From cd9cbe8aeb0780673049c2c6def1eea84a4fc899 Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Wed, 14 Aug 2024 15:30:49 -0700
Subject: [PATCH 1/5] add pypi publish gh action with trusted publisher

---
 .github/workflows/pypi-publish.yaml | 35 +++++++++++++++++++++++++++++
 .gitignore                          |  2 --
 2 files changed, 35 insertions(+), 2 deletions(-)
 create mode 100644 .github/workflows/pypi-publish.yaml

diff --git a/.github/workflows/pypi-publish.yaml b/.github/workflows/pypi-publish.yaml
new file mode 100644
index 00000000..8885ff71
--- /dev/null
+++ b/.github/workflows/pypi-publish.yaml
@@ -0,0 +1,35 @@
+---
+name: Publish Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+    # Specifying a GitHub environment is optional, but strongly encouraged
+    environment: release
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install Poetry
+        run: |
+          pipx install poetry
+          poetry self add "poetry-dynamic-versioning[plugin]"
+
+      - name: Build source and wheel archives
+        run: poetry build
+
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
index 5da2b71f..e83aea43 100644
--- a/.gitignore
+++ b/.gitignore
@@ -25,8 +25,6 @@ var/
 *.egg
 # keep poetry files out of the repo for now, until we decide if we are moving to a .toml file specification
 # for requirements in the future.
-pyproject.toml
-poetry.lock
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

From cda1bbc8759d8e14c64bf2c56927758ddc0d17db Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Wed, 14 Aug 2024 15:31:21 -0700
Subject: [PATCH 2/5] add poetry lock and pyproject.toml to the repo so that GH
 actions can use it to build the dist and push to pypi

---
 poetry.lock    | 1962 ++++++++++++++++++++++++++++++++++++++++++++++++
 pyproject.toml |   52 ++
 2 files changed, 2014 insertions(+)
 create mode 100644 poetry.lock
 create mode 100644 pyproject.toml

diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 00000000..7d8519b8
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,1962 @@
+# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
+
+[[package]]
+name = "antlr4-python3-runtime"
+version = "4.9.3"
+description = "ANTLR 4.9.3 runtime for Python 3.7"
+optional = false
+python-versions = "*"
+files = [
+    {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"},
+]
+
+[[package]]
+name = "backports-tarfile"
+version = "1.2.0"
+description = "Backport of CPython tarfile module"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "backports.tarfile-1.2.0-py3-none-any.whl", hash = "sha256:77e284d754527b01fb1e6fa8a1afe577858ebe4e9dad8919e34c862cb399bc34"},
+    {file = "backports_tarfile-1.2.0.tar.gz", hash = "sha256:d75e02c268746e1b8144c278978b6e98e85de6ad16f8e4b0844a154557eca991"},
+]
+
+[package.extras]
+docs = ["furo", "jaraco.packaging (>=9.3)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["jaraco.test", "pytest (!=8.0.*)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)"]
+
+[[package]]
+name = "bidict"
+version = "0.23.1"
+description = "The bidirectional mapping library for Python."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "bidict-0.23.1-py3-none-any.whl", hash = "sha256:5dae8d4d79b552a71cbabc7deb25dfe8ce710b17ff41711e13010ead2abfc3e5"},
+    {file = "bidict-0.23.1.tar.gz", hash = "sha256:03069d763bc387bbd20e7d49914e75fc4132a41937fa3405417e1a5a2d006d71"},
+]
+
+[[package]]
+name = "certifi"
+version = "2024.7.4"
+description = "Python package for providing Mozilla's CA Bundle."
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "certifi-2024.7.4-py3-none-any.whl", hash = "sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90"},
+    {file = "certifi-2024.7.4.tar.gz", hash = "sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b"},
+]
+
+[[package]]
+name = "cffi"
+version = "1.16.0"
+description = "Foreign Function Interface for Python calling C code."
+optional = false
+python-versions = ">=3.8"
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+python-versions = ">=3.7.0"
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+
+[package.extras]
+brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+h2 = ["h2 (>=4,<5)"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
+
+[[package]]
+name = "wheel"
+version = "0.43.0"
+description = "A built-package format for Python"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "wheel-0.43.0-py3-none-any.whl", hash = "sha256:55c570405f142630c6b9f72fe09d9b67cf1477fcf543ae5b8dcb1f5b7377da81"},
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+]
+
+[package.extras]
+test = ["pytest (>=6.0.0)", "setuptools (>=65)"]
+
+[[package]]
+name = "yamldown"
+version = "0.1.8"
+description = "Python library for loading and dumping \"yamldown\" (markdown with embedded yaml) files."
+optional = false
+python-versions = "*"
+files = [
+    {file = "yamldown-0.1.8-py3-none-any.whl", hash = "sha256:936ad7bdbde725d0bd3adb77236aae4eb75388619f31232595f7dd45f7006598"},
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+]
+
+[package.dependencies]
+pyYaml = "*"
+
+[[package]]
+name = "zipp"
+version = "3.19.2"
+description = "Backport of pathlib-compatible object wrapper for zip files"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "zipp-3.19.2-py3-none-any.whl", hash = "sha256:f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c"},
+    {file = "zipp-3.19.2.tar.gz", hash = "sha256:bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19"},
+]
+
+[package.extras]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+
+[metadata]
+lock-version = "2.0"
+python-versions = "^3.10"
+content-hash = "d8dd22255e91cffe40aed1fa49bb1a6c896246bd7d7ebe4bbd9373479cf1cea6"
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 00000000..fe88c28b
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,52 @@
+[tool.poetry]
+name = "ontobio"
+version = "0.0.0"
+description = ""
+authors = ["Gene Ontology Consortium <helpdesk@geneontology.org>"]
+readme = "README.rst"
+
+packages = [
+    { include = "bin" },
+    { include = "ontobio"}
+]
+
+[tool.poetry.scripts]
+validate = "bin.validate:cli"
+
+[tool.poetry.dependencies]
+python = "^3.10"
+rdflib = ">=6.0.0"
+marshmallow = ">=3.0.0b11, <4.0.0"
+jsobject = ">=0.0"
+prefixcommons = ">=0.1.9"
+requests = ">=0.0"
+pip = ">=9.0.1"
+wheel = ">0.25.0"
+pysolr = ">=3.6.0"
+networkx = ">=2.3"
+matplotlib = "^3.9.2"
+sparqlwrapper = ">=1.8.0"
+pandas = ">=0.0"
+scipy = ">=1.2.0"
+jsonpickle = ">=0.0"
+jsonpath-rw = ">=0.0"
+pyshex = ">=0.7.11"
+pytest = ">=0.0"
+pytest-logging = ">=0.0"
+pydotplus = ">=0.0"
+plotly = ">=2.0.7"
+yamldown = ">=0.1.7"
+diskcache = ">=4.0.0"
+bidict = ">=0.20.0"
+dacite = ">=1.6.0"
+pyparsing = "2.4.7"
+twine = "^4.0.2"
+PyYAML = "^6.0.1"
+click = "^8.1.7"
+chardet = "^5.2.0"
+pytest-mock = "^3.14.0"
+
+
+[build-system]
+requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
+build-backend = "poetry_dynamic_versioning.backend"
\ No newline at end of file

From bfa27f01c6b711765d651b30f82d824c771d7bed Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Wed, 14 Aug 2024 15:50:23 -0700
Subject: [PATCH 3/5] rebuild poetry.lock

---
 poetry.lock | 303 +++++++++++++++++++++++++++-------------------------
 1 file changed, 160 insertions(+), 143 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 7d8519b8..07cdafa4 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -49,63 +49,78 @@ files = [
 
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 description = "Foreign Function Interface for Python calling C code."
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 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -524,13 +539,13 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "8.0.0"
+version = "8.2.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -604,21 +619,21 @@ testing = ["portend", "pytest (>=6,!=8.1.1)", "pytest-checkdocs (>=2.4)", "pytes
 
 [[package]]
 name = "jaraco-functools"
-version = "4.0.1"
+version = "4.0.2"
 description = "Functools like those found in stdlib"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 more-itertools = "*"
 
 [package.extras]
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+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+test = ["jaraco.classes", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
 
 [[package]]
 name = "jeepney"
@@ -689,13 +704,13 @@ testing = ["bson", "ecdsa", "feedparser", "gmpy2", "numpy", "pandas", "pymongo",
 
 [[package]]
 name = "keyring"
-version = "25.2.1"
+version = "25.3.0"
 description = "Store and access your passwords safely."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -709,8 +724,8 @@ SecretStorage = {version = ">=3.2", markers = "sys_platform == \"linux\""}
 
 [package.extras]
 completion = ["shtab (>=1.1.0)"]
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+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+test = ["pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
 
 [[package]]
 name = "kiwisolver"
@@ -944,13 +959,13 @@ files = [
 
 [[package]]
 name = "more-itertools"
-version = "10.3.0"
+version = "10.4.0"
 description = "More routines for operating on iterables, beyond itertools"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
@@ -1233,13 +1248,13 @@ xmp = ["defusedxml"]
 
 [[package]]
 name = "pip"
-version = "24.1.2"
+version = "24.2"
 description = "The PyPA recommended tool for installing Python packages."
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "pip-24.2-py3-none-any.whl", hash = "sha256:2cd581cf58ab7fcfca4ce8efa6dcacd0de5bf8d0a3eb9ec927e07405f4d9e2a2"},
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 ]
 
 [[package]]
@@ -1258,13 +1273,13 @@ testing = ["pytest", "pytest-cov", "wheel"]
 
 [[package]]
 name = "plotly"
-version = "5.22.0"
+version = "5.23.0"
 description = "An open-source, interactive data visualization library for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "plotly-5.23.0.tar.gz", hash = "sha256:89e57d003a116303a34de6700862391367dd564222ab71f8531df70279fc0193"},
 ]
 
 [package.dependencies]
@@ -1437,13 +1452,13 @@ solrcloud = ["kazoo (>=2.5.0)"]
 
 [[package]]
 name = "pytest"
-version = "8.3.1"
+version = "8.3.2"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "PyYAML-6.0.2-cp39-cp39-win32.whl", hash = "sha256:6395c297d42274772abc367baaa79683958044e5d3835486c16da75d2a694631"},
+    {file = "PyYAML-6.0.2-cp39-cp39-win_amd64.whl", hash = "sha256:39693e1f8320ae4f43943590b49779ffb98acb81f788220ea932a6b6c51004d8"},
+    {file = "pyyaml-6.0.2.tar.gz", hash = "sha256:d584d9ec91ad65861cc08d42e834324ef890a082e591037abe114850ff7bbc3e"},
 ]
 
 [[package]]
@@ -1839,13 +1856,13 @@ pandas = ["pandas (>=1.3.5)"]
 
 [[package]]
 name = "tenacity"
-version = "8.5.0"
+version = "9.0.0"
 description = "Retry code until it succeeds"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "tenacity-8.5.0-py3-none-any.whl", hash = "sha256:b594c2a5945830c267ce6b79a166228323ed52718f30302c1359836112346687"},
-    {file = "tenacity-8.5.0.tar.gz", hash = "sha256:8bc6c0c8a09b31e6cad13c47afbed1a567518250a9a171418582ed8d9c20ca78"},
+    {file = "tenacity-9.0.0-py3-none-any.whl", hash = "sha256:93de0c98785b27fcf659856aa9f54bfbd399e29969b0621bc7f762bd441b4539"},
+    {file = "tenacity-9.0.0.tar.gz", hash = "sha256:807f37ca97d62aa361264d497b0e31e92b8027044942bfa756160d908320d73b"},
 ]
 
 [package.extras]
@@ -1915,13 +1932,13 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "wheel"
-version = "0.43.0"
+version = "0.44.0"
 description = "A built-package format for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "wheel-0.43.0-py3-none-any.whl", hash = "sha256:55c570405f142630c6b9f72fe09d9b67cf1477fcf543ae5b8dcb1f5b7377da81"},
-    {file = "wheel-0.43.0.tar.gz", hash = "sha256:465ef92c69fa5c5da2d1cf8ac40559a8c940886afcef87dcf14b9470862f1d85"},
+    {file = "wheel-0.44.0-py3-none-any.whl", hash = "sha256:2376a90c98cc337d18623527a97c31797bd02bad0033d41547043a1cbfbe448f"},
+    {file = "wheel-0.44.0.tar.gz", hash = "sha256:a29c3f2817e95ab89aa4660681ad547c0e9547f20e75b0562fe7723c9a2a9d49"},
 ]
 
 [package.extras]
@@ -1943,13 +1960,13 @@ pyYaml = "*"
 
 [[package]]
 name = "zipp"
-version = "3.19.2"
+version = "3.20.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.19.2-py3-none-any.whl", hash = "sha256:f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c"},
-    {file = "zipp-3.19.2.tar.gz", hash = "sha256:bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19"},
+    {file = "zipp-3.20.0-py3-none-any.whl", hash = "sha256:58da6168be89f0be59beb194da1250516fdaa062ccebd30127ac65d30045e10d"},
+    {file = "zipp-3.20.0.tar.gz", hash = "sha256:0145e43d89664cfe1a2e533adc75adafed82fe2da404b4bbb6b026c0157bdb31"},
 ]
 
 [package.extras]

From 897c61be3a00a9267087622d3d155b64869dea10 Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Wed, 14 Aug 2024 15:57:51 -0700
Subject: [PATCH 4/5] add config to pyproject.toml for dynamic version

---
 pyproject.toml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index fe88c28b..c26d1407 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -46,7 +46,11 @@ click = "^8.1.7"
 chardet = "^5.2.0"
 pytest-mock = "^3.14.0"
 
-
 [build-system]
 requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
-build-backend = "poetry_dynamic_versioning.backend"
\ No newline at end of file
+build-backend = "poetry_dynamic_versioning.backend"
+
+[tool.poetry-dynamic-versioning]
+enable = true
+vcs = "git"
+style = "pep440"
\ No newline at end of file

From e4dd8409528d98816b28ab765500b419ca9cf03a Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Thu, 15 Aug 2024 12:07:04 -0700
Subject: [PATCH 5/5] change version of python to match in workflows

---
 .github/workflows/make-tests.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/make-tests.yaml b/.github/workflows/make-tests.yaml
index 41bf5586..3a4d1b35 100644
--- a/.github/workflows/make-tests.yaml
+++ b/.github/workflows/make-tests.yaml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: [ "3.9", "3.10", "3.11" ]
+        python: [ "3.10", "3.11" ]
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps: