37 -0700
Subject: [PATCH 19/47] Add typing extensions

---
 .readthedocs.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 0e179d326..4bd1c3868 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -15,6 +15,7 @@ build:
       - pip install poetry==1.3.0
       - poetry config virtualenvs.create false
       - poetry install --all-extras
+      - pip install typing-extensions
     #Poetry will install my dependencies into the virtualenv created by readthedocs if I set virtualenvs.create=false
     # You can also specify other tool versions:
     # nodejs: "16"

From 7292112ec323a7cd83cd7a43e46841331ea77d38 Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Fri, 1 Nov 2024 22:50:17 -0700
Subject: [PATCH 20/47] Add details

---
 docs/source/cli_reference.rst | 25 ++++++++++++++++---------
 1 file changed, 16 insertions(+), 9 deletions(-)

diff --git a/docs/source/cli_reference.rst b/docs/source/cli_reference.rst
index 0acb08627..69c886511 100644
--- a/docs/source/cli_reference.rst
+++ b/docs/source/cli_reference.rst
@@ -2,37 +2,44 @@
 CLI Reference
 =============
 
+When you're using this tool `-d` flag is referring to the Synapse ID of a folder that would be found under the files tab
+that contains a manifest and data. This would be referring to a Schematic Dataset. It is not required to provide a dataset_id
+but if you're trying to pull existing annotations by using the `-a` flag and the manifest is file-based then you would
+need to provide a dataset_id.
+
+
+Generate a new manifest as a Google Sheet
+-----------------------------------------
 
-1. Generate a new manifest as a Google Sheet
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. code-block:: shell
 
    schematic manifest -c /path/to/config.yml get -dt <your data type> -s
 
-2. Grab an existing manifest from Synapse
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Generate an existing manifest from Synapse
+------------------------------------------
 
 .. code-block:: shell
 
    schematic manifest -c /path/to/config.yml get -dt <your data type> -d <your synapse dataset folder id> -s
 
-3. Validate a manifest
-~~~~~~~~~~~~~~~~~~~~~~
+Validate a manifest
+-------------------
 
 .. code-block:: shell
 
    schematic model -c /path/to/config.yml validate -dt <your data type> -mp <your csv manifest path>
 
-4. Submit a manifest as a file
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Submit a manifest as a file
+---------------------------
 
 .. code-block:: shell
 
    schematic model -c /path/to/config.yml submit -mp <your csv manifest path> -d <your synapse dataset folder id> -vc <your data type> -mrt file_only
 
 
-
+In depth guide
+--------------
 
 .. click:: schematic.__main__:main
   :prog: schematic

From 8d272ef1ff2d86028fcbd55afd526cc5bbfb074d Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Sat, 2 Nov 2024 15:01:33 -0700
Subject: [PATCH 21/47] Add documentation

---
 docs/source/index.rst | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/docs/source/index.rst b/docs/source/index.rst
index 565dc2c78..99a5850e1 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -105,6 +105,11 @@ Data Model Visualization
 These endpoints allows you to visulize your data models and their relationships with each other.
 
 
+API reference
+-------------
+
+For the entire Python API reference documentation, you can visit the docs here: https://sage-bionetworks.github.io/schematic/
+
 .. toctree::
    :maxdepth: 1
    :hidden:

From 625d7126ff347cc0645a552b1bb7dec7249c0eb7 Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Mon, 4 Nov 2024 18:34:51 -0800
Subject: [PATCH 22/47] Add tutorials and troubleshooting docs

---
 docs/source/index.rst           |  6 ++++
 docs/source/troubleshooting.rst | 52 +++++++++++++++++++++++++++++++++
 docs/source/tutorials.rst       |  6 ++++
 3 files changed, 64 insertions(+)
 create mode 100644 docs/source/troubleshooting.rst
 create mode 100644 docs/source/tutorials.rst

diff --git a/docs/source/index.rst b/docs/source/index.rst
index 99a5850e1..508d10f6f 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -6,6 +6,10 @@
 Welcome to Schematic's documentation!
 =====================================
 
+.. warning::
+   This documentation site is a work in progress, and the sublinks may change.  Apologies for the inconvenience.
+
+
 **SCHEMATIC** is an acronym for *Schema Engine for Manifest Ingress and Curation*. The Python-based infrastructure provides a *novel* schema-based, metadata ingress ecosystem, which is meant to streamline the process of biomedical dataset annotation, metadata validation, and submission to a data repository for various data contributors.
 
 Schematic tackles these goals:
@@ -117,4 +121,6 @@ For the entire Python API reference documentation, you can visit the docs here:
    installation
    asset_store
    configuration
+   tutorials
+   troubleshooting
    cli_reference
diff --git a/docs/source/troubleshooting.rst b/docs/source/troubleshooting.rst
new file mode 100644
index 000000000..98781c78d
--- /dev/null
+++ b/docs/source/troubleshooting.rst
@@ -0,0 +1,52 @@
+Troubleshooting
+===============
+
+These are some common issues you may encounter when using schematic
+
+
+Manifest Generate: `KeyError: entityId`
+---------------------------------------
+
+If there is currently a manifest in your Schematic Dataset folder on Synapse with an incorrect Filename BUT entityId column.
+You will be able to run manifest generate to create a new manifest with the new Filenames. However, If this manifest on Synapse does
+NOT have the entityId column you will encounter that error. 
+
+To fix: Please submit your manifest using schematic.
+
+
+Manifest Submit: `RuntimeError: failed with SynapseHTTPError('400 Client Error: nan is not a valid Synapse ID.')`
+-----------------------------------------------------------------------------------------------------------------
+
+As for 24.10.2 version of Schematic, we require the `Filename` column to have the full paths to the file on Synapse including the project name.
+If you try and submit a manifest with invalid Filenames (not containing full path), you will encounter the `nan`.  This is because we join the `Filename`
+column together with what's in Synapse to append the `entityId` column if it's missing.
+
+To fix: Please generate a manifest with schematic which should fix the Filenames
+
+
+Manifest Submit: `TypeError: boolean value of NA is ambiguous`
+--------------------------------------------------------------
+
+You may encounter this error if your manifest has a Component column but it is empty.  This may occur if the manifest in your Schematic Dataset folder
+does not contain this column.  During manifest generate, it will create an empty column for you.  
+
+To fix: Please fill out this column with the correct Component values and submit the manifest again.
+
+
+Manifest validation: `The submitted metadata does not contain all required column(s)`
+-------------------------------------------------------------------------------------
+
+The required columns are determined by the data model, but `Component` should be a required column even if it's not set that way in the data model.
+This is the validation error you may get if you don't have the `Component` column.
+
+To fix: Please add the `Component` column (and fill it out) or any other required columns.
+
+
+Manifest validation: `The submitted metadata contains << 'string' >> in the Component column, but requested validation for << expected string >>`
+-------------------------------------------------------------------------------------------------------------------------------------------------
+
+If the manifest has incorrect Component values, you might get the validation error message above. This is because the Component value is incorrect,
+and the validation rule uses the "display" value of what's expected in the Component column.  For example, the display name could be "Imaging Assay"
+but the actual Component name is "ImagingAssayTemplate".
+
+To fix: Using the above example, fill out your Component column with "ImagingAssayTemplate"
diff --git a/docs/source/tutorials.rst b/docs/source/tutorials.rst
new file mode 100644
index 000000000..ff3ef29b9
--- /dev/null
+++ b/docs/source/tutorials.rst
@@ -0,0 +1,6 @@
+Tutorials
+=========
+
+
+Contributing your manifest
+--------------------------

From 198ed52380cb91ca0d0d63a0267e75a1ac7f65eb Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Mon, 4 Nov 2024 18:59:57 -0800
Subject: [PATCH 23/47] Add tutorial for contributing manifests

---
 docs/source/tutorials.rst | 87 ++++++++++++++++++++++++++++++++++++++-
 1 file changed, 85 insertions(+), 2 deletions(-)

diff --git a/docs/source/tutorials.rst b/docs/source/tutorials.rst
index ff3ef29b9..bd19a7e13 100644
--- a/docs/source/tutorials.rst
+++ b/docs/source/tutorials.rst
@@ -2,5 +2,88 @@ Tutorials
 =========
 
 
-Contributing your manifest
---------------------------
+Contributing your manifest with the CLI
+---------------------------------------
+
+In this tutorial, you'll learn how to contribute your metadata manifests to Synapse using the `CLI`. Following best practices,
+we will cover generating, validating, and submitting your manifest in a structured workflow.
+
+.. note::
+
+    Whether you have submitted manifests before to your dataset OR are submitting a new manifest, we **strongly recommend** you to follow this workflow.
+    If you deviate from this workflow or upload files to Synapse directly without using schematic, you risk the errors outlined in the
+    troubleshooting section of the documentation.
+
+    Question: What if I've already gone through this workflow, can I download the manifest, modify it and upload it to Synapse without Schematic?
+    Answer: Yes, but you risk running into errors when others use these commands.  We strongly recommend not doing that.
+
+
+Prerequisites
+~~~~~~~~~~~~~
+1. **Install and configure Schematic**: Ensure that you have installed `schematic` and set up its dependencies. See "Installation Guide For: Users" for more information.
+2. **Important Concepts**: Make sure you know the important concepts outlined on the home page of the doc site.
+3. **Configuration**: Read more here about each of the attributes in the configuration file.
+
+Steps to Contribute a Manifest
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The contribution process includes three main commands.
+For information about the parameters of each of these commands, please refer to the CLI Reference section.
+
+1. **Generate** a manifest to fill out
+2. **Validate** the manifest (optional, since it's included in submission)
+3. **Submit** the manifest to Synapse
+
+
+Step 1: Generate a Manifest
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The `schematic manifest get` command that creates a manifest template based on a data model and existing manifests.
+
+.. note::
+
+    This step is crucial for ensuring that your manifest includes all the necessary columns and headers. As of v24.10.2, you will
+    want to generate the manifest to ensure the right Filenames are populated in your manifest.
+
+.. code-block:: bash
+
+    schematic manifest -c /path/to/config.yml get -dt <your data type> -s
+
+- **Data Type**: The data type or schema model for your manifest (e.g., "Patient", "Biospecimen")..
+
+This command will create a CSV file with the necessary columns and headers, which you can then fill with your metadata.
+
+Step 2: Validate the Manifest (Optional)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Though optional, `schematic model validate`` is a useful step to ensure that your manifest meets the required standards before submission.
+It checks for any errors, such as missing or incorrectly formatted values.
+
+.. note::
+
+    If your manifest has an empty Component column, you will need to fill it out before validation.
+
+.. code-block:: bash
+
+    schematic model -c /path/to/config.yml validate -dt <your data type> -mp <your csv manifest path>
+
+If validation passes, you'll see a success message; if there are errors, `schematic` will list them. Correct any issues before proceeding to submission.
+
+Step 3: Submit the Manifest to Synapse
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The `schematic model submit` command uploads your manifest to Synapse. This command will automatically validate
+the manifest as part of the submission process, so if you prefer, you can skip the standalone validation step.
+
+.. note::
+
+    During the manifest submission, it will fill out the entityId column if it's missing.
+
+.. code-block:: bash
+
+    schematic model -c /path/to/config.yml submit -mp <your csv manifest path> -d <your synapse dataset folder id> -vc <your data type> -mrt file_only
+
+This command will:
+
+- Validate your manifest
+- If validation is successful, submit it to the specified Schematic Dataset folder in Synapse.

From b759ba8729ccff334a09bc13c315407aed8f660c Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Mon, 4 Nov 2024 19:06:38 -0800
Subject: [PATCH 24/47] Add a line

---
 docs/source/tutorials.rst | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/source/tutorials.rst b/docs/source/tutorials.rst
index bd19a7e13..a6162ec23 100644
--- a/docs/source/tutorials.rst
+++ b/docs/source/tutorials.rst
@@ -15,6 +15,7 @@ we will cover generating, validating, and submitting your manifest in a structur
     troubleshooting section of the documentation.
 
     Question: What if I've already gone through this workflow, can I download the manifest, modify it and upload it to Synapse without Schematic?
+
     Answer: Yes, but you risk running into errors when others use these commands.  We strongly recommend not doing that.
 
 

From c67ce6177cb2d7d65a7ae80d87c520a9592aea5e Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Mon, 4 Nov 2024 19:14:17 -0800
Subject: [PATCH 25/47] Add to documentation

---
 docs/source/asset_store.rst     |  3 +++
 docs/source/troubleshooting.rst | 12 +++++++-----
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/docs/source/asset_store.rst b/docs/source/asset_store.rst
index f98c02549..db1be4ecb 100644
--- a/docs/source/asset_store.rst
+++ b/docs/source/asset_store.rst
@@ -1,6 +1,9 @@
 Setting up your asset store
 ===========================
 
+.. note::
+
+   You can ignore this section if you are just trying to contribute manifests.
 
 This document covers the minimal recommended elements needed in Synapse to interface with the Data Curator App (DCA) and provides options for Synapse project layout.
 
diff --git a/docs/source/troubleshooting.rst b/docs/source/troubleshooting.rst
index 98781c78d..bf75a539d 100644
--- a/docs/source/troubleshooting.rst
+++ b/docs/source/troubleshooting.rst
@@ -11,7 +11,8 @@ If there is currently a manifest in your Schematic Dataset folder on Synapse wit
 You will be able to run manifest generate to create a new manifest with the new Filenames. However, If this manifest on Synapse does
 NOT have the entityId column you will encounter that error. 
 
-To fix: Please submit your manifest using schematic.
+To fix: You will want to first check if your Schematic Dataset folder has a manifest without the entityId column.
+If so, you can either submit your manifest using schematic OR (the less preferred solution) manually add the entityId column to the manifest on Synapse.
 
 
 Manifest Submit: `RuntimeError: failed with SynapseHTTPError('400 Client Error: nan is not a valid Synapse ID.')`
@@ -21,7 +22,8 @@ As for 24.10.2 version of Schematic, we require the `Filename` column to have th
 If you try and submit a manifest with invalid Filenames (not containing full path), you will encounter the `nan`.  This is because we join the `Filename`
 column together with what's in Synapse to append the `entityId` column if it's missing.
 
-To fix: Please generate a manifest with schematic which should fix the Filenames
+To fix: You will want to first check if your Schematic Dataset folder has a manifest with invalid Filename values in the column.
+If so, please generate a manifest with schematic which should fix the Filenames OR (the less preferred solution) manually update the Filenames to include the full path to the file and manually upload.
 
 
 Manifest Submit: `TypeError: boolean value of NA is ambiguous`
@@ -30,7 +32,7 @@ Manifest Submit: `TypeError: boolean value of NA is ambiguous`
 You may encounter this error if your manifest has a Component column but it is empty.  This may occur if the manifest in your Schematic Dataset folder
 does not contain this column.  During manifest generate, it will create an empty column for you.  
 
-To fix: Please fill out this column with the correct Component values and submit the manifest again.
+To fix: Check if your manifest has an empty Component column.  Please fill out this column with the correct Component values and submit the manifest again.
 
 
 Manifest validation: `The submitted metadata does not contain all required column(s)`
@@ -39,7 +41,7 @@ Manifest validation: `The submitted metadata does not contain all required colum
 The required columns are determined by the data model, but `Component` should be a required column even if it's not set that way in the data model.
 This is the validation error you may get if you don't have the `Component` column.
 
-To fix: Please add the `Component` column (and fill it out) or any other required columns.
+To fix: Check if your manifest has a Component column or missing other required columns. Please add the `Component` column (and fill it out) or any other required columns.
 
 
 Manifest validation: `The submitted metadata contains << 'string' >> in the Component column, but requested validation for << expected string >>`
@@ -49,4 +51,4 @@ If the manifest has incorrect Component values, you might get the validation err
 and the validation rule uses the "display" value of what's expected in the Component column.  For example, the display name could be "Imaging Assay"
 but the actual Component name is "ImagingAssayTemplate".
 
-To fix: Using the above example, fill out your Component column with "ImagingAssayTemplate"
+To fix: Check if your manifest has invalid Component values and fill it out correctly.  Using the above example, fill out your Component column with "ImagingAssayTemplate"

From 8cf43429b1d76b62c38b91fca2135c3ac2949ac0 Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Mon, 4 Nov 2024 19:29:27 -0800
Subject: [PATCH 26/47] Remove precommit

---
 docs/source/installation.rst | 22 +++-------------------
 1 file changed, 3 insertions(+), 19 deletions(-)

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
index d07414cae..315e42a8f 100644
--- a/docs/source/installation.rst
+++ b/docs/source/installation.rst
@@ -265,6 +265,8 @@ Once you've copied the file, modify its contents according to your use case. For
 
 .. important::
    Be sure to update your ``config.yml`` with the location of your ``.synapseConfig`` created in the step above to avoid authentication errors. Paths can be specified relative to the ``config.yml`` file or as absolute paths.
+   By default, the ``.synapseConfig`` file is created in your home directory, so as an example, the configuration file will have to contain `/full/path/to/.synapseConfig` as the path to the ``.synapseConfig`` file or be in the same
+   directory as the ``config.yml`` file.
 
 .. note::
    ``config.yml`` is ignored by git.
@@ -294,26 +296,8 @@ Once you have obtained credentials, ensure that the JSON file generated is named
 .. note::
    Use the ``schematic_service_account_creds.json`` file for the service account mode of authentication (*for Google services/APIs*). Service accounts are special Google accounts that can be used by applications to access Google APIs programmatically via OAuth2.0, with the advantage being that they do not require human authorization.
 
-7. Set up pre-commit hooks
-~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-This repository is configured to utilize pre-commit hooks as part of the development process. To enable these hooks, run the following command and look for the success message:
-
-.. code-block:: shell
-
-   pre-commit install
-
-   pre-commit installed at .git/hooks/pre-commit
-
-You can run ``pre-commit`` manually across the entire repository like so:
-
-.. code-block:: shell
-
-   pre-commit run --all-files
-
-After running this step, your setup is complete, and you can test it in a Python instance or by running a command based on the examples in the command line usage section.
-
-8. Verify your setup
+7. Verify your setup
 ~~~~~~~~~~~~~~~~~~~~
 
 After running the steps above, your setup is complete, and you can test it in a ``python`` instance or by running a command based on the examples

From 2c1f49149ca0f01b8e9e684140c6641768e6cf76 Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Mon, 4 Nov 2024 22:45:16 -0800
Subject: [PATCH 27/47] Add etag value error

---
 docs/source/troubleshooting.rst | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/docs/source/troubleshooting.rst b/docs/source/troubleshooting.rst
index bf75a539d..828ac55ab 100644
--- a/docs/source/troubleshooting.rst
+++ b/docs/source/troubleshooting.rst
@@ -14,6 +14,13 @@ NOT have the entityId column you will encounter that error.
 To fix: You will want to first check if your Schematic Dataset folder has a manifest without the entityId column.
 If so, you can either submit your manifest using schematic OR (the less preferred solution) manually add the entityId column to the manifest on Synapse.
 
+Manifest Generate: `ValueError: cannot insert eTag, already exists`
+-------------------------------------------------------------------
+
+If there is currently a manifest in your Schematic Dataset folder on Synapse with the 'eTag' column and you try to generate a manifest, it will fail.
+
+To fix: You will want to first check if your Schematic Dataset folder has a manifest with the 'eTag' column and remove that column.
+
 
 Manifest Submit: `RuntimeError: failed with SynapseHTTPError('400 Client Error: nan is not a valid Synapse ID.')`
 -----------------------------------------------------------------------------------------------------------------

From abef1f6930eb7f233691e2c2934cadd8373eecd9 Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Mon, 4 Nov 2024 23:03:50 -0800
Subject: [PATCH 28/47] Add schematic config section

---
 docs/source/configuration.rst | 50 ++++++++++++++++++++++++++++-------
 1 file changed, 41 insertions(+), 9 deletions(-)

diff --git a/docs/source/configuration.rst b/docs/source/configuration.rst
index f84fa49e9..5ab4111ec 100644
--- a/docs/source/configuration.rst
+++ b/docs/source/configuration.rst
@@ -1,17 +1,12 @@
 Configure Schematic
 ===================
 
-Schematic takes a configuration file with the following structure:
+This is an example config for Schematic. All listed values are those that are the default if a config is not used. Remove any fields in the config you don't want to change.
+If you remove all fields from a section, the entire section should be removed including the header.
+Change the values of any fields you do want to change.  Please view the installation section for details on how to set some of this up.
 
 .. code-block:: yaml
 
-    # This is an example config for Schematic.
-    # All listed values are those that are the default if a config is not used.
-    # Save this as config.yml, this will be gitignored.
-    # Remove any fields in the config you don't want to change
-    # If you remove all fields from a section, the entire section should be removed including the header.
-    # Change the values of any fields you do want to change
-
     # This describes where assets such as manifests are stored
     asset_store:
         # This is when assets are stored in a synapse project
@@ -41,7 +36,7 @@ Schematic takes a configuration file with the following structure:
 
     # This section is for using google sheets with Schematic
     google_sheets:
-        # Path to the synapse config file, either absolute or relative to this file
+        # Path to the google service account creds, either absolute or relative to this file
         service_acct_creds: "schematic_service_account_creds.json"
         # When doing google sheet validation (regex match) with the validation rules.
         #   true is alerting the user and not allowing entry of bad values.
@@ -50,3 +45,40 @@ Schematic takes a configuration file with the following structure:
 
 
 This document will go into detail what each of these configurations mean.
+
+Asset Store
+-----------
+
+Synapse
+~~~~~~~
+This describes where assets such as manifests are stored and the configurations of the asset store is described
+under the asset store section.
+
+* master_fileview_id: Synapse ID of the file view listing all project data assets.
+* config: Path to the synapse config file, either absolute or relative to this file. Note, if you use `synapse config` command, you will have to provide the full path to the configuration file.
+* manifest_basename: Base name that manifest files will be saved as on Synapse. The Component will be appended to it so for example: `synapse_storage_manifest_biospecimen.csv`
+
+Manifest
+--------
+This describes information about manifests as it relates to generation and validation.  Note: some of these configurations can be overwritten by the CLI commands.
+
+* manifest_folder: Location where manifests will saved to. This can be a relative or absolute path on your local machine.
+* title: Title or title prefix given to generated manifest(s). This is used to name the manifest file saved locally.
+* data_type: Data types of manifests to be generated or data type (singular) to validate manifest against. If you wanted all the available manifests, you can input "all manifests"
+
+
+Model
+-----
+Describes the location of your schema
+
+* location: This is the location of your schema jsonld, it must be a path relative to this file or absolute path.  Currently URL's are NOT supported, so you will have to download the jsonld data model.  Here is an example: https://raw.githubusercontent.com/ncihtan/data-models/v24.9.1/HTAN.model.jsonld
+
+Google Sheets
+-------------
+Schematic leverages the Google API to generate manifests. This section is for using google sheets with Schematic
+
+* service_acct_creds: Path to the google service account creds, either absolute or relative to this file. This is the path to the service account credentials file that you download from Google Cloud Platform.
+* strict_validation: When doing google sheet validation (regex match) with the validation rules.
+
+    * True is alerting the user and not allowing entry of bad values.
+    * False is warning but allowing the entry on to the sheet.

From ad3b4025848ac5b19318f97da43874d1dd62f659 Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Mon, 4 Nov 2024 23:17:19 -0800
Subject: [PATCH 29/47] Add documentation

---
 docs/source/troubleshooting.rst | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/docs/source/troubleshooting.rst b/docs/source/troubleshooting.rst
index 828ac55ab..030a671ca 100644
--- a/docs/source/troubleshooting.rst
+++ b/docs/source/troubleshooting.rst
@@ -3,6 +3,29 @@ Troubleshooting
 
 These are some common issues you may encounter when using schematic
 
+Debugging
+---------
+Whether you are using DCA or schematic API or schematic library/CLI, the following are some steps that you want to take to debug your issues.  Here are some steps to walk you through the process.
+
+1. What was the command that caused the error?
+2. Is the error listed down below?
+3. Did you follow the workflow outlined in the tutorials section under: "Contributing your manifest with the CLI"?
+4. Create a Github issue or reach out to your respective DCC service desks.  What is the schematic or DCA configuration used? Specifically, it's most important to capture the following:
+
+    1. `data_type`: This is the same as Component in the data model.
+    2. `master_fileview_id`: This is the Synapse ID of the file view listing all project datasets.
+    3. `data model url`: This is the link to your data model.
+    4. `dataset_id`: This is the Schematic Dataset folder (folder annoated with contentType: Datatset).
+    5. What is the command or API call that you made?  If you are using DCA, please provide the step at which you encountered the error (manifest generate, validate, submit, etc)
+
+        .. code-block:: bash
+
+            schematic manifest -c /path/to/config.yml get -dt <your data type> -s
+            # OR (PLEASE REDACT YOUR BEARER TOKEN)
+            curl -X 'GET' \
+                'https://schematic.api.sagebionetworks.org/v1/manifest/generate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2Fnf-osi%2Fnf-metadata-dictionary%2Fv9.8.0%2FNF.jsonld&title=Example&data_type=EpigeneticsAssayTemplate&use_annotations=true&dataset_id=syn63305821&asset_view=syn16858331&output_format=google_sheet&strict_validation=true&data_model_labels=class_label' \
+                -H 'accept: application/json' ...
+
 
 Manifest Generate: `KeyError: entityId`
 ---------------------------------------

From 04799618124749e564f8152caee3c6469fc7969e Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Mon, 4 Nov 2024 23:44:57 -0800
Subject: [PATCH 30/47] Add debugging string

---
 docs/source/troubleshooting.rst | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/docs/source/troubleshooting.rst b/docs/source/troubleshooting.rst
index 030a671ca..ce6d21839 100644
--- a/docs/source/troubleshooting.rst
+++ b/docs/source/troubleshooting.rst
@@ -10,7 +10,10 @@ Whether you are using DCA or schematic API or schematic library/CLI, the followi
 1. What was the command that caused the error?
 2. Is the error listed down below?
 3. Did you follow the workflow outlined in the tutorials section under: "Contributing your manifest with the CLI"?
-4. Create a Github issue or reach out to your respective DCC service desks.  What is the schematic or DCA configuration used? Specifically, it's most important to capture the following:
+
+    1. If you are validating or submitting the manifest, how was the manifest initiatially generated?  If manually and NOT using schematic, there may be errors.
+
+5. Create a Github issue or reach out to your respective DCC service desks.  What is the schematic or DCA configuration used? Specifically, it's most important to capture the following:
 
     1. `data_type`: This is the same as Component in the data model.
     2. `master_fileview_id`: This is the Synapse ID of the file view listing all project datasets.

From ed2b231cad94d6820c895619381aa48b0a2c7168 Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Tue, 5 Nov 2024 00:09:13 -0800
Subject: [PATCH 31/47] Add notes

---
 docs/source/troubleshooting.rst | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/source/troubleshooting.rst b/docs/source/troubleshooting.rst
index ce6d21839..06157237d 100644
--- a/docs/source/troubleshooting.rst
+++ b/docs/source/troubleshooting.rst
@@ -12,6 +12,7 @@ Whether you are using DCA or schematic API or schematic library/CLI, the followi
 3. Did you follow the workflow outlined in the tutorials section under: "Contributing your manifest with the CLI"?
 
     1. If you are validating or submitting the manifest, how was the manifest initiatially generated?  If manually and NOT using schematic, there may be errors.
+    2. If the manifest was generated by schematic, when was it generated?  Did you download the previously submitted manifest from Synapse and modify it?  Did you download it and resubmit it?  Please run the manifest generate command again to have a fresh manifest.
 
 5. Create a Github issue or reach out to your respective DCC service desks.  What is the schematic or DCA configuration used? Specifically, it's most important to capture the following:
 

From 9bf1200d93dca8b2d4f9b4eb73fdf233eb0cb805 Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Tue, 5 Nov 2024 14:20:19 -0800
Subject: [PATCH 32/47] Use top level fodler

---
 docs/source/cli_reference.rst   | 12 ++++++------
 docs/source/index.rst           | 24 ++++++++++++++++--------
 docs/source/installation.rst    |  6 +++---
 docs/source/troubleshooting.rst | 16 ++++++++--------
 docs/source/tutorials.rst       | 10 ++++++----
 5 files changed, 39 insertions(+), 29 deletions(-)

diff --git a/docs/source/cli_reference.rst b/docs/source/cli_reference.rst
index 69c886511..83cda3e2c 100644
--- a/docs/source/cli_reference.rst
+++ b/docs/source/cli_reference.rst
@@ -2,10 +2,10 @@
 CLI Reference
 =============
 
-When you're using this tool `-d` flag is referring to the Synapse ID of a folder that would be found under the files tab
-that contains a manifest and data. This would be referring to a Schematic Dataset. It is not required to provide a dataset_id
-but if you're trying to pull existing annotations by using the `-a` flag and the manifest is file-based then you would
-need to provide a dataset_id.
+When you're using this tool ``-d`` flag is referring to the Synapse ID of a folder that would be found under the files tab
+that contains a manifest and data. This would be referring to a "Top Level Folder". It is not required to provide a ``dataset_id``
+but if you're trying to pull existing annotations by using the ``-a`` flag and the manifest is file-based then you would
+need to provide a ``dataset_id``.
 
 
 Generate a new manifest as a Google Sheet
@@ -21,7 +21,7 @@ Generate an existing manifest from Synapse
 
 .. code-block:: shell
 
-   schematic manifest -c /path/to/config.yml get -dt <your data type> -d <your synapse dataset folder id> -s
+   schematic manifest -c /path/to/config.yml get -dt <your data type> -d <your synapse "Top Level Folder" folder id> -s
 
 Validate a manifest
 -------------------
@@ -35,7 +35,7 @@ Submit a manifest as a file
 
 .. code-block:: shell
 
-   schematic model -c /path/to/config.yml submit -mp <your csv manifest path> -d <your synapse dataset folder id> -vc <your data type> -mrt file_only
+   schematic model -c /path/to/config.yml submit -mp <your csv manifest path> -d <your synapse "Top Level Folder" id> -vc <your data type> -mrt file_only
 
 
 In depth guide
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 508d10f6f..ab4ae30ed 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -41,13 +41,21 @@ Synapse Folders
 
 Folders in Synapse allow users to organize data within projects. More details on uploading and organizing data can be found at `Synapse folders <https://help.synapse.org/docs/Uploading-and-Organizing-Data-Into-Projects,-Files,-and-Folders.2048327716.html>`_
 
-Datasets
-~~~~~~~~
-You will hear the term **dataset** used frequently. The term dataset refers to three different concepts:
+Synapse Datasets
+~~~~~~~~~~~~~~~~
+
+This is an object in Synapse which appears under the "Dataset" tab and represents a user-defined collection of Synapse files and versions. https://help.synapse.org/docs/Datasets.2611281979.html
+
+Top Level Folders
+~~~~~~~~~~~~~~~~~
+
+.. note::
+   This concept is subject to feedback and _can_ be changed.  Schematic currently has parameters in the API and CLI that refer to ``dataset``.  This is actually referring to
+   the top level folders.
+
+This is a schematic specific term, this refers to top level Synapse folders that contain Synapse associated to a group of files.
+These folders are often annotated with ``contentType: dataset`` or the name of the folder is used when there is a multi-project setup (This needs to fact check)
 
-1. Dataset: A collection of data that is organized and curated for analysis, processing, and/or sharing.
-2. Schematic Dataset: This refers to a folder containing files. These folders are annotated with `contentType:dataset`.
-3. Synapse Dataset Entity: This is an object in Synapse which appears under the "Dataset" tab and represents a user-defined collection of Synapse files and versions.
 
 JSON-LD
 ~~~~~~~
@@ -55,10 +63,10 @@ JSON-LD is a lightweight Linked Data format. The usage of JSON-LD to capture our
 
 Manifest
 ~~~~~~~~
-A manifest is a structured file that contains metadata about a dataset.
+A manifest is a structured file that contains metadata about a files under a "top level folder".
 It is a list of files and their associated metadata. The metadata includes information such as the file name,
 file type, and file size. The manifest is used to validate the metadata before it is uploaded to Synapse.
-The manifest can also used to create a view in Synapse that displays the metadata for each file in the dataset.
+The manifest can also used to create a view in Synapse that displays the metadata for each file in the "top level folder".
 
 Component/Data type
 ~~~~~~~~~~~~~~~~~~~
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
index 315e42a8f..fce22159a 100644
--- a/docs/source/installation.rst
+++ b/docs/source/installation.rst
@@ -88,7 +88,7 @@ If you run into ``ERROR: Failed building wheel for numpy``, the error might be a
 4. Get your data model as a ``JSON-LD`` schema file
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Now you need a schema file, e.g. ``model.jsonld``, to have a data model that schematic can work with. While you can download a super basic `example data model <https://raw.githubusercontent.com/Sage-Bionetworks/schematic/refs/heads/develop/tests/data/example.model.jsonld>`_, you’ll probably be working with a DCC-specific data model. For non-Sage employees/contributors using the CLI, you might care only about the minimum needed artifact, which is the  ``.jsonld``; locate and download only that from the right repo.
+Now you need a schema file, e.g. ``model.jsonld``, to have a data model that schematic can work with. While you can download a super basic `example data model <https://raw.githubusercontent.com/Sage-Bionetworks/schematic/refs/heads/develop/tests/data/example.model.jsonld>`_, you'll probably be working with a DCC-specific data model. For non-Sage employees/contributors using the CLI, you might care only about the minimum needed artifact, which is the  ``.jsonld``; locate and download only that from the right repo.
 
 Here are some example repos with schema files:
 
@@ -111,7 +111,7 @@ Any function that interacts with a Google sheet (such as ``schematic manifest ge
 Once you have obtained credentials, be sure that the json file generated is named in the same way as the ``service_acct_creds`` parameter in your ``config.yml`` file. You will find more context on the ``config.yml`` in section [6. Set up configuration files](#6-set-up-configuration-files).
 
 .. note::
-   Running ``schematic init`` is no longer supported due to security concerns. To obtain ``schematic_service_account_creds.json``, please follow the `instructions <https://scribehow.com/shared/Enable_Google_Drive_and_Google_Sheets_APIs_for_project__yqfcJz_rQVeyTcg0KQCINA>`_. Schematic uses Google’s API to generate Google sheet templates that users fill in to provide (meta)data. Most Google sheet functionality could be authenticated with service account. However, more complex Google sheet functionality requires token-based authentication. As browser support that requires the token-based authentication diminishes, we are hoping to deprecate token-based authentication and keep only service account authentication in the future.
+   Running ``schematic init`` is no longer supported due to security concerns. To obtain ``schematic_service_account_creds.json``, please follow the `instructions <https://scribehow.com/shared/Enable_Google_Drive_and_Google_Sheets_APIs_for_project__yqfcJz_rQVeyTcg0KQCINA>`_. Schematic uses Google's API to generate Google sheet templates that users fill in to provide (meta)data. Most Google sheet functionality could be authenticated with service account. However, more complex Google sheet functionality requires token-based authentication. As browser support that requires the token-based authentication diminishes, we are hoping to deprecate token-based authentication and keep only service account authentication in the future.
 
 .. note::
    Use the ``schematic_service_account_creds.json`` file for the service account mode of authentication (*for Google services/APIs*). Service accounts are special Google accounts that can be used by applications to access Google APIs programmatically via OAuth2.0, with the advantage being that they do not require human authorization.
@@ -290,7 +290,7 @@ Once you have obtained credentials, ensure that the JSON file generated is named
    For testing, ensure there is no environment variable ``SCHEMATIC_SERVICE_ACCOUNT_CREDS``. Check the file ``.env`` to ensure this is not set. Also, verify that config files used for testing, such as ``config_example.yml``, do not contain ``service_acct_creds_synapse_id``.
 
 .. note::
-   Running ``schematic init`` is no longer supported due to security concerns. To obtain  ``schematic_service_account_creds.json``, please follow the `instructions <https://scribehow.com/shared/Enable_Google_Drive_and_Google_Sheets_APIs_for_project__yqfcJz_rQVeyTcg0KQCINA>`_. Schematic uses Google’s API to generate Google Sheet templates that users fill in to provide (meta)data.
+   Running ``schematic init`` is no longer supported due to security concerns. To obtain  ``schematic_service_account_creds.json``, please follow the `instructions <https://scribehow.com/shared/Enable_Google_Drive_and_Google_Sheets_APIs_for_project__yqfcJz_rQVeyTcg0KQCINA>`_. Schematic uses Google's API to generate Google Sheet templates that users fill in to provide (meta)data.
    Most Google Sheet functionality could be authenticated with a service account. However, more complex Google Sheet functionality requires token-based authentication. As browser support that requires token-based authentication diminishes, we hope to deprecate token-based authentication and keep only service account authentication in the future.
 
 .. note::
diff --git a/docs/source/troubleshooting.rst b/docs/source/troubleshooting.rst
index 06157237d..5ce8de8a4 100644
--- a/docs/source/troubleshooting.rst
+++ b/docs/source/troubleshooting.rst
@@ -17,9 +17,9 @@ Whether you are using DCA or schematic API or schematic library/CLI, the followi
 5. Create a Github issue or reach out to your respective DCC service desks.  What is the schematic or DCA configuration used? Specifically, it's most important to capture the following:
 
     1. `data_type`: This is the same as Component in the data model.
-    2. `master_fileview_id`: This is the Synapse ID of the file view listing all project datasets.
+    2. `master_fileview_id`: This is the Synapse ID of the file view listing all project data.
     3. `data model url`: This is the link to your data model.
-    4. `dataset_id`: This is the Schematic Dataset folder (folder annoated with contentType: Datatset).
+    4. `dataset_id`: This is the "top level folder" (folder annoated with contentType: Datatset).
     5. What is the command or API call that you made?  If you are using DCA, please provide the step at which you encountered the error (manifest generate, validate, submit, etc)
 
         .. code-block:: bash
@@ -34,19 +34,19 @@ Whether you are using DCA or schematic API or schematic library/CLI, the followi
 Manifest Generate: `KeyError: entityId`
 ---------------------------------------
 
-If there is currently a manifest in your Schematic Dataset folder on Synapse with an incorrect Filename BUT entityId column.
+If there is currently a manifest in your "Top Level Folder" on Synapse with an incorrect Filename BUT entityId column.
 You will be able to run manifest generate to create a new manifest with the new Filenames. However, If this manifest on Synapse does
 NOT have the entityId column you will encounter that error. 
 
-To fix: You will want to first check if your Schematic Dataset folder has a manifest without the entityId column.
+To fix: You will want to first check if your "Top Level Folder" has a manifest without the entityId column.
 If so, you can either submit your manifest using schematic OR (the less preferred solution) manually add the entityId column to the manifest on Synapse.
 
 Manifest Generate: `ValueError: cannot insert eTag, already exists`
 -------------------------------------------------------------------
 
-If there is currently a manifest in your Schematic Dataset folder on Synapse with the 'eTag' column and you try to generate a manifest, it will fail.
+If there is currently a manifest in your "Top Level Folder" on Synapse with the 'eTag' column and you try to generate a manifest, it will fail.
 
-To fix: You will want to first check if your Schematic Dataset folder has a manifest with the 'eTag' column and remove that column.
+To fix: You will want to first check if your "Top Level Folder" has a manifest with the 'eTag' column and remove that column.
 
 
 Manifest Submit: `RuntimeError: failed with SynapseHTTPError('400 Client Error: nan is not a valid Synapse ID.')`
@@ -56,14 +56,14 @@ As for 24.10.2 version of Schematic, we require the `Filename` column to have th
 If you try and submit a manifest with invalid Filenames (not containing full path), you will encounter the `nan`.  This is because we join the `Filename`
 column together with what's in Synapse to append the `entityId` column if it's missing.
 
-To fix: You will want to first check if your Schematic Dataset folder has a manifest with invalid Filename values in the column.
+To fix: You will want to first check if your "Top Level Folder" has a manifest with invalid Filename values in the column.
 If so, please generate a manifest with schematic which should fix the Filenames OR (the less preferred solution) manually update the Filenames to include the full path to the file and manually upload.
 
 
 Manifest Submit: `TypeError: boolean value of NA is ambiguous`
 --------------------------------------------------------------
 
-You may encounter this error if your manifest has a Component column but it is empty.  This may occur if the manifest in your Schematic Dataset folder
+You may encounter this error if your manifest has a Component column but it is empty.  This may occur if the manifest in your "Top Level Folder"
 does not contain this column.  During manifest generate, it will create an empty column for you.  
 
 To fix: Check if your manifest has an empty Component column.  Please fill out this column with the correct Component values and submit the manifest again.
diff --git a/docs/source/tutorials.rst b/docs/source/tutorials.rst
index a6162ec23..4ffa8ac30 100644
--- a/docs/source/tutorials.rst
+++ b/docs/source/tutorials.rst
@@ -10,13 +10,15 @@ we will cover generating, validating, and submitting your manifest in a structur
 
 .. note::
 
-    Whether you have submitted manifests before to your dataset OR are submitting a new manifest, we **strongly recommend** you to follow this workflow.
+    Whether you have submitted manifests before to your "Top Level Folder" (see important terminology) OR are submitting a new manifest, we **strongly recommend** you to follow this workflow.
     If you deviate from this workflow or upload files to Synapse directly without using schematic, you risk the errors outlined in the
     troubleshooting section of the documentation.
 
     Question: What if I've already gone through this workflow, can I download the manifest, modify it and upload it to Synapse without Schematic?
 
-    Answer: Yes, but you risk running into errors when others use these commands.  We strongly recommend not doing that.
+    Answer: Yes, but you risk running into errors when others use these commands.
+    Updates may have been made to the data model by the DCC and these changes won't be reflected unless you regenerate your manfiest.
+    We strongly recommend not doing that.
 
 
 Prerequisites
@@ -82,9 +84,9 @@ the manifest as part of the submission process, so if you prefer, you can skip t
 
 .. code-block:: bash
 
-    schematic model -c /path/to/config.yml submit -mp <your csv manifest path> -d <your synapse dataset folder id> -vc <your data type> -mrt file_only
+    schematic model -c /path/to/config.yml submit -mp <your csv manifest path> -d <your synapse top level folder id> -vc <your data type> -mrt file_only
 
 This command will:
 
 - Validate your manifest
-- If validation is successful, submit it to the specified Schematic Dataset folder in Synapse.
+- If validation is successful, submit it to the specified "Top Level Folder" (see important terminology) in Synapse.

From b49ec859aa84a80efe6cc419fa0546b9d5966d18 Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Tue, 5 Nov 2024 14:23:39 -0800
Subject: [PATCH 33/47] Fix

---
 docs/source/troubleshooting.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/troubleshooting.rst b/docs/source/troubleshooting.rst
index 5ce8de8a4..53d79c404 100644
--- a/docs/source/troubleshooting.rst
+++ b/docs/source/troubleshooting.rst
@@ -14,7 +14,7 @@ Whether you are using DCA or schematic API or schematic library/CLI, the followi
     1. If you are validating or submitting the manifest, how was the manifest initiatially generated?  If manually and NOT using schematic, there may be errors.
     2. If the manifest was generated by schematic, when was it generated?  Did you download the previously submitted manifest from Synapse and modify it?  Did you download it and resubmit it?  Please run the manifest generate command again to have a fresh manifest.
 
-5. Create a Github issue or reach out to your respective DCC service desks.  What is the schematic or DCA configuration used? Specifically, it's most important to capture the following:
+4. Create a Github issue or reach out to your respective DCC service desks.  What is the schematic or DCA configuration used? Specifically, it's most important to capture the following:
 
     1. `data_type`: This is the same as Component in the data model.
     2. `master_fileview_id`: This is the Synapse ID of the file view listing all project data.

From 1d36c3736ba246f8dd1dff30d80f0b8d684824bc Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Tue, 5 Nov 2024 14:32:24 -0800
Subject: [PATCH 34/47] Edit

---
 docs/source/index.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/source/index.rst b/docs/source/index.rst
index ab4ae30ed..95041b019 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -50,11 +50,11 @@ Top Level Folders
 ~~~~~~~~~~~~~~~~~
 
 .. note::
-   This concept is subject to feedback and _can_ be changed.  Schematic currently has parameters in the API and CLI that refer to ``dataset``.  This is actually referring to
+   This concept is subject to feedback and `can` be changed.  Schematic currently has parameters in the API and CLI that refer to ``dataset``.  This is actually referring to
    the top level folders.
 
 This is a schematic specific term, this refers to top level Synapse folders that contain Synapse associated to a group of files.
-These folders are often annotated with ``contentType: dataset`` or the name of the folder is used when there is a multi-project setup (This needs to fact check)
+These folders are often annotated with ``contentType: dataset``.  Until users add this Synapse Annotation to their folder, it will NOT be a "Top Level Folder"
 
 
 JSON-LD

From 1ee5a8013ffdbaf19108947cf75e41ed3a8c23ce Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Tue, 5 Nov 2024 15:41:36 -0800
Subject: [PATCH 35/47] Add more documentation around asset stores

---
 docs/source/asset_store.rst | 50 +++++++++++++++++++++++++++++++------
 1 file changed, 43 insertions(+), 7 deletions(-)

diff --git a/docs/source/asset_store.rst b/docs/source/asset_store.rst
index db1be4ecb..d2fa45ddc 100644
--- a/docs/source/asset_store.rst
+++ b/docs/source/asset_store.rst
@@ -9,8 +9,31 @@ This document covers the minimal recommended elements needed in Synapse to inter
 
 There are two options for setting up a DCC Synapse project:
 
-1. Each team of DCC contributors has its own Synapse project that stores the team's datasets.
-2. All DCC datasets are stored in the same Synapse project.
+1. **Distributed Projects**: Each team of DCC contributors has its own Synapse project that stores the team's datasets.
+2. **Single Project**: All DCC datasets are stored in the same Synapse project.
+
+In each of these project setups, there are two ways you can lay out your data:
+
+1. **Flat Data Layout**: All top level folders structured under the project
+
+   .. code-block:: shell
+
+      my_flat_project
+      ├── biospecimen
+      └── clinical
+
+2. **Hierarchical Data Layout**: Top level folders are stored within nested folders annotated with ``contentType: dataset``
+
+   .. code-block:: shell
+
+      my_heirarchical_project
+      ├── biospecimen
+      │   ├── experiment_1 <- annotated
+      │   └── experiment_2 <- annotated
+      └── clinical
+         ├── batch_1 <- annotated
+         └── batch_2 <- annotated
+
 
 Option 1: Distributed Synapse Projects
 --------------------------------------
@@ -20,7 +43,7 @@ Pick **option 1** if you answer "yes" to one or more of the following questions:
 - Does the DCC have multiple contributing institutions/labs, each with different data governance and access controls?
 - Does the DCC have multiple institutions with limited cross-institutional sharing?
 - Will contributors submit more than 100 datasets per release or per month?
-- Are you not willing to annotate each DCC dataset folder with the annotation `contentType:dataset`?
+- Are you not willing to annotate each DCC dataset folder with the annotation ``contentType:dataset``?
 
 Access & Project Setup - Multiple Contributing Projects
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -29,10 +52,11 @@ Access & Project Setup - Multiple Contributing Projects
 2. Create a Team for each data contributing institution. Begin with a "Test Team" if all teams are not yet identified.
 3. Create a Synapse Project for each institution and grant the respective team **Edit** level access.
    - E.g., for institutions A, B, and C, create Projects A, B, and C with Teams A, B, and C. Team A has **Edit** access to Project A, etc.
-4. Within each project, create top-level dataset folders in the **Files** tab for each dataset type.
+4. Within each project, create "top level folders" in the **Files** tab for each dataset type.
 5. Create another Synapse Project (e.g., MyDCC) containing the main **Fileview** that includes in the scope all the DCC projects.
    - Ensure all teams have **Download** level access to this file view.
    - Include both file and folder entities and add ALL default columns.
+   - Note: If you want to upload data according to hierachical data layout, you can still use distributed projects, just the ``contentType`` column to your fileview, and you will have to annotate your top level folders with ``contentType:dataset``.
 
 
 Option 2: Single Synapse Project
@@ -42,7 +66,7 @@ Pick **option 2** if you don't select option 1 and you answer "yes" to any of th
 
 - Does the DCC have a project with pre-existing datasets in a complex folder hierarchy?
 - Does the DCC envision collaboration on the same dataset collection across multiple teams with shared access controls?
-- Are you willing to set up local access control for each dataset folder and annotate each with `contentType:dataset`?
+- Are you willing to set up local access control for each dataset folder and annotate each with ``contentType: dataset``?
 
 If neither option fits, select option 1.
 
@@ -53,8 +77,20 @@ Access & Project Setup - Single Contributing Project
 1. Create a Team for each data contributing institution.
 2. Create a single Synapse Project (e.g., MyDCC).
 3. Within this project, create dataset folders for each contributor. Organize them as needed.
-   - Use `contentType:dataset` for each dataset folder, which should not nest inside other dataset folders and must have unique names.
-4. In MyDCC, create the main **DCC Fileview** with `MyDCC` as scope. Add column `contentType` to the schema and grant teams **Download** level access.
+   - Annotate ``contentType: dataset`` for each top level folder, which should not nest inside other dataset folders and must have unique names.
+     Taking the above example, you cannot have something like this:
+
+      .. code-block:: shell
+
+         my_heirarchical_project
+         ├── biospecimen
+         │   ├── experiment_1 <- annotated
+         │   └── experiment_2 <- annotated
+         └── clinical
+            ├── experiment_1 <- this is not allowed, because experiment_1 is duplicated
+            └── batch_2 <- annotated
+
+4. In MyDCC, create the main **DCC Fileview** with `MyDCC` as the scope. Add column ``contentType`` to the schema and grant teams **Download** level access.
    - Add both file and folder entities and add ALL default columns.
 
 

From d50e7a66d7b08763b7df59095dc69aec929f813f Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Tue, 5 Nov 2024 15:56:18 -0800
Subject: [PATCH 36/47] Update section title

---
 docs/source/installation.rst | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
index fce22159a..0e38f3894 100644
--- a/docs/source/installation.rst
+++ b/docs/source/installation.rst
@@ -149,8 +149,11 @@ The ``.synapseConfig`` is used to log into Synapse if you are not using an envir
 
 In this repository there is a ``config_example.yml`` file with default configurations to various components that are required before running ``schematic``, such as the Synapse ID of the main file view containing all your project assets, the
 
-Installation Guide For: Contributors
-------------------------------------
+Installation Guide For: Developers
+----------------------------------
+
+.. note::
+   This section is for people developing on Schematic only
 
 The instructions below assume you have already installed `python <https://www.python.org/downloads/>`_, with the release version meeting the constraints set in the `Installation Requirements`_ section, and do not have an environment already active (e.g., with ``pyenv``). For development, we recommend working with versions > python 3.9 to avoid issues with ``pre-commit``'s default hook configuration.
 

From 42101f7dabe080d92043fe6aad29786b51f8610b Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Tue, 5 Nov 2024 16:02:59 -0800
Subject: [PATCH 37/47] Fix formatting

---
 docs/source/asset_store.rst | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/docs/source/asset_store.rst b/docs/source/asset_store.rst
index d2fa45ddc..b4f8e5c99 100644
--- a/docs/source/asset_store.rst
+++ b/docs/source/asset_store.rst
@@ -51,9 +51,12 @@ Access & Project Setup - Multiple Contributing Projects
 1. Create a DCC Admin Team with admin permissions.
 2. Create a Team for each data contributing institution. Begin with a "Test Team" if all teams are not yet identified.
 3. Create a Synapse Project for each institution and grant the respective team **Edit** level access.
+
    - E.g., for institutions A, B, and C, create Projects A, B, and C with Teams A, B, and C. Team A has **Edit** access to Project A, etc.
+
 4. Within each project, create "top level folders" in the **Files** tab for each dataset type.
 5. Create another Synapse Project (e.g., MyDCC) containing the main **Fileview** that includes in the scope all the DCC projects.
+
    - Ensure all teams have **Download** level access to this file view.
    - Include both file and folder entities and add ALL default columns.
    - Note: If you want to upload data according to hierachical data layout, you can still use distributed projects, just the ``contentType`` column to your fileview, and you will have to annotate your top level folders with ``contentType:dataset``.
@@ -77,6 +80,7 @@ Access & Project Setup - Single Contributing Project
 1. Create a Team for each data contributing institution.
 2. Create a single Synapse Project (e.g., MyDCC).
 3. Within this project, create dataset folders for each contributor. Organize them as needed.
+
    - Annotate ``contentType: dataset`` for each top level folder, which should not nest inside other dataset folders and must have unique names.
      Taking the above example, you cannot have something like this:
 
@@ -91,6 +95,7 @@ Access & Project Setup - Single Contributing Project
             └── batch_2 <- annotated
 
 4. In MyDCC, create the main **DCC Fileview** with `MyDCC` as the scope. Add column ``contentType`` to the schema and grant teams **Download** level access.
+
    - Add both file and folder entities and add ALL default columns.
 
 
@@ -101,6 +106,7 @@ If DCC contributors require external cloud buckets, select one of the following
 set this up on Synapse, view this documentation: https://help.synapse.org/docs/Custom-Storage-Locations.2048327803.html
 
 1. **Basic External Storage Bucket (Default)**:
+
    - Create an S3 bucket for Synapse uploads via web or CLI. Contributors will upload data without needing AWS credentials.
    - Provision an S3 bucket, attach it to the Synapse project, and create folders for specific assay types.
 

From 3f4b5636e1b4cb26bafea58d30bf00aeccbebee9 Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Tue, 5 Nov 2024 18:59:49 -0800
Subject: [PATCH 38/47] Edit troubleshotting docs

---
 docs/source/troubleshooting.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/source/troubleshooting.rst b/docs/source/troubleshooting.rst
index 53d79c404..86a65dd5a 100644
--- a/docs/source/troubleshooting.rst
+++ b/docs/source/troubleshooting.rst
@@ -44,9 +44,9 @@ If so, you can either submit your manifest using schematic OR (the less preferre
 Manifest Generate: `ValueError: cannot insert eTag, already exists`
 -------------------------------------------------------------------
 
-If there is currently a manifest in your "Top Level Folder" on Synapse with the 'eTag' column and you try to generate a manifest, it will fail.
+If you do NOT have a manifest in your "Top Level Folder" on Synapse and your File entities in this folder are annotated with 'eTag' key and you try to generate a manifest, it will fail.
 
-To fix: You will want to first check if your "Top Level Folder" has a manifest with the 'eTag' column and remove that column.
+To fix: This should be fixed in schematic, but for now, remove the 'eTag' annotation from your file.
 
 
 Manifest Submit: `RuntimeError: failed with SynapseHTTPError('400 Client Error: nan is not a valid Synapse ID.')`

From 3abe8efe41232468677831a01c05b35974439886 Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Tue, 5 Nov 2024 19:08:15 -0800
Subject: [PATCH 39/47] Add more inforamtion

---
 docs/source/index.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/source/index.rst b/docs/source/index.rst
index 95041b019..0a4e314ac 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -53,8 +53,8 @@ Top Level Folders
    This concept is subject to feedback and `can` be changed.  Schematic currently has parameters in the API and CLI that refer to ``dataset``.  This is actually referring to
    the top level folders.
 
-This is a schematic specific term, this refers to top level Synapse folders that contain Synapse associated to a group of files.
-These folders are often annotated with ``contentType: dataset``.  Until users add this Synapse Annotation to their folder, it will NOT be a "Top Level Folder"
+This is a schematic specific term, this refers to top level Synapse folders associated to a group of files.
+Depending on whether you pick a flat and hiearchical data project layout, these folders are either annotated with ``contentType: dataset`` or are folders that live directly under the project.
 
 
 JSON-LD

From fb91a47bda56a7109180628c1134b2f1ecd6b797 Mon Sep 17 00:00:00 2001
From: thomasyu888 <thomasyu888@gmail.com>
Date: Tue, 5 Nov 2024 23:26:18 -0800
Subject: [PATCH 40/47] Add notes

---
 docs/source/asset_store.rst | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/docs/source/asset_store.rst b/docs/source/asset_store.rst
index b4f8e5c99..675f59dbb 100644
--- a/docs/source/asset_store.rst
+++ b/docs/source/asset_store.rst
@@ -24,6 +24,10 @@ In each of these project setups, there are two ways you can lay out your data:
 
 2. **Hierarchical Data Layout**: Top level folders are stored within nested folders annotated with ``contentType: dataset``
 
+   .. note::
+
+      This requires you to add the column ``contentType`` to your fileview schema.
+
    .. code-block:: shell
 
       my_heirarchical_project
@@ -59,7 +63,12 @@ Access & Project Setup - Multiple Contributing Projects
 
    - Ensure all teams have **Download** level access to this file view.
    - Include both file and folder entities and add ALL default columns.
-   - Note: If you want to upload data according to hierachical data layout, you can still use distributed projects, just the ``contentType`` column to your fileview, and you will have to annotate your top level folders with ``contentType:dataset``.
+
+.. note::
+
+   Note: If you want to upload data according to hierachical data layout, you can still use
+   distributed projects, just the ``contentType`` column to your fileview, and you will have
+   to annotate your top level folders with ``contentType:dataset``.
 
 
 Option 2: Single Synapse Project
@@ -98,6 +107,11 @@ Access & Project Setup - Single Contributing Project
 
    - Add both file and folder entities and add ALL default columns.
 
+.. note::
+
+   You can technically use the flat data layout with a single project setup, but it is not recommended
+   as if you have different data contributors contributing similar datatypes, it would lead to a
+   proliferation of folders per contributor and data type.
 
 Synapse External Cloud Buckets Setup
 ------------------------------------

From 0b6ef684b3d29a2c50f41dc11575d17069b4d234 Mon Sep 17 00:00:00 2001
From: thomasyu888 <thomasyu888@gmail.com>
Date: Tue, 5 Nov 2024 23:35:55 -0800
Subject: [PATCH 41/47] Update docs

---
 docs/source/index.rst | 37 +++++++++++++++++++++++++------------
 1 file changed, 25 insertions(+), 12 deletions(-)

diff --git a/docs/source/index.rst b/docs/source/index.rst
index 0a4e314ac..c4eecbe23 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -10,13 +10,17 @@ Welcome to Schematic's documentation!
    This documentation site is a work in progress, and the sublinks may change.  Apologies for the inconvenience.
 
 
-**SCHEMATIC** is an acronym for *Schema Engine for Manifest Ingress and Curation*. The Python-based infrastructure provides a *novel* schema-based, metadata ingress ecosystem, which is meant to streamline the process of biomedical dataset annotation, metadata validation, and submission to a data repository for various data contributors.
+**SCHEMATIC** is an acronym for *Schema Engine for Manifest Ingress and Curation*.
+The Python-based infrastructure provides a *novel* schema-based, metadata ingress ecosystem,
+which is meant to streamline the process of biomedical dataset annotation, metadata validation,
+and submission to a data repository for various data contributors.  This tool is a recommened to be
+used as a command line tool (CLI) and as an API.
 
 Schematic tackles these goals:
 
-- Ensure the highest quality structured data or metadata be contributed to Synapse before it lands in Synapse
-- Provide excel templates that correspond to a data model that can be filled out by data contributors
-- Visualize data models and their relationships with each other
+- Ensure the highest quality structured data or metadata be contributed to Synapse.
+- Provide excel templates that correspond to a data model that can be filled out by data contributors.
+- Visualize and manage data models and their relationships with each other
 
 .. contents::
    :depth: 2
@@ -26,6 +30,7 @@ Important Concepts
 ------------------
 
 .. important::
+
    Before moving reading more about schematic, this section covers essential concepts relevant for using the Schematic tool effectively.
 
 Synapse FileViews
@@ -33,6 +38,7 @@ Synapse FileViews
 Users are responsible for setting up a **FileView** that integrates with Schematic. Note that FileViews appear under the "Tables" tab in Synapse and can be named according to the project's needs. For instance, a FileView for the **Project A** could have a different name than a FileView for the **Project B**.
 
 For more information on Synapse projects, visit:
+
 - `Synapse projects <https://help.synapse.org/docs/Uploading-and-Organizing-Data-Into-Projects,-Files,-and-Folders.2048327716.html>`_
 - `Synapse annotations <https://help.synapse.org/docs/Annotating-Data-With-Metadata.2667708522.html>`_
 
@@ -50,23 +56,30 @@ Top Level Folders
 ~~~~~~~~~~~~~~~~~
 
 .. note::
-   This concept is subject to feedback and `can` be changed.  Schematic currently has parameters in the API and CLI that refer to ``dataset``.  This is actually referring to
-   the top level folders.
 
-This is a schematic specific term, this refers to top level Synapse folders associated to a group of files.
+   This concept is subject to feedback and `can` be changed.  Schematic currently has parameters in
+   the API and CLI that refer to ``dataset``.  This is referring to the "top level folders".
+
+Top level folders refers to Synapse folders that contains a group of files.
 Depending on whether you pick a flat and hiearchical data project layout, these folders are either annotated with ``contentType: dataset`` or are folders that live directly under the project.
 
 
 JSON-LD
 ~~~~~~~
-JSON-LD is a lightweight Linked Data format. The usage of JSON-LD to capture our data models extends beyond the creation, validation, and submission of annotations/manifests into Synapse. It can create relationships between different data models and, in the future, drive transformation of data from one data model to another. Visualization of these data models and their relationships is also possible (see *Schema Visualization - Design & Platform*), which allows the community to see the depth of connections between all the data uploaded into Synapse. As with all products, we must start somewhere.
+JSON-LD is a lightweight Linked Data format. The usage of JSON-LD to capture our data models
+extends beyond the creation, validation, and submission of annotations/manifests into Synapse
+It can create relationships between different data models and, in the future, drive
+transformation of data from one data model to another. Visualization of these data models
+and their relationships is also possible which allows the community to see the depth of
+connections between all the data uploaded into Synapse.
 
 Manifest
 ~~~~~~~~
-A manifest is a structured file that contains metadata about a files under a "top level folder".
-It is a list of files and their associated metadata. The metadata includes information such as the file name,
-file type, and file size. The manifest is used to validate the metadata before it is uploaded to Synapse.
-The manifest can also used to create a view in Synapse that displays the metadata for each file in the "top level folder".
+
+A manifest is a structured file that contains metadata about files under a "top level folder".
+The metadata includes information of the files such as data type and etc.
+The manifest can also used to annotate the data on Synapse and create a file view
+that enables the FAIR principles on each of the files in the "top level folder".
 
 Component/Data type
 ~~~~~~~~~~~~~~~~~~~

From 9bd4055304097beec9497f77b8f5ba9af3145a5e Mon Sep 17 00:00:00 2001
From: thomasyu888 <thomasyu888@gmail.com>
Date: Tue, 5 Nov 2024 23:39:13 -0800
Subject: [PATCH 42/47] Update docs

---
 docs/source/index.rst | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/docs/source/index.rst b/docs/source/index.rst
index c4eecbe23..db15f0c05 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -113,14 +113,14 @@ Given a filled-out manifest:
 Manifest Submission
 ~~~~~~~~~~~~~~~~~~~
 
-- Validates the manifest. If errors are present, the manifest is not stored.
-- If valid:
-  - Stores the manifest in Synapse.
-  - Uploads the manifest to a view, updating file views with annotations as follows:
+Given a filled out manifest, this will allow you to submit the manifest to the "top level folder".
+This is validates the manifest and...
+
+- If manifest is invalid, erorr messages will be returned.
+- If the manifest is valid:
 
-      - **Store manifest only**
-      - **Store manifest and annotations** (to update a file view)
-      - **Store manifest and update a corresponding Synapse table**
+  - Stores the manifest in Synapse.
+  - Uploads the manifest as a Synapse File, Annotations on Files, and/or Synapse Table.
 
 More validation documentation can be found here: https://sagebionetworks.jira.com/wiki/spaces/SCHEM/pages/3302785036/Schematic+Validation
 

From 1b4307883815ae05f34edec05e210228f0524fb8 Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Wed, 6 Nov 2024 15:19:57 -0800
Subject: [PATCH 43/47] Add data layout

---
 docs/source/index.rst | 26 +++++++++++++++-----------
 1 file changed, 15 insertions(+), 11 deletions(-)

diff --git a/docs/source/index.rst b/docs/source/index.rst
index 0a4e314ac..7edb7f340 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -46,17 +46,6 @@ Synapse Datasets
 
 This is an object in Synapse which appears under the "Dataset" tab and represents a user-defined collection of Synapse files and versions. https://help.synapse.org/docs/Datasets.2611281979.html
 
-Top Level Folders
-~~~~~~~~~~~~~~~~~
-
-.. note::
-   This concept is subject to feedback and `can` be changed.  Schematic currently has parameters in the API and CLI that refer to ``dataset``.  This is actually referring to
-   the top level folders.
-
-This is a schematic specific term, this refers to top level Synapse folders associated to a group of files.
-Depending on whether you pick a flat and hiearchical data project layout, these folders are either annotated with ``contentType: dataset`` or are folders that live directly under the project.
-
-
 JSON-LD
 ~~~~~~~
 JSON-LD is a lightweight Linked Data format. The usage of JSON-LD to capture our data models extends beyond the creation, validation, and submission of annotations/manifests into Synapse. It can create relationships between different data models and, in the future, drive transformation of data from one data model to another. Visualization of these data models and their relationships is also possible (see *Schema Visualization - Design & Platform*), which allows the community to see the depth of connections between all the data uploaded into Synapse. As with all products, we must start somewhere.
@@ -75,6 +64,21 @@ If the string "component" exists in the depends on column, the "Attribute" value
 Examples of a data type is "Biospecimen", "Patient": https://github.com/Sage-Bionetworks/schematic/blob/develop/tests/data/example.model.csv#L3.
 Each data type/component should a manifest template that has different columns.
 
+Project Data Layout
+~~~~~~~~~~~~~~~~~~~
+
+Regardless of data layout, the data in your Synapse Project(s) are uploaded into Synapse Folders to be curated and annotated by schematic.
+In both layouts listed below, the project administrators along with the data contributors may have preferences on how the
+data is organized. The organization of your data is specified with the "Component / data type" attribute of your data model and
+act as logical groupings for your data. Schematic has a concept of a ``dataset`` (parameters for the API/library/CLI), but this means
+different things under these two layouts.
+
+* **Hierarchical**: The "dataset" parameter under this data layout is associated with any folder that has ``contentType: dataset`` annotated
+  and is often associated with a "dataset".
+* **Flat**: The "dataset" parameter under this data layout is often referred to as "top level folders".
+
+In both of these layouts, these are really just groupings of resources.
+
 
 Schematic services
 ------------------

From 35a116d9943a917f4cddda69bcdcb5434fd10efe Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Wed, 6 Nov 2024 23:18:50 -0800
Subject: [PATCH 44/47] Fix lock file

---
 poetry.lock | 259 +++-------------------------------------------------
 1 file changed, 13 insertions(+), 246 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 7e8d64135..b0f123002 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,10 +1,9 @@
-# This file is automatically @generated by Poetry and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
 version = "0.7.16"
 description = "A light, configurable Sphinx theme"
-category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -16,7 +15,6 @@ files = [
 name = "altair"
 version = "4.2.0"
 description = "Altair: A declarative statistical visualization library for Python."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -39,7 +37,6 @@ dev = ["black", "docutils", "flake8", "ipython", "m2r", "mistune (<2.0.0)", "pyt
 name = "anyio"
 version = "4.6.2.post1"
 description = "High level compatibility layer for multiple asynchronous event loop implementations"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -62,7 +59,6 @@ trio = ["trio (>=0.26.1)"]
 name = "appnope"
 version = "0.1.4"
 description = "Disable App Nap on macOS >= 10.9"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -74,7 +70,6 @@ files = [
 name = "argon2-cffi"
 version = "23.1.0"
 description = "Argon2 for Python"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -95,7 +90,6 @@ typing = ["mypy"]
 name = "argon2-cffi-bindings"
 version = "21.2.0"
 description = "Low-level CFFI bindings for Argon2"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -133,7 +127,6 @@ tests = ["pytest"]
 name = "arrow"
 version = "1.3.0"
 description = "Better dates & times for Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -147,13 +140,12 @@ types-python-dateutil = ">=2.8.10"
 
 [package.extras]
 doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"]
-test = ["dateparser (>=1.0.0,<2.0.0)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (>=3.0.0,<4.0.0)"]
+test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"]
 
 [[package]]
 name = "astroid"
 version = "2.15.8"
 description = "An abstract syntax tree for Python with inference support."
-category = "dev"
 optional = false
 python-versions = ">=3.7.2"
 files = [
@@ -170,7 +162,6 @@ wrapt = {version = ">=1.11,<2", markers = "python_version < \"3.11\""}
 name = "asttokens"
 version = "2.4.1"
 description = "Annotate AST trees with source code positions"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -189,7 +180,6 @@ test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
 name = "async-lru"
 version = "2.0.4"
 description = "Simple LRU cache for asyncio"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -204,7 +194,6 @@ typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
 name = "asyncio"
 version = "3.4.3"
 description = "reference implementation of PEP 3156"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -218,7 +207,6 @@ files = [
 name = "asyncio-atexit"
 version = "1.0.1"
 description = "Like atexit, but for asyncio"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -233,7 +221,6 @@ test = ["pytest", "uvloop"]
 name = "attrs"
 version = "24.2.0"
 description = "Classes Without Boilerplate"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -253,7 +240,6 @@ tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
 name = "babel"
 version = "2.16.0"
 description = "Internationalization utilities"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -268,7 +254,6 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
 name = "beautifulsoup4"
 version = "4.12.3"
 description = "Screen-scraping library"
-category = "main"
 optional = false
 python-versions = ">=3.6.0"
 files = [
@@ -290,7 +275,6 @@ lxml = ["lxml"]
 name = "black"
 version = "23.12.1"
 description = "The uncompromising code formatter."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -337,7 +321,6 @@ uvloop = ["uvloop (>=0.15.2)"]
 name = "bleach"
 version = "6.2.0"
 description = "An easy safelist-based HTML-sanitizing tool."
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -355,7 +338,6 @@ css = ["tinycss2 (>=1.1.0,<1.5)"]
 name = "cachetools"
 version = "5.5.0"
 description = "Extensible memoizing collections and decorators"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -367,7 +349,6 @@ files = [
 name = "certifi"
 version = "2024.8.30"
 description = "Python package for providing Mozilla's CA Bundle."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -379,7 +360,6 @@ files = [
 name = "cffi"
 version = "1.17.1"
 description = "Foreign Function Interface for Python calling C code."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -459,7 +439,6 @@ pycparser = "*"
 name = "cfgv"
 version = "3.4.0"
 description = "Validate configuration and produce human readable error messages."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -471,7 +450,6 @@ files = [
 name = "charset-normalizer"
 version = "3.4.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
-category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -586,7 +564,6 @@ files = [
 name = "click"
 version = "8.1.7"
 description = "Composable command line interface toolkit"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -601,7 +578,6 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 name = "click-log"
 version = "0.4.0"
 description = "Logging integration for Click"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -616,7 +592,6 @@ click = "*"
 name = "clickclick"
 version = "20.10.2"
 description = "Click utility functions"
-category = "main"
 optional = true
 python-versions = "*"
 files = [
@@ -632,7 +607,6 @@ PyYAML = ">=3.11"
 name = "colorama"
 version = "0.4.6"
 description = "Cross-platform colored terminal text."
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
@@ -644,7 +618,6 @@ files = [
 name = "comm"
 version = "0.2.2"
 description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -662,7 +635,6 @@ test = ["pytest"]
 name = "connexion"
 version = "2.14.2"
 description = "Connexion - API first applications with OpenAPI/Swagger and Flask"
-category = "main"
 optional = true
 python-versions = ">=3.6"
 files = [
@@ -693,7 +665,6 @@ tests = ["MarkupSafe (>=0.23)", "aiohttp (>=2.3.10,<4)", "aiohttp-jinja2 (>=0.14
 name = "coverage"
 version = "7.6.4"
 description = "Code coverage measurement for Python"
-category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -771,7 +742,6 @@ toml = ["tomli"]
 name = "cryptography"
 version = "41.0.7"
 description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -817,7 +787,6 @@ test-randomorder = ["pytest-randomly"]
 name = "dataclasses-json"
 version = "0.6.7"
 description = "Easily serialize dataclasses to and from JSON."
-category = "main"
 optional = false
 python-versions = "<4.0,>=3.7"
 files = [
@@ -833,7 +802,6 @@ typing-inspect = ">=0.4.0,<1"
 name = "dateparser"
 version = "1.2.0"
 description = "Date parsing library designed to parse dates from HTML pages"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -856,7 +824,6 @@ langdetect = ["langdetect"]
 name = "debugpy"
 version = "1.8.7"
 description = "An implementation of the Debug Adapter Protocol for Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -892,7 +859,6 @@ files = [
 name = "decorator"
 version = "5.1.1"
 description = "Decorators for Humans"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -904,7 +870,6 @@ files = [
 name = "defusedxml"
 version = "0.7.1"
 description = "XML bomb protection for Python stdlib modules"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -916,7 +881,6 @@ files = [
 name = "deprecated"
 version = "1.2.14"
 description = "Python @deprecated decorator to deprecate old python classes, functions or methods."
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -934,7 +898,6 @@ dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"]
 name = "dill"
 version = "0.3.9"
 description = "serialize all of Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -950,7 +913,6 @@ profile = ["gprof2dot (>=2022.7.29)"]
 name = "distlib"
 version = "0.3.9"
 description = "Distribution utilities"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -962,7 +924,6 @@ files = [
 name = "docutils"
 version = "0.21.2"
 description = "Docutils -- Python Documentation Utilities"
-category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -974,7 +935,6 @@ files = [
 name = "entrypoints"
 version = "0.4"
 description = "Discover and load entry points from installed packages."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -986,7 +946,6 @@ files = [
 name = "et-xmlfile"
 version = "2.0.0"
 description = "An implementation of lxml.xmlfile for the standard library"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -998,7 +957,6 @@ files = [
 name = "exceptiongroup"
 version = "1.2.2"
 description = "Backport of PEP 654 (exception groups)"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1013,7 +971,6 @@ test = ["pytest (>=6)"]
 name = "execnet"
 version = "2.1.1"
 description = "execnet: rapid multi-Python deployment"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1028,7 +985,6 @@ testing = ["hatch", "pre-commit", "pytest", "tox"]
 name = "executing"
 version = "2.1.0"
 description = "Get the currently executing AST node of a frame, and other information"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1043,7 +999,6 @@ tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipyth
 name = "fastjsonschema"
 version = "2.20.0"
 description = "Fastest Python implementation of JSON schema"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1058,7 +1013,6 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc
 name = "filelock"
 version = "3.16.1"
 description = "A platform independent file lock."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1075,7 +1029,6 @@ typing = ["typing-extensions (>=4.12.2)"]
 name = "flake8"
 version = "6.1.0"
 description = "the modular source code checker: pep8 pyflakes and co"
-category = "dev"
 optional = false
 python-versions = ">=3.8.1"
 files = [
@@ -1092,7 +1045,6 @@ pyflakes = ">=3.1.0,<3.2.0"
 name = "flask"
 version = "2.1.3"
 description = "A simple framework for building complex web applications."
-category = "main"
 optional = true
 python-versions = ">=3.7"
 files = [
@@ -1115,7 +1067,6 @@ dotenv = ["python-dotenv"]
 name = "flask-cors"
 version = "3.0.10"
 description = "A Flask extension adding a decorator for CORS support"
-category = "main"
 optional = true
 python-versions = "*"
 files = [
@@ -1131,7 +1082,6 @@ Six = "*"
 name = "fqdn"
 version = "1.5.1"
 description = "Validates fully-qualified domain names against RFC 1123, so that they are acceptable to modern bowsers"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4"
 files = [
@@ -1143,7 +1093,6 @@ files = [
 name = "google-api-core"
 version = "2.21.0"
 description = "Google API client core library"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1168,7 +1117,6 @@ grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"]
 name = "google-api-python-client"
 version = "2.123.0"
 description = "Google API Client Library for Python"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1177,7 +1125,7 @@ files = [
 ]
 
 [package.dependencies]
-google-api-core = ">=1.31.5,<2.0.0 || >2.3.0,<3.0.0.dev0"
+google-api-core = ">=1.31.5,<2.0.dev0 || >2.3.0,<3.0.0.dev0"
 google-auth = ">=1.19.0,<3.0.0.dev0"
 google-auth-httplib2 = ">=0.1.0"
 httplib2 = ">=0.15.0,<1.dev0"
@@ -1187,7 +1135,6 @@ uritemplate = ">=3.0.1,<5"
 name = "google-auth"
 version = "2.35.0"
 description = "Google Authentication Library"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1211,7 +1158,6 @@ requests = ["requests (>=2.20.0,<3.0.0.dev0)"]
 name = "google-auth-httplib2"
 version = "0.1.1"
 description = "Google Authentication Library: httplib2 transport"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1227,7 +1173,6 @@ httplib2 = ">=0.19.0"
 name = "google-auth-oauthlib"
 version = "0.8.0"
 description = "Google Authentication Library"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1246,7 +1191,6 @@ tool = ["click (>=6.0.0)"]
 name = "googleapis-common-protos"
 version = "1.65.0"
 description = "Common protobufs used in Google APIs"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1264,7 +1208,6 @@ grpc = ["grpcio (>=1.44.0,<2.0.0.dev0)"]
 name = "graphviz"
 version = "0.20.3"
 description = "Simple Python interface for Graphviz"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1281,7 +1224,6 @@ test = ["coverage", "pytest (>=7,<8.1)", "pytest-cov", "pytest-mock (>=3)"]
 name = "great-expectations"
 version = "0.15.50"
 description = "Always know what to expect from your data."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1356,7 +1298,6 @@ vertica = ["sqlalchemy (>=1.3.18,<2.0.0)", "sqlalchemy-vertica-python (>=0.5.10)
 name = "grpcio"
 version = "1.67.0"
 description = "HTTP/2-based RPC framework"
-category = "main"
 optional = true
 python-versions = ">=3.8"
 files = [
@@ -1424,7 +1365,6 @@ protobuf = ["grpcio-tools (>=1.67.0)"]
 name = "h11"
 version = "0.14.0"
 description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1436,7 +1376,6 @@ files = [
 name = "httpcore"
 version = "1.0.6"
 description = "A minimal low-level HTTP client."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1458,7 +1397,6 @@ trio = ["trio (>=0.22.0,<1.0)"]
 name = "httplib2"
 version = "0.22.0"
 description = "A comprehensive HTTP client library."
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -1473,7 +1411,6 @@ pyparsing = {version = ">=2.4.2,<3.0.0 || >3.0.0,<3.0.1 || >3.0.1,<3.0.2 || >3.0
 name = "httpx"
 version = "0.27.2"
 description = "The next generation HTTP client."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1484,22 +1421,21 @@ files = [
 [package.dependencies]
 anyio = "*"
 certifi = "*"
-httpcore = ">=1.0.0,<2.0.0"
+httpcore = "==1.*"
 idna = "*"
 sniffio = "*"
 
 [package.extras]
 brotli = ["brotli", "brotlicffi"]
-cli = ["click (>=8.0.0,<9.0.0)", "pygments (>=2.0.0,<3.0.0)", "rich (>=10,<14)"]
+cli = ["click (==8.*)", "pygments (==2.*)", "rich (>=10,<14)"]
 http2 = ["h2 (>=3,<5)"]
-socks = ["socksio (>=1.0.0,<2.0.0)"]
+socks = ["socksio (==1.*)"]
 zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "identify"
 version = "2.6.1"
 description = "File identification library for Python"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1514,7 +1450,6 @@ license = ["ukkonen"]
 name = "idna"
 version = "3.10"
 description = "Internationalized Domain Names in Applications (IDNA)"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1529,7 +1464,6 @@ all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2
 name = "imagesize"
 version = "1.4.1"
 description = "Getting image size from png/jpeg/jpeg2000/gif file"
-category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -1541,7 +1475,6 @@ files = [
 name = "importlib-metadata"
 version = "8.4.0"
 description = "Read metadata from Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1561,7 +1494,6 @@ test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "p
 name = "inflection"
 version = "0.5.1"
 description = "A port of Ruby on Rails inflector to Python"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -1573,7 +1505,6 @@ files = [
 name = "iniconfig"
 version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1585,7 +1516,6 @@ files = [
 name = "ipykernel"
 version = "6.29.5"
 description = "IPython Kernel for Jupyter"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1599,7 +1529,7 @@ comm = ">=0.1.1"
 debugpy = ">=1.6.5"
 ipython = ">=7.23.1"
 jupyter-client = ">=6.1.12"
-jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 matplotlib-inline = ">=0.1"
 nest-asyncio = "*"
 packaging = "*"
@@ -1619,7 +1549,6 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio
 name = "ipython"
 version = "8.18.1"
 description = "IPython: Productive Interactive Computing"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1657,7 +1586,6 @@ test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.22)", "pa
 name = "ipywidgets"
 version = "8.1.5"
 description = "Jupyter interactive widgets"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1679,7 +1607,6 @@ test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"]
 name = "isodate"
 version = "0.6.1"
 description = "An ISO 8601 date/time/duration parser and formatter"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -1694,7 +1621,6 @@ six = "*"
 name = "isoduration"
 version = "20.11.0"
 description = "Operations with ISO 8601 durations"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1709,7 +1635,6 @@ arrow = ">=0.15.0"
 name = "isort"
 version = "5.13.2"
 description = "A Python utility / library to sort Python imports."
-category = "dev"
 optional = false
 python-versions = ">=3.8.0"
 files = [
@@ -1724,7 +1649,6 @@ colors = ["colorama (>=0.4.6)"]
 name = "itsdangerous"
 version = "2.2.0"
 description = "Safely pass data to untrusted environments and back."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1736,7 +1660,6 @@ files = [
 name = "jedi"
 version = "0.19.1"
 description = "An autocompletion tool for Python that can be used for text editors."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -1756,7 +1679,6 @@ testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
 name = "jinja2"
 version = "3.1.4"
 description = "A very fast and expressive template engine."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1774,7 +1696,6 @@ i18n = ["Babel (>=2.7)"]
 name = "json5"
 version = "0.9.25"
 description = "A Python implementation of the JSON5 data format."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1786,7 +1707,6 @@ files = [
 name = "jsonpatch"
 version = "1.33"
 description = "Apply JSON-Patches (RFC 6902)"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
 files = [
@@ -1801,7 +1721,6 @@ jsonpointer = ">=1.9"
 name = "jsonpointer"
 version = "3.0.0"
 description = "Identify specific nodes in a JSON document (RFC 6901)"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -1813,7 +1732,6 @@ files = [
 name = "jsonschema"
 version = "4.23.0"
 description = "An implementation of JSON Schema validation for Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1843,7 +1761,6 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 name = "jsonschema-specifications"
 version = "2024.10.1"
 description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -1858,7 +1775,6 @@ referencing = ">=0.31.0"
 name = "jupyter-client"
 version = "8.6.3"
 description = "Jupyter protocol implementation and client libraries"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1868,7 +1784,7 @@ files = [
 
 [package.dependencies]
 importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""}
-jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 python-dateutil = ">=2.8.2"
 pyzmq = ">=23.0"
 tornado = ">=6.2"
@@ -1882,7 +1798,6 @@ test = ["coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pyt
 name = "jupyter-core"
 version = "5.7.2"
 description = "Jupyter core package. A base package on which Jupyter projects rely."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1903,7 +1818,6 @@ test = ["ipykernel", "pre-commit", "pytest (<8)", "pytest-cov", "pytest-timeout"
 name = "jupyter-events"
 version = "0.10.0"
 description = "Jupyter Event System library"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1929,7 +1843,6 @@ test = ["click", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.19.0)", "p
 name = "jupyter-lsp"
 version = "2.2.5"
 description = "Multi-Language Server WebSocket proxy for Jupyter Notebook/Lab server"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1945,7 +1858,6 @@ jupyter-server = ">=1.1.2"
 name = "jupyter-server"
 version = "2.14.2"
 description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -1958,7 +1870,7 @@ anyio = ">=3.1.0"
 argon2-cffi = ">=21.1"
 jinja2 = ">=3.0.3"
 jupyter-client = ">=7.4.4"
-jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 jupyter-events = ">=0.9.0"
 jupyter-server-terminals = ">=0.4.4"
 nbconvert = ">=6.4.4"
@@ -1982,7 +1894,6 @@ test = ["flaky", "ipykernel", "pre-commit", "pytest (>=7.0,<9)", "pytest-console
 name = "jupyter-server-terminals"
 version = "0.5.3"
 description = "A Jupyter Server Extension Providing Terminals."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2002,7 +1913,6 @@ test = ["jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-jupyter[server] (>
 name = "jupyterlab"
 version = "4.2.5"
 description = "JupyterLab computational environment"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2038,7 +1948,6 @@ upgrade-extension = ["copier (>=9,<10)", "jinja2-time (<0.3)", "pydantic (<3.0)"
 name = "jupyterlab-pygments"
 version = "0.3.0"
 description = "Pygments theme using JupyterLab CSS variables"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2050,7 +1959,6 @@ files = [
 name = "jupyterlab-server"
 version = "2.27.3"
 description = "A set of server components for JupyterLab and JupyterLab like applications."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2077,7 +1985,6 @@ test = ["hatch", "ipykernel", "openapi-core (>=0.18.0,<0.19.0)", "openapi-spec-v
 name = "jupyterlab-widgets"
 version = "3.0.13"
 description = "Jupyter interactive widgets for JupyterLab"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2089,7 +1996,6 @@ files = [
 name = "lazy-object-proxy"
 version = "1.10.0"
 description = "A fast and thorough lazy object proxy."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2136,7 +2042,6 @@ files = [
 name = "makefun"
 version = "1.15.6"
 description = "Small library to dynamically create python functions."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2148,7 +2053,6 @@ files = [
 name = "markupsafe"
 version = "3.0.2"
 description = "Safely add untrusted strings to HTML/XML markup."
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2219,7 +2123,6 @@ files = [
 name = "marshmallow"
 version = "3.23.0"
 description = "A lightweight library for converting complex datatypes to and from native Python datatypes."
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2239,7 +2142,6 @@ tests = ["pytest", "simplejson"]
 name = "matplotlib-inline"
 version = "0.1.7"
 description = "Inline Matplotlib backend for Jupyter"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2254,7 +2156,6 @@ traitlets = "*"
 name = "mccabe"
 version = "0.7.0"
 description = "McCabe checker, plugin for flake8"
-category = "dev"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2266,7 +2167,6 @@ files = [
 name = "mistune"
 version = "3.0.2"
 description = "A sane and fast Markdown parser with useful plugins and renderers"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2278,7 +2178,6 @@ files = [
 name = "mypy"
 version = "1.13.0"
 description = "Optional static typing for Python"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2332,7 +2231,6 @@ reports = ["lxml"]
 name = "mypy-extensions"
 version = "1.0.0"
 description = "Type system extensions for programs checked with the mypy type checker."
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -2344,7 +2242,6 @@ files = [
 name = "nbclient"
 version = "0.10.0"
 description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor."
-category = "main"
 optional = false
 python-versions = ">=3.8.0"
 files = [
@@ -2354,7 +2251,7 @@ files = [
 
 [package.dependencies]
 jupyter-client = ">=6.1.12"
-jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 nbformat = ">=5.1"
 traitlets = ">=5.4"
 
@@ -2367,7 +2264,6 @@ test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>=
 name = "nbconvert"
 version = "7.16.4"
 description = "Converting Jupyter Notebooks (.ipynb files) to other formats.  Output formats include asciidoc, html, latex, markdown, pdf, py, rst, script.  nbconvert can be used both as a Python library (`import nbconvert`) or as a command line tool (invoked as `jupyter nbconvert ...`)."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2406,7 +2302,6 @@ webpdf = ["playwright"]
 name = "nbformat"
 version = "5.10.4"
 description = "The Jupyter Notebook format"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2417,7 +2312,7 @@ files = [
 [package.dependencies]
 fastjsonschema = ">=2.15"
 jsonschema = ">=2.6"
-jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
 traitlets = ">=5.1"
 
 [package.extras]
@@ -2428,7 +2323,6 @@ test = ["pep440", "pre-commit", "pytest", "testpath"]
 name = "nest-asyncio"
 version = "1.6.0"
 description = "Patch asyncio to allow nested event loops"
-category = "main"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -2440,7 +2334,6 @@ files = [
 name = "networkx"
 version = "3.2.1"
 description = "Python package for creating and manipulating graphs and networks"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2459,7 +2352,6 @@ test = ["pytest (>=7.2)", "pytest-cov (>=4.0)"]
 name = "nodeenv"
 version = "1.9.1"
 description = "Node.js virtual environment builder"
-category = "dev"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
@@ -2471,7 +2363,6 @@ files = [
 name = "notebook"
 version = "7.2.2"
 description = "Jupyter Notebook - A web-based notebook environment for interactive computing"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2495,7 +2386,6 @@ test = ["importlib-resources (>=5.0)", "ipykernel", "jupyter-server[test] (>=2.4
 name = "notebook-shim"
 version = "0.2.4"
 description = "A shim layer for notebook traits and config"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2513,7 +2403,6 @@ test = ["pytest", "pytest-console-scripts", "pytest-jupyter", "pytest-tornasync"
 name = "numpy"
 version = "1.26.4"
 description = "Fundamental package for array computing in Python"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -2559,7 +2448,6 @@ files = [
 name = "oauth2client"
 version = "4.1.3"
 description = "OAuth 2.0 client library"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -2578,7 +2466,6 @@ six = ">=1.6.1"
 name = "oauthlib"
 version = "3.2.2"
 description = "A generic, spec-compliant, thorough implementation of the OAuth request-signing logic"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2595,7 +2482,6 @@ signedtoken = ["cryptography (>=3.0.0)", "pyjwt (>=2.0.0,<3)"]
 name = "openpyxl"
 version = "3.1.5"
 description = "A Python library to read/write Excel 2010 xlsx/xlsm files"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2610,7 +2496,6 @@ et-xmlfile = "*"
 name = "opentelemetry-api"
 version = "1.27.0"
 description = "OpenTelemetry Python API"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2626,7 +2511,6 @@ importlib-metadata = ">=6.0,<=8.4.0"
 name = "opentelemetry-exporter-otlp-proto-common"
 version = "1.27.0"
 description = "OpenTelemetry Protobuf encoding"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2641,7 +2525,6 @@ opentelemetry-proto = "1.27.0"
 name = "opentelemetry-exporter-otlp-proto-grpc"
 version = "1.27.0"
 description = "OpenTelemetry Collector Protobuf over gRPC Exporter"
-category = "main"
 optional = true
 python-versions = ">=3.8"
 files = [
@@ -2662,7 +2545,6 @@ opentelemetry-sdk = ">=1.27.0,<1.28.0"
 name = "opentelemetry-exporter-otlp-proto-http"
 version = "1.27.0"
 description = "OpenTelemetry Collector Protobuf over HTTP Exporter"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2683,7 +2565,6 @@ requests = ">=2.7,<3.0"
 name = "opentelemetry-instrumentation"
 version = "0.48b0"
 description = "Instrumentation Tools & Auto Instrumentation for OpenTelemetry Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2700,7 +2581,6 @@ wrapt = ">=1.0.0,<2.0.0"
 name = "opentelemetry-instrumentation-flask"
 version = "0.48b0"
 description = "Flask instrumentation for OpenTelemetry"
-category = "main"
 optional = true
 python-versions = ">=3.8"
 files = [
@@ -2724,7 +2604,6 @@ instruments = ["flask (>=1.0)"]
 name = "opentelemetry-instrumentation-httpx"
 version = "0.48b0"
 description = "OpenTelemetry HTTPX Instrumentation"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2745,7 +2624,6 @@ instruments = ["httpx (>=0.18.0)"]
 name = "opentelemetry-instrumentation-requests"
 version = "0.48b0"
 description = "OpenTelemetry requests instrumentation"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2766,7 +2644,6 @@ instruments = ["requests (>=2.0,<3.0)"]
 name = "opentelemetry-instrumentation-threading"
 version = "0.48b0"
 description = "Thread context propagation support for OpenTelemetry"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2783,7 +2660,6 @@ wrapt = ">=1.0.0,<2.0.0"
 name = "opentelemetry-instrumentation-urllib"
 version = "0.48b0"
 description = "OpenTelemetry urllib instrumentation"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2801,7 +2677,6 @@ opentelemetry-util-http = "0.48b0"
 name = "opentelemetry-instrumentation-wsgi"
 version = "0.48b0"
 description = "WSGI Middleware for OpenTelemetry"
-category = "main"
 optional = true
 python-versions = ">=3.8"
 files = [
@@ -2819,7 +2694,6 @@ opentelemetry-util-http = "0.48b0"
 name = "opentelemetry-proto"
 version = "1.27.0"
 description = "OpenTelemetry Python Proto"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2834,7 +2708,6 @@ protobuf = ">=3.19,<5.0"
 name = "opentelemetry-sdk"
 version = "1.27.0"
 description = "OpenTelemetry Python SDK"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2851,7 +2724,6 @@ typing-extensions = ">=3.7.4"
 name = "opentelemetry-semantic-conventions"
 version = "0.48b0"
 description = "OpenTelemetry Semantic Conventions"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2867,7 +2739,6 @@ opentelemetry-api = "1.27.0"
 name = "opentelemetry-util-http"
 version = "0.48b0"
 description = "Web util for OpenTelemetry"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2879,7 +2750,6 @@ files = [
 name = "overrides"
 version = "7.7.0"
 description = "A decorator to automatically detect mismatch when overriding a method."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -2891,7 +2761,6 @@ files = [
 name = "packaging"
 version = "24.1"
 description = "Core utilities for Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -2903,7 +2772,6 @@ files = [
 name = "pandarallel"
 version = "1.6.5"
 description = "An easy to use library to speed up computation (by parallelizing on multi CPUs) with pandas."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -2923,7 +2791,6 @@ doc = ["mkdocs-material"]
 name = "pandas"
 version = "2.2.3"
 description = "Powerful data structures for data analysis, time series, and statistics"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -3006,7 +2873,6 @@ xml = ["lxml (>=4.9.2)"]
 name = "pandocfilters"
 version = "1.5.1"
 description = "Utilities for writing pandoc filters in python"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -3018,7 +2884,6 @@ files = [
 name = "parso"
 version = "0.8.4"
 description = "A Python Parser"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -3034,7 +2899,6 @@ testing = ["docopt", "pytest"]
 name = "pathspec"
 version = "0.12.1"
 description = "Utility library for gitignore style pattern matching of file paths."
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3046,7 +2910,6 @@ files = [
 name = "pdoc"
 version = "14.7.0"
 description = "API Documentation for Python Projects"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3066,7 +2929,6 @@ dev = ["hypothesis", "mypy", "pdoc-pyo3-sample-library (==1.0.11)", "pygments (>
 name = "pexpect"
 version = "4.9.0"
 description = "Pexpect allows easy control of interactive console applications."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -3081,7 +2943,6 @@ ptyprocess = ">=0.5"
 name = "platformdirs"
 version = "4.3.6"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3098,7 +2959,6 @@ type = ["mypy (>=1.11.2)"]
 name = "pluggy"
 version = "1.5.0"
 description = "plugin and hook calling mechanisms for python"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3114,7 +2974,6 @@ testing = ["pytest", "pytest-benchmark"]
 name = "pre-commit"
 version = "3.8.0"
 description = "A framework for managing and maintaining multi-language pre-commit hooks."
-category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -3133,7 +2992,6 @@ virtualenv = ">=20.10.0"
 name = "prometheus-client"
 version = "0.21.0"
 description = "Python client for the Prometheus monitoring system."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3148,7 +3006,6 @@ twisted = ["twisted"]
 name = "prompt-toolkit"
 version = "3.0.48"
 description = "Library for building powerful interactive command lines in Python"
-category = "main"
 optional = false
 python-versions = ">=3.7.0"
 files = [
@@ -3163,7 +3020,6 @@ wcwidth = "*"
 name = "proto-plus"
 version = "1.25.0"
 description = "Beautiful, Pythonic protocol buffers."
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3181,7 +3037,6 @@ testing = ["google-api-core (>=1.31.5)"]
 name = "protobuf"
 version = "4.25.5"
 description = ""
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3202,7 +3057,6 @@ files = [
 name = "psutil"
 version = "5.9.8"
 description = "Cross-platform lib for process and system monitoring in Python."
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
@@ -3231,7 +3085,6 @@ test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"]
 name = "ptyprocess"
 version = "0.7.0"
 description = "Run a subprocess in a pseudo terminal"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -3243,7 +3096,6 @@ files = [
 name = "pure-eval"
 version = "0.2.3"
 description = "Safely evaluate AST nodes without side effects"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -3258,7 +3110,6 @@ tests = ["pytest"]
 name = "pyasn1"
 version = "0.6.1"
 description = "Pure-Python implementation of ASN.1 types and DER/BER/CER codecs (X.208)"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3270,7 +3121,6 @@ files = [
 name = "pyasn1-modules"
 version = "0.4.1"
 description = "A collection of ASN.1-based protocols modules"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3285,7 +3135,6 @@ pyasn1 = ">=0.4.6,<0.7.0"
 name = "pycodestyle"
 version = "2.11.1"
 description = "Python style guide checker"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3297,7 +3146,6 @@ files = [
 name = "pycparser"
 version = "2.22"
 description = "C parser in Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3309,7 +3157,6 @@ files = [
 name = "pydantic"
 version = "1.10.18"
 description = "Data validation and settings management using python type hints"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3369,7 +3216,6 @@ email = ["email-validator (>=1.0.3)"]
 name = "pyflakes"
 version = "3.1.0"
 description = "passive checker of Python programs"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3381,7 +3227,6 @@ files = [
 name = "pygments"
 version = "2.18.0"
 description = "Pygments is a syntax highlighting package written in Python."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3396,7 +3241,6 @@ windows-terminal = ["colorama (>=0.4.6)"]
 name = "pygsheets"
 version = "2.0.6"
 description = "Google Spreadsheets Python API v4"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
@@ -3415,7 +3259,6 @@ pandas = ["pandas (>=0.14.0)"]
 name = "pyjwt"
 version = "2.9.0"
 description = "JSON Web Token implementation in Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3433,7 +3276,6 @@ tests = ["coverage[toml] (==5.0.4)", "pytest (>=6.0.0,<7.0.0)"]
 name = "pylint"
 version = "2.17.7"
 description = "python code static checker"
-category = "dev"
 optional = false
 python-versions = ">=3.7.2"
 files = [
@@ -3460,7 +3302,6 @@ testutils = ["gitpython (>3)"]
 name = "pyopenssl"
 version = "23.3.0"
 description = "Python wrapper module around the OpenSSL library"
-category = "main"
 optional = true
 python-versions = ">=3.7"
 files = [
@@ -3479,7 +3320,6 @@ test = ["flaky", "pretend", "pytest (>=3.0.1)"]
 name = "pyparsing"
 version = "3.2.0"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -3494,7 +3334,6 @@ diagrams = ["jinja2", "railroad-diagrams"]
 name = "pytest"
 version = "8.3.3"
 description = "pytest: simple powerful testing with Python"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3517,7 +3356,6 @@ dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments
 name = "pytest-asyncio"
 version = "0.24.0"
 description = "Pytest support for asyncio"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3536,7 +3374,6 @@ testing = ["coverage (>=6.2)", "hypothesis (>=5.7.1)"]
 name = "pytest-cov"
 version = "4.1.0"
 description = "Pytest plugin for measuring coverage."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3555,7 +3392,6 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtuale
 name = "pytest-mock"
 version = "3.14.0"
 description = "Thin-wrapper around the mock package for easier use with pytest"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3573,7 +3409,6 @@ dev = ["pre-commit", "pytest-asyncio", "tox"]
 name = "pytest-rerunfailures"
 version = "12.0"
 description = "pytest plugin to re-run tests to eliminate flaky failures"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3589,7 +3424,6 @@ pytest = ">=6.2"
 name = "pytest-xdist"
 version = "3.6.1"
 description = "pytest xdist plugin for distributed testing, most importantly across multiple CPUs"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3610,7 +3444,6 @@ testing = ["filelock"]
 name = "python-dateutil"
 version = "2.9.0.post0"
 description = "Extensions to the standard Python datetime module"
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
@@ -3625,7 +3458,6 @@ six = ">=1.5"
 name = "python-dotenv"
 version = "0.21.1"
 description = "Read key-value pairs from a .env file and set them as environment variables"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3640,7 +3472,6 @@ cli = ["click (>=5.0)"]
 name = "python-json-logger"
 version = "2.0.7"
 description = "A python library adding a json log formatter"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -3652,7 +3483,6 @@ files = [
 name = "pytz"
 version = "2024.2"
 description = "World timezone definitions, modern and historical"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -3664,7 +3494,6 @@ files = [
 name = "pywin32"
 version = "308"
 description = "Python for Window Extensions"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -3692,7 +3521,6 @@ files = [
 name = "pywinpty"
 version = "2.0.14"
 description = "Pseudo terminal support for Windows from Python."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3708,7 +3536,6 @@ files = [
 name = "pyyaml"
 version = "6.0.2"
 description = "YAML parser and emitter for Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3771,7 +3598,6 @@ files = [
 name = "pyzmq"
 version = "26.2.0"
 description = "Python bindings for 0MQ"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -3893,7 +3719,6 @@ cffi = {version = "*", markers = "implementation_name == \"pypy\""}
 name = "rdflib"
 version = "6.3.2"
 description = "RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information."
-category = "main"
 optional = false
 python-versions = ">=3.7,<4.0"
 files = [
@@ -3915,7 +3740,6 @@ networkx = ["networkx (>=2.0.0,<3.0.0)"]
 name = "referencing"
 version = "0.35.1"
 description = "JSON Referencing + Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -3931,7 +3755,6 @@ rpds-py = ">=0.7.0"
 name = "regex"
 version = "2024.9.11"
 description = "Alternative regular expression module, to replace re."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4035,7 +3858,6 @@ files = [
 name = "requests"
 version = "2.32.3"
 description = "Python HTTP for Humans."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4057,7 +3879,6 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 name = "requests-oauthlib"
 version = "2.0.0"
 description = "OAuthlib authentication support for Requests."
-category = "main"
 optional = false
 python-versions = ">=3.4"
 files = [
@@ -4076,7 +3897,6 @@ rsa = ["oauthlib[signedtoken] (>=3.0.0)"]
 name = "rfc3339-validator"
 version = "0.1.4"
 description = "A pure python RFC3339 validator"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -4091,7 +3911,6 @@ six = "*"
 name = "rfc3986-validator"
 version = "0.1.1"
 description = "Pure python rfc3986 validator"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 files = [
@@ -4103,7 +3922,6 @@ files = [
 name = "rpds-py"
 version = "0.20.1"
 description = "Python bindings to Rust's persistent data structures (rpds)"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4216,7 +4034,6 @@ files = [
 name = "rsa"
 version = "4.9"
 description = "Pure-Python RSA implementation"
-category = "main"
 optional = false
 python-versions = ">=3.6,<4"
 files = [
@@ -4231,7 +4048,6 @@ pyasn1 = ">=0.1.3"
 name = "ruamel-yaml"
 version = "0.17.17"
 description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order"
-category = "main"
 optional = false
 python-versions = ">=3"
 files = [
@@ -4250,7 +4066,6 @@ jinja2 = ["ruamel.yaml.jinja2 (>=0.2)"]
 name = "ruamel-yaml-clib"
 version = "0.2.12"
 description = "C version of reader, parser and emitter for ruamel.yaml derived from libyaml"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -4301,7 +4116,6 @@ files = [
 name = "scipy"
 version = "1.13.1"
 description = "Fundamental algorithms for scientific computing in Python"
-category = "main"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -4344,7 +4158,6 @@ test = ["array-api-strict", "asv", "gmpy2", "hypothesis (>=6.30)", "mpmath", "po
 name = "send2trash"
 version = "1.8.3"
 description = "Send file to trash natively under Mac OS X, Windows and Linux"
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
 files = [
@@ -4361,7 +4174,6 @@ win32 = ["pywin32"]
 name = "setuptools"
 version = "66.1.1"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4378,7 +4190,6 @@ testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (
 name = "six"
 version = "1.16.0"
 description = "Python 2 and 3 compatibility utilities"
-category = "main"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
@@ -4390,7 +4201,6 @@ files = [
 name = "sniffio"
 version = "1.3.1"
 description = "Sniff out which async library your code is running under"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4402,7 +4212,6 @@ files = [
 name = "snowballstemmer"
 version = "2.2.0"
 description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms."
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -4414,7 +4223,6 @@ files = [
 name = "soupsieve"
 version = "2.6"
 description = "A modern CSS selector implementation for Beautiful Soup."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4426,7 +4234,6 @@ files = [
 name = "sphinx"
 version = "7.3.7"
 description = "Python documentation generator"
-category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -4463,7 +4270,6 @@ test = ["cython (>=3.0)", "defusedxml (>=0.7.1)", "pytest (>=6.0)", "setuptools
 name = "sphinx-click"
 version = "4.4.0"
 description = "Sphinx extension that automatically documents click applications"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4480,7 +4286,6 @@ sphinx = ">=2.0"
 name = "sphinx-rtd-theme"
 version = "3.0.1"
 description = "Read the Docs theme for Sphinx"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4500,7 +4305,6 @@ dev = ["bump2version", "transifex-client", "twine", "wheel"]
 name = "sphinxcontrib-applehelp"
 version = "2.0.0"
 description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
-category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -4517,7 +4321,6 @@ test = ["pytest"]
 name = "sphinxcontrib-devhelp"
 version = "2.0.0"
 description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
-category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -4534,7 +4337,6 @@ test = ["pytest"]
 name = "sphinxcontrib-htmlhelp"
 version = "2.1.0"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
-category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -4551,7 +4353,6 @@ test = ["html5lib", "pytest"]
 name = "sphinxcontrib-jquery"
 version = "4.1"
 description = "Extension to include jQuery on newer Sphinx releases"
-category = "dev"
 optional = false
 python-versions = ">=2.7"
 files = [
@@ -4566,7 +4367,6 @@ Sphinx = ">=1.8"
 name = "sphinxcontrib-jsmath"
 version = "1.0.1"
 description = "A sphinx extension which renders display math in HTML via JavaScript"
-category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -4581,7 +4381,6 @@ test = ["flake8", "mypy", "pytest"]
 name = "sphinxcontrib-qthelp"
 version = "2.0.0"
 description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
-category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -4598,7 +4397,6 @@ test = ["defusedxml (>=0.7.1)", "pytest"]
 name = "sphinxcontrib-serializinghtml"
 version = "2.0.0"
 description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
-category = "dev"
 optional = false
 python-versions = ">=3.9"
 files = [
@@ -4615,7 +4413,6 @@ test = ["pytest"]
 name = "stack-data"
 version = "0.6.3"
 description = "Extract data from python stack frames and tracebacks for informative displays"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -4635,7 +4432,6 @@ tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
 name = "swagger-ui-bundle"
 version = "0.0.9"
 description = "swagger_ui_bundle - swagger-ui files in a pip package"
-category = "main"
 optional = true
 python-versions = "*"
 files = [
@@ -4650,7 +4446,6 @@ Jinja2 = ">=2.0"
 name = "synapseclient"
 version = "4.6.0"
 description = "A client for Synapse, a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate."
-category = "main"
 optional = false
 python-versions = "<3.13,>=3.9"
 files = [
@@ -4688,7 +4483,6 @@ tests = ["flake8 (>=3.7.0,<4.0)", "func-timeout (>=4.3,<5.0)", "pandas (>=1.5,<3
 name = "tenacity"
 version = "8.5.0"
 description = "Retry code until it succeeds"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4704,7 +4498,6 @@ test = ["pytest", "tornado (>=4.5)", "typeguard"]
 name = "terminado"
 version = "0.18.1"
 description = "Tornado websocket backend for the Xterm.js Javascript terminal emulator library."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4726,7 +4519,6 @@ typing = ["mypy (>=1.6,<2.0)", "traitlets (>=5.11.1)"]
 name = "tinycss2"
 version = "1.4.0"
 description = "A tiny CSS parser"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4745,7 +4537,6 @@ test = ["pytest", "ruff"]
 name = "toml"
 version = "0.10.2"
 description = "Python Library for Tom's Obvious, Minimal Language"
-category = "main"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
@@ -4757,7 +4548,6 @@ files = [
 name = "tomli"
 version = "2.0.2"
 description = "A lil' TOML parser"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4769,7 +4559,6 @@ files = [
 name = "tomlkit"
 version = "0.13.2"
 description = "Style preserving TOML library"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4781,7 +4570,6 @@ files = [
 name = "toolz"
 version = "1.0.0"
 description = "List processing tools and functional utilities"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4793,7 +4581,6 @@ files = [
 name = "tornado"
 version = "6.4.1"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4814,7 +4601,6 @@ files = [
 name = "tqdm"
 version = "4.66.6"
 description = "Fast, Extensible Progress Meter"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4835,7 +4621,6 @@ telegram = ["requests"]
 name = "traitlets"
 version = "5.14.3"
 description = "Traitlets Python configuration system"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4851,7 +4636,6 @@ test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,
 name = "types-python-dateutil"
 version = "2.9.0.20241003"
 description = "Typing stubs for python-dateutil"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4863,7 +4647,6 @@ files = [
 name = "typing-extensions"
 version = "4.12.2"
 description = "Backported and Experimental Type Hints for Python 3.8+"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4875,7 +4658,6 @@ files = [
 name = "typing-inspect"
 version = "0.9.0"
 description = "Runtime inspection utilities for typing module."
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -4891,7 +4673,6 @@ typing-extensions = ">=3.7.4"
 name = "tzdata"
 version = "2024.2"
 description = "Provider of IANA time zone data"
-category = "main"
 optional = false
 python-versions = ">=2"
 files = [
@@ -4903,7 +4684,6 @@ files = [
 name = "tzlocal"
 version = "5.2"
 description = "tzinfo object for the local timezone"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4921,7 +4701,6 @@ devenv = ["check-manifest", "pytest (>=4.3)", "pytest-cov", "pytest-mock (>=3.3)
 name = "uri-template"
 version = "1.3.0"
 description = "RFC 6570 URI Template Processor"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -4936,7 +4715,6 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake
 name = "uritemplate"
 version = "4.1.1"
 description = "Implementation of RFC 6570 URI Templates"
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -4948,7 +4726,6 @@ files = [
 name = "urllib3"
 version = "1.26.20"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
-category = "main"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
 files = [
@@ -4965,7 +4742,6 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 name = "uwsgi"
 version = "2.0.27"
 description = "The uWSGI server"
-category = "main"
 optional = true
 python-versions = "*"
 files = [
@@ -4976,7 +4752,6 @@ files = [
 name = "virtualenv"
 version = "20.27.0"
 description = "Virtual Python Environment builder"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -4997,7 +4772,6 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess
 name = "wcwidth"
 version = "0.2.13"
 description = "Measures the displayed width of unicode strings in a terminal"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -5009,7 +4783,6 @@ files = [
 name = "webcolors"
 version = "24.8.0"
 description = "A library for working with the color formats defined by HTML and CSS."
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -5025,7 +4798,6 @@ tests = ["coverage[toml]"]
 name = "webencodings"
 version = "0.5.1"
 description = "Character encoding aliases for legacy web content"
-category = "main"
 optional = false
 python-versions = "*"
 files = [
@@ -5037,7 +4809,6 @@ files = [
 name = "websocket-client"
 version = "1.8.0"
 description = "WebSocket client for Python with low level API options"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -5054,7 +4825,6 @@ test = ["websockets"]
 name = "werkzeug"
 version = "2.2.3"
 description = "The comprehensive WSGI web application library."
-category = "main"
 optional = true
 python-versions = ">=3.7"
 files = [
@@ -5072,7 +4842,6 @@ watchdog = ["watchdog"]
 name = "widgetsnbextension"
 version = "4.0.13"
 description = "Jupyter interactive widgets for Jupyter Notebook"
-category = "main"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -5084,7 +4853,6 @@ files = [
 name = "wrapt"
 version = "1.16.0"
 description = "Module for decorators, wrappers and monkey patching."
-category = "main"
 optional = false
 python-versions = ">=3.6"
 files = [
@@ -5164,7 +4932,6 @@ files = [
 name = "zipp"
 version = "3.20.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -5181,10 +4948,10 @@ test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools",
 type = ["pytest-mypy"]
 
 [extras]
-api = ["connexion", "Flask", "Flask-Cors", "Jinja2", "pyopenssl", "opentelemetry-api", "opentelemetry-sdk", "opentelemetry-exporter-otlp-proto-grpc", "opentelemetry-instrumentation-flask"]
+api = ["Flask", "Flask-Cors", "Jinja2", "connexion", "opentelemetry-api", "opentelemetry-exporter-otlp-proto-grpc", "opentelemetry-instrumentation-flask", "opentelemetry-sdk", "pyopenssl"]
 aws = ["uWSGI"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9.0,<3.11"
-content-hash = "38eaaeb34ea2fe3ba10c11767ba864c4dbab46ff425352256e4ba09ed2369430"
+content-hash = "a1c3716705c45d674e62e3639a613c0d59d9e64f1e4a851b30b3f562c011ef3e"

From a0d9da840a5b51342edd3358b9cf9c1ab53c0cae Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Mon, 18 Nov 2024 23:13:46 -0800
Subject: [PATCH 45/47] Add in permissions

---
 docs/source/asset_store.rst | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/docs/source/asset_store.rst b/docs/source/asset_store.rst
index 675f59dbb..80cbd008b 100644
--- a/docs/source/asset_store.rst
+++ b/docs/source/asset_store.rst
@@ -62,7 +62,7 @@ Access & Project Setup - Multiple Contributing Projects
 5. Create another Synapse Project (e.g., MyDCC) containing the main **Fileview** that includes in the scope all the DCC projects.
 
    - Ensure all teams have **Download** level access to this file view.
-   - Include both file and folder entities and add ALL default columns.
+   - Include both file and folder entities and add **ALL default columns**.
 
 .. note::
 
@@ -105,7 +105,8 @@ Access & Project Setup - Single Contributing Project
 
 4. In MyDCC, create the main **DCC Fileview** with `MyDCC` as the scope. Add column ``contentType`` to the schema and grant teams **Download** level access.
 
-   - Add both file and folder entities and add ALL default columns.
+   - Ensure all teams have **Download** level access to this file view.
+   - Add both file and folder entities and add **ALL default columns**.
 
 .. note::
 

From 970d0a69b298d9c641df29d9dc14c5ac125a6c50 Mon Sep 17 00:00:00 2001
From: thomasyu888 <thomasyu888@gmail.com>
Date: Fri, 13 Dec 2024 00:17:25 -0800
Subject: [PATCH 46/47] Update docs

---
 docs/source/troubleshooting.rst | 40 ++++++++++++++++++---------------
 1 file changed, 22 insertions(+), 18 deletions(-)

diff --git a/docs/source/troubleshooting.rst b/docs/source/troubleshooting.rst
index 86a65dd5a..cc04d4134 100644
--- a/docs/source/troubleshooting.rst
+++ b/docs/source/troubleshooting.rst
@@ -31,24 +31,6 @@ Whether you are using DCA or schematic API or schematic library/CLI, the followi
                 -H 'accept: application/json' ...
 
 
-Manifest Generate: `KeyError: entityId`
----------------------------------------
-
-If there is currently a manifest in your "Top Level Folder" on Synapse with an incorrect Filename BUT entityId column.
-You will be able to run manifest generate to create a new manifest with the new Filenames. However, If this manifest on Synapse does
-NOT have the entityId column you will encounter that error. 
-
-To fix: You will want to first check if your "Top Level Folder" has a manifest without the entityId column.
-If so, you can either submit your manifest using schematic OR (the less preferred solution) manually add the entityId column to the manifest on Synapse.
-
-Manifest Generate: `ValueError: cannot insert eTag, already exists`
--------------------------------------------------------------------
-
-If you do NOT have a manifest in your "Top Level Folder" on Synapse and your File entities in this folder are annotated with 'eTag' key and you try to generate a manifest, it will fail.
-
-To fix: This should be fixed in schematic, but for now, remove the 'eTag' annotation from your file.
-
-
 Manifest Submit: `RuntimeError: failed with SynapseHTTPError('400 Client Error: nan is not a valid Synapse ID.')`
 -----------------------------------------------------------------------------------------------------------------
 
@@ -86,3 +68,25 @@ and the validation rule uses the "display" value of what's expected in the Compo
 but the actual Component name is "ImagingAssayTemplate".
 
 To fix: Check if your manifest has invalid Component values and fill it out correctly.  Using the above example, fill out your Component column with "ImagingAssayTemplate"
+
+
+Manifest Generate: `KeyError: entityId`
+---------------------------------------
+
+Fixed: v24.12.1
+
+If there is currently a manifest in your "Top Level Folder" on Synapse with an incorrect Filename BUT entityId column.
+You will be able to run manifest generate to create a new manifest with the new Filenames. However, If this manifest on Synapse does
+NOT have the entityId column you will encounter that error.
+
+To fix: You will want to first check if your "Top Level Folder" has a manifest without the entityId column.
+If so, you can either submit your manifest using schematic OR (the less preferred solution) manually add the entityId column to the manifest on Synapse.
+
+Manifest Generate: `ValueError: cannot insert eTag, already exists`
+-------------------------------------------------------------------
+
+Fixed: v24.11.2
+
+If you do NOT have a manifest in your "Top Level Folder" on Synapse and your File entities in this folder are annotated with 'eTag' key and you try to generate a manifest, it will fail.
+
+To fix: This should be fixed in schematic, but for now, remove the 'eTag' annotation from your file.

From 8fd545bce9c3166af3690eb8c7c0facebec5f02a Mon Sep 17 00:00:00 2001
From: Thomas Yu <thomas.yu@sagebase.org>
Date: Mon, 16 Dec 2024 23:04:07 -0800
Subject: [PATCH 47/47] Add documentation

---
 docs/source/troubleshooting.rst | 10 ++++++++--
 docs/source/tutorials.rst       |  5 ++++-
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/docs/source/troubleshooting.rst b/docs/source/troubleshooting.rst
index cc04d4134..3ffb16b1e 100644
--- a/docs/source/troubleshooting.rst
+++ b/docs/source/troubleshooting.rst
@@ -35,8 +35,14 @@ Manifest Submit: `RuntimeError: failed with SynapseHTTPError('400 Client Error:
 -----------------------------------------------------------------------------------------------------------------
 
 As for 24.10.2 version of Schematic, we require the `Filename` column to have the full paths to the file on Synapse including the project name.
-If you try and submit a manifest with invalid Filenames (not containing full path), you will encounter the `nan`.  This is because we join the `Filename`
-column together with what's in Synapse to append the `entityId` column if it's missing.
+You will encounter this issue if you try an submit a manifest with wrong filenames.  For example, if your file in your project has this full path
+`my_project/my_folder/my_file.txt`, you will get this error by:
+
+* not containing full path (e.g. `my_file.txt`)
+* Wrong filename (e.g. `my_project/my_folder/wrong_file_name.txt`)
+* Wrong filepath (e.g. `my_project/wrong_folder/my_file.txt`)
+
+This is because we join the `Filename` column together with what's in Synapse to append the `entityId` column if it's missing.
 
 To fix: You will want to first check if your "Top Level Folder" has a manifest with invalid Filename values in the column.
 If so, please generate a manifest with schematic which should fix the Filenames OR (the less preferred solution) manually update the Filenames to include the full path to the file and manually upload.
diff --git a/docs/source/tutorials.rst b/docs/source/tutorials.rst
index 4ffa8ac30..6ecc1f6ff 100644
--- a/docs/source/tutorials.rst
+++ b/docs/source/tutorials.rst
@@ -23,6 +23,7 @@ we will cover generating, validating, and submitting your manifest in a structur
 
 Prerequisites
 ~~~~~~~~~~~~~
+
 1. **Install and configure Schematic**: Ensure that you have installed `schematic` and set up its dependencies. See "Installation Guide For: Users" for more information.
 2. **Important Concepts**: Make sure you know the important concepts outlined on the home page of the doc site.
 3. **Configuration**: Read more here about each of the attributes in the configuration file.
@@ -46,7 +47,9 @@ The `schematic manifest get` command that creates a manifest template based on a
 .. note::
 
     This step is crucial for ensuring that your manifest includes all the necessary columns and headers. As of v24.10.2, you will
-    want to generate the manifest to ensure the right Filenames are populated in your manifest.
+    want to generate the manifest to ensure the right Filenames are populated in your manifest. If you just uploaded your folder
+    with data or files to a folder, you may see that this files are missing or get a `LookUp` error.  This is an artifact of Synapse
+    fileviews, please run this command again.
 
 .. code-block:: bash