From 9bdfd00574a34bc8aafef69cebdc70ced836f87a Mon Sep 17 00:00:00 2001
From: Alexander Berger <alexander.berger@jax.org>
Date: Wed, 15 Jan 2025 13:50:07 -0500
Subject: [PATCH 1/2] Updating version and deps

---
 poetry.lock    | 877 +++++++++++++++++++++++++++++++------------------
 pyproject.toml |   4 +-
 2 files changed, 565 insertions(+), 316 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 7e20e0f..869b3d4 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,37 +1,34 @@
-# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
 
 [[package]]
 name = "black"
-version = "23.3.0"
+version = "23.12.1"
 description = "The uncompromising code formatter."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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-    {file = "black-23.3.0-cp310-cp310-macosx_10_16_universal2.whl", hash = "sha256:67de8d0c209eb5b330cce2469503de11bca4085880d62f1628bd9972cc3366b9"},
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-    {file = "black-23.3.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:32daa9783106c28815d05b724238e30718f34155653d4d6e125dc7daec8e260c"},
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+    {file = "black-23.12.1-py3-none-any.whl", hash = "sha256:78baad24af0f033958cad29731e27363183e140962595def56423e626f4bee3e"},
+    {file = "black-23.12.1.tar.gz", hash = "sha256:4ce3ef14ebe8d9509188014d96af1c456a910d5b5cbf434a09fef7e024b3d0d5"},
 ]
 
 [package.dependencies]
@@ -41,23 +38,135 @@ packaging = ">=22.0"
 pathspec = ">=0.9.0"
 platformdirs = ">=2"
 tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
-typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}
+typing-extensions = {version = ">=4.0.1", markers = "python_version < \"3.11\""}
 
 [package.extras]
 colorama = ["colorama (>=0.4.3)"]
-d = ["aiohttp (>=3.7.4)"]
+d = ["aiohttp (>=3.7.4)", "aiohttp (>=3.7.4,!=3.9.0)"]
 jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
 uvloop = ["uvloop (>=0.15.2)"]
 
+[[package]]
+name = "certifi"
+version = "2024.12.14"
+description = "Python package for providing Mozilla's CA Bundle."
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "certifi-2024.12.14-py3-none-any.whl", hash = "sha256:1275f7a45be9464efc1173084eaa30f866fe2e47d389406136d332ed4967ec56"},
+    {file = "certifi-2024.12.14.tar.gz", hash = "sha256:b650d30f370c2b724812bee08008be0c4163b163ddaec3f2546c1caf65f191db"},
+]
+
+[[package]]
+name = "charset-normalizer"
+version = "3.4.1"
+description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
+optional = false
+python-versions = ">=3.7"
+files = [
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 ]
 
 [package.dependencies]
@@ -151,24 +262,24 @@ toml = ["tomli"]
 
 [[package]]
 name = "et-xmlfile"
-version = "1.1.0"
+version = "2.0.0"
 description = "An implementation of lxml.xmlfile for the standard library"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
 name = "exceptiongroup"
-version = "1.1.2"
+version = "1.2.2"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
@@ -176,20 +287,21 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "geneweaver-core"
-version = "0.6.0a0"
+version = "0.9.1"
 description = "The core of the Jax-Geneweaver Python library"
 optional = false
-python-versions = ">=3.9,<4.0"
+python-versions = "<4.0,>=3.9"
 files = [
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 ]
 
 [package.dependencies]
-numpy = ">=1.25.2,<2.0.0"
+numpy = ">=1.22,<2"
 openpyxl = ">=3.1.2,<4.0.0"
-pandas = ">=2.0.3,<3.0.0"
-pydantic = {version = ">=1.10.7,<2.0.0", extras = ["dotenv"]}
+pandas = ">=1.5,<3"
+pydantic = {version = ">=1.10,<2.0", extras = ["dotenv"]}
+requests = ">=2.31.0,<3.0.0"
 
 [[package]]
 name = "geneweaver-testing"
@@ -211,6 +323,20 @@ pytest-cov = ">=4.1.0,<5.0.0"
 ruff = ">=0.0.277,<0.0.278"
 tomli = ">=2.0.1,<3.0.0"
 
+[[package]]
+name = "idna"
+version = "3.10"
+description = "Internationalized Domain Names in Applications (IDNA)"
+optional = false
+python-versions = ">=3.6"
+files = [
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+]
+
+[package.extras]
+all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2)"]
+
 [[package]]
 name = "iniconfig"
 version = "2.0.0"
@@ -224,65 +350,75 @@ files = [
 
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 name = "isort"
-version = "5.12.0"
+version = "5.13.2"
 description = "A Python utility / library to sort Python imports."
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 python-versions = ">=3.8.0"
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-plugins = ["setuptools"]
-requirements-deprecated-finder = ["pip-api", "pipreqs"]
+colors = ["colorama (>=0.4.6)"]
 
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 name = "mypy"
-version = "1.4.1"
+version = "1.14.1"
 description = "Optional static typing for Python"
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 [package.extras]
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 install-types = ["pip"]
-python2 = ["typed-ast (>=1.4.0,<2)"]
+mypyc = ["setuptools (>=50)"]
 reports = ["lxml"]
 
 [[package]]
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+version = "3.1.5"
 description = "A Python library to read/write Excel 2010 xlsx/xlsm files"
 optional = false
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+python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -346,117 +493,137 @@ et-xmlfile = "*"
 
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 description = "Core utilities for Python packages"
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 [package.dependencies]
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 python-dateutil = ">=2.8.2"
 pytz = ">=2020.1"
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 ]
 
 [[package]]
 name = "platformdirs"
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+version = "4.3.6"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 [package.extras]
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-test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.3.1)", "pytest-cov (>=4.1)", "pytest-mock (>=3.10)"]
+docs = ["furo (>=2024.8.6)", "proselint (>=0.14)", "sphinx (>=8.0.2)", "sphinx-autodoc-typehints (>=2.4)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=8.3.2)", "pytest-cov (>=5)", "pytest-mock (>=3.14)"]
+type = ["mypy (>=1.11.2)"]
 
 [[package]]
 name = "pluggy"
-version = "1.2.0"
+version = "1.5.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "pluggy-1.5.0-py3-none-any.whl", hash = "sha256:44e1ad92c8ca002de6377e165f3e0f1be63266ab4d554740532335b9d75ea669"},
+    {file = "pluggy-1.5.0.tar.gz", hash = "sha256:2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1"},
 ]
 
 [package.extras]
@@ -465,47 +632,61 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "pydantic"
-version = "1.10.11"
+version = "1.10.21"
 description = "Data validation and settings management using python type hints"
 optional = false
 python-versions = ">=3.7"
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 [package.dependencies]
@@ -518,13 +699,13 @@ email = ["email-validator (>=1.0.3)"]
 
 [[package]]
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+version = "7.4.4"
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@@ -558,13 +739,13 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtuale
 
 [[package]]
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+version = "2.9.0.post0"
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 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
-    {file = "python-dateutil-2.8.2.tar.gz", hash = "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86"},
-    {file = "python_dateutil-2.8.2-py2.py3-none-any.whl", hash = "sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9"},
+    {file = "python-dateutil-2.9.0.post0.tar.gz", hash = "sha256:37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3"},
+    {file = "python_dateutil-2.9.0.post0-py2.py3-none-any.whl", hash = "sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427"},
 ]
 
 [package.dependencies]
@@ -572,13 +753,13 @@ six = ">=1.5"
 
 [[package]]
 name = "python-dotenv"
-version = "1.0.0"
+version = "1.0.1"
 description = "Read key-value pairs from a .env file and set them as environment variables"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "python-dotenv-1.0.0.tar.gz", hash = "sha256:a8df96034aae6d2d50a4ebe8216326c61c3eb64836776504fcca410e5937a3ba"},
-    {file = "python_dotenv-1.0.0-py3-none-any.whl", hash = "sha256:f5971a9226b701070a4bf2c38c89e5a3f0d64de8debda981d1db98583009122a"},
+    {file = "python-dotenv-1.0.1.tar.gz", hash = "sha256:e324ee90a023d808f1959c46bcbc04446a10ced277783dc6ee09987c37ec10ca"},
+    {file = "python_dotenv-1.0.1-py3-none-any.whl", hash = "sha256:f7b63ef50f1b690dddf550d03497b66d609393b40b564ed0d674909a68ebf16a"},
 ]
 
 [package.extras]
@@ -586,15 +767,36 @@ cli = ["click (>=5.0)"]
 
 [[package]]
 name = "pytz"
-version = "2023.3"
+version = "2024.2"
 description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
 files = [
-    {file = "pytz-2023.3-py2.py3-none-any.whl", hash = "sha256:a151b3abb88eda1d4e34a9814df37de2a80e301e68ba0fd856fb9b46bfbbbffb"},
-    {file = "pytz-2023.3.tar.gz", hash = "sha256:1d8ce29db189191fb55338ee6d0387d82ab59f3d00eac103412d64e0ebd0c588"},
+    {file = "pytz-2024.2-py2.py3-none-any.whl", hash = "sha256:31c7c1817eb7fae7ca4b8c7ee50c72f93aa2dd863de768e1ef4245d426aa0725"},
+    {file = "pytz-2024.2.tar.gz", hash = "sha256:2aa355083c50a0f93fa581709deac0c9ad65cca8a9e9beac660adcbd493c798a"},
+]
+
+[[package]]
+name = "requests"
+version = "2.32.3"
+description = "Python HTTP for Humans."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "requests-2.32.3-py3-none-any.whl", hash = "sha256:70761cfe03c773ceb22aa2f671b4757976145175cdfca038c02654d061d6dcc6"},
+    {file = "requests-2.32.3.tar.gz", hash = "sha256:55365417734eb18255590a9ff9eb97e9e1da868d4ccd6402399eaf68af20a760"},
 ]
 
+[package.dependencies]
+certifi = ">=2017.4.17"
+charset-normalizer = ">=2,<4"
+idna = ">=2.5,<4"
+urllib3 = ">=1.21.1,<3"
+
+[package.extras]
+socks = ["PySocks (>=1.5.6,!=1.5.7)"]
+use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
+
 [[package]]
 name = "ruff"
 version = "0.0.277"
@@ -623,49 +825,96 @@ files = [
 
 [[package]]
 name = "six"
-version = "1.16.0"
+version = "1.17.0"
 description = "Python 2 and 3 compatibility utilities"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
-    {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
-    {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
+    {file = "six-1.17.0-py2.py3-none-any.whl", hash = "sha256:4721f391ed90541fddacab5acf947aa0d3dc7d27b2e1e8eda2be8970586c3274"},
+    {file = "six-1.17.0.tar.gz", hash = "sha256:ff70335d468e7eb6ec65b95b99d3a2836546063f63acc5171de367e834932a81"},
 ]
 
 [[package]]
 name = "tomli"
-version = "2.0.1"
+version = "2.2.1"
 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-2.2.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:678e4fa69e4575eb77d103de3df8a895e1591b48e740211bd1067378c69e8249"},
+    {file = "tomli-2.2.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:023aa114dd824ade0100497eb2318602af309e5a55595f76b626d6d9f3b7b0a6"},
+    {file = "tomli-2.2.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:ece47d672db52ac607a3d9599a9d48dcb2f2f735c6c2d1f34130085bb12b112a"},
+    {file = "tomli-2.2.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6972ca9c9cc9f0acaa56a8ca1ff51e7af152a9f87fb64623e31d5c83700080ee"},
+    {file = "tomli-2.2.1-cp311-cp311-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:c954d2250168d28797dd4e3ac5cf812a406cd5a92674ee4c8f123c889786aa8e"},
+    {file = "tomli-2.2.1-cp311-cp311-musllinux_1_2_aarch64.whl", hash = "sha256:8dd28b3e155b80f4d54beb40a441d366adcfe740969820caf156c019fb5c7ec4"},
+    {file = "tomli-2.2.1-cp311-cp311-musllinux_1_2_i686.whl", hash = "sha256:e59e304978767a54663af13c07b3d1af22ddee3bb2fb0618ca1593e4f593a106"},
+    {file = "tomli-2.2.1-cp311-cp311-musllinux_1_2_x86_64.whl", hash = "sha256:33580bccab0338d00994d7f16f4c4ec25b776af3ffaac1ed74e0b3fc95e885a8"},
+    {file = "tomli-2.2.1-cp311-cp311-win32.whl", hash = "sha256:465af0e0875402f1d226519c9904f37254b3045fc5084697cefb9bdde1ff99ff"},
+    {file = "tomli-2.2.1-cp311-cp311-win_amd64.whl", hash = "sha256:2d0f2fdd22b02c6d81637a3c95f8cd77f995846af7414c5c4b8d0545afa1bc4b"},
+    {file = "tomli-2.2.1-cp312-cp312-macosx_10_13_x86_64.whl", hash = "sha256:4a8f6e44de52d5e6c657c9fe83b562f5f4256d8ebbfe4ff922c495620a7f6cea"},
+    {file = "tomli-2.2.1-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:8d57ca8095a641b8237d5b079147646153d22552f1c637fd3ba7f4b0b29167a8"},
+    {file = "tomli-2.2.1-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:4e340144ad7ae1533cb897d406382b4b6fede8890a03738ff1683af800d54192"},
+    {file = "tomli-2.2.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:db2b95f9de79181805df90bedc5a5ab4c165e6ec3fe99f970d0e302f384ad222"},
+    {file = "tomli-2.2.1-cp312-cp312-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:40741994320b232529c802f8bc86da4e1aa9f413db394617b9a256ae0f9a7f77"},
+    {file = "tomli-2.2.1-cp312-cp312-musllinux_1_2_aarch64.whl", hash = "sha256:400e720fe168c0f8521520190686ef8ef033fb19fc493da09779e592861b78c6"},
+    {file = "tomli-2.2.1-cp312-cp312-musllinux_1_2_i686.whl", hash = "sha256:02abe224de6ae62c19f090f68da4e27b10af2b93213d36cf44e6e1c5abd19fdd"},
+    {file = "tomli-2.2.1-cp312-cp312-musllinux_1_2_x86_64.whl", hash = "sha256:b82ebccc8c8a36f2094e969560a1b836758481f3dc360ce9a3277c65f374285e"},
+    {file = "tomli-2.2.1-cp312-cp312-win32.whl", hash = "sha256:889f80ef92701b9dbb224e49ec87c645ce5df3fa2cc548664eb8a25e03127a98"},
+    {file = "tomli-2.2.1-cp312-cp312-win_amd64.whl", hash = "sha256:7fc04e92e1d624a4a63c76474610238576942d6b8950a2d7f908a340494e67e4"},
+    {file = "tomli-2.2.1-cp313-cp313-macosx_10_13_x86_64.whl", hash = "sha256:f4039b9cbc3048b2416cc57ab3bda989a6fcf9b36cf8937f01a6e731b64f80d7"},
+    {file = "tomli-2.2.1-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:286f0ca2ffeeb5b9bd4fcc8d6c330534323ec51b2f52da063b11c502da16f30c"},
+    {file = "tomli-2.2.1-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a92ef1a44547e894e2a17d24e7557a5e85a9e1d0048b0b5e7541f76c5032cb13"},
+    {file = "tomli-2.2.1-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9316dc65bed1684c9a98ee68759ceaed29d229e985297003e494aa825ebb0281"},
+    {file = "tomli-2.2.1-cp313-cp313-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:e85e99945e688e32d5a35c1ff38ed0b3f41f43fad8df0bdf79f72b2ba7bc5272"},
+    {file = "tomli-2.2.1-cp313-cp313-musllinux_1_2_aarch64.whl", hash = "sha256:ac065718db92ca818f8d6141b5f66369833d4a80a9d74435a268c52bdfa73140"},
+    {file = "tomli-2.2.1-cp313-cp313-musllinux_1_2_i686.whl", hash = "sha256:d920f33822747519673ee656a4b6ac33e382eca9d331c87770faa3eef562aeb2"},
+    {file = "tomli-2.2.1-cp313-cp313-musllinux_1_2_x86_64.whl", hash = "sha256:a198f10c4d1b1375d7687bc25294306e551bf1abfa4eace6650070a5c1ae2744"},
+    {file = "tomli-2.2.1-cp313-cp313-win32.whl", hash = "sha256:d3f5614314d758649ab2ab3a62d4f2004c825922f9e370b29416484086b264ec"},
+    {file = "tomli-2.2.1-cp313-cp313-win_amd64.whl", hash = "sha256:a38aa0308e754b0e3c67e344754dff64999ff9b513e691d0e786265c93583c69"},
+    {file = "tomli-2.2.1-py3-none-any.whl", hash = "sha256:cb55c73c5f4408779d0cf3eef9f762b9c9f147a77de7b258bef0a5628adc85cc"},
+    {file = "tomli-2.2.1.tar.gz", hash = "sha256:cd45e1dc79c835ce60f7404ec8119f2eb06d38b1deba146f07ced3bbc44505ff"},
 ]
 
 [[package]]
 name = "typing-extensions"
-version = "4.7.1"
-description = "Backported and Experimental Type Hints for Python 3.7+"
+version = "4.12.2"
+description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "typing_extensions-4.7.1-py3-none-any.whl", hash = "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36"},
-    {file = "typing_extensions-4.7.1.tar.gz", hash = "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"},
+    {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 = "tzdata"
-version = "2023.3"
+version = "2024.2"
 description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
 files = [
-    {file = "tzdata-2023.3-py2.py3-none-any.whl", hash = "sha256:7e65763eef3120314099b6939b5546db7adce1e7d6f2e179e3df563c70511eda"},
-    {file = "tzdata-2023.3.tar.gz", hash = "sha256:11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a"},
+    {file = "tzdata-2024.2-py2.py3-none-any.whl", hash = "sha256:a48093786cdcde33cad18c2555e8532f34422074448fbc874186f0abd79565cd"},
+    {file = "tzdata-2024.2.tar.gz", hash = "sha256:7d85cc416e9382e69095b7bdf4afd9e3880418a2413feec7069d533d6b4e31cc"},
 ]
 
+[[package]]
+name = "urllib3"
+version = "2.3.0"
+description = "HTTP library with thread-safe connection pooling, file post, and more."
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "urllib3-2.3.0-py3-none-any.whl", hash = "sha256:1cee9ad369867bfdbbb48b7dd50374c0967a0bb7710050facf0dd6911440e3df"},
+    {file = "urllib3-2.3.0.tar.gz", hash = "sha256:f8c5449b3cf0861679ce7e0503c7b44b5ec981bec0d1d3795a07f1ba96f0204d"},
+]
+
+[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)"]
+
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "e68363bf0b9bcc4dd6b5fa33b376ad153c4b367d7b920c48498541c22faf90f6"
+content-hash = "dcf048cb58a0bd3598432119977145802aa5203748a100ca3d5129fc31d3bd0f"
diff --git a/pyproject.toml b/pyproject.toml
index 3c46e5d..a92f3e8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-tools"
-version = "0.0.2"
+version = "0.0.3"
 description = "A framework to allow for consistent implementation of tools for the GeneWeaver project."
 authors = ["Alexander Berger <alexander.berger@jax.org>"]
 readme = "README.md"
@@ -12,7 +12,7 @@ packages = [{include = "geneweaver/tools", from = "src"}]
 [tool.poetry.dependencies]
 python = "^3.9"
 pydantic = "^1.10.7"
-geneweaver-core = "^0.6.0a0"
+geneweaver-core = "^0.9.1"
 
 [tool.poetry.group.dev.dependencies]
 geneweaver-testing = "^0.0.2"

From 91e939027ca85e11b9b72e7f119b15267000a54c Mon Sep 17 00:00:00 2001
From: Alexander Berger <alexander.berger@jax.org>
Date: Wed, 15 Jan 2025 13:54:04 -0500
Subject: [PATCH 2/2] Pinning ruff and black versions

---
 .github/workflows/_format-lint-action.yml | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/.github/workflows/_format-lint-action.yml b/.github/workflows/_format-lint-action.yml
index 58baffe..565836a 100644
--- a/.github/workflows/_format-lint-action.yml
+++ b/.github/workflows/_format-lint-action.yml
@@ -16,6 +16,16 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ inputs.python-version }}
+      - name: Install Poetry
+        run: |
+          curl -sSL https://install.python-poetry.org | python3 -
+          if [[ "$RUNNER_OS" == "macOS" ]]; then
+            echo "/Users/runner/.local/bin:$PATH" >> $GITHUB_PATH
+          fi
+      - name: Configure Poetry
+        run: poetry config virtualenvs.create false
+      - name: Install Black and Ruff
+        run: poetry install --only dev
       - name: Install Black and Ruff
         run: pip install black ruff
       - name: Run Ruff Linter