From a63c4926f86607930dd0a58aeb75523e79a350f0 Mon Sep 17 00:00:00 2001
From: Ted Brookings <ted@fulcrumgenomics.com>
Date: Tue, 3 Dec 2024 13:08:19 -0500
Subject: [PATCH] Respond to some reviewer comments

---
 .github/workflows/pythonpackage.yml |   2 -
 .github/workflows/wheels.yml        |   2 -
 .gitmodules                         |   0
 poetry.lock                         | 547 ++++++++++++++++------------
 pyproject.toml                      |   5 +-
 5 files changed, 315 insertions(+), 241 deletions(-)
 delete mode 100644 .gitmodules

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index fe3b9cc..dc6e7d8 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -13,8 +13,6 @@ jobs:
         PYTHON_VERSION: ["3.8", "3.9", "3.10", "3.11"]
     steps:
     - uses: actions/checkout@v2
-      with:
-        submodules: 'true'
 
     - name: Set up Python ${{matrix.PYTHON_VERSION}}
       uses: actions/setup-python@v4
diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
index 97fec73..bfb2d5d 100644
--- a/.github/workflows/wheels.yml
+++ b/.github/workflows/wheels.yml
@@ -37,8 +37,6 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-        with:
-          submodules: "false"
 
       # Used to host cibuildwheel
       - uses: actions/setup-python@v4
diff --git a/.gitmodules b/.gitmodules
deleted file mode 100644
index e69de29..0000000
diff --git a/poetry.lock b/poetry.lock
index 7fb94dc..6fe95cb 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -32,13 +32,13 @@ tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "p
 
 [[package]]
 name = "babel"
-version = "2.14.0"
+version = "2.16.0"
 description = "Internationalization utilities"
 optional = true
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
-    {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
+    {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"},
+    {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"},
 ]
 
 [package.dependencies]
@@ -95,112 +95,127 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "certifi"
-version = "2024.2.2"
+version = "2024.8.30"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = true
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"},
-    {file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"},
+    {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"},
+    {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"},
 ]
 
 [[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 = true
 python-versions = ">=3.7.0"
 files = [
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-    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:25baf083bf6f6b341f4121c2f3c548875ee6f5339300e08be3f2b2ba1721cdd3"},
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 [package.dependencies]
@@ -383,13 +418,13 @@ files = [
 
 [[package]]
 name = "exceptiongroup"
-version = "1.2.1"
+version = "1.2.2"
 description = "Backport of PEP 654 (exception groups)"
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 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
@@ -413,15 +448,18 @@ pyflakes = ">=2.5.0,<2.6.0"
 
 [[package]]
 name = "idna"
-version = "3.7"
+version = "3.10"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = true
-python-versions = ">=3.5"
+python-versions = ">=3.6"
 files = [
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 ]
 
+[package.extras]
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+
 [[package]]
 name = "imagesize"
 version = "1.4.1"
@@ -435,22 +473,26 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "7.1.0"
+version = "8.5.0"
 description = "Read metadata from Python packages"
 optional = true
 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
-zipp = ">=0.5"
+zipp = ">=3.20"
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+enabler = ["pytest-enabler (>=2.2)"]
 perf = ["ipython"]
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+type = ["pytest-mypy"]
 
 [[package]]
 name = "iniconfig"
@@ -479,13 +521,13 @@ colors = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "jinja2"
-version = "3.1.3"
+version = "3.1.4"
 description = "A very fast and expressive template engine."
 optional = true
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -576,47 +618,53 @@ files = [
 
 [[package]]
 name = "mypy"
-version = "1.10.0"
+version = "1.13.0"
 description = "Optional static typing for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 mypy-extensions = ">=1.0.0"
 tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
-typing-extensions = ">=4.1.0"
+typing-extensions = ">=4.6.0"
 
 [package.extras]
 dmypy = ["psutil (>=4.0)"]
+faster-cache = ["orjson"]
 install-types = ["pip"]
 mypyc = ["setuptools (>=50)"]
 reports = ["lxml"]
@@ -634,13 +682,13 @@ files = [
 
 [[package]]
 name = "packaging"
-version = "24.0"
+version = "24.2"
 description = "Core utilities for Python packages"
 optional = false
-python-versions = ">=3.7"
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 [[package]]
@@ -656,19 +704,19 @@ files = [
 
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 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
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 python-versions = ">=3.8"
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-type = ["mypy (>=1.8)"]
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+type = ["mypy (>=1.11.2)"]
 
 [[package]]
 name = "pluggy"
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 [package.extras]
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 [[package]]
@@ -764,24 +811,24 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtuale
 
 [[package]]
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+version = "2024.2"
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 [package.dependencies]
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 [[package]]
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 description = "A lil' TOML parser"
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+    {file = "tomli-2.2.1.tar.gz", hash = "sha256:cd45e1dc79c835ce60f7404ec8119f2eb06d38b1deba146f07ced3bbc44505ff"},
 ]
 
 [[package]]
 name = "typing-extensions"
-version = "4.11.0"
+version = "4.12.2"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "typing_extensions-4.11.0-py3-none-any.whl", hash = "sha256:c1f94d72897edaf4ce775bb7558d5b79d8126906a14ea5ed1635921406c0387a"},
-    {file = "typing_extensions-4.11.0.tar.gz", hash = "sha256:83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0"},
+    {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"},
+    {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"},
 ]
 
 [[package]]
 name = "urllib3"
-version = "2.2.1"
+version = "2.2.3"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = true
 python-versions = ">=3.8"
 files = [
-    {file = "urllib3-2.2.1-py3-none-any.whl", hash = "sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d"},
-    {file = "urllib3-2.2.1.tar.gz", hash = "sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19"},
+    {file = "urllib3-2.2.3-py3-none-any.whl", hash = "sha256:ca899ca043dcb1bafa3e262d73aa25c465bfb49e0bd9dd5d59f1d0acba2f8fac"},
+    {file = "urllib3-2.2.3.tar.gz", hash = "sha256:e7d814a81dad81e6caf2ec9fdedb284ecc9c73076b62654547cc64ccdcae26e9"},
 ]
 
 [package.extras]
@@ -983,18 +1060,22 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "zipp"
-version = "3.18.1"
+version = "3.20.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = true
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"},
-    {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"},
+    {file = "zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"},
+    {file = "zipp-3.20.2.tar.gz", hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
+type = ["pytest-mypy"]
 
 [extras]
 docs = ["sphinx"]
diff --git a/pyproject.toml b/pyproject.toml
index 85b51c6..6325d71 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -44,9 +44,6 @@ pytest-cov = "^4.0.0"
 [tool.poetry.extras]
 docs = ["sphinx"]
 
-[tool.poetry.build]
-generate-setup-file = true
-
 [build-system]
-requires = ["poetry-core", "setuptools", "cython"]
+requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"