From 2fdf343bdfa9ae7e0fc3d1d436ce9bdad3b14c3c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Irene=20L=C3=B3pez=20Santiago?=
 <45119610+ireneisdoomed@users.noreply.github.com>
Date: Thu, 12 Dec 2024 16:25:33 +0000
Subject: [PATCH 1/7] build: define dependency version constraints + other
 fixes (#945)

* build(deps): bump wandb from 0.18.5 to 0.19.0

Bumps [wandb](https://github.com/wandb/wandb) from 0.18.5 to 0.19.0.
- [Release notes](https://github.com/wandb/wandb/releases)
- [Changelog](https://github.com/wandb/wandb/blob/main/CHANGELOG.md)
- [Commits](https://github.com/wandb/wandb/compare/v0.18.5...v0.19.0)

---
updated-dependencies:
- dependency-name: wandb
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

* fix: lock `skops` and `scikit-learn` versions

* build: define next major release as upper bound

* test: add `test_all_modules_are_importable`

* build: make version constraints more flexible for some packages

* chore: move dev dependencies to same group

* build: change caret to more explicit requirements
---
 poetry.lock                    | 2970 ++++++++++++++++----------------
 pyproject.toml                 |   81 +-
 tests/gentropy/test_imports.py |   27 +
 3 files changed, 1589 insertions(+), 1489 deletions(-)
 create mode 100644 tests/gentropy/test_imports.py

diff --git a/poetry.lock b/poetry.lock
index 53d95babf..e9a6b7e00 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand.
 
 [[package]]
 name = "aiodns"
@@ -16,123 +16,109 @@ pycares = ">=3.0.0"
 
 [[package]]
 name = "aiohappyeyeballs"
-version = "2.4.3"
+version = "2.4.4"
 description = "Happy Eyeballs for asyncio"
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "aiohappyeyeballs-2.4.3.tar.gz", hash = "sha256:75cf88a15106a5002a8eb1dab212525c00d1f4c0fa96e551c9fbe6f09a621586"},
+    {file = "aiohappyeyeballs-2.4.4-py3-none-any.whl", hash = "sha256:a980909d50efcd44795c4afeca523296716d50cd756ddca6af8c65b996e27de8"},
+    {file = "aiohappyeyeballs-2.4.4.tar.gz", hash = "sha256:5fdd7d87889c63183afc18ce9271f9b0a7d32c2303e394468dd45d514a757745"},
 ]
 
 [[package]]
 name = "aiohttp"
-version = "3.10.10"
+version = "3.11.10"
 description = "Async http client/server framework (asyncio)"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
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 ]
 
 [package.dependencies]
 aiohappyeyeballs = ">=2.3.0"
 aiosignal = ">=1.1.2"
-async-timeout = {version = ">=4.0,<5.0", markers = "python_version < \"3.11\""}
+async-timeout = {version = ">=4.0,<6.0", markers = "python_version < \"3.11\""}
 attrs = ">=17.3.0"
 frozenlist = ">=1.1.1"
 multidict = ">=4.5,<7.0"
-yarl = ">=1.12.0,<2.0"
+propcache = ">=0.2.0"
+yarl = ">=1.17.0,<2.0"
 
 [package.extras]
 speedups = ["Brotli", "aiodns (>=3.2.0)", "brotlicffi"]
@@ -151,6 +137,17 @@ files = [
 [package.dependencies]
 frozenlist = ">=1.1.0"
 
+[[package]]
+name = "annotated-types"
+version = "0.7.0"
+description = "Reusable constraint types to use with typing.Annotated"
+optional = false
+python-versions = ">=3.8"
+files = [
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+    {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"},
+]
+
 [[package]]
 name = "antlr4-python3-runtime"
 version = "4.9.3"
@@ -174,31 +171,28 @@ files = [
 
 [[package]]
 name = "asttokens"
-version = "2.4.1"
+version = "3.0.0"
 description = "Annotate AST trees with source code positions"
 optional = false
-python-versions = "*"
+python-versions = ">=3.8"
 files = [
-    {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"},
-    {file = "asttokens-2.4.1.tar.gz", hash = "sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0"},
+    {file = "asttokens-3.0.0-py3-none-any.whl", hash = "sha256:e3078351a059199dd5138cb1c706e6430c05eff2ff136af5eb4790f9d28932e2"},
+    {file = "asttokens-3.0.0.tar.gz", hash = "sha256:0dcd8baa8d62b0c1d118b399b2ddba3c4aff271d0d7a9e0d4c1681c79035bbc7"},
 ]
 
-[package.dependencies]
-six = ">=1.12.0"
-
 [package.extras]
-astroid = ["astroid (>=1,<2)", "astroid (>=2,<4)"]
-test = ["astroid (>=1,<2)", "astroid (>=2,<4)", "pytest"]
+astroid = ["astroid (>=2,<4)"]
+test = ["astroid (>=2,<4)", "pytest", "pytest-cov", "pytest-xdist"]
 
 [[package]]
 name = "async-timeout"
-version = "4.0.3"
+version = "5.0.1"
 description = "Timeout context manager for asyncio programs"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "async-timeout-4.0.3.tar.gz", hash = "sha256:4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f"},
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+    {file = "async_timeout-5.0.1.tar.gz", hash = "sha256:d9321a7a3d5a6a5e187e824d2fa0793ce379a202935782d555d6e9d2735677d3"},
 ]
 
 [[package]]
@@ -247,13 +241,13 @@ files = [
 
 [[package]]
 name = "azure-core"
-version = "1.31.0"
+version = "1.32.0"
 description = "Microsoft Azure Core Library for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "azure_core-1.32.0-py3-none-any.whl", hash = "sha256:eac191a0efb23bfa83fddf321b27b122b4ec847befa3091fa736a5c32c50d7b4"},
+    {file = "azure_core-1.32.0.tar.gz", hash = "sha256:22b3c35d6b2dae14990f6c1be2912bf23ffe50b220e708a28ab1bb92b1c730e5"},
 ]
 
 [package.dependencies]
@@ -284,17 +278,17 @@ typing-extensions = ">=4.0.0"
 
 [[package]]
 name = "azure-mgmt-core"
-version = "1.4.0"
+version = "1.5.0"
 description = "Microsoft Azure Management Core Library for Python"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "azure_mgmt_core-1.5.0-py3-none-any.whl", hash = "sha256:18aaa5a723ee8ae05bf1bfc9f6d0ffb996631c7ea3c922cc86f522973ce07b5f"},
+    {file = "azure_mgmt_core-1.5.0.tar.gz", hash = "sha256:380ae3dfa3639f4a5c246a7db7ed2d08374e88230fd0da3eb899f7c11e5c441a"},
 ]
 
 [package.dependencies]
-azure-core = ">=1.26.2,<2.0.0"
+azure-core = ">=1.31.0"
 
 [[package]]
 name = "azure-mgmt-storage"
@@ -314,13 +308,13 @@ msrest = ">=0.6.21"
 
 [[package]]
 name = "azure-storage-blob"
-version = "12.23.1"
+version = "12.24.0"
 description = "Microsoft Azure Blob Storage Client Library for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -369,13 +363,13 @@ lxml = ["lxml"]
 
 [[package]]
 name = "bokeh"
-version = "3.6.0"
+version = "3.6.2"
 description = "Interactive plots and applications in the browser from Python"
 optional = false
 python-versions = ">=3.10"
 files = [
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-    {file = "bokeh-3.6.0.tar.gz", hash = "sha256:0032dc1e76ad097b07626e51584685ff48c65481fbaaad105663b1046165867a"},
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 ]
 
 [package.dependencies]
@@ -391,17 +385,17 @@ xyzservices = ">=2021.09.1"
 
 [[package]]
 name = "boto3"
-version = "1.35.51"
+version = "1.35.77"
 description = "The AWS SDK for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
-botocore = ">=1.35.51,<1.36.0"
+botocore = ">=1.35.77,<1.36.0"
 jmespath = ">=0.7.1,<2.0.0"
 s3transfer = ">=0.10.0,<0.11.0"
 
@@ -410,13 +404,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "botocore"
-version = "1.35.51"
+version = "1.35.77"
 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -733,76 +727,65 @@ test = ["flake8 (==3.7.8)", "hypothesis (==3.55.3)"]
 
 [[package]]
 name = "contourpy"
-version = "1.3.0"
+version = "1.3.1"
 description = "Python library for calculating contours of 2D quadrilateral grids"
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.10"
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 [package.dependencies]
@@ -817,73 +800,73 @@ test-no-images = ["pytest", "pytest-cov", "pytest-rerunfailures", "pytest-xdist"
 
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 test-randomorder = ["pytest-randomly"]
 
 [[package]]
@@ -969,13 +954,13 @@ files = [
 
 [[package]]
 name = "db-dtypes"
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 description = "Pandas Data Types for SQL systems (BigQuery, Spanner)"
 optional = false
 python-versions = ">=3.7"
 files = [
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 description = "Python @deprecated decorator to deprecate old python classes, functions or methods."
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 ]
 
 [package.extras]
@@ -1509,13 +1496,13 @@ beautifulsoup4 = "*"
 
 [[package]]
 name = "google-api-core"
-version = "2.22.0"
+version = "2.24.0"
 description = "Google API client core library"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -1535,13 +1522,13 @@ grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.dev0)"]
 
 [[package]]
 name = "google-auth"
-version = "2.35.0"
+version = "2.36.0"
 description = "Google Authentication Library"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -1576,13 +1563,13 @@ tool = ["click (>=6.0.0)"]
 
 [[package]]
 name = "google-cloud-bigquery"
-version = "3.26.0"
+version = "3.27.0"
 description = "Google BigQuery API client library"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -1625,31 +1612,30 @@ grpc = ["grpcio (>=1.38.0,<2.0dev)", "grpcio-status (>=1.38.0,<2.0.dev0)"]
 
 [[package]]
 name = "google-cloud-dataproc"
-version = "5.15.0"
+version = "5.8.0"
 description = "Google Cloud Dataproc API client library"
 optional = false
 python-versions = ">=3.7"
 files = [
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 [package.dependencies]
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-google-auth = ">=2.14.1,<2.24.0 || >2.24.0,<2.25.0 || >2.25.0,<3.0.0dev"
+google-api-core = {version = ">=1.34.0,<2.0.dev0 || >=2.11.dev0,<3.0.0dev", extras = ["grpc"]}
 grpc-google-iam-v1 = ">=0.12.4,<1.0.0dev"
 proto-plus = ">=1.22.3,<2.0.0dev"
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 [[package]]
 name = "google-cloud-secret-manager"
-version = "2.21.0"
+version = "2.20.2"
 description = "Google Cloud Secret Manager API client library"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -1661,13 +1647,13 @@ protobuf = ">=3.20.2,<4.21.0 || >4.21.0,<4.21.1 || >4.21.1,<4.21.2 || >4.21.2,<4
 
 [[package]]
 name = "google-cloud-storage"
-version = "2.18.2"
+version = "2.19.0"
 description = "Google Cloud Storage API client library"
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "google_cloud_storage-2.19.0-py2.py3-none-any.whl", hash = "sha256:aeb971b5c29cf8ab98445082cbfe7b161a1f48ed275822f59ed3f1524ea54fba"},
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 ]
 
 [package.dependencies]
@@ -1741,13 +1727,13 @@ requests = ["requests (>=2.18.0,<3.0.0dev)"]
 
 [[package]]
 name = "googleapis-common-protos"
-version = "1.65.0"
+version = "1.66.0"
 description = "Common protobufs used in Google APIs"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -1789,70 +1775,70 @@ protobuf = ">=3.20.2,<4.21.1 || >4.21.1,<4.21.2 || >4.21.2,<4.21.3 || >4.21.3,<4
 
 [[package]]
 name = "grpcio"
-version = "1.67.1"
+version = "1.68.1"
 description = "HTTP/2-based RPC framework"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
-protobuf = ["grpcio-tools (>=1.67.1)"]
+protobuf = ["grpcio-tools (>=1.68.1)"]
 
 [[package]]
 name = "grpcio-status"
@@ -1919,13 +1905,13 @@ uvloop = {version = ">=0.19.0,<1", markers = "sys_platform != \"win32\""}
 
 [[package]]
 name = "huggingface-hub"
-version = "0.26.2"
+version = "0.26.5"
 description = "Client library to download and publish models, datasets and other repos on the huggingface.co hub"
 optional = false
 python-versions = ">=3.8.0"
 files = [
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 ]
 
 [package.dependencies]
@@ -1983,13 +1969,13 @@ packaging = "*"
 
 [[package]]
 name = "identify"
-version = "2.6.1"
+version = "2.6.3"
 description = "File identification library for Python"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.extras]
@@ -2047,13 +2033,13 @@ tests = ["coverage[toml]", "pytest", "pytest-cov", "pytest-mock"]
 
 [[package]]
 name = "ipykernel"
-version = "6.29.5"
+version = "6.28.0"
 description = "IPython Kernel for Jupyter"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -2076,17 +2062,17 @@ cov = ["coverage[toml]", "curio", "matplotlib", "pytest-cov", "trio"]
 docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "trio"]
 pyqt5 = ["pyqt5"]
 pyside6 = ["pyside6"]
-test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.23.5)", "pytest-cov", "pytest-timeout"]
+test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio", "pytest-cov", "pytest-timeout"]
 
 [[package]]
 name = "ipython"
-version = "8.30.0"
+version = "8.29.0"
 description = "IPython: Productive Interactive Computing"
 optional = false
 python-versions = ">=3.10"
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 ]
 
 [package.dependencies]
@@ -2096,16 +2082,16 @@ exceptiongroup = {version = "*", markers = "python_version < \"3.11\""}
 jedi = ">=0.16"
 matplotlib-inline = "*"
 pexpect = {version = ">4.3", markers = "sys_platform != \"win32\" and sys_platform != \"emscripten\""}
-prompt_toolkit = ">=3.0.41,<3.1.0"
+prompt-toolkit = ">=3.0.41,<3.1.0"
 pygments = ">=2.4.0"
-stack_data = "*"
+stack-data = "*"
 traitlets = ">=5.13.0"
-typing_extensions = {version = ">=4.6", markers = "python_version < \"3.12\""}
+typing-extensions = {version = ">=4.6", markers = "python_version < \"3.12\""}
 
 [package.extras]
 all = ["ipython[black,doc,kernel,matplotlib,nbconvert,nbformat,notebook,parallel,qtconsole]", "ipython[test,test-extra]"]
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+doc = ["docrepr", "exceptiongroup", "intersphinx-registry", "ipykernel", "ipython[test]", "matplotlib", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "sphinxcontrib-jquery", "tomli", "typing-extensions"]
 kernel = ["ipykernel"]
 matplotlib = ["matplotlib"]
 nbconvert = ["nbconvert"]
@@ -2157,22 +2143,22 @@ typing-extensions = ">=3.7.4.3"
 
 [[package]]
 name = "jedi"
-version = "0.19.1"
+version = "0.19.2"
 description = "An autocompletion tool for Python that can be used for text editors."
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 python-versions = ">=3.6"
 files = [
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 [package.dependencies]
-parso = ">=0.8.3,<0.9.0"
+parso = ">=0.8.4,<0.9.0"
 
 [package.extras]
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-testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
+testing = ["Django", "attrs", "colorama", "docopt", "pytest (<9.0.0)"]
 
 [[package]]
 name = "jinja2"
@@ -2424,157 +2410,91 @@ files = [
 
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 python-versions = ">=3.6"
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-html-clean = ["lxml-html-clean"]
 html5 = ["html5lib"]
 htmlsoup = ["BeautifulSoup4"]
-source = ["Cython (>=3.0.11)"]
+source = ["Cython (>=3.0.9)"]
 
 [[package]]
 name = "markdown"
@@ -2767,13 +2687,13 @@ files = [
 
 [[package]]
 name = "mkdocs"
-version = "1.6.1"
+version = "1.5.3"
 description = "Project documentation with Markdown."
 optional = false
-python-versions = ">=3.8"
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 ghp-import = ">=1.0"
 jinja2 = ">=2.11.1"
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 packaging = ">=20.5"
 pathspec = ">=0.11.1"
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 pyyaml = ">=5.1"
 pyyaml-env-tag = ">=0.1"
 watchdog = ">=2.0"
 
 [package.extras]
 i18n = ["babel (>=2.9.0)"]
-min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-import (==1.0)", "importlib-metadata (==4.4)", "jinja2 (==2.11.1)", "markdown (==3.3.6)", "markupsafe (==2.0.1)", "mergedeep (==1.3.4)", "mkdocs-get-deps (==0.2.0)", "packaging (==20.5)", "pathspec (==0.11.1)", "pyyaml (==5.1)", "pyyaml-env-tag (==0.1)", "watchdog (==2.0)"]
+min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-import (==1.0)", "importlib-metadata (==4.3)", "jinja2 (==2.11.1)", "markdown (==3.2.1)", "markupsafe (==2.0.1)", "mergedeep (==1.3.4)", "packaging (==20.5)", "pathspec (==0.11.1)", "platformdirs (==2.2.0)", "pyyaml (==5.1)", "pyyaml-env-tag (==0.1)", "typing-extensions (==3.10)", "watchdog (==2.0)"]
 
 [[package]]
 name = "mkdocs-autolinks-plugin"
@@ -2854,31 +2774,15 @@ files = [
 [package.dependencies]
 mkdocs = "*"
 
-[[package]]
-name = "mkdocs-get-deps"
-version = "0.2.0"
-description = "MkDocs extension that lists all dependencies according to a mkdocs.yml file"
-optional = false
-python-versions = ">=3.8"
-files = [
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-    {file = "mkdocs_get_deps-0.2.0.tar.gz", hash = "sha256:162b3d129c7fad9b19abfdcb9c1458a651628e4b1dea628ac68790fb3061c60c"},
-]
-
-[package.dependencies]
-mergedeep = ">=1.3.4"
-platformdirs = ">=2.2.0"
-pyyaml = ">=5.1"
-
 [[package]]
 name = "mkdocs-git-committers-plugin-2"
-version = "2.4.1"
+version = "2.2.3"
 description = "An MkDocs plugin to create a list of contributors on the page. The git-committers plugin will seed the template context with a list of GitHub or GitLab committers and other useful GIT info such as last modified date"
 optional = false
-python-versions = "<4,>=3.8"
+python-versions = ">=3.8,<4"
 files = [
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-    {file = "mkdocs_git_committers_plugin_2-2.4.1.tar.gz", hash = "sha256:ea1f80a79cedc42289e0b8e973276df04fb94f56e0ae3efc5385fb28547cf5cb"},
+    {file = "mkdocs-git-committers-plugin-2-2.2.3.tar.gz", hash = "sha256:e0dddef4e3e321d97bcb83123fd963a839d9f9fa801c3125efeb6544bd8b247c"},
+    {file = "mkdocs_git_committers_plugin_2-2.2.3-py3-none-any.whl", hash = "sha256:0f20d61a9315174f30d5a0266d4a457d3d88909ca5c5bd7d0e0dd2e1841f2af0"},
 ]
 
 [package.dependencies]
@@ -2888,13 +2792,13 @@ requests = "*"
 
 [[package]]
 name = "mkdocs-git-revision-date-localized-plugin"
-version = "1.3.0"
+version = "1.2.9"
 description = "Mkdocs plugin that enables displaying the localized date of the last git modification of a markdown file."
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "mkdocs_git_revision_date_localized_plugin-1.3.0.tar.gz", hash = "sha256:439e2f14582204050a664c258861c325064d97cdc848c541e48bb034a6c4d0cb"},
+    {file = "mkdocs_git_revision_date_localized_plugin-1.2.9-py3-none-any.whl", hash = "sha256:dea5c8067c23df30275702a1708885500fadf0abfb595b60e698bffc79c7a423"},
+    {file = "mkdocs_git_revision_date_localized_plugin-1.2.9.tar.gz", hash = "sha256:df9a50873fba3a42ce9123885f8c53d589e90ef6c2443fe3280ef1e8d33c8f65"},
 ]
 
 [package.dependencies]
@@ -2910,13 +2814,13 @@ dev = ["click", "codecov", "mkdocs-gen-files", "mkdocs-git-authors-plugin", "mkd
 
 [[package]]
 name = "mkdocs-material"
-version = "9.5.42"
+version = "9.5.18"
 description = "Documentation that simply works"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "mkdocs_material-9.5.42-py3-none-any.whl", hash = "sha256:452a7c5d21284b373f36b981a2cbebfff59263feebeede1bc28652e9c5bbe316"},
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+    {file = "mkdocs_material-9.5.18-py3-none-any.whl", hash = "sha256:1e0e27fc9fe239f9064318acf548771a4629d5fd5dfd45444fd80a953fe21eb4"},
+    {file = "mkdocs_material-9.5.18.tar.gz", hash = "sha256:a43f470947053fa2405c33995f282d24992c752a50114f23f30da9d8d0c57e62"},
 ]
 
 [package.dependencies]
@@ -2924,7 +2828,7 @@ babel = ">=2.10,<3.0"
 colorama = ">=0.4,<1.0"
 jinja2 = ">=3.0,<4.0"
 markdown = ">=3.2,<4.0"
-mkdocs = ">=1.6,<2.0"
+mkdocs = ">=1.5.3,<1.6.0"
 mkdocs-material-extensions = ">=1.3,<2.0"
 paginate = ">=0.5,<1.0"
 pygments = ">=2.16,<3.0"
@@ -2964,13 +2868,13 @@ mkdocs = ">=1.2"
 
 [[package]]
 name = "mkdocstrings"
-version = "0.26.2"
+version = "0.27.0"
 description = "Automatic documentation from sources, for MkDocs."
 optional = false
 python-versions = ">=3.9"
 files = [
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+    {file = "mkdocstrings-0.27.0-py3-none-any.whl", hash = "sha256:6ceaa7ea830770959b55a16203ac63da24badd71325b96af950e59fd37366332"},
+    {file = "mkdocstrings-0.27.0.tar.gz", hash = "sha256:16adca6d6b0a1f9e0c07ff0b02ced8e16f228a9d65a37c063ec4c14d7b76a657"},
 ]
 
 [package.dependencies]
@@ -3006,13 +2910,13 @@ mkdocstrings = ">=0.26"
 
 [[package]]
 name = "msal"
-version = "1.31.0"
+version = "1.31.1"
 description = "The Microsoft Authentication Library (MSAL) for Python library enables your app to access the Microsoft Cloud by supporting authentication of users with Microsoft Azure Active Directory accounts (AAD) and Microsoft Accounts (MSA) using industry standard OAuth2 and OpenID Connect."
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "msal-1.31.1.tar.gz", hash = "sha256:11b5e6a3f802ffd3a72107203e20c4eac6ef53401961b880af2835b723d80578"},
 ]
 
 [package.dependencies]
@@ -3376,80 +3280,97 @@ PyYAML = ">=5.1.0"
 
 [[package]]
 name = "orjson"
-version = "3.10.10"
+version = "3.10.12"
 description = "Fast, correct Python JSON library supporting dataclasses, datetimes, and numpy"
 optional = false
 python-versions = ">=3.8"
 files = [
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+
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+version = "1.9.0"
 description = "PyData helpers for authenticating to Google APIs"
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-google-auth-oauthlib = {version = ">=0.4.0", markers = "python_version >= \"3.6\""}
+google-auth = ">=1.25.0,<3.0dev"
+google-auth-oauthlib = ">=0.4.0"
 setuptools = "*"
 
 [[package]]
 name = "pydoclint"
-version = "0.5.9"
+version = "0.5.10"
 description = "A Python docstring linter that checks arguments, returns, yields, and raises sections"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
 click = ">=8.1.0"
-docstring-parser-fork = ">=0.0.9"
+docstring_parser_fork = ">=0.0.9"
 tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""}
 
 [package.extras]
@@ -4310,13 +4356,13 @@ windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "pyjwt"
-version = "2.9.0"
+version = "2.10.1"
 description = "JSON Web Token implementation in Python"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
@@ -4341,17 +4387,17 @@ files = [
 
 [[package]]
 name = "pymdown-extensions"
-version = "10.12"
+version = "10.7.1"
 description = "Extension pack for Python Markdown."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
-markdown = ">=3.6"
+markdown = ">=3.5"
 pyyaml = "*"
 
 [package.extras]
@@ -4359,13 +4405,13 @@ extra = ["pygments (>=2.12)"]
 
 [[package]]
 name = "pyparsing"
-version = "3.2.0"
+version = "3.1.4"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.6.8"
 files = [
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 ]
 
 [package.extras]
@@ -4392,13 +4438,13 @@ sql = ["pandas (>=1.0.5)", "pyarrow (>=1.0.0)"]
 
 [[package]]
 name = "pytest"
-version = "8.3.3"
+version = "8.3.4"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -4451,18 +4497,18 @@ dev = ["black", "flake8", "pre-commit"]
 
 [[package]]
 name = "pytest-xdist"
-version = "3.6.1"
+version = "3.5.0"
 description = "pytest xdist plugin for distributed testing, most importantly across multiple CPUs"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.7"
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 [package.dependencies]
-execnet = ">=2.1"
-pytest = ">=7.0.0"
+execnet = ">=1.1"
+pytest = ">=6.2.0"
 
 [package.extras]
 psutil = ["psutil (>=3.0)"]
@@ -4731,105 +4777,105 @@ cffi = {version = "*", markers = "implementation_name == \"pypy\""}
 
 [[package]]
 name = "regex"
-version = "2024.9.11"
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 description = "Alternative regular expression module, to replace re."
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 [[package]]
@@ -4905,40 +4951,40 @@ pyasn1 = ">=0.1.3"
 
 [[package]]
 name = "ruff"
-version = "0.8.1"
+version = "0.8.2"
 description = "An extremely fast Python linter and code formatter, written in Rust."
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 [[package]]
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 description = "An Amazon S3 Transfer Manager"
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 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
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 ]
 
 [package.dependencies]
@@ -4991,11 +5041,11 @@ threadpoolctl = ">=3.1.0"
 [package.extras]
 benchmark = ["matplotlib (>=3.3.4)", "memory_profiler (>=0.57.0)", "pandas (>=1.1.5)"]
 build = ["cython (>=3.0.10)", "meson-python (>=0.16.0)", "numpy (>=1.19.5)", "scipy (>=1.6.0)"]
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 examples = ["matplotlib (>=3.3.4)", "pandas (>=1.1.5)", "plotly (>=5.14.0)", "pooch (>=1.6.0)", "scikit-image (>=0.17.2)", "seaborn (>=0.9.0)"]
 install = ["joblib (>=1.2.0)", "numpy (>=1.19.5)", "scipy (>=1.6.0)", "threadpoolctl (>=3.1.0)"]
 maintenance = ["conda-lock (==2.5.6)"]
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+tests = ["black (>=24.3.0)", "matplotlib (>=3.3.4)", "mypy (>=1.9)", "numpydoc (>=1.2.0)", "pandas (>=1.1.5)", "polars (>=0.20.30)", "pooch (>=1.6.0)", "pyamg (>=4.0.0)", "pyarrow (>=12.0.0)", "pytest (>=7.1.2)", "pytest-cov (>=2.9.0)", "ruff (>=0.5.1)", "scikit-image (>=0.17.2)"]
 
 [[package]]
 name = "scipy"
@@ -5041,13 +5091,13 @@ test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeo
 
 [[package]]
 name = "sentry-sdk"
-version = "2.17.0"
+version = "2.19.2"
 description = "Python client for Sentry (https://sentry.io)"
 optional = false
 python-versions = ">=3.6"
 files = [
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 ]
 
 [package.dependencies]
@@ -5073,14 +5123,16 @@ grpcio = ["grpcio (>=1.21.1)", "protobuf (>=3.8.0)"]
 http2 = ["httpcore[http2] (==1.*)"]
 httpx = ["httpx (>=0.16.0)"]
 huey = ["huey (>=2)"]
-huggingface-hub = ["huggingface-hub (>=0.22)"]
+huggingface-hub = ["huggingface_hub (>=0.22)"]
 langchain = ["langchain (>=0.0.210)"]
+launchdarkly = ["launchdarkly-server-sdk (>=9.8.0)"]
 litestar = ["litestar (>=2.0.0)"]
 loguru = ["loguru (>=0.5)"]
 openai = ["openai (>=1.0.0)", "tiktoken (>=0.3.0)"]
+openfeature = ["openfeature-sdk (>=0.7.1)"]
 opentelemetry = ["opentelemetry-distro (>=0.35b0)"]
 opentelemetry-experimental = ["opentelemetry-distro"]
-pure-eval = ["asttokens", "executing", "pure-eval"]
+pure-eval = ["asttokens", "executing", "pure_eval"]
 pymongo = ["pymongo (>=3.1)"]
 pyspark = ["pyspark (>=2.4.4)"]
 quart = ["blinker (>=1.1)", "quart (>=0.16.1)"]
@@ -5093,99 +5145,96 @@ tornado = ["tornado (>=6)"]
 
 [[package]]
 name = "setproctitle"
-version = "1.3.3"
+version = "1.3.4"
 description = "A Python module to customize the process title"
 optional = false
-python-versions = ">=3.7"
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 [package.extras]
@@ -5193,23 +5242,23 @@ test = ["pytest"]
 
 [[package]]
 name = "setuptools"
-version = "75.3.0"
+version = "75.6.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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-core = ["importlib-metadata (>=6)", "importlib-resources (>=5.10.2)", "jaraco.collections", "jaraco.functools", "jaraco.text (>=3.7)", "more-itertools", "more-itertools (>=8.8)", "packaging", "packaging (>=24)", "platformdirs (>=4.2.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)", "ruff (>=0.7.0)"]
+core = ["importlib_metadata (>=6)", "jaraco.collections", "jaraco.functools (>=4)", "jaraco.text (>=3.7)", "more_itertools", "more_itertools (>=8.8)", "packaging", "packaging (>=24.2)", "platformdirs (>=4.2.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"]
 cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
 enabler = ["pytest-enabler (>=2.2)"]
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-type = ["importlib-metadata (>=7.0.2)", "jaraco.develop (>=7.21)", "mypy (==1.12.*)", "pytest-mypy"]
+test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test (>=5.5)", "packaging (>=24.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-home (>=0.5)", "pytest-perf", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel (>=0.44.0)"]
+type = ["importlib_metadata (>=7.0.2)", "jaraco.develop (>=7.21)", "mypy (>=1.12,<1.14)", "pytest-mypy"]
 
 [[package]]
 name = "setuptools-scm"
@@ -5298,36 +5347,34 @@ 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 = [
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 ]
 
 [[package]]
 name = "skops"
-version = "0.10.0"
-description = "A set of tools to push scikit-learn based models to and pull from Hugging Face Hub"
+version = "0.11.0"
+description = "A set of tools, related to machine learning in production."
 optional = false
 python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
 huggingface-hub = ">=0.17.0"
 packaging = ">=17.0"
-scikit-learn = ">=0.24"
+scikit-learn = ">=1.1"
 tabulate = ">=0.8.8"
 
 [package.extras]
-docs = ["fairlearn (>=0.7.0)", "matplotlib (>=3.3)", "numpydoc (>=1.0.0)", "pandas (>=1)", "sphinx (>=3.2.0)", "sphinx-gallery (>=0.7.0)", "sphinx-issues (>=1.2.0)", "sphinx-prompt (>=1.3.0)", "sphinx-rtd-theme (>=1)"]
 rich = ["rich (>=12)"]
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 [[package]]
 name = "slicer"
@@ -5448,51 +5495,82 @@ files = [
 
 [[package]]
 name = "tomli"
-version = "2.0.2"
+version = "2.2.1"
 description = "A lil' TOML parser"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
 name = "tornado"
-version = "6.4.1"
+version = "6.4.2"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
 name = "tqdm"
-version = "4.66.6"
+version = "4.67.1"
 description = "Fast, Extensible Progress Meter"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
 [package.extras]
-dev = ["pytest (>=6)", "pytest-cov", "pytest-timeout", "pytest-xdist"]
+dev = ["nbval", "pytest (>=6)", "pytest-asyncio (>=0.24)", "pytest-cov", "pytest-timeout"]
+discord = ["requests"]
 notebook = ["ipywidgets (>=6)"]
 slack = ["slack-sdk"]
 telegram = ["requests"]
@@ -5514,13 +5592,13 @@ test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,
 
 [[package]]
 name = "typer"
-version = "0.12.5"
+version = "0.15.1"
 description = "Typer, build great CLIs. Easy to code. Based on Python type hints."
 optional = false
 python-versions = ">=3.7"
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 [package.dependencies]
@@ -5531,13 +5609,13 @@ typing-extensions = ">=3.7.4.3"
 
 [[package]]
 name = "typing-extensions"
-version = "4.12.2"
+version = "4.9.0"
 description = "Backported and Experimental Type Hints for Python 3.8+"
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 python-versions = ">=3.8"
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 [[package]]
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 [[package]]
 name = "virtualenv"
-version = "20.27.1"
+version = "20.28.0"
 description = "Virtual Python Environment builder"
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -5641,21 +5719,21 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess
 
 [[package]]
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-version = "0.18.5"
+version = "0.19.0"
 description = "A CLI and library for interacting with the Weights & Biases API."
 optional = false
-python-versions = ">=3.7"
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 ]
 
 [package.dependencies]
@@ -5665,6 +5743,7 @@ gitpython = ">=1.0.0,<3.1.29 || >3.1.29"
 platformdirs = "*"
 protobuf = {version = ">=3.19.0,<4.21.0 || >4.21.0,<5.28.0 || >5.28.0,<6", markers = "python_version > \"3.9\" or sys_platform != \"linux\""}
 psutil = ">=5.0.0"
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 pyyaml = "*"
 requests = ">=2.0.0,<3"
 sentry-sdk = ">=2.0.0"
@@ -5687,41 +5766,41 @@ workspaces = ["wandb-workspaces"]
 
 [[package]]
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+version = "6.0.0"
 description = "Filesystem events monitoring"
 optional = false
 python-versions = ">=3.9"
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 ]
 
 [package.extras]
@@ -5754,81 +5833,76 @@ files = [
 
 [[package]]
 name = "wrapt"
-version = "1.16.0"
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 description = "Module for decorators, wrappers and monkey patching."
 optional = false
-python-versions = ">=3.6"
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+    {file = "yarl-1.18.3-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:88a19f62ff30117e706ebc9090b8ecc79aeb77d0b1f5ec10d2d27a12bc9f66d0"},
+    {file = "yarl-1.18.3-cp313-cp313-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:e17c9361d46a4d5addf777c6dd5eab0715a7684c2f11b88c67ac37edfba6c482"},
+    {file = "yarl-1.18.3-cp313-cp313-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:1a74a13a4c857a84a845505fd2d68e54826a2cd01935a96efb1e9d86c728e186"},
+    {file = "yarl-1.18.3-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:41f7ce59d6ee7741af71d82020346af364949314ed3d87553763a2df1829cc58"},
+    {file = "yarl-1.18.3-cp313-cp313-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:f52a265001d830bc425f82ca9eabda94a64a4d753b07d623a9f2863fde532b53"},
+    {file = "yarl-1.18.3-cp313-cp313-musllinux_1_2_aarch64.whl", hash = "sha256:82123d0c954dc58db301f5021a01854a85bf1f3bb7d12ae0c01afc414a882ca2"},
+    {file = "yarl-1.18.3-cp313-cp313-musllinux_1_2_armv7l.whl", hash = "sha256:2ec9bbba33b2d00999af4631a3397d1fd78290c48e2a3e52d8dd72db3a067ac8"},
+    {file = "yarl-1.18.3-cp313-cp313-musllinux_1_2_i686.whl", hash = "sha256:fbd6748e8ab9b41171bb95c6142faf068f5ef1511935a0aa07025438dd9a9bc1"},
+    {file = "yarl-1.18.3-cp313-cp313-musllinux_1_2_ppc64le.whl", hash = "sha256:877d209b6aebeb5b16c42cbb377f5f94d9e556626b1bfff66d7b0d115be88d0a"},
+    {file = "yarl-1.18.3-cp313-cp313-musllinux_1_2_s390x.whl", hash = "sha256:b464c4ab4bfcb41e3bfd3f1c26600d038376c2de3297760dfe064d2cb7ea8e10"},
+    {file = "yarl-1.18.3-cp313-cp313-musllinux_1_2_x86_64.whl", hash = "sha256:8d39d351e7faf01483cc7ff7c0213c412e38e5a340238826be7e0e4da450fdc8"},
+    {file = "yarl-1.18.3-cp313-cp313-win32.whl", hash = "sha256:61ee62ead9b68b9123ec24bc866cbef297dd266175d53296e2db5e7f797f902d"},
+    {file = "yarl-1.18.3-cp313-cp313-win_amd64.whl", hash = "sha256:578e281c393af575879990861823ef19d66e2b1d0098414855dd367e234f5b3c"},
+    {file = "yarl-1.18.3-cp39-cp39-macosx_10_9_universal2.whl", hash = "sha256:61e5e68cb65ac8f547f6b5ef933f510134a6bf31bb178be428994b0cb46c2a04"},
+    {file = "yarl-1.18.3-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:fe57328fbc1bfd0bd0514470ac692630f3901c0ee39052ae47acd1d90a436719"},
+    {file = "yarl-1.18.3-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:a440a2a624683108a1b454705ecd7afc1c3438a08e890a1513d468671d90a04e"},
+    {file = "yarl-1.18.3-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:09c7907c8548bcd6ab860e5f513e727c53b4a714f459b084f6580b49fa1b9cee"},
+    {file = "yarl-1.18.3-cp39-cp39-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:b4f6450109834af88cb4cc5ecddfc5380ebb9c228695afc11915a0bf82116789"},
+    {file = "yarl-1.18.3-cp39-cp39-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:a9ca04806f3be0ac6d558fffc2fdf8fcef767e0489d2684a21912cc4ed0cd1b8"},
+    {file = "yarl-1.18.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:77a6e85b90a7641d2e07184df5557132a337f136250caafc9ccaa4a2a998ca2c"},
+    {file = "yarl-1.18.3-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:6333c5a377c8e2f5fae35e7b8f145c617b02c939d04110c76f29ee3676b5f9a5"},
+    {file = "yarl-1.18.3-cp39-cp39-musllinux_1_2_aarch64.whl", hash = "sha256:0b3c92fa08759dbf12b3a59579a4096ba9af8dd344d9a813fc7f5070d86bbab1"},
+    {file = "yarl-1.18.3-cp39-cp39-musllinux_1_2_armv7l.whl", hash = "sha256:4ac515b860c36becb81bb84b667466885096b5fc85596948548b667da3bf9f24"},
+    {file = "yarl-1.18.3-cp39-cp39-musllinux_1_2_i686.whl", hash = "sha256:045b8482ce9483ada4f3f23b3774f4e1bf4f23a2d5c912ed5170f68efb053318"},
+    {file = "yarl-1.18.3-cp39-cp39-musllinux_1_2_ppc64le.whl", hash = "sha256:a4bb030cf46a434ec0225bddbebd4b89e6471814ca851abb8696170adb163985"},
+    {file = "yarl-1.18.3-cp39-cp39-musllinux_1_2_s390x.whl", hash = "sha256:54d6921f07555713b9300bee9c50fb46e57e2e639027089b1d795ecd9f7fa910"},
+    {file = "yarl-1.18.3-cp39-cp39-musllinux_1_2_x86_64.whl", hash = "sha256:1d407181cfa6e70077df3377938c08012d18893f9f20e92f7d2f314a437c30b1"},
+    {file = "yarl-1.18.3-cp39-cp39-win32.whl", hash = "sha256:ac36703a585e0929b032fbaab0707b75dc12703766d0b53486eabd5139ebadd5"},
+    {file = "yarl-1.18.3-cp39-cp39-win_amd64.whl", hash = "sha256:ba87babd629f8af77f557b61e49e7c7cac36f22f871156b91e10a6e9d4f829e9"},
+    {file = "yarl-1.18.3-py3-none-any.whl", hash = "sha256:b57f4f58099328dfb26c6a771d09fb20dbbae81d20cfb66141251ea063bd101b"},
+    {file = "yarl-1.18.3.tar.gz", hash = "sha256:ac1801c45cbf77b6c99242eeff4fffb5e4e73a800b5c4ad4fc0be5def634d2e1"},
 ]
 
 [package.dependencies]
@@ -5958,5 +6032,5 @@ propcache = ">=0.2.0"
 
 [metadata]
 lock-version = "2.0"
-python-versions = "^3.10, <3.11"
-content-hash = "b47b8a546db802a97c4656174b4417d844f3af383cf6617b7743c43f7e2a5381"
+python-versions = ">=3.10, <3.11"
+content-hash = "31b6cab2e7afafb35fa84376f0428e6e5b4eabe7a9ca28a7bf197391ab7b8834"
diff --git a/pyproject.toml b/pyproject.toml
index ebdacef7d..4e6c97cb5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,64 +19,63 @@ packages = [{ include = "gentropy", from = "src" }]
 gentropy = "gentropy.cli:main"
 
 [tool.poetry.dependencies]
-python = "^3.10, <3.11"
+python = ">=3.10, <3.11"
 pyspark = "3.3.4"
-scipy = "^1.11.4"
-hydra-core = "^1.3.2"
-pyliftover = "^0.4"
-numpy = "^1.26.2"
+scipy = ">=1.11.4, <1.12.0"
+hydra-core = ">=1.3.2, <1.4.0"
+pyliftover = ">=0.4, <0.5"
+numpy = ">=1.26.2, <1.27.0"
 hail = "0.2.127"
-wandb = ">=0.16.2,<0.19.0"
-google = "^3.0.0"
-omegaconf = "^2.3.0"
-typing-extensions = "^4.9.0"
-scikit-learn = "^1.3.2"
-pandas = { extras = ["gcp", "parquet"], version = "^2.2.2" }
-skops = ">=0.9,<0.11"
-google-cloud-secret-manager = "^2.20.0"
-shap = "^0.46.0"
-matplotlib = "3.7.3"
-
-[tool.poetry.dev-dependencies]
-pre-commit = "^4.0.0"
-mypy = "^1.13"
-pep8-naming = "^0.14.1"
-interrogate = "^1.7.0"
-isort = "^5.13.2"
-darglint = "^1.8.1"
-ruff = "^0.8.1"
+wandb = ">=0.19.0, <0.20.0"
+google = ">=3.0.0, <3.1.0"
+omegaconf = ">=2.3.0, <2.4.0"
+typing-extensions = ">=4.9.0, <4.13.0"
+scikit-learn = ">=1.6.0, <1.7.0"
+pandas = { extras = ["gcp", "parquet"], version = ">=2.2.2, <2.3.0" }
+skops = ">=0.11, <0.12"
+google-cloud-secret-manager = ">=2.20.0, <2.22.0"
+shap = ">=0.46.0, <0.47.0"
+matplotlib = ">=3.7.3, <3.8.0"
+
 
 [tool.poetry.group.docs.dependencies]
-mkdocs = "^1.5.3"
-mkdocstrings-python = "^1.8.0"
+mkdocs = ">=1.5.3, <1.6.0"
+mkdocstrings-python = ">=1.12.2, <1.13.0"
 mkdocs-material = "*"
-mkdocs-section-index = "^0.3.4"
-mkdocs-git-revision-date-localized-plugin = "^1.2.2"
-mkdocs-autolinks-plugin = "^0.7.1"
-mkdocs-awesome-pages-plugin = "^2.9.2"
-mkdocs-exclude = "^1.0.2"
-mkdocs-git-committers-plugin-2 = "^2.2.3"
-lxml = "^5.1.0"
-pymdown-extensions = "^10.7"
+mkdocs-section-index = ">=0.3.4, <0.4.0"
+mkdocs-git-revision-date-localized-plugin = ">=1.2.2, <1.4.0"
+mkdocs-autolinks-plugin = ">=0.7.1, <0.8.0"
+mkdocs-awesome-pages-plugin = ">=2.9.2, <3.0.0"
+mkdocs-exclude = ">=1.0.2, <1.1.0"
+mkdocs-git-committers-plugin-2 = ">=2.2.3, <2.5.0"
+lxml = ">=5.1.0, <5.4.0"
+pymdown-extensions = ">=10.7, <10.13"
 
 
 [tool.poetry.group.tests.dependencies]
 pytest-cov = ">=4.1,<7.0"
 pytest-sugar = ">=0.9.5,<1.1.0"
 dbldatagen = ">=0.3.1,<0.5.0"
-pyparsing = "^3.1.1"
+pyparsing = ">=3.1.1, <3.3.0"
 pytest = ">=7.4.4,<9.0.0"
-pytest-xdist = "^3.5.0"
+pytest-xdist = ">=3.5.0, <3.7.0"
 
 
 [tool.poetry.group.dev.dependencies]
-ipython = "^8.19.0"
-ipykernel = "^6.28.0"
-google-cloud-dataproc = "^5.8.0"
+ipython = ">=8.19.0, <8.31.0"
+ipykernel = ">=6.28.0, <6.30.0"
+google-cloud-dataproc = ">=5.8.0, <5.16.0"
 pydoclint = ">=0.3.8,<0.6.0"
-prettier = "^0.0.7"
+prettier = ">=0.0.7, <0.1.0"
 deptry = ">=0.12,<0.21"
-yamllint = "^1.33.0"
+yamllint = ">=1.33.0, <1.36.0"
+pre-commit = ">=4.0.0, <4.1.0"
+mypy = ">=1.13, <1.14"
+pep8-naming = ">=0.14.1, <0.15.0"
+interrogate = ">=1.7.0, <1.8.0"
+isort = ">=5.13.2, <5.14.0"
+darglint = ">=1.8.1, <1.9.0"
+ruff = ">=0.8.1, <0.9.0"
 
 [tool.semantic_release]
 logging_use_named_masks = true
diff --git a/tests/gentropy/test_imports.py b/tests/gentropy/test_imports.py
new file mode 100644
index 000000000..39ae77b43
--- /dev/null
+++ b/tests/gentropy/test_imports.py
@@ -0,0 +1,27 @@
+"""Test that all modules can be imported. This ensures the lack of major compatibility issues."""
+
+import importlib
+import pkgutil
+
+import gentropy
+
+
+def test_all_modules_are_importable() -> None:
+    """Test that all modules in the gentropy package can be imported."""
+    import_errors = []
+
+    def try_import(module_name: str) -> None:
+        """Given a module name, attempt to import it."""
+        try:
+            importlib.import_module(module_name)
+        except ImportError as e:
+            import_errors.append(f"{module_name}: {str(e)}")
+
+    # Iterate over all modules in Gentropy
+    package = gentropy
+    for _, name, _ in pkgutil.walk_packages(package.__path__, f"{package.__name__}."):
+        try_import(name)
+    if import_errors:
+        raise AssertionError(
+            "The following modules failed to import:\n" + "\n".join(import_errors)
+        )

From 3ae76f89479ed9c5672c1984f88a5bf915198596 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 16 Dec 2024 10:21:14 +0000
Subject: [PATCH 2/7] build(deps-dev): bump ipykernel from 6.28.0 to 6.29.5
 (#953)

Bumps [ipykernel](https://github.com/ipython/ipykernel) from 6.28.0 to 6.29.5.
- [Release notes](https://github.com/ipython/ipykernel/releases)
- [Changelog](https://github.com/ipython/ipykernel/blob/main/CHANGELOG.md)
- [Commits](https://github.com/ipython/ipykernel/compare/v6.28.0...v6.29.5)

---
updated-dependencies:
- dependency-name: ipykernel
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index e9a6b7e00..25176244a 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -888,7 +888,6 @@ files = [
     {file = "cryptography-44.0.0-cp37-abi3-manylinux_2_28_aarch64.whl", hash = "sha256:761817a3377ef15ac23cd7834715081791d4ec77f9297ee694ca1ee9c2c7e5eb"},
     {file = "cryptography-44.0.0-cp37-abi3-manylinux_2_28_x86_64.whl", hash = "sha256:3c672a53c0fb4725a29c303be906d3c1fa99c32f58abe008a82705f9ee96f40b"},
     {file = "cryptography-44.0.0-cp37-abi3-manylinux_2_34_aarch64.whl", hash = "sha256:4ac4c9f37eba52cb6fbeaf5b59c152ea976726b865bd4cf87883a7e7006cc543"},
-    {file = "cryptography-44.0.0-cp37-abi3-manylinux_2_34_x86_64.whl", hash = "sha256:60eb32934076fa07e4316b7b2742fa52cbb190b42c2df2863dbc4230a0a9b385"},
     {file = "cryptography-44.0.0-cp37-abi3-musllinux_1_2_aarch64.whl", hash = "sha256:ed3534eb1090483c96178fcb0f8893719d96d5274dfde98aa6add34614e97c8e"},
     {file = "cryptography-44.0.0-cp37-abi3-musllinux_1_2_x86_64.whl", hash = "sha256:f3f6fdfa89ee2d9d496e2c087cebef9d4fcbb0ad63c40e821b39f74bf48d9c5e"},
     {file = "cryptography-44.0.0-cp37-abi3-win32.whl", hash = "sha256:eb33480f1bad5b78233b0ad3e1b0be21e8ef1da745d8d2aecbb20671658b9053"},
@@ -899,7 +898,6 @@ files = [
     {file = "cryptography-44.0.0-cp39-abi3-manylinux_2_28_aarch64.whl", hash = "sha256:c5eb858beed7835e5ad1faba59e865109f3e52b3783b9ac21e7e47dc5554e289"},
     {file = "cryptography-44.0.0-cp39-abi3-manylinux_2_28_x86_64.whl", hash = "sha256:f53c2c87e0fb4b0c00fa9571082a057e37690a8f12233306161c8f4b819960b7"},
     {file = "cryptography-44.0.0-cp39-abi3-manylinux_2_34_aarch64.whl", hash = "sha256:9e6fc8a08e116fb7c7dd1f040074c9d7b51d74a8ea40d4df2fc7aa08b76b9e6c"},
-    {file = "cryptography-44.0.0-cp39-abi3-manylinux_2_34_x86_64.whl", hash = "sha256:9abcc2e083cbe8dde89124a47e5e53ec38751f0d7dfd36801008f316a127d7ba"},
     {file = "cryptography-44.0.0-cp39-abi3-musllinux_1_2_aarch64.whl", hash = "sha256:d2436114e46b36d00f8b72ff57e598978b37399d2786fd39793c36c6d5cb1c64"},
     {file = "cryptography-44.0.0-cp39-abi3-musllinux_1_2_x86_64.whl", hash = "sha256:a01956ddfa0a6790d594f5b34fc1bfa6098aca434696a03cfdbe469b8ed79285"},
     {file = "cryptography-44.0.0-cp39-abi3-win32.whl", hash = "sha256:eca27345e1214d1b9f9490d200f9db5a874479be914199194e746c893788d417"},
@@ -2033,13 +2031,13 @@ tests = ["coverage[toml]", "pytest", "pytest-cov", "pytest-mock"]
 
 [[package]]
 name = "ipykernel"
-version = "6.28.0"
+version = "6.29.5"
 description = "IPython Kernel for Jupyter"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "ipykernel-6.28.0-py3-none-any.whl", hash = "sha256:c6e9a9c63a7f4095c0a22a79f765f079f9ec7be4f2430a898ddea889e8665661"},
-    {file = "ipykernel-6.28.0.tar.gz", hash = "sha256:69c11403d26de69df02225916f916b37ea4b9af417da0a8c827f84328d88e5f3"},
+    {file = "ipykernel-6.29.5-py3-none-any.whl", hash = "sha256:afdb66ba5aa354b09b91379bac28ae4afebbb30e8b39510c9690afb7a10421b5"},
+    {file = "ipykernel-6.29.5.tar.gz", hash = "sha256:f093a22c4a40f8828f8e330a9c297cb93dcab13bd9678ded6de8e5cf81c56215"},
 ]
 
 [package.dependencies]
@@ -2062,7 +2060,7 @@ cov = ["coverage[toml]", "curio", "matplotlib", "pytest-cov", "trio"]
 docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "trio"]
 pyqt5 = ["pyqt5"]
 pyside6 = ["pyside6"]
-test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio", "pytest-cov", "pytest-timeout"]
+test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.23.5)", "pytest-cov", "pytest-timeout"]
 
 [[package]]
 name = "ipython"

From 2405464c73d9dad19bff72ceac719f291b2ce708 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 16 Dec 2024 11:10:33 +0000
Subject: [PATCH 3/7] build(deps-dev): bump pytest-xdist from 3.5.0 to 3.6.1
 (#952)

Bumps [pytest-xdist](https://github.com/pytest-dev/pytest-xdist) from 3.5.0 to 3.6.1.
- [Release notes](https://github.com/pytest-dev/pytest-xdist/releases)
- [Changelog](https://github.com/pytest-dev/pytest-xdist/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest-xdist/compare/v3.5.0...v3.6.1)

---
updated-dependencies:
- dependency-name: pytest-xdist
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
---
 poetry.lock | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 25176244a..825fe9af0 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -4495,18 +4495,18 @@ dev = ["black", "flake8", "pre-commit"]
 
 [[package]]
 name = "pytest-xdist"
-version = "3.5.0"
+version = "3.6.1"
 description = "pytest xdist plugin for distributed testing, most importantly across multiple CPUs"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
-execnet = ">=1.1"
-pytest = ">=6.2.0"
+execnet = ">=2.1"
+pytest = ">=7.0.0"
 
 [package.extras]
 psutil = ["psutil (>=3.0)"]

From ea7b98338e08230f38923f91d2ae28f220101d4a Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 16 Dec 2024 11:22:49 +0000
Subject: [PATCH 4/7] build(deps-dev): bump lxml from 5.1.1 to 5.3.0 (#950)

Bumps [lxml](https://github.com/lxml/lxml) from 5.1.1 to 5.3.0.
- [Release notes](https://github.com/lxml/lxml/releases)
- [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt)
- [Commits](https://github.com/lxml/lxml/compare/lxml-5.1.1...lxml-5.3.0)

---
updated-dependencies:
- dependency-name: lxml
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock | 216 ++++++++++++++++++++++++++++++++++------------------
 1 file changed, 141 insertions(+), 75 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 825fe9af0..29570e030 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2408,91 +2408,157 @@ files = [
 
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+    {file = "lxml-5.3.0.tar.gz", hash = "sha256:4e109ca30d1edec1ac60cdbe341905dc3b8f55b16855e03a54aaf59e51ec8c6f"},
 ]
 
 [package.extras]
 cssselect = ["cssselect (>=0.7)"]
+html-clean = ["lxml-html-clean"]
 html5 = ["html5lib"]
 htmlsoup = ["BeautifulSoup4"]
-source = ["Cython (>=3.0.9)"]
+source = ["Cython (>=3.0.11)"]
 
 [[package]]
 name = "markdown"

From 3f867a7d3308b3f1f2581afd843f4796588231c0 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 16 Dec 2024 11:34:54 +0000
Subject: [PATCH 5/7] build(deps-dev): bump google-cloud-dataproc from 5.8.0 to
 5.10.1 (#951)

Bumps [google-cloud-dataproc](https://github.com/googleapis/google-cloud-python) from 5.8.0 to 5.10.1.
- [Release notes](https://github.com/googleapis/google-cloud-python/releases)
- [Changelog](https://github.com/googleapis/google-cloud-python/blob/main/packages/google-cloud-documentai/CHANGELOG.md)
- [Commits](https://github.com/googleapis/google-cloud-python/compare/google-cloud-dataproc-v5.8.0...google-cloud-dataproc-v5.10.1)

---
updated-dependencies:
- dependency-name: google-cloud-dataproc
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 poetry.lock | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 29570e030..d162df5b2 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1610,20 +1610,21 @@ grpc = ["grpcio (>=1.38.0,<2.0dev)", "grpcio-status (>=1.38.0,<2.0.dev0)"]
 
 [[package]]
 name = "google-cloud-dataproc"
-version = "5.8.0"
+version = "5.15.1"
 description = "Google Cloud Dataproc API client library"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "google-cloud-dataproc-5.8.0.tar.gz", hash = "sha256:b03412dd63cb84dc0bb0844cd9e9a9eef40e1d0d719649659052cccf0d3e95d7"},
-    {file = "google_cloud_dataproc-5.8.0-py2.py3-none-any.whl", hash = "sha256:1b3dd086d8ee7d1055b93230338a93091e77aca167cf7e32edc0b92e8288667d"},
+    {file = "google_cloud_dataproc-5.15.1-py2.py3-none-any.whl", hash = "sha256:c89dde89d3d70bcc0aa37d0da8734f7ec27bfae46e05e6fe56cb6d340b880910"},
+    {file = "google_cloud_dataproc-5.15.1.tar.gz", hash = "sha256:ab7b3806a905c50dd64ceb5a854b1dcdc8ddcea092aaf7162083fdfd2e1943aa"},
 ]
 
 [package.dependencies]
-google-api-core = {version = ">=1.34.0,<2.0.dev0 || >=2.11.dev0,<3.0.0dev", extras = ["grpc"]}
+google-api-core = {version = ">=1.34.1,<2.0.dev0 || >=2.11.dev0,<3.0.0dev", extras = ["grpc"]}
+google-auth = ">=2.14.1,<2.24.0 || >2.24.0,<2.25.0 || >2.25.0,<3.0.0dev"
 grpc-google-iam-v1 = ">=0.12.4,<1.0.0dev"
 proto-plus = ">=1.22.3,<2.0.0dev"
-protobuf = ">=3.19.5,<3.20.0 || >3.20.0,<3.20.1 || >3.20.1,<4.21.0 || >4.21.0,<4.21.1 || >4.21.1,<4.21.2 || >4.21.2,<4.21.3 || >4.21.3,<4.21.4 || >4.21.4,<4.21.5 || >4.21.5,<5.0.0dev"
+protobuf = ">=3.20.2,<4.21.0 || >4.21.0,<4.21.1 || >4.21.1,<4.21.2 || >4.21.2,<4.21.3 || >4.21.3,<4.21.4 || >4.21.4,<4.21.5 || >4.21.5,<6.0.0dev"
 
 [[package]]
 name = "google-cloud-secret-manager"

From bc4727213328798b88cf73d51df7eaa27ff5e2b9 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 16 Dec 2024 11:37:10 +0000
Subject: [PATCH 6/7] build(deps-dev): bump ipython from 8.29.0 to 8.30.0

Bumps [ipython](https://github.com/ipython/ipython) from 8.29.0 to 8.30.0.
- [Release notes](https://github.com/ipython/ipython/releases)
- [Commits](https://github.com/ipython/ipython/compare/8.29.0...8.30.0)

---
updated-dependencies:
- dependency-name: ipython
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 poetry.lock | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index d162df5b2..d5e3b3696 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2065,13 +2065,13 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio
 
 [[package]]
 name = "ipython"
-version = "8.29.0"
+version = "8.30.0"
 description = "IPython: Productive Interactive Computing"
 optional = false
 python-versions = ">=3.10"
 files = [
-    {file = "ipython-8.29.0-py3-none-any.whl", hash = "sha256:0188a1bd83267192123ccea7f4a8ed0a78910535dbaa3f37671dca76ebd429c8"},
-    {file = "ipython-8.29.0.tar.gz", hash = "sha256:40b60e15b22591450eef73e40a027cf77bd652e757523eebc5bd7c7c498290eb"},
+    {file = "ipython-8.30.0-py3-none-any.whl", hash = "sha256:85ec56a7e20f6c38fce7727dcca699ae4ffc85985aa7b23635a8008f918ae321"},
+    {file = "ipython-8.30.0.tar.gz", hash = "sha256:cb0a405a306d2995a5cbb9901894d240784a9f341394c6ba3f4fe8c6eb89ff6e"},
 ]
 
 [package.dependencies]
@@ -2081,16 +2081,16 @@ exceptiongroup = {version = "*", markers = "python_version < \"3.11\""}
 jedi = ">=0.16"
 matplotlib-inline = "*"
 pexpect = {version = ">4.3", markers = "sys_platform != \"win32\" and sys_platform != \"emscripten\""}
-prompt-toolkit = ">=3.0.41,<3.1.0"
+prompt_toolkit = ">=3.0.41,<3.1.0"
 pygments = ">=2.4.0"
-stack-data = "*"
+stack_data = "*"
 traitlets = ">=5.13.0"
-typing-extensions = {version = ">=4.6", markers = "python_version < \"3.12\""}
+typing_extensions = {version = ">=4.6", markers = "python_version < \"3.12\""}
 
 [package.extras]
 all = ["ipython[black,doc,kernel,matplotlib,nbconvert,nbformat,notebook,parallel,qtconsole]", "ipython[test,test-extra]"]
 black = ["black"]
-doc = ["docrepr", "exceptiongroup", "intersphinx-registry", "ipykernel", "ipython[test]", "matplotlib", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "sphinxcontrib-jquery", "tomli", "typing-extensions"]
+doc = ["docrepr", "exceptiongroup", "intersphinx_registry", "ipykernel", "ipython[test]", "matplotlib", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "sphinxcontrib-jquery", "tomli", "typing_extensions"]
 kernel = ["ipykernel"]
 matplotlib = ["matplotlib"]
 nbconvert = ["nbconvert"]

From 4820e655fa6715dae5c6d0e9af81c86b3b4bbd10 Mon Sep 17 00:00:00 2001
From: Szymon Szyszkowski <69353402+project-defiant@users.noreply.github.com>
Date: Mon, 16 Dec 2024 13:11:26 +0100
Subject: [PATCH 7/7] refactor: drop version_engine (#940)

* refactor: drop use_version_from_input flag

* chore: drop version engine

---------

Co-authored-by: project-defiant <szymonszyszkowski@gmail.com>
Co-authored-by: Szymon Szyszkowski <ss60@mib117351s.internal.sanger.ac.uk>
Co-authored-by: Daniel Suveges <daniel.suveges@protonmail.com>
---
 docs/python_api/common/version_engine.md     |  12 --
 src/gentropy/common/version_engine.py        | 158 -------------------
 src/gentropy/config.py                       |  30 ++--
 src/gentropy/gnomad_ingestion.py             |  22 +--
 tests/gentropy/common/test_version_engine.py | 115 --------------
 5 files changed, 20 insertions(+), 317 deletions(-)
 delete mode 100644 docs/python_api/common/version_engine.md
 delete mode 100644 src/gentropy/common/version_engine.py
 delete mode 100644 tests/gentropy/common/test_version_engine.py

diff --git a/docs/python_api/common/version_engine.md b/docs/python_api/common/version_engine.md
deleted file mode 100644
index 28d9b4b2e..000000000
--- a/docs/python_api/common/version_engine.md
+++ /dev/null
@@ -1,12 +0,0 @@
----
-title: VersionEngine
----
-
-**VersionEngine**:
-
-Version engine allows for registering datasource specific version seeker class to retrieve datasource version used as input to gentropy steps. Currently implemented only for GnomAD datasource.
-
-This class can be then used to produce automation over output directory versioning.
-
-:::gentropy.common.version_engine.VersionEngine
-:::gentropy.common.version_engine.GnomADVersionSeeker
diff --git a/src/gentropy/common/version_engine.py b/src/gentropy/common/version_engine.py
deleted file mode 100644
index d852d8f5d..000000000
--- a/src/gentropy/common/version_engine.py
+++ /dev/null
@@ -1,158 +0,0 @@
-"""Mechanism to seek version from specific datasource."""
-
-from __future__ import annotations
-
-import re
-from abc import ABC, abstractmethod
-from pathlib import Path
-from typing import Callable
-
-from gentropy.common.types import DataSourceType
-
-
-class VersionEngine:
-    """Seek version from the datasource."""
-
-    def __init__(self, datasource: DataSourceType) -> None:
-        """Initialize VersionEngine.
-
-        Args:
-            datasource (DataSourceType): datasource to seek the version from
-        """
-        self.datasource = datasource
-
-    @staticmethod
-    def version_seekers() -> dict[DataSourceType, DatasourceVersionSeeker]:
-        """List version seekers.
-
-        Returns:
-            dict[DataSourceType, DatasourceVersionSeeker]: list of available data sources.
-        """
-        return {
-            "gnomad": GnomADVersionSeeker(),
-        }
-
-    def seek(self, text: str | Path) -> str:
-        """Interface for inferring the version from text by using registered data source version iner method.
-
-        Args:
-            text (str | Path): text to seek version from
-
-        Returns:
-            str: inferred version
-
-        Raises:
-            TypeError: if version can not be found in the text
-
-        Examples:
-            >>> VersionEngine("gnomad").seek("gs://gcp-public-data--gnomad/release/2.1.1/vcf/genomes/gnomad.genomes.r2.1.1.sites.vcf.bgz")
-            '2.1.1'
-        """
-        match text:
-            case Path() | str():
-                text = str(text)
-            case _:
-                msg = f"Can not find version in {text}"
-                raise TypeError(msg)
-        infer_method = self._get_version_seek_method()
-        return infer_method(text)
-
-    def _get_version_seek_method(self) -> Callable[[str], str]:
-        """Method that gets the version seeker for the datasource.
-
-        Returns:
-            Callable[[str], str]: Method to seek version based on the initialized datasource
-
-        Raises:
-            ValueError: if datasource is not registered in the list of version seekers
-        """
-        if self.datasource not in self.version_seekers():
-            raise ValueError(f"Invalid datasource {self.datasource}")
-        return self.version_seekers()[self.datasource].seek_version
-
-    def amend_version(
-        self, analysis_input_path: str | Path, analysis_output_path: str | Path
-    ) -> str:
-        """Amend version to the analysis output path if it is not already present.
-
-        Path can be path to g3:// or Path object, absolute or relative.
-        The analysis_input_path has to contain the version number.
-        If the analysis_output_path contains the same version as inferred from input version already,
-        then it will not be appended.
-
-        Args:
-            analysis_input_path (str | Path): step input path
-            analysis_output_path (str | Path): step output path
-
-        Returns:
-            str: Path with the ammended version, does not return Path object!
-
-        Examples:
-            >>> VersionEngine("gnomad").amend_version("gs://gcp-public-data--gnomad/release/2.1.1/vcf/genomes/gnomad.genomes.r2.1.1.sites.vcf.bgz", "/some/path/without/version")
-            '/some/path/without/version/2.1.1'
-        """
-        version = self.seek(analysis_input_path)
-        output_path = str(analysis_output_path)
-        if version in output_path:
-            return output_path
-        if output_path.endswith("/"):
-            return f"{analysis_output_path}{version}"
-        return f"{analysis_output_path}/{version}"
-
-
-class DatasourceVersionSeeker(ABC):
-    """Interface for datasource version seeker.
-
-    Raises:
-        NotImplementedError: if method is not implemented in the subclass
-    """
-
-    @staticmethod
-    @abstractmethod
-    def seek_version(text: str) -> str:
-        """Seek version from text. Implement this method in the subclass.
-
-        Args:
-            text (str): text to seek version from
-
-        Returns:
-            str: seeked version
-
-        Raises:
-            NotImplementedError: if method is not implemented in the subclass
-
-        """
-        raise NotImplementedError
-
-
-class GnomADVersionSeeker(DatasourceVersionSeeker):
-    """Seek version from GnomAD datasource."""
-
-    @staticmethod
-    def seek_version(text: str) -> str:
-        """Seek GnomAD version from provided text by using regex.
-
-        Up to 3 digits are allowed in the version number.
-        Historically gnomAD version numbers have been in the format
-        2.1.1, 3.1, etc. as of 2024-05. GnomAD versions can be found by
-        running `"gs://gcp-public-data--gnomad/release/*/*/*"`
-
-        Args:
-            text (str): text to seek version from
-
-        Raises:
-            ValueError: if version can not be seeked
-
-        Returns:
-            str: seeked version
-
-        Examples:
-            >>> GnomADVersionSeeker.seek_version("gs://gcp-public-data--gnomad/release/2.1.1/vcf/genomes/gnomad.genomes.r2.1.1.sites.vcf.bgz")
-            '2.1.1'
-        """
-        result = re.search(r"v?((\d+){1}\.(\d+){1}\.?(\d+)?)", text)
-        match result:
-            case None:
-                raise ValueError(f"No GnomAD version found in provided text: {text}")
-            case _:
-                return result.group(1)
diff --git a/src/gentropy/config.py b/src/gentropy/config.py
index 9c454d41b..0d9d6abf1 100644
--- a/src/gentropy/config.py
+++ b/src/gentropy/config.py
@@ -17,7 +17,8 @@ class SessionConfig:
     write_mode: str = "errorifexists"
     spark_uri: str = "local[*]"
     hail_home: str = os.path.dirname(hail_location)
-    extended_spark_conf: dict[str, str] | None = field(default_factory=dict[str, str])
+    extended_spark_conf: dict[str, str] | None = field(
+        default_factory=dict[str, str])
     output_partitions: int = 200
     _target_: str = "gentropy.common.session.Session"
 
@@ -39,7 +40,8 @@ class ColocalisationConfig(StepConfig):
     credible_set_path: str = MISSING
     coloc_path: str = MISSING
     colocalisation_method: str = MISSING
-    colocalisation_method_params: dict[str, Any] = field(default_factory=dict[str, Any])
+    colocalisation_method_params: dict[str, Any] = field(
+        default_factory=dict[str, Any])
     _target_: str = "gentropy.colocalisation.ColocalisationStep"
 
 
@@ -124,7 +126,8 @@ class EqtlCatalogueConfig(StepConfig):
     eqtl_catalogue_paths_imported: str = MISSING
     eqtl_catalogue_study_index_out: str = MISSING
     eqtl_catalogue_credible_sets_out: str = MISSING
-    mqtl_quantification_methods_blacklist: list[str] = field(default_factory=lambda: [])
+    mqtl_quantification_methods_blacklist: list[str] = field(
+        default_factory=lambda: [])
     eqtl_lead_pvalue_threshold: float = 1e-3
     _target_: str = "gentropy.eqtl_catalogue.EqtlCatalogueStep"
 
@@ -146,7 +149,8 @@ class FinngenStudiesConfig(StepConfig):
     )
     finngen_summary_stats_url_suffix: str = ".gz"
     efo_curation_mapping_url: str = "https://raw.githubusercontent.com/opentargets/curation/24.09.1/mappings/disease/manual_string.tsv"
-    sample_size: int = 453733  # https://www.finngen.fi/en/access_results#:~:text=Total%20sample%20size%3A%C2%A0453%2C733%C2%A0(254%2C618%C2%A0females%20and%C2%A0199%2C115%20males)
+    # https://www.finngen.fi/en/access_results#:~:text=Total%20sample%20size%3A%C2%A0453%2C733%C2%A0(254%2C618%C2%A0females%20and%C2%A0199%2C115%20males)
+    sample_size: int = 453733
     _target_: str = "gentropy.finngen_studies.FinnGenStudiesStep"
 
 
@@ -199,7 +203,6 @@ class LDIndexConfig(StepConfig):
             "nfe",  # Non-Finnish European
         ]
     )
-    use_version_from_input: bool = False
     _target_: str = "gentropy.gnomad_ingestion.LDIndexStep"
 
 
@@ -409,7 +412,6 @@ class GnomadVariantConfig(StepConfig):
             "remaining",  # Other
         ]
     )
-    use_version_from_input: bool = False
     _target_: str = "gentropy.gnomad_ingestion.GnomadVariantIndexStep"
 
 
@@ -432,7 +434,6 @@ class PanUKBBConfig(StepConfig):
             "EUR",  # European
         ]
     )
-    use_version_from_input: bool = False
     _target_: str = "gentropy.pan_ukb_ingestion.PanUKBBVariantIndexStep"
 
 
@@ -680,7 +681,8 @@ class Config:
     """Application configuration."""
 
     # this is unfortunately verbose due to @dataclass limitations
-    defaults: List[Any] = field(default_factory=lambda: ["_self_", {"step": MISSING}])
+    defaults: List[Any] = field(default_factory=lambda: [
+                                "_self_", {"step": MISSING}])
     step: StepConfig = MISSING
     datasets: dict[str, str] = field(default_factory=dict)
 
@@ -714,7 +716,8 @@ def register_config() -> None:
         name="gwas_catalog_top_hit_ingestion",
         node=GWASCatalogTopHitIngestionConfig,
     )
-    cs.store(group="step", name="ld_based_clumping", node=LDBasedClumpingConfig)
+    cs.store(group="step", name="ld_based_clumping",
+             node=LDBasedClumpingConfig)
     cs.store(group="step", name="ld_index", node=LDIndexConfig)
     cs.store(group="step", name="locus_to_gene", node=LocusToGeneConfig)
     cs.store(
@@ -732,7 +735,8 @@ def register_config() -> None:
 
     cs.store(group="step", name="pics", node=PICSConfig)
     cs.store(group="step", name="gnomad_variants", node=GnomadVariantConfig)
-    cs.store(group="step", name="ukb_ppp_eur_sumstat_preprocess", node=UkbPppEurConfig)
+    cs.store(group="step", name="ukb_ppp_eur_sumstat_preprocess",
+             node=UkbPppEurConfig)
     cs.store(group="step", name="variant_index", node=VariantIndexConfig)
     cs.store(group="step", name="variant_to_vcf", node=ConvertToVcfStepConfig)
     cs.store(
@@ -765,5 +769,7 @@ def register_config() -> None:
         name="locus_to_gene_associations",
         node=LocusToGeneAssociationsStepConfig,
     )
-    cs.store(group="step", name="finngen_ukb_meta_ingestion", node=FinngenUkbMetaConfig)
-    cs.store(group="step", name="credible_set_qc", node=CredibleSetQCStepConfig)
+    cs.store(group="step", name="finngen_ukb_meta_ingestion",
+             node=FinngenUkbMetaConfig)
+    cs.store(group="step", name="credible_set_qc",
+             node=CredibleSetQCStepConfig)
diff --git a/src/gentropy/gnomad_ingestion.py b/src/gentropy/gnomad_ingestion.py
index d930b54c6..e0960c8f7 100644
--- a/src/gentropy/gnomad_ingestion.py
+++ b/src/gentropy/gnomad_ingestion.py
@@ -4,7 +4,6 @@
 
 from gentropy.common.session import Session
 from gentropy.common.types import LD_Population, VariantPopulation
-from gentropy.common.version_engine import VersionEngine
 from gentropy.config import GnomadVariantConfig, LDIndexConfig
 from gentropy.datasource.gnomad.ld import GnomADLDMatrix
 from gentropy.datasource.gnomad.variants import GnomADVariants
@@ -26,10 +25,10 @@ def __init__(
         min_r2: float = LDIndexConfig().min_r2,
         ld_matrix_template: str = LDIndexConfig().ld_matrix_template,
         ld_index_raw_template: str = LDIndexConfig().ld_index_raw_template,
-        ld_populations: list[LD_Population | str] = LDIndexConfig().ld_populations,
+        ld_populations: list[LD_Population |
+                             str] = LDIndexConfig().ld_populations,
         liftover_ht_path: str = LDIndexConfig().liftover_ht_path,
         grch37_to_grch38_chain_path: str = LDIndexConfig().grch37_to_grch38_chain_path,
-        use_version_from_input: bool = LDIndexConfig().use_version_from_input,
     ) -> None:
         """Run step.
 
@@ -42,17 +41,9 @@ def __init__(
             ld_populations (list[LD_Population | str]): Population names derived from the ld file paths
             liftover_ht_path (str): Path to the liftover ht file
             grch37_to_grch38_chain_path (str): Path to the chain file used to lift over the coordinates.
-            use_version_from_input (bool): Append version derived from input ld_matrix_template to the output ld_index_out. Defaults to False.
 
-        In case use_version_from_input is set to True,
-        data source version inferred from ld_matrix_temolate is appended as the last path segment to the output path.
         Default values are provided in LDIndexConfig.
         """
-        if use_version_from_input:
-            # amend data source version to output path
-            ld_index_out = VersionEngine("gnomad").amend_version(
-                ld_matrix_template, ld_index_out
-            )
         (
             GnomADLDMatrix(
                 ld_matrix_template=ld_matrix_template,
@@ -84,7 +75,6 @@ def __init__(
         gnomad_variant_populations: list[
             VariantPopulation | str
         ] = GnomadVariantConfig().gnomad_variant_populations,
-        use_version_from_input: bool = GnomadVariantConfig().use_version_from_input,
     ) -> None:
         """Run Variant Annotation step.
 
@@ -93,18 +83,10 @@ def __init__(
             variant_annotation_path (str): Path to resulting dataset.
             gnomad_genomes_path (str): Path to gnomAD genomes hail table, e.g. `gs://gcp-public-data--gnomad/release/4.0/ht/genomes/gnomad.genomes.v4.0.sites.ht/`.
             gnomad_variant_populations (list[VariantPopulation | str]): List of populations to include.
-            use_version_from_input (bool): Append version derived from input gnomad_genomes_path to the output variant_annotation_path. Defaults to False.
 
-        In case use_version_from_input is set to True,
-        data source version inferred from gnomad_genomes_path is appended as the last path segment to the output path.
         All defaults are stored in the GnomadVariantConfig.
         """
         # amend data source version to output path
-        if use_version_from_input:
-            variant_annotation_path = VersionEngine("gnomad").amend_version(
-                gnomad_genomes_path, variant_annotation_path
-            )
-
         session.logger.info("Gnomad variant annotation path:")
         session.logger.info(variant_annotation_path)
         # Parse variant info from source.
diff --git a/tests/gentropy/common/test_version_engine.py b/tests/gentropy/common/test_version_engine.py
deleted file mode 100644
index 2ee2e12ce..000000000
--- a/tests/gentropy/common/test_version_engine.py
+++ /dev/null
@@ -1,115 +0,0 @@
-"""Tests version engine class."""
-
-from __future__ import annotations
-
-from pathlib import Path
-
-import pytest
-
-from gentropy.common.version_engine import GnomADVersionSeeker, VersionEngine
-
-
-@pytest.mark.parametrize(
-    ["text", "version"],
-    [
-        pytest.param(
-            "gcp-public-data--gnomad/release/2.1.1/vcf/genomes/gnomad.genomes.r2.1.1.sites.7.vcf",
-            "2.1.1",
-            id="GnomAD v2.1.1",
-        ),
-        pytest.param(
-            "/gcp-public-data--gnomad/release/3.0/vcf/genomes/gnomad.genomes.r3.0.sites.chr6.vcf",
-            "3.0",
-            id="GnomAD v3.0",
-        ),
-        pytest.param(
-            "gs://gcp-public-data--gnomad/release/3.1.1/vcf/genomes/gnomad.genomes.v3.1.1.sites.chr1.vcf",
-            "3.1.1",
-            id="GnomAD v3.1.1",
-        ),
-        pytest.param(
-            "gs://gcp-public-data--gnomad/release/3.1.2/vcf/genomes/gnomad.genomes.v3.1.2.sites.chrY.vcf",
-            "3.1.2",
-            id="GnomAD v3.1.2",
-        ),
-        pytest.param(
-            "gsa://gcp-public-data--gnomad/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chrY.vcf",
-            "4.0",
-            id="GnomAD v4.0",
-        ),
-        pytest.param(
-            "gs://gcp-public-data--gnomad/release/4.1/vcf/genomes/gnomad.genomes.v4.1.sites.chr18.vcf",
-            "4.1",
-            id="GnomAD v4.1",
-        ),
-        pytest.param(
-            "/some/path/to/the/version/r20.111.44",
-            "20.111.44",
-            id="Extreme version number",
-        ),
-    ],
-)
-def test_extracting_version_with_gnomad_seeker(text: str, version: str) -> None:
-    """Test gnomad version extraction with GnomADVersionSeeker."""
-    version_seeker = GnomADVersionSeeker().seek_version
-    assert version_seeker(text) == version
-
-
-def test_not_registered_datasource_raises_error() -> None:
-    """Test that unknown datasource raises error."""
-    with pytest.raises(ValueError) as e:
-        VersionEngine("ClinVar").seek("some/path/to/the/version/v20.111.44")  # type: ignore
-        assert e.value.args[0].startswith("Invalid datasource ClinVar")
-
-
-def test_extracting_version_when_no_version_is_found() -> None:
-    """Test that unknown datasource raises error."""
-    with pytest.raises(ValueError) as e:
-        VersionEngine("ClinVar").seek("some/path/without/version")  # type: ignore
-        assert e.value.args[0].startswith(
-            "Can not find version in some/path/without/version"
-        )
-
-
-def test_non_string_path_raises_error() -> None:
-    """Test that non-string path raises error."""
-    with pytest.raises(TypeError) as e:
-        VersionEngine("gnomad").seek(123)  # type: ignore
-        assert e.value.args[0].startswith("Can not infer version from 123")
-
-
-@pytest.mark.parametrize(
-    ["text", "version"],
-    [
-        pytest.param(Path("some/file/path/v3.1.1"), "3.1.1", id="Path object"),
-        pytest.param("s3://some/file/path/v3.1.1", "3.1.1", id="S3 protocol"),
-        pytest.param("gs://some/file/path/v3.1.1", "3.1.1", id="GS protocol"),
-    ],
-)
-def test_extracting_version_with_version_engine(text: str | Path, version: str) -> None:
-    """Check if concrete data types and file protocols does not return an error while passed to VersionEngine."""
-    assert VersionEngine("gnomad").seek(text) == version
-
-
-@pytest.mark.parametrize(
-    ["input_path", "output_path", "expected_output"],
-    [
-        pytest.param(
-            "input/v20.111.44", "output", "output/20.111.44", id="Append version"
-        ),
-        pytest.param(
-            "input/1.0.0",
-            "output/1.0.0",
-            "output/1.0.0",
-            id="Do not append version, already present",
-        ),
-        pytest.param(
-            Path("input/1.0.0"), Path("output/"), "output/1.0.0", id="Path objects"
-        ),
-    ],
-)
-def test_appending_version_to_path(
-    input_path: Path | str, output_path: Path | str, expected_output: str
-) -> None:
-    """Test that the version is ammended at the end of the output path."""
-    VersionEngine("gnomad").amend_version(input_path, output_path) == expected_output