From 0a958f8fae5d4fa218773d25950dc7c06275a337 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Irene=20L=C3=B3pez=20Santiago?= <45119610+ireneisdoomed@users.noreply.github.com> Date: Tue, 14 Jan 2025 12:28:43 +0000 Subject: [PATCH] chore: update poetry to version 2 (#969) * fix: `poetry shell` is deprecated * chore: update versionin precommit hook * chore: update versionin precommit hook * chore: migrate toml * chore: update version in dockerfile * chore: pre-commit auto fixes [...] * chore: do not use typing deprecated classes according to ruff * build: update `deptry` * build: update `deptry` --- .pre-commit-config.yaml | 3 +- Dockerfile | 2 +- poetry.lock | 308 +++++++++++++++++- pyproject.toml | 58 ++-- src/gentropy/colocalisation.py | 9 +- src/gentropy/common/spark_helpers.py | 3 +- src/gentropy/config.py | 28 +- src/gentropy/dataset/l2g_feature_matrix.py | 4 +- src/gentropy/dataset/l2g_gold_standard.py | 4 +- src/gentropy/dataset/l2g_prediction.py | 4 +- .../datasource/gwas_catalog/study_splitter.py | 6 +- .../open_targets/l2g_gold_standard.py | 6 +- src/gentropy/method/l2g/feature_factory.py | 3 +- src/gentropy/method/l2g/model.py | 6 +- .../finngen/test_finngen_study_index.py | 2 +- .../gentropy/step/test_colocalisation_step.py | 3 +- tests/gentropy/test_cli.py | 12 +- utils/install_dependencies.sh | 3 - 18 files changed, 364 insertions(+), 100 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 5bf5e6239..ddcee97c4 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -103,8 +103,7 @@ repos: - id: pydoclint - repo: https://github.com/python-poetry/poetry - rev: "1.8.0" + rev: "2.0.0" hooks: - id: poetry-check - id: poetry-lock - args: ["--no-update"] diff --git a/Dockerfile b/Dockerfile index ff8706b62..6a66c53ef 100644 --- a/Dockerfile +++ b/Dockerfile @@ -11,7 +11,7 @@ ENV POETRY_NO_INTERACTION=1 \ POETRY_CACHE_DIR=/tmp/poetry_cache \ JAVA_HOME=/usr -RUN pip install poetry==1.7.1 +RUN pip install poetry>=2.0.0 WORKDIR /app COPY pyproject.toml poetry.lock ./ diff --git a/poetry.lock b/poetry.lock index d5e3b3696..9044db42a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.0.0 and should not be changed by hand. [[package]] name = "aiodns" @@ -6,6 +6,7 @@ version = "2.0.0" description = "Simple DNS resolver for asyncio" optional = false python-versions = "*" +groups = ["main"] files = [ {file = "aiodns-2.0.0-py2.py3-none-any.whl", hash = "sha256:aaa5ac584f40fe778013df0aa6544bf157799bd3f608364b451840ed2c8688de"}, {file = "aiodns-2.0.0.tar.gz", hash = "sha256:815fdef4607474295d68da46978a54481dd1e7be153c7d60f9e72773cd38d77d"}, @@ -20,6 +21,7 @@ version = "2.4.4" description = "Happy Eyeballs for asyncio" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "aiohappyeyeballs-2.4.4-py3-none-any.whl", hash = "sha256:a980909d50efcd44795c4afeca523296716d50cd756ddca6af8c65b996e27de8"}, {file = "aiohappyeyeballs-2.4.4.tar.gz", hash = "sha256:5fdd7d87889c63183afc18ce9271f9b0a7d32c2303e394468dd45d514a757745"}, @@ -31,6 +33,7 @@ version = "3.11.10" description = "Async http client/server framework (asyncio)" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "aiohttp-3.11.10-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:cbad88a61fa743c5d283ad501b01c153820734118b65aee2bd7dbb735475ce0d"}, {file = "aiohttp-3.11.10-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:80886dac673ceaef499de2f393fc80bb4481a129e6cb29e624a12e3296cc088f"}, @@ -129,6 +132,7 @@ version = "1.3.1" description = "aiosignal: a list of registered asynchronous callbacks" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "aiosignal-1.3.1-py3-none-any.whl", hash = "sha256:f8376fb07dd1e86a584e4fcdec80b36b7f81aac666ebc724e2c090300dd83b17"}, {file = "aiosignal-1.3.1.tar.gz", hash = "sha256:54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc"}, @@ -143,6 +147,7 @@ version = "0.7.0" description = "Reusable constraint types to use with typing.Annotated" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, @@ -154,6 +159,7 @@ version = "4.9.3" description = "ANTLR 4.9.3 runtime for Python 3.7" optional = false python-versions = "*" +groups = ["main"] files = [ {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"}, ] @@ -164,6 +170,8 @@ version = "0.1.4" description = "Disable App Nap on macOS >= 10.9" optional = false python-versions = ">=3.6" +groups = ["dev"] +markers = "platform_system == \"Darwin\"" files = [ {file = "appnope-0.1.4-py2.py3-none-any.whl", hash = "sha256:502575ee11cd7a28c0205f379b525beefebab9d161b7c964670864014ed7213c"}, {file = "appnope-0.1.4.tar.gz", hash = "sha256:1de3860566df9caf38f01f86f65e0e13e379af54f9e4bee1e66b48f2efffd1ee"}, @@ -175,6 +183,7 @@ version = "3.0.0" description = "Annotate AST trees with source code positions" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "asttokens-3.0.0-py3-none-any.whl", hash = "sha256:e3078351a059199dd5138cb1c706e6430c05eff2ff136af5eb4790f9d28932e2"}, {file = "asttokens-3.0.0.tar.gz", hash = "sha256:0dcd8baa8d62b0c1d118b399b2ddba3c4aff271d0d7a9e0d4c1681c79035bbc7"}, @@ -190,6 +199,7 @@ version = "5.0.1" description = "Timeout context manager for asyncio programs" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "async_timeout-5.0.1-py3-none-any.whl", hash = "sha256:39e3809566ff85354557ec2398b55e096c8364bacac9405a7a1fa429e77fe76c"}, {file = "async_timeout-5.0.1.tar.gz", hash = "sha256:d9321a7a3d5a6a5e187e824d2fa0793ce379a202935782d555d6e9d2735677d3"}, @@ -201,6 +211,7 @@ version = "24.2.0" description = "Classes Without Boilerplate" optional = false python-versions = ">=3.7" +groups = ["main", "dev"] files = [ {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"}, {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"}, @@ -220,6 +231,7 @@ version = "1.11.3" description = "Avro is a serialization and RPC framework." optional = false python-versions = ">=3.6" +groups = ["main"] files = [ {file = "avro-1.11.3.tar.gz", hash = "sha256:3393bb5139f9cf0791d205756ce1e39a5b58586af5b153d6a3b5a199610e9d17"}, ] @@ -234,6 +246,7 @@ version = "1.1.28" description = "Microsoft Azure Client Library for Python (Common)" optional = false python-versions = "*" +groups = ["main"] files = [ {file = "azure-common-1.1.28.zip", hash = "sha256:4ac0cd3214e36b6a1b6a442686722a5d8cc449603aa833f3f0f40bda836704a3"}, {file = "azure_common-1.1.28-py2.py3-none-any.whl", hash = "sha256:5c12d3dcf4ec20599ca6b0d3e09e86e146353d443e7fcc050c9a19c1f9df20ad"}, @@ -245,6 +258,7 @@ version = "1.32.0" description = "Microsoft Azure Core Library for Python" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "azure_core-1.32.0-py3-none-any.whl", hash = "sha256:eac191a0efb23bfa83fddf321b27b122b4ec847befa3091fa736a5c32c50d7b4"}, {file = "azure_core-1.32.0.tar.gz", hash = "sha256:22b3c35d6b2dae14990f6c1be2912bf23ffe50b220e708a28ab1bb92b1c730e5"}, @@ -264,6 +278,7 @@ version = "1.19.0" description = "Microsoft Azure Identity Library for Python" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "azure_identity-1.19.0-py3-none-any.whl", hash = "sha256:e3f6558c181692d7509f09de10cca527c7dce426776454fb97df512a46527e81"}, {file = "azure_identity-1.19.0.tar.gz", hash = "sha256:500144dc18197d7019b81501165d4fa92225f03778f17d7ca8a2a180129a9c83"}, @@ -282,6 +297,7 @@ version = "1.5.0" description = "Microsoft Azure Management Core Library for Python" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {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"}, @@ -296,6 +312,7 @@ version = "20.1.0" description = "Microsoft Azure Storage Management Client Library for Python" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "azure-mgmt-storage-20.1.0.zip", hash = "sha256:214f3fde8c91e27d53f2e654a28d15003ad3f6f15c8438a8205f0c88a48d9451"}, {file = "azure_mgmt_storage-20.1.0-py3-none-any.whl", hash = "sha256:afdc830329c674d96a91c963fa03ac81a4e387dfbf9f5a4e823950dc1fe95659"}, @@ -312,6 +329,7 @@ version = "12.24.0" description = "Microsoft Azure Blob Storage Client Library for Python" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "azure_storage_blob-12.24.0-py3-none-any.whl", hash = "sha256:4f0bb4592ea79a2d986063696514c781c9e62be240f09f6397986e01755bc071"}, {file = "azure_storage_blob-12.24.0.tar.gz", hash = "sha256:eaaaa1507c8c363d6e1d1342bd549938fdf1adec9b1ada8658c8f5bf3aea844e"}, @@ -332,6 +350,7 @@ version = "2.16.0" description = "Internationalization utilities" optional = false python-versions = ">=3.8" +groups = ["docs"] files = [ {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"}, {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"}, @@ -346,6 +365,7 @@ version = "4.12.3" description = "Screen-scraping library" optional = false python-versions = ">=3.6.0" +groups = ["main"] files = [ {file = "beautifulsoup4-4.12.3-py3-none-any.whl", hash = "sha256:b80878c9f40111313e55da8ba20bdba06d8fa3969fc68304167741bbf9e082ed"}, {file = "beautifulsoup4-4.12.3.tar.gz", hash = "sha256:74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051"}, @@ -367,6 +387,7 @@ version = "3.6.2" description = "Interactive plots and applications in the browser from Python" optional = false python-versions = ">=3.10" +groups = ["main"] files = [ {file = "bokeh-3.6.2-py3-none-any.whl", hash = "sha256:fddc4b91f8b40178c0e3e83dfcc33886d7803a3a1f041a840834255e435a18c2"}, {file = "bokeh-3.6.2.tar.gz", hash = "sha256:2f3043d9ecb3d5dc2e8c0ebf8ad55727617188d4e534f3e7208b36357e352396"}, @@ -389,6 +410,7 @@ version = "1.35.77" description = "The AWS SDK for Python" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "boto3-1.35.77-py3-none-any.whl", hash = "sha256:a09871805f8e462349a1c33c23eb413668df0bf68424e61d53518e1a7d883b2f"}, {file = "boto3-1.35.77.tar.gz", hash = "sha256:cc819cdbccbc2d0dc185f1dcfe74cf3809489c4cae63c2e5d6a557aa0c5ab928"}, @@ -408,6 +430,7 @@ version = "1.35.77" description = "Low-level, data-driven core of boto 3." optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "botocore-1.35.77-py3-none-any.whl", hash = "sha256:3faa27d65841499762228902d7e215fa99a4c2fdc76c9113e1c3f339bdf685b8"}, {file = "botocore-1.35.77.tar.gz", hash = "sha256:17b778016644e9342ca3ff2f430c1d1db0c6126e9b41a57cff52ac58e7a455e0"}, @@ -427,6 +450,7 @@ version = "2.5.post1" description = "Bash style brace expander." optional = false python-versions = ">=3.8" +groups = ["docs"] files = [ {file = "bracex-2.5.post1-py3-none-any.whl", hash = "sha256:13e5732fec27828d6af308628285ad358047cec36801598368cb28bc631dbaf6"}, {file = "bracex-2.5.post1.tar.gz", hash = "sha256:12c50952415bfa773d2d9ccb8e79651b8cdb1f31a42f6091b804f6ba2b4a66b6"}, @@ -438,6 +462,7 @@ version = "5.5.0" description = "Extensible memoizing collections and decorators" optional = false python-versions = ">=3.7" +groups = ["main", "dev"] files = [ {file = "cachetools-5.5.0-py3-none-any.whl", hash = "sha256:02134e8439cdc2ffb62023ce1debca2944c3f289d66bb17ead3ab3dede74b292"}, {file = "cachetools-5.5.0.tar.gz", hash = "sha256:2cc24fb4cbe39633fb7badd9db9ca6295d766d9c2995f245725a46715d050f2a"}, @@ -449,6 +474,7 @@ version = "2024.8.30" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.6" +groups = ["main", "dev", "docs"] files = [ {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"}, {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"}, @@ -460,6 +486,7 @@ version = "1.17.1" description = "Foreign Function Interface for Python calling C code." optional = false python-versions = ">=3.8" +groups = ["main", "dev"] files = [ {file = "cffi-1.17.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:df8b1c11f177bc2313ec4b2d46baec87a5f3e71fc8b45dab2ee7cae86d9aba14"}, {file = "cffi-1.17.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8f2cdc858323644ab277e9bb925ad72ae0e67f69e804f4898c070998d50b1a67"}, @@ -529,6 +556,7 @@ files = [ {file = "cffi-1.17.1-cp39-cp39-win_amd64.whl", hash = "sha256:d016c76bdd850f3c626af19b0542c9677ba156e4ee4fccfdd7848803533ef662"}, {file = "cffi-1.17.1.tar.gz", hash = "sha256:1c39c6016c32bc48dd54561950ebd6836e1670f2ae46128f67cf49e789c52824"}, ] +markers = {dev = "implementation_name == \"pypy\""} [package.dependencies] pycparser = "*" @@ -539,6 +567,7 @@ version = "3.4.0" description = "Validate configuration and produce human readable error messages." optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"}, {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"}, @@ -550,6 +579,7 @@ version = "3.4.0" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." optional = false python-versions = ">=3.7.0" +groups = ["main", "dev", "docs"] files = [ {file = "charset_normalizer-3.4.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:4f9fc98dad6c2eaa32fc3af1417d95b5e3d08aff968df0cd320066def971f9a6"}, {file = "charset_normalizer-3.4.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:0de7b687289d3c1b3e8660d0741874abe7888100efe14bd0f9fd7141bcbda92b"}, @@ -664,6 +694,7 @@ version = "8.1.7" description = "Composable command line interface toolkit" optional = false python-versions = ">=3.7" +groups = ["main", "dev", "docs"] files = [ {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"}, {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"}, @@ -678,6 +709,7 @@ version = "3.1.0" description = "Pickler class to extend the standard pickle.Pickler functionality" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "cloudpickle-3.1.0-py3-none-any.whl", hash = "sha256:fe11acda67f61aaaec473e3afe030feb131d78a43461b718185363384f1ba12e"}, {file = "cloudpickle-3.1.0.tar.gz", hash = "sha256:81a929b6e3c7335c863c771d673d105f02efdb89dfaba0c90495d1c64796601b"}, @@ -689,10 +721,12 @@ version = "0.4.6" description = "Cross-platform colored terminal text." optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" +groups = ["main", "dev", "docs", "tests"] files = [ {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"}, {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"}, ] +markers = {main = "platform_system == \"Windows\"", tests = "sys_platform == \"win32\""} [[package]] name = "comm" @@ -700,6 +734,7 @@ version = "0.2.2" description = 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"sha256:eda2d8a4116d4f2429db8550f2457da57279247dd930bb12f821b58391359493"}, @@ -1411,6 +1478,7 @@ version = "2024.10.0" description = "Convenient Filesystem interface over GCS" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "gcsfs-2024.10.0-py2.py3-none-any.whl", hash = "sha256:bb2d23547e61203ea2dda5fa6c4b91a0c34b74ebe8bb6ab1926f6c33381bceb2"}, {file = "gcsfs-2024.10.0.tar.gz", hash = "sha256:5df54cfe568e8fdeea5aafa7fed695cdc69a9a674e991ca8c1ce634f5df1d314"}, @@ -1435,6 +1503,7 @@ version = "2.1.0" description = "Copy your docs directly to the gh-pages branch." optional = false python-versions = "*" +groups = ["docs"] files = [ {file = "ghp-import-2.1.0.tar.gz", hash = "sha256:9c535c4c61193c2df8871222567d7fd7e5014d835f97dc7b7439069e2413d343"}, {file = "ghp_import-2.1.0-py3-none-any.whl", hash = "sha256:8337dd7b50877f163d4c0289bc1f1c7f127550241988d568c1db512c4324a619"}, @@ -1452,6 +1521,7 @@ version = "4.0.11" description = "Git Object Database" optional = false python-versions = ">=3.7" +groups = ["main", "docs"] files = [ {file = "gitdb-4.0.11-py3-none-any.whl", hash = "sha256:81a3407ddd2ee8df444cbacea00e2d038e40150acfa3001696fe0dcf1d3adfa4"}, {file = "gitdb-4.0.11.tar.gz", hash = "sha256:bf5421126136d6d0af55bc1e7c1af1c397a34f5b7bd79e776cd3e89785c2b04b"}, @@ -1466,6 +1536,7 @@ version = "3.1.43" description = "GitPython is a Python library used to interact with Git repositories" optional = false python-versions = ">=3.7" +groups = ["main", "docs"] files = [ {file = "GitPython-3.1.43-py3-none-any.whl", hash = "sha256:eec7ec56b92aad751f9912a73404bc02ba212a23adb2c7098ee668417051a1ff"}, {file = "GitPython-3.1.43.tar.gz", hash = "sha256:35f314a9f878467f5453cc1fee295c3e18e52f1b99f10f6cf5b1682e968a9e7c"}, @@ -1484,6 +1555,7 @@ version = "3.0.0" description = "Python bindings to the Google search engine." optional = false python-versions = "*" +groups = ["main"] files = [ {file = "google-3.0.0-py2.py3-none-any.whl", hash = "sha256:889cf695f84e4ae2c55fbc0cfdaf4c1e729417fa52ab1db0485202ba173e4935"}, {file = "google-3.0.0.tar.gz", hash = "sha256:143530122ee5130509ad5e989f0512f7cb218b2d4eddbafbad40fd10e8d8ccbe"}, @@ -1498,6 +1570,7 @@ version = "2.24.0" description = "Google API client core library" optional = false python-versions = ">=3.7" +groups = ["main", "dev"] files = [ {file = "google_api_core-2.24.0-py3-none-any.whl", hash = "sha256:10d82ac0fca69c82a25b3efdeefccf6f28e02ebb97925a8cce8edbfe379929d9"}, {file = "google_api_core-2.24.0.tar.gz", hash = "sha256:e255640547a597a4da010876d333208ddac417d60add22b6851a0c66a831fcaf"}, @@ -1524,6 +1597,7 @@ version = "2.36.0" description = "Google Authentication Library" optional = false python-versions = ">=3.7" +groups = ["main", "dev"] files = [ {file = "google_auth-2.36.0-py2.py3-none-any.whl", hash = "sha256:51a15d47028b66fd36e5c64a82d2d57480075bccc7da37cde257fc94177a61fb"}, {file = "google_auth-2.36.0.tar.gz", hash = "sha256:545e9618f2df0bcbb7dcbc45a546485b1212624716975a1ea5ae8149ce769ab1"}, @@ -1547,6 +1621,7 @@ version = "0.8.0" description = "Google Authentication Library" optional = false python-versions = ">=3.6" +groups = ["main"] files = [ {file = "google-auth-oauthlib-0.8.0.tar.gz", hash = "sha256:81056a310fb1c4a3e5a7e1a443e1eb96593c6bbc55b26c0261e4d3295d3e6593"}, {file = "google_auth_oauthlib-0.8.0-py2.py3-none-any.whl", hash = "sha256:40cc612a13c3336d5433e94e2adb42a0c88f6feb6c55769e44500fc70043a576"}, @@ -1565,6 +1640,7 @@ version = "3.27.0" description = "Google BigQuery API client library" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "google_cloud_bigquery-3.27.0-py2.py3-none-any.whl", hash = "sha256:b53b0431e5ba362976a4cd8acce72194b4116cdf8115030c7b339b884603fcc3"}, {file = "google_cloud_bigquery-3.27.0.tar.gz", hash = "sha256:379c524054d7b090fa56d0c22662cc6e6458a6229b6754c0e7177e3a73421d2c"}, @@ -1596,6 +1672,7 @@ version = "2.4.1" description = "Google Cloud API client core library" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "google-cloud-core-2.4.1.tar.gz", hash = "sha256:9b7749272a812bde58fff28868d0c5e2f585b82f37e09a1f6ed2d4d10f134073"}, {file = "google_cloud_core-2.4.1-py2.py3-none-any.whl", hash = "sha256:a9e6a4422b9ac5c29f79a0ede9485473338e2ce78d91f2370c01e730eab22e61"}, @@ -1614,6 +1691,7 @@ version = "5.15.1" description = "Google Cloud Dataproc API client library" optional = false python-versions = ">=3.7" +groups = ["dev"] files = [ {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"}, @@ -1632,6 +1710,7 @@ version = "2.20.2" description = "Google Cloud Secret Manager API client library" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "google_cloud_secret_manager-2.20.2-py2.py3-none-any.whl", hash = "sha256:99b342ff722feef78aa5bad1c05c6be204f8fee01373a2eb6f05dba710b32879"}, {file = "google_cloud_secret_manager-2.20.2.tar.gz", hash = "sha256:bbe24825e334f9e679e825e70d932118a7ff536e67c1ceb048da44111c87a45c"}, @@ -1650,6 +1729,7 @@ version = "2.19.0" description = "Google Cloud Storage API client library" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "google_cloud_storage-2.19.0-py2.py3-none-any.whl", hash = "sha256:aeb971b5c29cf8ab98445082cbfe7b161a1f48ed275822f59ed3f1524ea54fba"}, {file = "google_cloud_storage-2.19.0.tar.gz", hash = "sha256:cd05e9e7191ba6cb68934d8eb76054d9be4562aa89dbc4236feee4d7d51342b2"}, @@ -1673,6 +1753,7 @@ version = "1.6.0" description = "A python wrapper of the C library 'Google CRC32C'" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "google_crc32c-1.6.0-cp310-cp310-macosx_12_0_arm64.whl", hash = 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Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API." optional = false python-versions = ">=3.9" +groups = ["docs"] files = [ {file = "griffe-1.5.1-py3-none-any.whl", hash = "sha256:ad6a7980f8c424c9102160aafa3bcdf799df0e75f7829d75af9ee5aef656f860"}, {file = "griffe-1.5.1.tar.gz", hash = "sha256:72964f93e08c553257706d6cd2c42d1c172213feb48b2be386f243380b405d4b"}, @@ -1762,6 +1846,7 @@ version = "0.13.1" description = "IAM API client library" optional = false python-versions = ">=3.7" +groups = ["main", "dev"] files = [ {file = "grpc-google-iam-v1-0.13.1.tar.gz", hash = "sha256:3ff4b2fd9d990965e410965253c0da6f66205d5a8291c4c31c6ebecca18a9001"}, {file = "grpc_google_iam_v1-0.13.1-py2.py3-none-any.whl", hash = "sha256:c3e86151a981811f30d5e7330f271cee53e73bb87755e88cc3b6f0c7b5fe374e"}, @@ -1778,6 +1863,7 @@ version = "1.68.1" description = "HTTP/2-based RPC framework" optional = false python-versions = ">=3.8" +groups = ["main", "dev"] files = [ {file = "grpcio-1.68.1-cp310-cp310-linux_armv7l.whl", hash = "sha256:d35740e3f45f60f3c37b1e6f2f4702c23867b9ce21c6410254c9c682237da68d"}, {file = "grpcio-1.68.1-cp310-cp310-macosx_12_0_universal2.whl", hash = "sha256:d99abcd61760ebb34bdff37e5a3ba333c5cc09feda8c1ad42547bea0416ada78"}, @@ -1845,6 +1931,7 @@ version = "1.48.2" description = "Status proto mapping for gRPC" optional = false python-versions = ">=3.6" +groups = ["main", "dev"] files = [ {file = "grpcio-status-1.48.2.tar.gz", hash = "sha256:53695f45da07437b7c344ee4ef60d370fd2850179f5a28bb26d8e2aa1102ec11"}, {file = "grpcio_status-1.48.2-py3-none-any.whl", hash = "sha256:2c33bbdbe20188b2953f46f31af669263b6ee2a9b2d38fa0d36ee091532e21bf"}, @@ -1861,6 +1948,7 @@ version = "0.2.127" description = "Scalable library for exploring and analyzing genomic data." optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "hail-0.2.127-py3-none-any.whl", hash = "sha256:cb6555373e4e9d265d1493696b959ffefee389d0522c162be7dd813b0f698bc9"}, ] @@ -1908,6 +1996,7 @@ 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" +groups = ["main"] files = [ {file = "huggingface_hub-0.26.5-py3-none-any.whl", hash = "sha256:fb7386090bbe892072e64b85f7c4479fd2d65eea5f2543327c970d5169e83924"}, {file = "huggingface_hub-0.26.5.tar.gz", hash = "sha256:1008bd18f60bfb65e8dbc0a97249beeeaa8c99d3c2fa649354df9fa5a13ed83b"}, @@ -1942,6 +2031,7 @@ version = "1.1.0" description = "Python humanize utilities" optional = false python-versions = ">=3.5" +groups = ["main"] files = [ {file = "humanize-1.1.0-py3-none-any.whl", hash = "sha256:3959c76f1f6c9b43258bb0b0f6b6161d6c07b8717b306c0b713ea36b7999331e"}, {file = "humanize-1.1.0.tar.gz", hash = "sha256:ad83016fae2453a7486f5be5dba8e19883020c77f6c12c63702f3b6c15ae3c5e"}, @@ -1956,6 +2046,7 @@ version = "1.3.2" description = "A framework for elegantly configuring complex applications" optional = false python-versions = "*" +groups = ["main"] files = [ {file = "hydra-core-1.3.2.tar.gz", hash = "sha256:8a878ed67216997c3e9d88a8e72e7b4767e81af37afb4ea3334b269a4390a824"}, {file = "hydra_core-1.3.2-py3-none-any.whl", hash = "sha256:fa0238a9e31df3373b35b0bfb672c34cc92718d21f81311d8996a16de1141d8b"}, @@ -1972,6 +2063,7 @@ version = "2.6.3" description = "File identification library for Python" optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "identify-2.6.3-py2.py3-none-any.whl", hash = "sha256:9edba65473324c2ea9684b1f944fe3191db3345e50b6d04571d10ed164f8d7bd"}, {file = "identify-2.6.3.tar.gz", hash = "sha256:62f5dae9b5fef52c84cc188514e9ea4f3f636b1d8799ab5ebc475471f9e47a02"}, @@ -1986,6 +2078,7 @@ version = "3.10" description = "Internationalized Domain Names in Applications (IDNA)" optional = false python-versions = ">=3.6" +groups = ["main", "dev", "docs"] files = [ {file = "idna-3.10-py3-none-any.whl", hash = "sha256:946d195a0d259cbba61165e88e65941f16e9b36ea6ddb97f00452bae8b1287d3"}, {file = "idna-3.10.tar.gz", hash = "sha256:12f65c9b470abda6dc35cf8e63cc574b1c52b11df2c86030af0ac09b01b13ea9"}, @@ -2000,6 +2093,7 @@ version = "2.0.0" description = "brain-dead simple config-ini parsing" optional = false python-versions = ">=3.7" +groups = ["tests"] files = [ {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"}, {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"}, @@ -2011,6 +2105,7 @@ version = "1.7.0" description = "Interrogate a codebase for docstring coverage." optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "interrogate-1.7.0-py3-none-any.whl", hash = "sha256:b13ff4dd8403369670e2efe684066de9fcb868ad9d7f2b4095d8112142dc9d12"}, {file = "interrogate-1.7.0.tar.gz", hash = "sha256:a320d6ec644dfd887cc58247a345054fc4d9f981100c45184470068f4b3719b0"}, @@ -2036,6 +2131,7 @@ version = "6.29.5" description = "IPython Kernel for Jupyter" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "ipykernel-6.29.5-py3-none-any.whl", hash = "sha256:afdb66ba5aa354b09b91379bac28ae4afebbb30e8b39510c9690afb7a10421b5"}, {file = "ipykernel-6.29.5.tar.gz", hash = "sha256:f093a22c4a40f8828f8e330a9c297cb93dcab13bd9678ded6de8e5cf81c56215"}, @@ -2069,6 +2165,7 @@ version = "8.30.0" description = "IPython: Productive Interactive Computing" optional = false python-versions = ">=3.10" +groups = ["dev"] files = [ {file = "ipython-8.30.0-py3-none-any.whl", hash = "sha256:85ec56a7e20f6c38fce7727dcca699ae4ffc85985aa7b23635a8008f918ae321"}, {file = "ipython-8.30.0.tar.gz", hash = "sha256:cb0a405a306d2995a5cbb9901894d240784a9f341394c6ba3f4fe8c6eb89ff6e"}, @@ -2107,6 +2204,7 @@ version = "0.7.2" description = "An ISO 8601 date/time/duration parser and formatter" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "isodate-0.7.2-py3-none-any.whl", hash = "sha256:28009937d8031054830160fce6d409ed342816b543597cece116d966c6d99e15"}, {file = "isodate-0.7.2.tar.gz", hash = "sha256:4cd1aa0f43ca76f4a6c6c0292a85f40b35ec2e43e315b59f06e6d32171a953e6"}, @@ -2118,6 +2216,7 @@ version = "5.13.2" description = "A Python utility / library to sort Python imports." optional = false python-versions = ">=3.8.0" +groups = ["dev"] files = [ {file = "isort-5.13.2-py3-none-any.whl", hash = "sha256:8ca5e72a8d85860d5a3fa69b8745237f2939afe12dbf656afbcb47fe72d947a6"}, {file = "isort-5.13.2.tar.gz", hash = "sha256:48fdfcb9face5d58a4f6dde2e72a1fb8dcaf8ab26f95ab49fab84c2ddefb0109"}, @@ -2132,6 +2231,7 @@ version = "1.0.0" description = "Mixed sync-async queue to interoperate between asyncio tasks and classic threads" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "janus-1.0.0-py3-none-any.whl", hash = "sha256:2596ea5482711c1ee3ef2df6c290aaf370a13c55a007826e8f7c32d696d1d00a"}, {file = "janus-1.0.0.tar.gz", hash = "sha256:df976f2cdcfb034b147a2d51edfc34ff6bfb12d4e2643d3ad0e10de058cb1612"}, @@ -2146,6 +2246,7 @@ version = "0.19.2" description = "An autocompletion tool for Python that can be used for text editors." optional = false python-versions = ">=3.6" +groups = ["dev"] files = [ {file = "jedi-0.19.2-py2.py3-none-any.whl", hash = "sha256:a8ef22bde8490f57fe5c7681a3c83cb58874daf72b4784de3cce5b6ef6edb5b9"}, {file = "jedi-0.19.2.tar.gz", hash = "sha256:4770dc3de41bde3966b02eb84fbcf557fb33cce26ad23da12c742fb50ecb11f0"}, @@ -2165,6 +2266,7 @@ version = "3.1.4" description = "A very fast and expressive template engine." optional = false python-versions = ">=3.7" +groups = ["main", "docs"] files = [ {file = "jinja2-3.1.4-py3-none-any.whl", hash = "sha256:bc5dd2abb727a5319567b7a813e6a2e7318c39f4f487cfe6c89c6f9c7d25197d"}, {file = "jinja2-3.1.4.tar.gz", hash = "sha256:4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369"}, @@ -2182,6 +2284,7 @@ version = "1.0.1" description = "JSON Matching Expressions" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "jmespath-1.0.1-py3-none-any.whl", hash = "sha256:02e2e4cc71b5bcab88332eebf907519190dd9e6e82107fa7f83b1003a6252980"}, {file = "jmespath-1.0.1.tar.gz", hash = "sha256:90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe"}, @@ -2193,6 +2296,7 @@ version = "1.4.2" description = "Lightweight pipelining with Python functions" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "joblib-1.4.2-py3-none-any.whl", hash = "sha256:06d478d5674cbc267e7496a410ee875abd68e4340feff4490bcb7afb88060ae6"}, {file = "joblib-1.4.2.tar.gz", hash = "sha256:2382c5816b2636fbd20a09e0f4e9dad4736765fdfb7dca582943b9c1366b3f0e"}, @@ -2204,6 +2308,7 @@ version = "2.1.2" description = "Java Property file parser and writer for Python" optional = false python-versions = ">=2.7" +groups = ["main"] files = [ {file = "jproperties-2.1.2-py2.py3-none-any.whl", hash = "sha256:4108e868353a9f4a12bb86a92df5462d0e18d00119169533972ce473029be79a"}, {file = "jproperties-2.1.2.tar.gz", hash = "sha256:036fcd52c10a8a1c21e6fa2a1c292c93892e759b76490acc4809213a36ddc329"}, @@ -2218,6 +2323,7 @@ version = "8.6.3" description = "Jupyter protocol implementation and client libraries" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "jupyter_client-8.6.3-py3-none-any.whl", hash = "sha256:e8a19cc986cc45905ac3362915f410f3af85424b4c0905e94fa5f2cb08e8f23f"}, {file = "jupyter_client-8.6.3.tar.gz", hash = "sha256:35b3a0947c4a6e9d589eb97d7d4cd5e90f910ee73101611f01283732bd6d9419"}, @@ -2240,6 +2346,7 @@ version = "5.7.2" description = "Jupyter core package. A base package on which Jupyter projects rely." optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "jupyter_core-5.7.2-py3-none-any.whl", hash = "sha256:4f7315d2f6b4bcf2e3e7cb6e46772eba760ae459cd1f59d29eb57b0a01bd7409"}, {file = "jupyter_core-5.7.2.tar.gz", hash = "sha256:aa5f8d32bbf6b431ac830496da7392035d6f61b4f54872f15c4bd2a9c3f536d9"}, @@ -2260,6 +2367,7 @@ version = "1.4.7" description = "A fast implementation of the Cassowary constraint solver" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "kiwisolver-1.4.7-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:8a9c83f75223d5e48b0bc9cb1bf2776cf01563e00ade8775ffe13b0b6e1af3a6"}, {file = "kiwisolver-1.4.7-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:58370b1ffbd35407444d57057b57da5d6549d2d854fa30249771775c63b5fe17"}, @@ -2383,6 +2491,7 @@ version = "0.43.0" description = "lightweight wrapper around basic LLVM functionality" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "llvmlite-0.43.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:a289af9a1687c6cf463478f0fa8e8aa3b6fb813317b0d70bf1ed0759eab6f761"}, {file = "llvmlite-0.43.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:6d4fd101f571a31acb1559ae1af30f30b1dc4b3186669f92ad780e17c81e91bc"}, @@ -2413,6 +2522,7 @@ version = "5.3.0" description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API." optional = false python-versions = ">=3.6" +groups = ["docs"] files = [ {file = "lxml-5.3.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:dd36439be765e2dde7660212b5275641edbc813e7b24668831a5c8ac91180656"}, {file = "lxml-5.3.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ae5fe5c4b525aa82b8076c1a59d642c17b6e8739ecf852522c6321852178119d"}, @@ -2567,6 +2677,7 @@ version = "3.7" description = "Python implementation of John Gruber's Markdown." optional = false python-versions = ">=3.8" +groups = ["docs"] files = [ {file = "Markdown-3.7-py3-none-any.whl", hash = "sha256:7eb6df5690b81a1d7942992c97fad2938e956e79df20cbc6186e9c3a77b1c803"}, {file = "markdown-3.7.tar.gz", hash = "sha256:2ae2471477cfd02dbbf038d5d9bc226d40def84b4fe2986e49b59b6b472bbed2"}, @@ -2582,6 +2693,7 @@ version = "3.0.2" description = "Safely add untrusted strings to HTML/XML markup." optional = false python-versions = ">=3.9" +groups = ["main", "docs"] files = [ {file = "MarkupSafe-3.0.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:7e94c425039cde14257288fd61dcfb01963e658efbc0ff54f5306b06054700f8"}, {file = "MarkupSafe-3.0.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:9e2d922824181480953426608b81967de705c3cef4d1af983af849d7bd619158"}, @@ -2652,6 +2764,7 @@ version = "3.7.3" description = "Python plotting package" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "matplotlib-3.7.3-cp310-cp310-macosx_10_12_universal2.whl", hash = "sha256:085c33b27561d9c04386789d5aa5eb4a932ddef43cfcdd0e01735f9a6e85ce0c"}, {file = "matplotlib-3.7.3-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:c568e80e1c17f68a727f30f591926751b97b98314d8e59804f54f86ae6fa6a22"}, @@ -2720,6 +2833,7 @@ version = "0.1.7" description = "Inline Matplotlib backend for Jupyter" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "matplotlib_inline-0.1.7-py3-none-any.whl", hash = "sha256:df192d39a4ff8f21b1895d72e6a13f5fcc5099f00fa84384e0ea28c2cc0653ca"}, {file = "matplotlib_inline-0.1.7.tar.gz", hash = "sha256:8423b23ec666be3d16e16b60bdd8ac4e86e840ebd1dd11a30b9f117f2fa0ab90"}, @@ -2734,6 +2848,7 @@ version = "0.7.0" description = "McCabe checker, plugin for flake8" optional = false python-versions = ">=3.6" +groups = ["dev"] files = [ {file = "mccabe-0.7.0-py2.py3-none-any.whl", hash = "sha256:6c2d30ab6be0e4a46919781807b4f0d834ebdd6c6e3dca0bda5a15f863427b6e"}, {file = "mccabe-0.7.0.tar.gz", hash = "sha256:348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325"}, @@ -2745,6 +2860,7 @@ version = "1.3.4" description = "A deep merge function for 🐍." optional = false python-versions = ">=3.6" +groups = ["docs"] files = [ {file = "mergedeep-1.3.4-py3-none-any.whl", hash = "sha256:70775750742b25c0d8f36c55aed03d24c3384d17c951b3175d898bd778ef0307"}, {file = "mergedeep-1.3.4.tar.gz", hash = "sha256:0096d52e9dad9939c3d975a774666af186eda617e6ca84df4c94dec30004f2a8"}, @@ -2756,6 +2872,7 @@ version = "1.5.3" description = "Project documentation with Markdown." optional = false python-versions = ">=3.7" +groups = ["docs"] files = [ {file = "mkdocs-1.5.3-py3-none-any.whl", hash = "sha256:3b3a78e736b31158d64dbb2f8ba29bd46a379d0c6e324c2246c3bc3d2189cfc1"}, {file = "mkdocs-1.5.3.tar.gz", hash = "sha256:eb7c99214dcb945313ba30426c2451b735992c73c2e10838f76d09e39ff4d0e2"}, @@ -2786,6 +2903,7 @@ version = "0.7.1" description = "An MkDocs plugin" optional = false python-versions = ">=3.4" +groups = ["docs"] files = [ {file = "mkdocs-autolinks-plugin-0.7.1.tar.gz", hash = "sha256:445ddb9b417b7795856c30801bb430773186c1daf210bdeecf8305f55a47d151"}, {file = "mkdocs_autolinks_plugin-0.7.1-py3-none-any.whl", hash = "sha256:5c6c17f6649b68e79a9ef0b2648d59f3072e18002b90ee1586a64c505f11ab12"}, @@ -2800,6 +2918,7 @@ version = "1.2.0" description = "Automatically link across pages in MkDocs." optional = false python-versions = ">=3.8" +groups = ["docs"] files = [ {file = "mkdocs_autorefs-1.2.0-py3-none-any.whl", hash = "sha256:d588754ae89bd0ced0c70c06f58566a4ee43471eeeee5202427da7de9ef85a2f"}, {file = "mkdocs_autorefs-1.2.0.tar.gz", hash = "sha256:a86b93abff653521bda71cf3fc5596342b7a23982093915cb74273f67522190f"}, @@ -2816,6 +2935,7 @@ version = "2.9.3" description = "An MkDocs plugin that simplifies configuring page titles and their order" optional = false python-versions = ">=3.8.1" +groups = ["docs"] files = [ {file = "mkdocs_awesome_pages_plugin-2.9.3-py3-none-any.whl", hash = "sha256:1ba433d4e7edaf8661b15b93267f78f78e2e06ca590fc0e651ea36b191d64ae4"}, {file = "mkdocs_awesome_pages_plugin-2.9.3.tar.gz", hash = "sha256:bdf6369871f41bb17f09c3cfb573367732dfcceb5673d7a2c5c76ac2567b242f"}, @@ -2832,6 +2952,7 @@ version = "1.0.2" description = "A mkdocs plugin that lets you exclude files or trees." optional = false python-versions = "*" +groups = ["docs"] files = [ {file = "mkdocs-exclude-1.0.2.tar.gz", hash = "sha256:ba6fab3c80ddbe3fd31d3e579861fd3124513708271180a5f81846da8c7e2a51"}, ] @@ -2845,6 +2966,7 @@ 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 = ">=3.8,<4" +groups = ["docs"] files = [ {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"}, @@ -2861,6 +2983,7 @@ 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" +groups = ["docs"] files = [ {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"}, @@ -2883,6 +3006,7 @@ version = "9.5.18" description = "Documentation that simply works" optional = false python-versions = ">=3.8" +groups = ["docs"] files = [ {file = "mkdocs_material-9.5.18-py3-none-any.whl", hash = "sha256:1e0e27fc9fe239f9064318acf548771a4629d5fd5dfd45444fd80a953fe21eb4"}, {file = "mkdocs_material-9.5.18.tar.gz", hash = "sha256:a43f470947053fa2405c33995f282d24992c752a50114f23f30da9d8d0c57e62"}, @@ -2912,6 +3036,7 @@ version = "1.3.1" description = "Extension pack for Python Markdown and MkDocs Material." optional = false python-versions = ">=3.8" +groups = ["docs"] files = [ {file = "mkdocs_material_extensions-1.3.1-py3-none-any.whl", hash = "sha256:adff8b62700b25cb77b53358dad940f3ef973dd6db797907c49e3c2ef3ab4e31"}, {file = "mkdocs_material_extensions-1.3.1.tar.gz", hash = "sha256:10c9511cea88f568257f960358a467d12b970e1f7b2c0e5fb2bb48cab1928443"}, @@ -2923,6 +3048,7 @@ version = "0.3.9" description = "MkDocs plugin to allow clickable sections that lead to an index page" optional = false python-versions = ">=3.8" +groups = ["docs"] files = [ {file = "mkdocs_section_index-0.3.9-py3-none-any.whl", hash = "sha256:5e5eb288e8d7984d36c11ead5533f376fdf23498f44e903929d72845b24dfe34"}, {file = "mkdocs_section_index-0.3.9.tar.gz", hash = "sha256:b66128d19108beceb08b226ee1ba0981840d14baf8a652b6c59e650f3f92e4f8"}, @@ -2937,6 +3063,7 @@ version = "0.27.0" description = "Automatic documentation from sources, for MkDocs." optional = false python-versions = ">=3.9" +groups = ["docs"] files = [ {file = "mkdocstrings-0.27.0-py3-none-any.whl", hash = "sha256:6ceaa7ea830770959b55a16203ac63da24badd71325b96af950e59fd37366332"}, {file = "mkdocstrings-0.27.0.tar.gz", hash = "sha256:16adca6d6b0a1f9e0c07ff0b02ced8e16f228a9d65a37c063ec4c14d7b76a657"}, @@ -2963,6 +3090,7 @@ version = "1.12.2" description = "A Python handler for mkdocstrings." optional = false python-versions = ">=3.9" +groups = ["docs"] files = [ {file = "mkdocstrings_python-1.12.2-py3-none-any.whl", hash = "sha256:7f7d40d6db3cb1f5d19dbcd80e3efe4d0ba32b073272c0c0de9de2e604eda62a"}, {file = "mkdocstrings_python-1.12.2.tar.gz", hash = "sha256:7a1760941c0b52a2cd87b960a9e21112ffe52e7df9d0b9583d04d47ed2e186f3"}, @@ -2979,6 +3107,7 @@ 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" +groups = ["main"] files = [ {file = "msal-1.31.1-py3-none-any.whl", hash = "sha256:29d9882de247e96db01386496d59f29035e5e841bcac892e6d7bf4390bf6bd17"}, {file = "msal-1.31.1.tar.gz", hash = "sha256:11b5e6a3f802ffd3a72107203e20c4eac6ef53401961b880af2835b723d80578"}, @@ -2998,6 +3127,7 @@ version = "1.2.0" description = "Microsoft Authentication Library extensions (MSAL EX) provides a persistence API that can save your data on disk, encrypted on Windows, macOS and Linux. Concurrent data access will be coordinated by a file lock mechanism." optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "msal_extensions-1.2.0-py3-none-any.whl", hash = "sha256:cf5ba83a2113fa6dc011a254a72f1c223c88d7dfad74cc30617c4679a417704d"}, {file = "msal_extensions-1.2.0.tar.gz", hash = "sha256:6f41b320bfd2933d631a215c91ca0dd3e67d84bd1a2f50ce917d5874ec646bef"}, @@ -3013,6 +3143,7 @@ version = "0.7.1" description = "AutoRest swagger generator Python client runtime." optional = false python-versions = ">=3.6" +groups = ["main"] files = [ {file = "msrest-0.7.1-py3-none-any.whl", hash = "sha256:21120a810e1233e5e6cc7fe40b474eeb4ec6f757a15d7cf86702c369f9567c32"}, {file = "msrest-0.7.1.zip", hash = "sha256:6e7661f46f3afd88b75667b7187a92829924446c7ea1d169be8c4bb7eeb788b9"}, @@ -3034,6 +3165,7 @@ version = "6.1.0" description = "multidict implementation" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "multidict-6.1.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:3380252550e372e8511d49481bd836264c009adb826b23fefcc5dd3c69692f60"}, {file = "multidict-6.1.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:99f826cbf970077383d7de805c0681799491cb939c25450b9b5b3ced03ca99f1"}, @@ -3138,6 +3270,7 @@ version = "1.13.0" description = "Optional static typing for Python" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "mypy-1.13.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:6607e0f1dd1fb7f0aca14d936d13fd19eba5e17e1cd2a14f808fa5f8f6d8f60a"}, {file = "mypy-1.13.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8a21be69bd26fa81b1f80a61ee7ab05b076c674d9b18fb56239d72e21d9f4c80"}, @@ -3191,6 +3324,7 @@ version = "1.0.0" description = "Type system extensions for programs checked with the mypy type checker." optional = false python-versions = ">=3.5" +groups = ["dev"] files = [ {file = "mypy_extensions-1.0.0-py3-none-any.whl", hash = "sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d"}, {file = "mypy_extensions-1.0.0.tar.gz", hash = "sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782"}, @@ -3202,6 +3336,7 @@ version = "8.4.0" description = "Simple yet flexible natural sorting in Python." optional = false python-versions = ">=3.7" +groups = ["docs"] files = [ {file = "natsort-8.4.0-py3-none-any.whl", hash = "sha256:4732914fb471f56b5cce04d7bae6f164a592c7712e1c85f9ef585e197299521c"}, {file = "natsort-8.4.0.tar.gz", hash = "sha256:45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581"}, @@ -3217,6 +3352,7 @@ version = "1.6.0" description = "Patch asyncio to allow nested event loops" optional = false python-versions = ">=3.5" +groups = ["main", "dev"] files = [ {file = "nest_asyncio-1.6.0-py3-none-any.whl", hash = "sha256:87af6efd6b5e897c81050477ef65c62e2b2f35d51703cae01aff2905b1852e1c"}, {file = "nest_asyncio-1.6.0.tar.gz", hash = "sha256:6f172d5449aca15afd6c646851f4e31e02c598d553a667e38cafa997cfec55fe"}, @@ -3228,6 +3364,7 @@ version = "1.9.1" description = "Node.js virtual environment builder" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" +groups = ["dev"] files = [ {file = "nodeenv-1.9.1-py2.py3-none-any.whl", hash = "sha256:ba11c9782d29c27c70ffbdda2d7415098754709be8a7056d79a737cd901155c9"}, {file = "nodeenv-1.9.1.tar.gz", hash = "sha256:6ec12890a2dab7946721edbfbcd91f3319c6ccc9aec47be7c7e6b7011ee6645f"}, @@ -3239,6 +3376,7 @@ version = "0.60.0" description = "compiling Python code using LLVM" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "numba-0.60.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:5d761de835cd38fb400d2c26bb103a2726f548dc30368853121d66201672e651"}, {file = "numba-0.60.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:159e618ef213fba758837f9837fb402bbe65326e60ba0633dbe6c7f274d42c1b"}, @@ -3273,6 +3411,7 @@ version = "1.26.4" description = "Fundamental package for array computing in Python" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "numpy-1.26.4-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:9ff0f4f29c51e2803569d7a51c2304de5554655a60c5d776e35b4a41413830d0"}, {file = "numpy-1.26.4-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:2e4ee3380d6de9c9ec04745830fd9e2eccb3e6cf790d39d7b98ffd19b0dd754a"}, @@ -3318,6 +3457,7 @@ version = "3.2.2" description = "A generic, spec-compliant, thorough implementation of the OAuth request-signing logic" optional = false python-versions = ">=3.6" +groups = ["main"] files = [ {file = "oauthlib-3.2.2-py3-none-any.whl", hash = "sha256:8139f29aac13e25d502680e9e19963e83f16838d48a0d71c287fe40e7067fbca"}, {file = "oauthlib-3.2.2.tar.gz", hash = "sha256:9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918"}, @@ -3334,6 +3474,7 @@ version = "2.3.0" description = "A flexible configuration library" optional = false python-versions = ">=3.6" +groups = ["main"] files = [ {file = "omegaconf-2.3.0-py3-none-any.whl", hash = "sha256:7b4df175cdb08ba400f45cae3bdcae7ba8365db4d165fc65fd04b050ab63b46b"}, {file = "omegaconf-2.3.0.tar.gz", hash = "sha256:d5d4b6d29955cc50ad50c46dc269bcd92c6e00f5f90d23ab5fee7bfca4ba4cc7"}, @@ -3349,6 +3490,7 @@ version = "3.10.12" description = "Fast, correct Python JSON library supporting dataclasses, datetimes, and numpy" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "orjson-3.10.12-cp310-cp310-macosx_10_15_x86_64.macosx_11_0_arm64.macosx_10_15_universal2.whl", hash = "sha256:ece01a7ec71d9940cc654c482907a6b65df27251255097629d0dea781f255c6d"}, {file = "orjson-3.10.12-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:c34ec9aebc04f11f4b978dd6caf697a2df2dd9b47d35aa4cc606cabcb9df69d7"}, @@ -3433,6 +3575,7 @@ version = "24.2" description = "Core utilities for Python packages" optional = false python-versions = ">=3.8" +groups = ["main", "dev", "docs", "tests"] files = [ {file = "packaging-24.2-py3-none-any.whl", hash = "sha256:09abb1bccd265c01f4a3aa3f7a7db064b36514d2cba19a2f694fe6150451a759"}, {file = "packaging-24.2.tar.gz", hash = "sha256:c228a6dc5e932d346bc5739379109d49e8853dd8223571c7c5b55260edc0b97f"}, @@ -3444,6 +3587,7 @@ version = "0.5.7" description = "Divides large result sets into pages for easier browsing" optional = false python-versions = "*" +groups = ["docs"] files = [ {file = "paginate-0.5.7-py2.py3-none-any.whl", hash = "sha256:b885e2af73abcf01d9559fd5216b57ef722f8c42affbb63942377668e35c7591"}, {file = "paginate-0.5.7.tar.gz", hash = "sha256:22bd083ab41e1a8b4f3690544afb2c60c25e5c9a63a30fa2f483f6c60c8e5945"}, @@ -3459,6 +3603,7 @@ version = "2.2.3" description = "Powerful data structures for data analysis, time series, and statistics" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = 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"sha256:ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f"}, @@ -3641,6 +3793,7 @@ version = "11.0.0" description = "Python Imaging Library (Fork)" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "pillow-11.0.0-cp310-cp310-macosx_10_10_x86_64.whl", hash = "sha256:6619654954dc4936fcff82db8eb6401d3159ec6be81e33c6000dfd76ae189947"}, {file = "pillow-11.0.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:b3c5ac4bed7519088103d9450a1107f76308ecf91d6dabc8a33a2fcfb18d0fba"}, @@ -3733,6 +3886,7 @@ 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 = ">=3.8" +groups = ["main", "dev", "docs"] files = [ {file = "platformdirs-4.3.6-py3-none-any.whl", hash = "sha256:73e575e1408ab8103900836b97580d5307456908a03e92031bab39e4554cc3fb"}, {file = "platformdirs-4.3.6.tar.gz", hash = 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portalocker recipe for easy usage" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "portalocker-2.10.1-py3-none-any.whl", hash = "sha256:53a5984ebc86a025552264b459b46a2086e269b21823cb572f8f28ee759e45bf"}, {file = "portalocker-2.10.1.tar.gz", hash = "sha256:ef1bf844e878ab08aee7e40184156e1151f228f103aa5c6bd0724cc330960f8f"}, @@ -3798,6 +3955,7 @@ version = "4.0.1" description = "A framework for managing and maintaining multi-language pre-commit hooks." optional = false python-versions = ">=3.9" +groups = ["dev"] files = [ {file = "pre_commit-4.0.1-py2.py3-none-any.whl", hash = "sha256:efde913840816312445dc98787724647c65473daefe420785f885e8ed9a06878"}, {file = "pre_commit-4.0.1.tar.gz", hash = "sha256:80905ac375958c0444c65e9cebebd948b3cdb518f335a091a670a89d652139d2"}, @@ -3816,6 +3974,7 @@ version = "0.0.7" description = "Properly pprint of nested objects" optional = false python-versions = "*" +groups = ["dev"] files = [ {file = 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"sha256:51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719"}, @@ -4046,6 +4214,7 @@ version = "0.10.9.5" description = "Enables Python programs to dynamically access arbitrary Java objects" optional = false python-versions = "*" +groups = ["main"] files = [ {file = "py4j-0.10.9.5-py2.py3-none-any.whl", hash = "sha256:52d171a6a2b031d8a5d1de6efe451cf4f5baff1a2819aabc3741c8406539ba04"}, {file = "py4j-0.10.9.5.tar.gz", hash = "sha256:276a4a3c5a2154df1860ef3303a927460e02e97b047dc0a47c1c3fb8cce34db6"}, @@ -4057,6 +4226,7 @@ version = "18.1.0" description = "Python library for Apache Arrow" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "pyarrow-18.1.0-cp310-cp310-macosx_12_0_arm64.whl", hash = "sha256:e21488d5cfd3d8b500b3238a6c4b075efabc18f0f6d80b29239737ebd69caa6c"}, {file = "pyarrow-18.1.0-cp310-cp310-macosx_12_0_x86_64.whl", hash = "sha256:b516dad76f258a702f7ca0250885fc93d1fa5ac13ad51258e39d402bd9e2e1e4"}, @@ -4111,6 +4281,7 @@ version = "0.6.1" description = "Pure-Python implementation of ASN.1 types and DER/BER/CER codecs (X.208)" optional = false python-versions = ">=3.8" +groups = ["main", "dev"] files = [ {file = "pyasn1-0.6.1-py3-none-any.whl", hash = "sha256:0d632f46f2ba09143da3a8afe9e33fb6f92fa2320ab7e886e2d0f7672af84629"}, {file = "pyasn1-0.6.1.tar.gz", hash = "sha256:6f580d2bdd84365380830acf45550f2511469f673cb4a5ae3857a3170128b034"}, @@ -4122,6 +4293,7 @@ version = "0.4.1" description = "A collection of ASN.1-based protocols modules" optional = false python-versions = ">=3.8" +groups = ["main", "dev"] files = [ {file = "pyasn1_modules-0.4.1-py3-none-any.whl", hash = "sha256:49bfa96b45a292b711e986f222502c1c9a5e1f4e568fc30e2574a6c7d07838fd"}, {file = "pyasn1_modules-0.4.1.tar.gz", hash = "sha256:c28e2dbf9c06ad61c71a075c7e0f9fd0f1b0bb2d2ad4377f240d33ac2ab60a7c"}, @@ -4136,6 +4308,7 @@ version = "4.5.0" description = "Python interface for c-ares" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "pycares-4.5.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:13a82fad8239d6fbcf916099bee17d8b5666d0ddb77dace431e0f7961c9427ab"}, {file = "pycares-4.5.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:fefc7bebbe39b2e3b4b9615471233a8f7356b96129a7db9030313a3ae4ecc42d"}, @@ -4222,6 +4395,7 @@ version = "2.12.1" description = "Python style guide checker" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "pycodestyle-2.12.1-py2.py3-none-any.whl", hash = "sha256:46f0fb92069a7c28ab7bb558f05bfc0110dac69a0cd23c61ea0040283a9d78b3"}, {file = "pycodestyle-2.12.1.tar.gz", hash = "sha256:6838eae08bbce4f6accd5d5572075c63626a15ee3e6f842df996bf62f6d73521"}, @@ -4233,10 +4407,12 @@ version = "2.22" description = "C parser in Python" optional = false python-versions = ">=3.8" +groups = ["main", "dev"] files = [ {file = "pycparser-2.22-py3-none-any.whl", hash = "sha256:c3702b6d3dd8c7abc1afa565d7e63d53a1d0bd86cdc24edd75470f4de499cfcc"}, {file = 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"sha256:bf68f88be5948afea3197eb83f72e554ea0e7888cb606b5d30df6fe7151bd0bf"}, @@ -4400,6 +4580,7 @@ version = "3.2.0" description = "passive checker of Python programs" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "pyflakes-3.2.0-py2.py3-none-any.whl", hash = "sha256:84b5be138a2dfbb40689ca07e2152deb896a65c3a3e24c251c5c62489568074a"}, {file = "pyflakes-3.2.0.tar.gz", hash = "sha256:1c61603ff154621fb2a9172037d84dca3500def8c8b630657d1701f026f8af3f"}, @@ -4411,6 +4592,7 @@ version = "2.18.0" description = "Pygments is a syntax highlighting package written in Python." optional = false python-versions = ">=3.8" +groups = ["main", "dev", "docs"] files = [ {file = "pygments-2.18.0-py3-none-any.whl", hash = "sha256:b8e6aca0523f3ab76fee51799c488e38782ac06eafcf95e7ba832985c8e7b13a"}, {file = "pygments-2.18.0.tar.gz", hash = "sha256:786ff802f32e91311bff3889f6e9a86e81505fe99f2735bb6d60ae0c5004f199"}, @@ -4425,6 +4607,7 @@ version = "2.10.1" description = "JSON Web Token implementation in Python" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "PyJWT-2.10.1-py3-none-any.whl", hash = "sha256:dcdd193e30abefd5debf142f9adfcdd2b58004e644f25406ffaebd50bd98dacb"}, {file = "pyjwt-2.10.1.tar.gz", hash = "sha256:3cc5772eb20009233caf06e9d8a0577824723b44e6648ee0a2aedb6cf9381953"}, @@ -4445,6 +4628,7 @@ version = "0.4.1" description = "Pure-python implementation of UCSC ``liftOver`` genome coordinate conversion." optional = false python-versions = "*" +groups = ["main"] files = [ {file = "pyliftover-0.4.1-py3-none-any.whl", hash = "sha256:49ef8938010d2e934abb483d3ef8073897ed6b88bcd978c486c8f7631c24dbc1"}, {file = "pyliftover-0.4.1.tar.gz", hash = "sha256:33ad187e35d1b6662ba446432f4dd1a808ac2914ce1645eef37598fa5a3860cd"}, @@ -4456,6 +4640,7 @@ version = "10.7.1" description = "Extension pack for Python Markdown." optional = false python-versions = ">=3.8" +groups = ["docs"] files = [ {file = 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+4694,7 @@ version = "8.3.4" description = "pytest: simple powerful testing with Python" optional = false python-versions = ">=3.8" +groups = ["tests"] files = [ {file = "pytest-8.3.4-py3-none-any.whl", hash = "sha256:50e16d954148559c9a74109af1eaf0c945ba2d8f30f0a3d3335edde19788b6f6"}, {file = "pytest-8.3.4.tar.gz", hash = "sha256:965370d062bce11e73868e0335abac31b4d3de0e82f4007408d242b4f8610761"}, @@ -4529,6 +4717,7 @@ version = "6.0.0" description = "Pytest plugin for measuring coverage." optional = false python-versions = ">=3.9" +groups = ["tests"] files = [ {file = "pytest-cov-6.0.0.tar.gz", hash = "sha256:fde0b595ca248bb8e2d76f020b465f3b107c9632e6a1d1705f17834c89dcadc0"}, {file = "pytest_cov-6.0.0-py3-none-any.whl", hash = "sha256:eee6f1b9e61008bd34975a4d5bab25801eb31898b032dd55addc93e96fcaaa35"}, @@ -4547,6 +4736,7 @@ version = "1.0.0" description = "pytest-sugar is a plugin for pytest that changes the default look and feel of pytest (e.g. progressbar, show tests that fail instantly)." optional = false python-versions = "*" +groups = ["tests"] files = [ {file = "pytest-sugar-1.0.0.tar.gz", hash = "sha256:6422e83258f5b0c04ce7c632176c7732cab5fdb909cb39cca5c9139f81276c0a"}, {file = "pytest_sugar-1.0.0-py3-none-any.whl", hash = "sha256:70ebcd8fc5795dc457ff8b69d266a4e2e8a74ae0c3edc749381c64b5246c8dfd"}, @@ -4566,6 +4756,7 @@ version = "3.6.1" description = "pytest xdist plugin for distributed testing, most importantly across multiple CPUs" optional = false python-versions = ">=3.8" +groups = ["tests"] files = [ {file = "pytest_xdist-3.6.1-py3-none-any.whl", hash = "sha256:9ed4adfb68a016610848639bb7e02c9352d5d9f03d04809919e2dafc3be4cca7"}, {file = "pytest_xdist-3.6.1.tar.gz", hash = "sha256:ead156a4db231eec769737f57668ef58a2084a34b2e55c4a8fa20d861107300d"}, @@ -4586,6 +4777,7 @@ version = "2.9.0.post0" description = "Extensions to the standard Python datetime module" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" +groups = ["main", "dev", "docs"] files = [ {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"}, @@ -4600,6 +4792,7 @@ version = "2.0.7" description = "A python library adding a json log formatter" optional = false python-versions = ">=3.6" +groups = ["main"] files = [ {file = "python-json-logger-2.0.7.tar.gz", hash = "sha256:23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c"}, {file = "python_json_logger-2.0.7-py3-none-any.whl", hash = "sha256:f380b826a991ebbe3de4d897aeec42760035ac760345e57b812938dc8b35e2bd"}, @@ -4611,6 +4804,7 @@ version = "2024.2" description = "World timezone definitions, modern and historical" optional = false python-versions = "*" +groups = ["main", "docs"] files = [ {file = "pytz-2024.2-py2.py3-none-any.whl", hash = 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platform_python_implementation != \"PyPy\""} [[package]] name = "pyyaml" @@ -4649,6 +4845,7 @@ version = "6.0.2" description = "YAML parser and emitter for Python" optional = false python-versions = ">=3.8" +groups = ["main", "dev", "docs"] files = [ {file = "PyYAML-6.0.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:0a9a2848a5b7feac301353437eb7d5957887edbf81d56e903999a75a3d743086"}, {file = "PyYAML-6.0.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:29717114e51c84ddfba879543fb232a6ed60086602313ca38cce623c1d62cfbf"}, @@ -4711,6 +4908,7 @@ version = "0.1" description = "A custom YAML tag for referencing environment variables in YAML files. " optional = false python-versions = ">=3.6" +groups = ["docs"] files = [ {file = "pyyaml_env_tag-0.1-py3-none-any.whl", hash = "sha256:af31106dec8a4d68c60207c1886031cbf839b68aa7abccdb19868200532c2069"}, {file = "pyyaml_env_tag-0.1.tar.gz", hash = "sha256:70092675bda14fdec33b31ba77e7543de9ddc88f2e5b99160396572d11525bdb"}, @@ -4725,6 +4923,7 @@ version = "26.2.0" description = "Python bindings for 0MQ" optional = false python-versions = ">=3.7" +groups = ["dev"] files = [ {file = "pyzmq-26.2.0-cp310-cp310-macosx_10_15_universal2.whl", hash = "sha256:ddf33d97d2f52d89f6e6e7ae66ee35a4d9ca6f36eda89c24591b0c40205a3629"}, {file = "pyzmq-26.2.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:dacd995031a01d16eec825bf30802fceb2c3791ef24bcce48fa98ce40918c27b"}, @@ -4846,6 +5045,7 @@ version = "2024.11.6" description = "Alternative regular expression module, to replace re." optional = false python-versions = ">=3.8" +groups = ["main", "docs"] files = [ {file = 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python-versions = ">=3.6.3,<4.0.0" +groups = ["main"] files = [ {file = "rich-12.6.0-py3-none-any.whl", hash = "sha256:a4eb26484f2c82589bd9a17c73d32a010b1e29d89f1604cd9bf3a2097b81bb5e"}, {file = "rich-12.6.0.tar.gz", hash = "sha256:ba3a3775974105c221d31141f2c116f4fd65c5ceb0698657a11e9f295ec93fd0"}, @@ -5006,6 +5225,7 @@ version = "4.9" description = "Pure-Python RSA implementation" optional = false python-versions = ">=3.6,<4" +groups = ["main", "dev"] files = [ {file = "rsa-4.9-py3-none-any.whl", hash = "sha256:90260d9058e514786967344d0ef75fa8727eed8a7d2e43ce9f4bcf1b536174f7"}, {file = "rsa-4.9.tar.gz", hash = "sha256:e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21"}, @@ -5020,6 +5240,7 @@ version = "0.8.2" description = "An extremely fast Python linter and code formatter, written in Rust." optional = false python-versions = ">=3.7" +groups = ["dev"] files = [ {file = "ruff-0.8.2-py3-none-linux_armv6l.whl", hash = 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@@ -5331,6 +5558,7 @@ version = "8.1.0" description = "the blessed package to manage your versions by scm tags" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "setuptools_scm-8.1.0-py3-none-any.whl", hash = "sha256:897a3226a6fd4a6eb2f068745e49733261a21f70b1bb28fce0339feb978d9af3"}, {file = "setuptools_scm-8.1.0.tar.gz", hash = "sha256:42dea1b65771cba93b7a515d65a65d8246e560768a66b9106a592c8e7f26c8a7"}, @@ -5352,6 +5580,7 @@ version = "0.46.0" description = "A unified approach to explain the output of any machine learning model." optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "shap-0.46.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:905b2d7a0262ef820785a7c0e3c7f24c9d281e6f934edb65cbe811fe0e971187"}, {file = "shap-0.46.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:bccbb30ffbf8b9ed53e476d0c1319fdfcbeac455fe9df277fb0d570d92790e80"}, @@ -5405,6 +5634,7 @@ version = "1.5.4" description = "Tool to Detect Surrounding Shell" optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "shellingham-1.5.4-py2.py3-none-any.whl", hash = "sha256:7ecfff8f2fd72616f7481040475a65b2bf8af90a56c89140852d1120324e8686"}, {file = "shellingham-1.5.4.tar.gz", hash = "sha256:8dbca0739d487e5bd35ab3ca4b36e11c4078f3a234bfce294b0a0291363404de"}, @@ -5416,6 +5646,7 @@ version = "1.17.0" description = "Python 2 and 3 compatibility utilities" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" +groups = ["main", "dev", "docs"] files = [ {file = "six-1.17.0-py2.py3-none-any.whl", hash = "sha256:4721f391ed90541fddacab5acf947aa0d3dc7d27b2e1e8eda2be8970586c3274"}, {file = "six-1.17.0.tar.gz", hash = "sha256:ff70335d468e7eb6ec65b95b99d3a2836546063f63acc5171de367e834932a81"}, @@ -5427,6 +5658,7 @@ version = "0.11.0" description = "A set of tools, related to machine learning in production." optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = 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"Extract data from python stack frames and tracebacks for informative displays" optional = false python-versions = "*" +groups = ["dev"] files = [ {file = "stack_data-0.6.3-py3-none-any.whl", hash = "sha256:d5558e0c25a4cb0853cddad3d77da9891a08cb85dd9f9f91b9f8cd66e511e695"}, {file = "stack_data-0.6.3.tar.gz", hash = "sha256:836a778de4fec4dcd1dcd89ed8abff8a221f58308462e1c4aa2a3cf30148f0b9"}, @@ -5510,6 +5747,7 @@ version = "0.9.0" description = "Pretty-print tabular data" optional = false python-versions = ">=3.7" +groups = ["main", "dev"] files = [ {file = "tabulate-0.9.0-py3-none-any.whl", hash = "sha256:024ca478df22e9340661486f85298cff5f6dcdba14f3813e8830015b9ed1948f"}, {file = "tabulate-0.9.0.tar.gz", hash = "sha256:0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c"}, @@ -5524,6 +5762,7 @@ version = "9.0.0" description = "Retry code until it succeeds" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "tenacity-9.0.0-py3-none-any.whl", hash 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Easy to code. Based on Python type hints." optional = false python-versions = ">=3.7" +groups = ["main"] files = [ {file = "typer-0.15.1-py3-none-any.whl", hash = "sha256:7994fb7b8155b64d3402518560648446072864beefd44aa2dc36972a5972e847"}, {file = "typer-0.15.1.tar.gz", hash = "sha256:a0588c0a7fa68a1978a069818657778f86abe6ff5ea6abf472f940a08bfe4f0a"}, @@ -5672,12 +5918,25 @@ rich = ">=10.11.0" shellingham = ">=1.3.0" typing-extensions = ">=3.7.4.3" +[[package]] +name = "types-setuptools" +version = "75.8.0.20250110" +description = "Typing stubs for setuptools" +optional = false +python-versions = ">=3.8" +groups = ["dev"] +files = [ + {file = "types_setuptools-75.8.0.20250110-py3-none-any.whl", hash = "sha256:a9f12980bbf9bcdc23ecd80755789085bad6bfce4060c2275bc2b4ca9f2bc480"}, + {file = "types_setuptools-75.8.0.20250110.tar.gz", hash = "sha256:96f7ec8bbd6e0a54ea180d66ad68ad7a1d7954e7281a710ea2de75e355545271"}, +] + [[package]] name = "typing-extensions" version = "4.9.0" description = "Backported and Experimental Type Hints for Python 3.8+" optional = false python-versions = ">=3.8" +groups = ["main", "dev"] files = [ {file = "typing_extensions-4.9.0-py3-none-any.whl", hash = "sha256:af72aea155e91adfc61c3ae9e0e342dbc0cba726d6cba4b6c72c1f34e47291cd"}, {file = "typing_extensions-4.9.0.tar.gz", hash = "sha256:23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783"}, @@ -5689,6 +5948,7 @@ version = "2024.2" description = "Provider of IANA time zone data" optional = false python-versions = ">=2" +groups = ["main"] files = [ {file = "tzdata-2024.2-py2.py3-none-any.whl", hash = "sha256:a48093786cdcde33cad18c2555e8532f34422074448fbc874186f0abd79565cd"}, {file = "tzdata-2024.2.tar.gz", hash = "sha256:7d85cc416e9382e69095b7bdf4afd9e3880418a2413feec7069d533d6b4e31cc"}, @@ -5700,6 +5960,7 @@ version = "2.2.3" description = "HTTP library with thread-safe connection pooling, file post, and more." optional = false python-versions = ">=3.8" +groups = ["main", "dev", "docs"] files = [ 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"1.17.0" description = "Module for decorators, wrappers and monkey patching." optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "wrapt-1.17.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:2a0c23b8319848426f305f9cb0c98a6e32ee68a36264f45948ccf8e7d2b941f8"}, {file = "wrapt-1.17.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:b1ca5f060e205f72bec57faae5bd817a1560fcfc4af03f414b08fa29106b7e2d"}, @@ -5976,6 +6245,7 @@ version = "2024.9.0" description = "Source of XYZ tiles providers" optional = false python-versions = ">=3.8" +groups = ["main"] files = [ {file = "xyzservices-2024.9.0-py3-none-any.whl", hash = "sha256:776ae82b78d6e5ca63dd6a94abb054df8130887a4a308473b54a6bd364de8644"}, {file = "xyzservices-2024.9.0.tar.gz", hash = "sha256:68fb8353c9dbba4f1ff6c0f2e5e4e596bb9e1db7f94f4f7dfbcb26e25aa66fde"}, @@ -5987,6 +6257,7 @@ version = "1.33.0" description = "A linter for YAML files." optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ {file = "yamllint-1.33.0-py3-none-any.whl", hash = "sha256:28a19f5d68d28d8fec538a1db21bb2d84c7dc2e2ea36266da8d4d1c5a683814d"}, {file = "yamllint-1.33.0.tar.gz", hash = "sha256:2dceab9ef2d99518a2fcf4ffc964d44250ac4459be1ba3ca315118e4a1a81f7d"}, @@ -6005,6 +6276,7 @@ version = "1.18.3" description = "Yet another URL library" optional = false python-versions = ">=3.9" +groups = ["main"] files = [ {file = "yarl-1.18.3-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:7df647e8edd71f000a5208fe6ff8c382a1de8edfbccdbbfe649d263de07d8c34"}, {file = "yarl-1.18.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:c69697d3adff5aa4f874b19c0e4ed65180ceed6318ec856ebc423aa5850d84f7"}, @@ -6096,6 +6368,6 @@ multidict = ">=4.0" propcache = ">=0.2.0" [metadata] -lock-version = "2.0" +lock-version = "2.1" python-versions = ">=3.10, <3.11" -content-hash = "31b6cab2e7afafb35fa84376f0428e6e5b4eabe7a9ca28a7bf197391ab7b8834" +content-hash = "ffa2d7b08bb50d41e5f6dfb2db6049061e79139ff04595d7960b853d889b4022" diff --git a/pyproject.toml b/pyproject.toml index 4e6c97cb5..185d548af 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,43 +1,45 @@ -[tool.poetry] +[project] name = "gentropy" # !! version is managed by semantic_release version = "0.0.0" description = "Open Targets python framework for post-GWAS analysis" -authors = ["Open Targets core team"] +authors = [ + { name = "Open Targets core team", email = "data@opentargets.org" } +] license = "Apache-2.0" readme = "README.md" documentation = "https://opentargets.github.io/gentropy/" -repository = "https://github.com/opentargets/gentropy" packages = [{ include = "gentropy", from = "src" }] +requires-poetry = ">=2.0" +requires-python = ">=3.10, <3.11" +dependencies = [ + "pyspark (==3.3.4)", + "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 (>=0.19.0, <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[gcp,parquet] (>=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.urls] +[project.urls] +Source = "https://github.com/opentargets/gentropy" "Bug Tracker" = "http://github.com/opentargets/issues" -"Funding" = "https://www.opentargets.org" -"Documentation" = "https://opentargets.github.io/gentropy/" +Funding = "https://www.opentargets.org" +Documentation = "https://opentargets.github.io/gentropy/" -[tool.poetry.scripts] +[project.scripts] gentropy = "gentropy.cli:main" -[tool.poetry.dependencies] -python = ">=3.10, <3.11" -pyspark = "3.3.4" -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 = ">=0.19.0, <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, <1.6.0" mkdocstrings-python = ">=1.12.2, <1.13.0" @@ -67,7 +69,7 @@ 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, <0.1.0" -deptry = ">=0.12,<0.21" +deptry = ">=0.22.0, <0.23.0" yamllint = ">=1.33.0, <1.36.0" pre-commit = ">=4.0.0, <4.1.0" mypy = ">=1.13, <1.14" diff --git a/src/gentropy/colocalisation.py b/src/gentropy/colocalisation.py index 6a4568397..282412525 100644 --- a/src/gentropy/colocalisation.py +++ b/src/gentropy/colocalisation.py @@ -3,7 +3,7 @@ from __future__ import annotations from functools import partial -from typing import Any, Type +from typing import Any from pyspark.sql.functions import col @@ -77,14 +77,14 @@ def __init__( @classmethod def _get_colocalisation_class( cls, method: str - ) -> Type[ColocalisationMethodInterface]: + ) -> type[ColocalisationMethodInterface]: """Get colocalisation class. Args: method (str): Colocalisation method. Returns: - Type[ColocalisationMethodInterface]: Class that implements the ColocalisationMethodInterface. + type[ColocalisationMethodInterface]: Class that implements the ColocalisationMethodInterface. Raises: ValueError: if method not available. @@ -96,5 +96,4 @@ def _get_colocalisation_class( method = method.lower() if method not in cls.__coloc_methods__: raise ValueError(f"Colocalisation method {method} not available.") - coloc_method = cls.__coloc_methods__[method] - return coloc_method + return cls.__coloc_methods__[method] diff --git a/src/gentropy/common/spark_helpers.py b/src/gentropy/common/spark_helpers.py index 64a8bceb7..fd84a9810 100644 --- a/src/gentropy/common/spark_helpers.py +++ b/src/gentropy/common/spark_helpers.py @@ -4,9 +4,10 @@ import re import sys +from collections.abc import Callable, Iterable from functools import reduce, wraps from itertools import chain -from typing import TYPE_CHECKING, Any, Callable, Iterable, Optional, TypeVar +from typing import TYPE_CHECKING, Any, Optional, TypeVar import pyspark.sql.functions as f import pyspark.sql.types as t diff --git a/src/gentropy/config.py b/src/gentropy/config.py index 0d9d6abf1..0c031395c 100644 --- a/src/gentropy/config.py +++ b/src/gentropy/config.py @@ -2,7 +2,7 @@ import os from dataclasses import dataclass, field -from typing import Any, ClassVar, List, TypedDict +from typing import Any, ClassVar, TypedDict from hail import __file__ as hail_location from hydra.core.config_store import ConfigStore @@ -17,8 +17,7 @@ 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" @@ -28,7 +27,7 @@ class StepConfig: """Base step configuration.""" session: SessionConfig - defaults: List[Any] = field( + defaults: list[Any] = field( default_factory=lambda: [{"session": "base_session"}, "_self_"] ) @@ -40,8 +39,7 @@ 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" @@ -126,8 +124,7 @@ 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" @@ -681,8 +678,7 @@ 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) @@ -716,8 +712,7 @@ 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( @@ -735,8 +730,7 @@ 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( @@ -769,7 +763,5 @@ 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/dataset/l2g_feature_matrix.py b/src/gentropy/dataset/l2g_feature_matrix.py index 8c3d97e88..596d5b480 100644 --- a/src/gentropy/dataset/l2g_feature_matrix.py +++ b/src/gentropy/dataset/l2g_feature_matrix.py @@ -3,7 +3,7 @@ from __future__ import annotations from functools import reduce -from typing import TYPE_CHECKING, Type +from typing import TYPE_CHECKING import pyspark.sql.functions as f from pyspark.sql import Window @@ -55,7 +55,7 @@ def __init__( @classmethod def from_features_list( - cls: Type[L2GFeatureMatrix], + cls: type[L2GFeatureMatrix], study_loci_to_annotate: StudyLocus | L2GGoldStandard, features_list: list[str], features_input_loader: L2GFeatureInputLoader, diff --git a/src/gentropy/dataset/l2g_gold_standard.py b/src/gentropy/dataset/l2g_gold_standard.py index 4acf96cd2..af34cf648 100644 --- a/src/gentropy/dataset/l2g_gold_standard.py +++ b/src/gentropy/dataset/l2g_gold_standard.py @@ -3,7 +3,7 @@ from __future__ import annotations from dataclasses import dataclass -from typing import TYPE_CHECKING, Type +from typing import TYPE_CHECKING import pyspark.sql.functions as f from pyspark.sql import Window @@ -74,7 +74,7 @@ def get_schema(cls: type[L2GGoldStandard]) -> StructType: @classmethod def process_gene_interactions( - cls: Type[L2GGoldStandard], interactions: DataFrame + cls: type[L2GGoldStandard], interactions: DataFrame ) -> DataFrame: """Extract top scoring gene-gene interaction from the interactions dataset of the Platform. diff --git a/src/gentropy/dataset/l2g_prediction.py b/src/gentropy/dataset/l2g_prediction.py index 915b2b7dc..02818b7db 100644 --- a/src/gentropy/dataset/l2g_prediction.py +++ b/src/gentropy/dataset/l2g_prediction.py @@ -3,7 +3,7 @@ from __future__ import annotations from dataclasses import dataclass -from typing import TYPE_CHECKING, Type +from typing import TYPE_CHECKING import pyspark.sql.functions as f from pyspark.sql import DataFrame @@ -40,7 +40,7 @@ def get_schema(cls: type[L2GPrediction]) -> StructType: @classmethod def from_credible_set( - cls: Type[L2GPrediction], + cls: type[L2GPrediction], session: Session, credible_set: StudyLocus, feature_matrix: L2GFeatureMatrix, diff --git a/src/gentropy/datasource/gwas_catalog/study_splitter.py b/src/gentropy/datasource/gwas_catalog/study_splitter.py index 0b11e797a..85cb92e28 100644 --- a/src/gentropy/datasource/gwas_catalog/study_splitter.py +++ b/src/gentropy/datasource/gwas_catalog/study_splitter.py @@ -2,7 +2,7 @@ from __future__ import annotations -from typing import TYPE_CHECKING, Tuple +from typing import TYPE_CHECKING import pyspark.sql.functions as f from pyspark.sql.window import Window @@ -84,7 +84,7 @@ def split( cls: type[GWASCatalogStudySplitter], studies: StudyIndexGWASCatalog, associations: StudyLocusGWASCatalog, - ) -> Tuple[StudyIndexGWASCatalog, StudyLocusGWASCatalog]: + ) -> tuple[StudyIndexGWASCatalog, StudyLocusGWASCatalog]: """Splitting multi-trait GWAS Catalog studies. If assigned disease of the study and the association don't agree, we assume the study needs to be split. @@ -95,7 +95,7 @@ def split( associations (StudyLocusGWASCatalog): GWAS Catalog associations. Returns: - Tuple[StudyIndexGWASCatalog, StudyLocusGWASCatalog]: Split studies and associations. + tuple[StudyIndexGWASCatalog, StudyLocusGWASCatalog]: Split studies and associations. """ # Composite of studies and associations to resolve scattered information st_ass = ( diff --git a/src/gentropy/datasource/open_targets/l2g_gold_standard.py b/src/gentropy/datasource/open_targets/l2g_gold_standard.py index 21edcc201..ac2599091 100644 --- a/src/gentropy/datasource/open_targets/l2g_gold_standard.py +++ b/src/gentropy/datasource/open_targets/l2g_gold_standard.py @@ -2,8 +2,6 @@ from __future__ import annotations -from typing import Type - import pyspark.sql.functions as f from pyspark.sql import DataFrame @@ -24,7 +22,7 @@ class OpenTargetsL2GGoldStandard: @classmethod def parse_positive_curation( - cls: Type[OpenTargetsL2GGoldStandard], gold_standard_curation: DataFrame + cls: type[OpenTargetsL2GGoldStandard], gold_standard_curation: DataFrame ) -> DataFrame: """Parse positive set from gold standard curation. @@ -60,7 +58,7 @@ def parse_positive_curation( @classmethod def expand_gold_standard_with_negatives( - cls: Type[OpenTargetsL2GGoldStandard], + cls: type[OpenTargetsL2GGoldStandard], positive_set: DataFrame, variant_index: VariantIndex, ) -> DataFrame: diff --git a/src/gentropy/method/l2g/feature_factory.py b/src/gentropy/method/l2g/feature_factory.py index fe792058a..ca1ffb339 100644 --- a/src/gentropy/method/l2g/feature_factory.py +++ b/src/gentropy/method/l2g/feature_factory.py @@ -3,7 +3,8 @@ from __future__ import annotations -from typing import Any, Iterator, Mapping +from typing import Any +from collections.abc import Iterator, Mapping from gentropy.dataset.l2g_features.colocalisation import ( EQtlColocClppMaximumFeature, diff --git a/src/gentropy/method/l2g/model.py b/src/gentropy/method/l2g/model.py index 1f18f227f..c1aea9e08 100644 --- a/src/gentropy/method/l2g/model.py +++ b/src/gentropy/method/l2g/model.py @@ -5,7 +5,7 @@ import json from dataclasses import dataclass, field from pathlib import Path -from typing import TYPE_CHECKING, Any, Type +from typing import TYPE_CHECKING, Any import pandas as pd import skops.io as sio @@ -51,7 +51,7 @@ def __post_init__(self: LocusToGeneModel) -> None: self.model.set_params(**self.hyperparameters_dict) @classmethod - def load_from_disk(cls: Type[LocusToGeneModel], path: str) -> LocusToGeneModel: + def load_from_disk(cls: type[LocusToGeneModel], path: str) -> LocusToGeneModel: """Load a fitted model from disk. Args: @@ -83,7 +83,7 @@ def load_from_disk(cls: Type[LocusToGeneModel], path: str) -> LocusToGeneModel: @classmethod def load_from_hub( - cls: Type[LocusToGeneModel], + cls: type[LocusToGeneModel], model_id: str, hf_token: str | None = None, model_name: str = "classifier.skops", diff --git a/tests/gentropy/datasource/finngen/test_finngen_study_index.py b/tests/gentropy/datasource/finngen/test_finngen_study_index.py index 0d0537413..c85629a09 100644 --- a/tests/gentropy/datasource/finngen/test_finngen_study_index.py +++ b/tests/gentropy/datasource/finngen/test_finngen_study_index.py @@ -18,8 +18,8 @@ from gentropy.finngen_studies import FinnGenStudiesStep if TYPE_CHECKING: + from collections.abc import Callable from pathlib import Path - from typing import Callable from pyspark.sql import SparkSession diff --git a/tests/gentropy/step/test_colocalisation_step.py b/tests/gentropy/step/test_colocalisation_step.py index e74dee234..4b06adb69 100644 --- a/tests/gentropy/step/test_colocalisation_step.py +++ b/tests/gentropy/step/test_colocalisation_step.py @@ -1,7 +1,6 @@ """Test colocalisation step.""" from pathlib import Path -from typing import Type import pytest @@ -208,7 +207,7 @@ def _setup(self, session: Session, tmp_path: Path) -> None: ], ) def test_get_colocalisation_class( - self, label: str, expected_method: Type[ColocalisationMethodInterface] + self, label: str, expected_method: type[ColocalisationMethodInterface] ) -> None: """Test _get_colocalisation_class method on ColocalisationStep.""" method = ColocalisationStep._get_colocalisation_class(label) diff --git a/tests/gentropy/test_cli.py b/tests/gentropy/test_cli.py index dbb5a8cac..aeac0c35c 100644 --- a/tests/gentropy/test_cli.py +++ b/tests/gentropy/test_cli.py @@ -14,15 +14,19 @@ def test_main_no_step() -> None: override_key = "step" expected = f"You must specify '{override_key}', e.g, {override_key}=