diff --git a/.github/workflows/make-json.yml b/.github/workflows/make-json.yml index 3499b0ee..e6a937ad 100644 --- a/.github/workflows/make-json.yml +++ b/.github/workflows/make-json.yml @@ -12,22 +12,18 @@ concurrency: jobs: mkjson: runs-on: ubuntu-latest - steps: - - name: Checkout repository - uses: actions/checkout@v4 - - name: setup-yq - run: | - sudo curl -L "https://github.com/mikefarah/yq/releases/download/v4.28.2/yq_linux_amd64" > /usr/local/bin/yq - sudo chmod +x /usr/local/bin/yq - - name: convert to json + - uses: actions/checkout@v5 + - uses: astral-sh/setup-uv@v7 + - name: Execute validation script and create output directory run: | - mkdir build - touch build/.nojekyll - cat packages/**/meta.yaml - yq -o=json packages/**/meta.yaml | jq -s . > build/ecosystem.json + uvx --from ./scripts validate-registry --registry-dir packages --outdir=build + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + FORCE_COLOR: "1" + COLUMNS: "150" - name: Upload GitHub Pages artifact - uses: actions/upload-pages-artifact@v3 + uses: actions/upload-pages-artifact@v4 with: path: "build" diff --git a/.github/workflows/register-template-repos.yml b/.github/workflows/register-template-repos.yml index 40cf2f86..eb8cc40e 100644 --- a/.github/workflows/register-template-repos.yml +++ b/.github/workflows/register-template-repos.yml @@ -10,23 +10,17 @@ jobs: register-template-repos: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v5 with: token: ${{ secrets.BOT_GH_TOKEN }} - - name: Set up Python 3.11 - uses: actions/setup-python@v5 - with: - python-version: "3.11" - cache: "pip" - cache-dependency-path: "**/pyproject.toml" - - name: Install build dependencies - run: python -m pip install --upgrade pip wheel - - name: Install package with scripts - run: pip install ./scripts + - name: Install uv + uses: astral-sh/setup-uv@v7 - name: Update template repo registry - run: register-template-repos template-repos.yml + run: uvx --from ./scripts register-template-repos template-repos.yml env: GITHUB_TOKEN: "${{ secrets.BOT_GH_TOKEN }}" + FORCE_COLOR: "1" + COLUMNS: "150" - uses: EndBug/add-and-commit@v9 with: add: ./template-repos.yml diff --git a/.gitignore b/.gitignore index 636e042e..7f101b64 100644 --- a/.gitignore +++ b/.gitignore @@ -3,3 +3,5 @@ __pycache__/ .*cache/ /.vscode/ +.venv +schema.pyi diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 3f9e75a8..1e3b74c9 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -17,36 +17,64 @@ repos: args: [--fix=lf] - id: trailing-whitespace - id: check-case-conflict - - repo: https://github.com/pre-commit/mirrors-prettier - rev: v4.0.0-alpha.8 + - repo: https://github.com/rbubley/mirrors-prettier + rev: v3.6.2 hooks: - id: prettier # package metadata - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.33.3 + rev: 0.35.0 hooks: - id: check-jsonschema - files: "schema.json" + files: "scripts/src/ecosystem_scripts/schema.json" args: ["--check-metaschema"] - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.33.3 + rev: 0.35.0 hooks: - id: check-jsonschema files: "packages/.*/meta.yaml" - args: ["--schemafile", "schema.json"] + args: ["--schemafile", "scripts/src/ecosystem_scripts/schema.json"] - repo: local hooks: - id: forbid-to-commit name: Check files in `packages` directory entry: | - Only files named `meta.yaml` are permitted in the packages directory + Only `meta.yaml` and logo files are permitted in the packages directory language: fail files: "^packages/.*$" - exclude: "^packages/.*/meta.yaml$" - # template repo registry + exclude: "^packages/.*/(meta.yaml|logo\\..*)$" + # scripts - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.13.0 + rev: v0.14.5 hooks: - - id: ruff + - id: ruff-check args: [--fix, --exit-non-zero-on-fix] + files: ^scripts/.*$ - id: ruff-format + files: ^scripts/.*$ + - repo: https://github.com/tox-dev/pyproject-fmt + rev: v2.11.1 + hooks: + - id: pyproject-fmt + - repo: https://github.com/camptocamp/jsonschema-gentypes + rev: "2.12.0" + hooks: + - id: jsonschema-gentypes + args: + - --json-schema=scripts/src/ecosystem_scripts/schema.json + - --python=scripts/src/ecosystem_scripts/schema.pyi + files: ^scripts/.*/schema.json$ + - repo: https://github.com/pre-commit/mirrors-mypy + rev: v1.18.2 + hooks: + - id: mypy + args: [--config-file=scripts/pyproject.toml, scripts] + pass_filenames: false + additional_dependencies: + - httpx + - types-jsonschema + - pillow + - pygithub + - types-PyYAML + - rich + files: ^scripts/.*$ diff --git a/README.md b/README.md index 541f54fb..e12766ba 100644 --- a/README.md +++ b/README.md @@ -16,9 +16,10 @@ It **does not** imply endorsement or that an in-depth review has been performed. Submit a pull-request adding a `meta.yaml` file for your package to the `packages` directory. -- Please refer to other entries for examples -- The full definition of available fields is available in [`schema.json`](schema.json) - Please copy the checklist from below into the pull request description and answer all questions. +- Please refer to other entries for examples +- The full definition of available fields is available in [`schema.json`](scripts/src/ecosystem_scripts/schema.json) +- You can add a logo in svg/png/webp format if you like. Currently it is not used on our website, though. ## What are the requirements for an ecosystem package? diff --git a/packages/CellAnnotator/meta.yaml b/packages/CellAnnotator/meta.yaml index 366e5cb4..bc84d0f2 100644 --- a/packages/CellAnnotator/meta.yaml +++ b/packages/CellAnnotator/meta.yaml @@ -1,6 +1,6 @@ name: CellAnnotator description: | - CellAnnotator is a leightweight tool to query large language models for cell type labels in scRNA-seq data. It can incorporate prior knowledge, and it creates consistent labels across samples in your study. + CellAnnotator is a lightweight tool to query large language models for cell type labels in scRNA-seq data. It can incorporate prior knowledge, and it creates consistent labels across samples in your study. project_home: https://github.com/quadbio/cell-annotator documentation_home: https://cell-annotator.readthedocs.io/en/latest/ install: @@ -13,6 +13,7 @@ tags: - cell state license: MIT version: v0.1.3 -authors: +contact: - Marius1311 test_command: pip install -e '.[test]' && pytest +category: ecosystem diff --git a/packages/CellCharter/meta.yaml b/packages/CellCharter/meta.yaml index 345ba462..f77a73bc 100644 --- a/packages/CellCharter/meta.yaml +++ b/packages/CellCharter/meta.yaml @@ -15,7 +15,8 @@ tags: - gaussian mixture model license: BSD-3-Clause version: v0.3.1 -authors: +contact: - marcovarrone test_command: | pip install ".[test]" && pytest +category: ecosystem diff --git a/packages/CellMapper/meta.yaml b/packages/CellMapper/meta.yaml index ee06b7b3..32f903cb 100644 --- a/packages/CellMapper/meta.yaml +++ b/packages/CellMapper/meta.yaml @@ -12,6 +12,7 @@ tags: - query-to-reference license: MIT version: v0.1.2 -authors: +contact: - Marius1311 test_command: pip install -e '.[test]' && pytest +category: ecosystem diff --git a/packages/CellOracle/meta.yaml b/packages/CellOracle/meta.yaml index 0375318f..503f0277 100644 --- a/packages/CellOracle/meta.yaml +++ b/packages/CellOracle/meta.yaml @@ -14,8 +14,8 @@ tags: - TF license: Apache-2.0 version: v0.10.12 -authors: - - KenjiKamimoto-wustl122 +contact: + - KenjiKamimoto-ac - sam-morris - cmhct7 test_command: | @@ -42,3 +42,4 @@ test_command: | pip install . # command to run tests pytest -v +category: ecosystem diff --git a/packages/CellRank/meta.yaml b/packages/CellRank/meta.yaml index fe8c414b..fa85b61a 100644 --- a/packages/CellRank/meta.yaml +++ b/packages/CellRank/meta.yaml @@ -17,9 +17,10 @@ tags: - trajectory-generation license: BSD-3-Clause version: v1.5.1 -authors: +contact: - Marius1311 - michalk8 - WeilerP test_command: | pip install ".[test]" && pytest +category: ecosystem diff --git a/packages/Cell_BLAST/meta.yaml b/packages/Cell_BLAST/meta.yaml index 028a294f..f0acb615 100644 --- a/packages/Cell_BLAST/meta.yaml +++ b/packages/Cell_BLAST/meta.yaml @@ -2,7 +2,7 @@ name: Cell_BLAST description: | Cell BLAST is a cell querying tool for single-cell transcriptomics data. project_home: https://github.com/gao-lab/Cell_BLAST -documentation_home: https://cblast.gao-lab.org/doc/index.html +documentation_home: https://cblast.readthedocs.io/en/latest/ publications: - 10.1038/s41467-020-17281-7 install: @@ -11,9 +11,10 @@ tags: - BLAST license: MIT version: v0.3.8 -authors: +contact: - Jeff1995 test_command: | pip install --upgrade pip flit flit install -s cd test && python test.py +category: ecosystem diff --git a/packages/CellphoneDB/meta.yaml b/packages/CellphoneDB/meta.yaml index 738cc542..dc3f69ec 100644 --- a/packages/CellphoneDB/meta.yaml +++ b/packages/CellphoneDB/meta.yaml @@ -20,7 +20,7 @@ tags: - jupyter license: MIT version: v5.0.0 -authors: +contact: - chapuzzo - datasome - ktroule @@ -31,3 +31,4 @@ authors: - zktuong test_command: | git clone git@github.com:ventolab/CellphoneDB.git && pip install cellphonedb && pip install pytest && cd CellphoneDB/cellphonedb/src/tests/ && python3 -m pytest method_tests.py +category: ecosystem diff --git a/packages/Cirrocumulus/meta.yaml b/packages/Cirrocumulus/meta.yaml index b4242ef8..8a0ba053 100644 --- a/packages/Cirrocumulus/meta.yaml +++ b/packages/Cirrocumulus/meta.yaml @@ -12,9 +12,10 @@ tags: - visualization license: BSD-3-Clause version: v1.1.41 -authors: +contact: - joshua-gould - yihming - gouwens test_command: | SETUPTOOLS_SCM_PRETEND_VERSION=0.0.1 pip install .[test,parquet] && pytest +category: ecosystem diff --git a/packages/DoubletDetection/meta.yaml b/packages/DoubletDetection/meta.yaml index b77a370b..38fbf16f 100644 --- a/packages/DoubletDetection/meta.yaml +++ b/packages/DoubletDetection/meta.yaml @@ -13,8 +13,9 @@ tags: - doublet license: MIT version: v4.2 -authors: +contact: - adamgayoso - JonathanShor - ambrosejcarr test_command: pip install ".[test]" && pytest +category: ecosystem diff --git a/packages/GPTBioInsightor/meta.yaml b/packages/GPTBioInsightor/meta.yaml index f65abb9b..8bd6f75e 100644 --- a/packages/GPTBioInsightor/meta.yaml +++ b/packages/GPTBioInsightor/meta.yaml @@ -13,6 +13,7 @@ tags: - AI license: BSD-3-Clause version: v0.3.0 -authors: +contact: - huangsh test_command: pip install "." && pytest +category: ecosystem diff --git a/packages/GRnnData/meta.yaml b/packages/GRnnData/meta.yaml index d3983e8a..3ed6f843 100644 --- a/packages/GRnnData/meta.yaml +++ b/packages/GRnnData/meta.yaml @@ -16,6 +16,7 @@ tags: - utilities license: MIT version: v1.1.4 -authors: - - jkobject (jeremie kalfon) +contact: + - jkobject test_command: pip install . && make test +category: ecosystem diff --git a/packages/LazySlide/meta.yaml b/packages/LazySlide/meta.yaml index ae8c9d5d..52f4a4fc 100644 --- a/packages/LazySlide/meta.yaml +++ b/packages/LazySlide/meta.yaml @@ -11,8 +11,9 @@ tags: - PyTorch license: MIT version: v0.3.0 -authors: +contact: - Mr-Milk - eabila - afrendeiro test_command: uv run task test +category: ecosystem diff --git a/packages/Mowgli/meta.yaml b/packages/Mowgli/meta.yaml index a1a90a0a..02e96f77 100644 --- a/packages/Mowgli/meta.yaml +++ b/packages/Mowgli/meta.yaml @@ -15,6 +15,7 @@ tags: - NMF license: GPL-3.0-only version: v0.2.0 -authors: +contact: - gjhuizing test_command: pip install . && pytest +category: ecosystem diff --git a/packages/Multivelo/meta.yaml b/packages/Multivelo/meta.yaml index bbf9de62..29abbdde 100644 --- a/packages/Multivelo/meta.yaml +++ b/packages/Multivelo/meta.yaml @@ -13,7 +13,8 @@ tags: - rna velocity license: BSD-3-Clause version: 0.1.3 -authors: +contact: - jw156605 - danielee0707 - jacobrepucci +category: ecosystem diff --git a/packages/PEAKQC/meta.yaml b/packages/PEAKQC/meta.yaml index 7ba4957a..7b4350a2 100644 --- a/packages/PEAKQC/meta.yaml +++ b/packages/PEAKQC/meta.yaml @@ -12,6 +12,8 @@ tags: - quality control license: MIT version: 0.1.3 -authors: - - loosolab +contact: + - jan1034 + - mlooso test_command: pip install . && pytest +category: ecosystem diff --git a/packages/PILOT/meta.yaml b/packages/PILOT/meta.yaml index 0fd32877..55a7a222 100644 --- a/packages/PILOT/meta.yaml +++ b/packages/PILOT/meta.yaml @@ -24,27 +24,13 @@ tags: - patient-level license: MIT version: v2.0.6 -authors: - - Mehdi Joodaki - - Mina Shaigan - - Victor Parra - - Roman D. Bülow - - Christoph Kuppe - - David L. Hölscher - - Mingbo Cheng - - James S. Nagai - - Michaël Goedertier - - Nassim Bouteldja - - Vladimir Tesar - - Jonathan Barratt - - Ian S.D. Roberts - - Rosanna Coppo - - Rafael Kramann - - Peter Boor - - Ivan G. Costa +contact: + - mehdijoodaki + - minashaigan test_command: | conda create --name PILOT python=3.11.5 r-base conda activate PILOT pip install pilotpy conda install pytest cd test && pytest test_pilot.py +category: ecosystem diff --git a/packages/ParTIpy/meta.yaml b/packages/ParTIpy/meta.yaml index 75438ffa..19bbc425 100644 --- a/packages/ParTIpy/meta.yaml +++ b/packages/ParTIpy/meta.yaml @@ -13,6 +13,7 @@ tags: - "division of labor" - "representation learning" version: v0.0.04 -authors: +contact: - psl-schaefer - leotenshii +category: ecosystem diff --git a/packages/PathML/meta.yaml b/packages/PathML/meta.yaml index 6d3432fc..49553080 100644 --- a/packages/PathML/meta.yaml +++ b/packages/PathML/meta.yaml @@ -12,12 +12,11 @@ tags: - pathology license: GPL-2.0-only version: v2.1.0 -authors: +contact: - jacob-rosenthal - ryanccarelli - BeeGass - MohamedOmar2020 - - Dana-Farber - Karenxzr - ella-dfci - surya-narayanan @@ -25,3 +24,4 @@ authors: - Yu-AnChen - jzhang1031 test_command: pip install "." && pytest +category: ecosystem diff --git a/packages/PyDESeq2/meta.yaml b/packages/PyDESeq2/meta.yaml index 9a7f2e1d..0f1d9156 100644 --- a/packages/PyDESeq2/meta.yaml +++ b/packages/PyDESeq2/meta.yaml @@ -14,10 +14,10 @@ tags: publications: - 10.1101/2022.12.14.520412 version: v0.3.0 -authors: +contact: - BorisMuzellec - maikia - vcabeli - - mandreux-owkin test_command: | pip install ."[dev]" && pytest +category: ecosystem diff --git a/packages/Rectangle/meta.yaml b/packages/Rectangle/meta.yaml index 8890fa25..10456308 100644 --- a/packages/Rectangle/meta.yaml +++ b/packages/Rectangle/meta.yaml @@ -12,7 +12,8 @@ tags: - rna-seq - deconvolution version: v0.1.6 -authors: +contact: - bernheder test_command: | pip install ."[dev,test]" && pytest +category: ecosystem diff --git a/packages/SC2Spa/meta.yaml b/packages/SC2Spa/meta.yaml index 9fd80d69..53687c5e 100644 --- a/packages/SC2Spa/meta.yaml +++ b/packages/SC2Spa/meta.yaml @@ -17,7 +17,7 @@ tags: - cell communication license: BSD-3-Clause version: v1.2 -authors: - - Linbu Liao - - Kyoung Jae Won +contact: + - linbuliao test_command: pip install "." && pytest +category: ecosystem diff --git a/packages/SCALEX/meta.yaml b/packages/SCALEX/meta.yaml index 475c7e73..25e442b6 100644 --- a/packages/SCALEX/meta.yaml +++ b/packages/SCALEX/meta.yaml @@ -14,6 +14,7 @@ tags: - scATAC-seq license: MIT version: v1.0.3 -authors: - - Lei Xiong +contact: + - jsxlei test_command: pip install ".[test]" && pytest +category: ecosystem diff --git a/packages/STMiner/meta.yaml b/packages/STMiner/meta.yaml index 336028af..f2a0e45f 100644 --- a/packages/STMiner/meta.yaml +++ b/packages/STMiner/meta.yaml @@ -12,6 +12,7 @@ tags: - mechine learning license: GPL-3.0-or-later version: v1.1.0 -authors: - - Peisen Sun +contact: + - PSSUN test_command: pip install "." && pytest +category: ecosystem diff --git a/packages/anndata-for-R/meta.yaml b/packages/anndata-for-R/meta.yaml index a20c4d58..055fd8a2 100644 --- a/packages/anndata-for-R/meta.yaml +++ b/packages/anndata-for-R/meta.yaml @@ -9,5 +9,6 @@ tags: - R package license: MIT version: 0.7.5.5 -authors: +contact: - rcannood +category: ecosystem diff --git a/packages/anndataR/logo.svg b/packages/anndataR/logo.svg new file mode 100644 index 00000000..568b20f9 --- /dev/null +++ b/packages/anndataR/logo.svg @@ -0,0 +1,108 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + anndataR + + + diff --git a/packages/anndataR/meta.yaml b/packages/anndataR/meta.yaml new file mode 100644 index 00000000..bb369d32 --- /dev/null +++ b/packages/anndataR/meta.yaml @@ -0,0 +1,24 @@ +name: anndataR +description: | + An R implementation of the AnnData object including native reading and writing + of H5AD files and conversion to common R data structures. +project_home: https://github.com/scverse/anndataR +documentation_home: https://bioconductor.org/packages/anndataR/ +tutorials_home: https://anndatar.data-intuitive.com/ +install: + bioconductor: anndataR +license: MIT +tags: + - data structures + - interoperability + - R + - Bioconductor +publications: + - 10.1101/2025.08.18.669052 # bioRxiv preprint +version: 1.0.0 +contact: + - lazappi + - rcannood + - LouiseDck +logo: logo.svg +category: ecosystem diff --git a/packages/annsel/meta.yaml b/packages/annsel/meta.yaml index e3eb527d..016dbf5c 100644 --- a/packages/annsel/meta.yaml +++ b/packages/annsel/meta.yaml @@ -9,7 +9,7 @@ install: pypi: annsel license: MIT version: v0.0.8 -authors: +contact: - srivarra tags: - narwhals @@ -18,3 +18,4 @@ tags: - utilities test_command: | pip install ".[test]" && pytest +category: ecosystem diff --git a/packages/benGRN/meta.yaml b/packages/benGRN/meta.yaml index 43d716b3..dc768cb1 100644 --- a/packages/benGRN/meta.yaml +++ b/packages/benGRN/meta.yaml @@ -15,6 +15,7 @@ tags: - benchmark license: MIT version: v1.2.1 -authors: - - jkobject (jeremie kalfon) +contact: + - jkobject test_command: pip install . && make test +category: ecosystem diff --git a/packages/bento-tools/meta.yaml b/packages/bento-tools/meta.yaml index f274ad64..f2799175 100644 --- a/packages/bento-tools/meta.yaml +++ b/packages/bento-tools/meta.yaml @@ -12,7 +12,8 @@ tags: - spatial analysis license: BSD-2-Clause version: v1.0.1 -authors: +contact: - ckmah - noor01 test_command: pip install "." && pytest +category: ecosystem diff --git a/packages/biolord/meta.yaml b/packages/biolord/meta.yaml index e291f52a..646dffa3 100644 --- a/packages/biolord/meta.yaml +++ b/packages/biolord/meta.yaml @@ -12,7 +12,8 @@ tags: - generative framework license: BSD-3-Clause version: v0.0.1 -authors: +contact: - zoepiran test_command: | pip install ".[dev,test]" && pytest +category: ecosystem diff --git a/packages/cell2location/meta.yaml b/packages/cell2location/meta.yaml index f9e5d446..297cc961 100644 --- a/packages/cell2location/meta.yaml +++ b/packages/cell2location/meta.yaml @@ -15,11 +15,11 @@ tags: - Bayesian license: Apache-2.0 version: v0.1 -authors: +contact: - vitkl - yozhikoff - mayerdev - emdann - - Alexander Aivazidis test_command: | pip install ".[dev]" && pytest +category: ecosystem diff --git a/packages/cellxgene/meta.yaml b/packages/cellxgene/meta.yaml index f7897545..b3900017 100644 --- a/packages/cellxgene/meta.yaml +++ b/packages/cellxgene/meta.yaml @@ -12,7 +12,7 @@ tags: - HCA license: MIT version: 1.1.1 -authors: +contact: - csweaver - bkmartinjr - seve @@ -27,3 +27,4 @@ authors: - mweiden test_command: | pip install ".[test]" && pytest +category: ecosystem diff --git a/packages/dandelion/meta.yaml b/packages/dandelion/meta.yaml index 93ef8399..bfa99e76 100644 --- a/packages/dandelion/meta.yaml +++ b/packages/dandelion/meta.yaml @@ -18,10 +18,11 @@ tags: - tcr license: AGPL-3.0-or-later version: v0.3.0 -authors: +contact: - zktuong - ktpolanski - suochenqu - grst test_command: | pip install "." && pytest +category: ecosystem diff --git a/packages/delnx/meta.yaml b/packages/delnx/meta.yaml index 350d7801..ec060be2 100644 --- a/packages/delnx/meta.yaml +++ b/packages/delnx/meta.yaml @@ -13,8 +13,9 @@ tags: - JAX license: MIT version: v0.2.3 -authors: +contact: - joschif - adaml9 test_command: | pip install ".[test]" && pytest +category: ecosystem diff --git a/packages/dynamo-release/meta.yaml b/packages/dynamo-release/meta.yaml index 10a657a0..5c761c99 100644 --- a/packages/dynamo-release/meta.yaml +++ b/packages/dynamo-release/meta.yaml @@ -14,8 +14,9 @@ tags: - vector license: BSD-3-Clause version: v1.1.0 -authors: +contact: - Xiaojieqiu - dummyindex - yaz62 test_command: pip install ".[test]" && pytest +category: ecosystem diff --git a/packages/epiScanpy/meta.yaml b/packages/epiScanpy/meta.yaml index ffd37151..2c60044d 100644 --- a/packages/epiScanpy/meta.yaml +++ b/packages/epiScanpy/meta.yaml @@ -14,7 +14,7 @@ tags: - epigenomics license: BSD-3-Clause version: v0.3.2 -authors: +contact: - DaneseAnna - mrichter23 - kridsadakorn @@ -24,3 +24,4 @@ authors: - michalk8 - mvinyard test_command: pip install ".[test]" && pytest +category: ecosystem diff --git a/packages/eschr/meta.yaml b/packages/eschr/meta.yaml index de9c36f4..40ac20b5 100644 --- a/packages/eschr/meta.yaml +++ b/packages/eschr/meta.yaml @@ -15,6 +15,7 @@ tags: - ensemble license: "MIT" version: v1.0.1 -authors: +contact: - smgoggin10 test_command: pip install ".[test]" && pytest +category: ecosystem diff --git a/packages/favapy/meta.yaml b/packages/favapy/meta.yaml index 52472033..56cbbf92 100644 --- a/packages/favapy/meta.yaml +++ b/packages/favapy/meta.yaml @@ -16,5 +16,6 @@ tags: - variational autoencoders license: MIT version: v0.3.9.4 -authors: +contact: - mikelkou +category: ecosystem diff --git a/packages/flowsom/meta.yaml b/packages/flowsom/meta.yaml index 3ddec752..c8a9c457 100644 --- a/packages/flowsom/meta.yaml +++ b/packages/flowsom/meta.yaml @@ -19,9 +19,10 @@ tags: - flowcytometry license: GPL-3.0-only version: v0.0.1 -authors: +contact: - artuurC - berombau - ysaeys - SofieVG test_command: pip install "." && pytest +category: ecosystem diff --git a/packages/gssnng/meta.yaml b/packages/gssnng/meta.yaml index df2327a8..6548cd02 100644 --- a/packages/gssnng/meta.yaml +++ b/packages/gssnng/meta.yaml @@ -16,8 +16,9 @@ tags: - python license: MIT version: v0.4.2 -authors: +contact: - gibbsdavidl - redst4r test_command: | git clone git@github.com:IlyaLab/gssnng.git && pip install gssnng && pip install pytest && cd gssnng/ && pytest +category: ecosystem diff --git a/packages/hotspot/meta.yaml b/packages/hotspot/meta.yaml index 522e8370..d86d5a3e 100644 --- a/packages/hotspot/meta.yaml +++ b/packages/hotspot/meta.yaml @@ -12,8 +12,9 @@ tags: - gene-signatures license: BSD-3-Clause version: v1.1.1 -authors: +contact: - deto - adamgayoso test_command: | pip install ".[test]" && pytest +category: ecosystem diff --git a/packages/infercnvpy/meta.yaml b/packages/infercnvpy/meta.yaml index e9d046f2..383d925c 100644 --- a/packages/infercnvpy/meta.yaml +++ b/packages/infercnvpy/meta.yaml @@ -2,14 +2,16 @@ name: infercnvpy description: | Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy. project_home: https://github.com/icbi-lab/infercnvpy -documentation_home: https://icbi-lab.github.io/infercnvpy +documentation_home: https://infercnvpy.readthedocs.io/en/latest/ +tutorials_home: https://infercnvpy.readthedocs.io/en/latest/tutorials.html install: pypi: infercnvpy tags: - CNV license: BSD-3-Clause version: v0.3.0 -authors: +contact: - grst test_command: | pip install ".[test]" && pytest +category: ecosystem diff --git a/packages/kompot/logo.png b/packages/kompot/logo.png new file mode 100644 index 00000000..afaea224 Binary files /dev/null and b/packages/kompot/logo.png differ diff --git a/packages/kompot/meta.yaml b/packages/kompot/meta.yaml new file mode 100644 index 00000000..4fd65c99 --- /dev/null +++ b/packages/kompot/meta.yaml @@ -0,0 +1,34 @@ +name: kompot +description: | + Statistical framework for holistic comparison of multi-condition single-cell datasets over continuous phenotypic manifolds. + Kompot performs differential abundance and expression analysis agnostically to cell-type annotation or clustering, + detecting differences that span the continuous manifold even when effects go in opposite directions across cell states. + It models cell distributions and gene expression as continuous functions over cell state representations of arbitrary + dimension (typically ~50 dimensions), enabling single-cell resolution + inference with calibrated uncertainty estimates and capturing both global and cell-state-specific effects of perturbation. +project_home: https://github.com/settylab/kompot +documentation_home: https://kompot.readthedocs.io/ +tutorials_home: https://kompot.readthedocs.io/en/latest/notebooks/01_getting_started.html +publications: + - 10.1101/2025.06.03.657769 +install: + pypi: kompot + conda: bioconda::kompot +tags: + - differential-expression + - differential-abundance + - mahalanobis-distance + - gaussian-process + - phenotypic manifold + - continuous representation + - jax + - anndata +license: GPL-3.0-or-later +version: v0.6.1 +contact: + - katosh + - ManuSetty +logo: logo.png +test_command: | + pip install ".[dev]" && pytest +category: ecosystem diff --git a/packages/liana/meta.yaml b/packages/liana/meta.yaml index c132e8b5..2e781340 100644 --- a/packages/liana/meta.yaml +++ b/packages/liana/meta.yaml @@ -13,9 +13,10 @@ tags: - cell-cell communication license: GPL-3.0-only version: v1.0.0a1 -authors: +contact: - dbdimitrov test_command: | pip install poetry && \ poetry install --extras "full" && \ poetry run pytest --disable-warnings . +category: ecosystem diff --git a/packages/maxspin/meta.yaml b/packages/maxspin/meta.yaml index d2466048..68bd66fe 100644 --- a/packages/maxspin/meta.yaml +++ b/packages/maxspin/meta.yaml @@ -13,6 +13,7 @@ tags: - spatial autocorrelation license: MIT version: v0.1.1 -authors: +contact: - dcjones test_command: pip install "." && pytest +category: ecosystem diff --git a/packages/moscot/meta.yaml b/packages/moscot/meta.yaml index 38de20b4..46decb5b 100644 --- a/packages/moscot/meta.yaml +++ b/packages/moscot/meta.yaml @@ -14,10 +14,11 @@ tags: - spatial license: BSD-3-Clause version: v0.4.0 -authors: +contact: - MUCDK - giovp - michalk8 - Marius1311 - zoepiran test_command: pip install -e '.[dev]' && pytest +category: ecosystem diff --git a/packages/novae/meta.yaml b/packages/novae/meta.yaml index e32704b7..ed19c3bc 100644 --- a/packages/novae/meta.yaml +++ b/packages/novae/meta.yaml @@ -15,6 +15,7 @@ tags: - deep learning license: BSD-3-Clause version: v0.2.1 -authors: +contact: - quentinblampey test_command: pip install ".[dev]" && pytest +category: ecosystem diff --git a/packages/omicverse/meta.yaml b/packages/omicverse/meta.yaml index 5219ed6c..92db0dba 100644 --- a/packages/omicverse/meta.yaml +++ b/packages/omicverse/meta.yaml @@ -16,8 +16,9 @@ tags: - bioinformatics license: GPL-3.0-only version: v1.4.12 -authors: +contact: - Starlitnightly - DBinary - JuliaMYQ test_command: pip install "." && pytest +category: ecosystem diff --git a/packages/palantir/meta.yaml b/packages/palantir/meta.yaml index 454b9bda..17bb6419 100644 --- a/packages/palantir/meta.yaml +++ b/packages/palantir/meta.yaml @@ -26,8 +26,8 @@ tags: - scrna-seq-analysis license: GPL-2.0-or-later version: v1.3.3 -authors: +contact: - ManuSetty - - dpeerlab - katosh test_command: pip install -e '.' && pip install flake8 pytest coverage typing-extensions && pytest +category: ecosystem diff --git a/packages/panpipes/meta.yaml b/packages/panpipes/meta.yaml index 0e4b4f47..17f2b343 100644 --- a/packages/panpipes/meta.yaml +++ b/packages/panpipes/meta.yaml @@ -16,7 +16,7 @@ tags: - bioinformatics license: BSD-3-Clause version: v0.5.0 -authors: +contact: - bio-la - crichgriffin - SarahOuologuem @@ -28,3 +28,4 @@ authors: - Zethson - wlason test_command: pip install -e '.[dev]' && pytest +category: ecosystem diff --git a/packages/pegasus/meta.yaml b/packages/pegasus/meta.yaml index 19e9c99a..a56b5f1d 100644 --- a/packages/pegasus/meta.yaml +++ b/packages/pegasus/meta.yaml @@ -12,7 +12,7 @@ tags: - transcriptome analysis license: BSD-3-Clause version: v1.7.1 -authors: +contact: - yihming - bli25 - YanayRosen @@ -24,3 +24,4 @@ authors: - slowkow - jlchang test_command: pip install "." && pytest +category: ecosystem diff --git a/packages/popV/meta.yaml b/packages/popV/meta.yaml index 03bc000d..5793656b 100644 --- a/packages/popV/meta.yaml +++ b/packages/popV/meta.yaml @@ -11,6 +11,7 @@ tags: - automatic annotation license: MIT version: v0.5.2 -authors: +contact: - canergen test_command: pip install -e '.[test]' && pytest +category: ecosystem diff --git a/packages/pyLemur/meta.yaml b/packages/pyLemur/meta.yaml index a7dc1d34..499e2607 100644 --- a/packages/pyLemur/meta.yaml +++ b/packages/pyLemur/meta.yaml @@ -14,6 +14,7 @@ tags: - multi-condition license: MIT version: v0.1.0 -authors: - - Constantin Ahlmann-Eltze +contact: + - const-ae test_command: pip install -e '.[dev]' && pytest +category: ecosystem diff --git a/packages/pySCENIC/meta.yaml b/packages/pySCENIC/meta.yaml index 586f1c82..b98dac82 100644 --- a/packages/pySCENIC/meta.yaml +++ b/packages/pySCENIC/meta.yaml @@ -18,7 +18,7 @@ tags: - clustering license: GPL-3.0-only version: v0.12.0 -authors: +contact: - bramvds - cflerin - ghuls @@ -29,3 +29,4 @@ authors: - simonvh - loremendez test_command: pip install "." && pytest +category: ecosystem diff --git a/packages/pyUCell/meta.yaml b/packages/pyUCell/meta.yaml new file mode 100644 index 00000000..9865f231 --- /dev/null +++ b/packages/pyUCell/meta.yaml @@ -0,0 +1,26 @@ +name: pyUCell +description: | + pyUCell is a package for evaluating gene signatures in single-cell datasets. + pyUCell signature scores, based on the Mann-Whitney U statistic, are robust + to dataset size and heterogeneity, and their calculation demands less + computing time and memory than other available methods, enabling the + processing of large datasets in a few minutes even on machines with limited + computing power. +project_home: https://github.com/carmonalab/pyucell +documentation_home: https://pyucell.readthedocs.io/en/latest +tutorials_home: https://pyucell.readthedocs.io/en/latest/notebooks/basic.html +publications: + - 10.1016/j.csbj.2021.06.043 +install: + pypi: pyucell +tags: + - single-cell + - signature scoring + - module scoring +license: MIT +version: v0.3.0 +contact: + - mass-a + - sjcarmona +test_command: pip install "." && pytest +category: ecosystem diff --git a/packages/pychromVAR/meta.yaml b/packages/pychromVAR/meta.yaml index 98ff5bf8..1ca7a414 100644 --- a/packages/pychromVAR/meta.yaml +++ b/packages/pychromVAR/meta.yaml @@ -11,7 +11,8 @@ tags: - scATAC-seq license: MIT version: v0.0.3 -authors: - - Zhijian Li +contact: + - lzj1769 test_command: | test_command: pip install ".[test]" && pytest +category: ecosystem diff --git a/packages/pytximport/meta.yaml b/packages/pytximport/meta.yaml index 835808e4..424627bd 100644 --- a/packages/pytximport/meta.yaml +++ b/packages/pytximport/meta.yaml @@ -12,9 +12,10 @@ tags: - differential-expression license: GPL-3.0-only version: v0.2.0 -authors: +contact: - maltekuehl test_command: | pip install flit poetry && \ flit install --deps all && \ coverage run -m pytest +category: ecosystem diff --git a/packages/scCellFie/meta.yaml b/packages/scCellFie/meta.yaml index 60f57423..8a63145e 100644 --- a/packages/scCellFie/meta.yaml +++ b/packages/scCellFie/meta.yaml @@ -14,10 +14,11 @@ tags: - cell-cell communication license: MIT version: v0.4.5 -authors: +contact: - earmingol test_command: | python -m pip install --upgrade pip python -m pip install -r requirements.txt python -m pip install -e . pytest -vv --cov --cov-report xml +category: ecosystem diff --git a/packages/scDataLoader/meta.yaml b/packages/scDataLoader/meta.yaml index 115553f7..bb77545f 100644 --- a/packages/scDataLoader/meta.yaml +++ b/packages/scDataLoader/meta.yaml @@ -19,6 +19,7 @@ tags: - preprocessing license: MIT version: v1.2.2 -authors: - - jkobject (jeremie kalfon) +contact: + - jkobject test_command: pip install . && make test +category: ecosystem diff --git a/packages/scFates/meta.yaml b/packages/scFates/meta.yaml index 11513770..ea8f7189 100644 --- a/packages/scFates/meta.yaml +++ b/packages/scFates/meta.yaml @@ -14,7 +14,7 @@ tags: - trajectory-generation license: BSD-3-Clause version: v1.0.0 -authors: +contact: - LouisFaure test_command: | sudo apt-get clean && sudo apt-get update @@ -24,3 +24,4 @@ test_command: | pip install rpy2==3.4.2 pip install . pytest scFates/tests/test_w_plots.py +category: ecosystem diff --git a/packages/scGen/meta.yaml b/packages/scGen/meta.yaml index 6640bf62..4e760fcd 100644 --- a/packages/scGen/meta.yaml +++ b/packages/scGen/meta.yaml @@ -13,16 +13,15 @@ tags: - perturbation license: GPL-3.0-only version: v2.1.0 -authors: - - mn7697np +contact: - M0hammadL - adamgayoso - Cottoneyejoe95 - watiss - ktpolanski - Naghipourfar - - k4ngyh - Zethson - alirezaomidi - mumichae test_command: pip install "." && pytest +category: ecosystem diff --git a/packages/scLiTr/meta.yaml b/packages/scLiTr/meta.yaml index 62679cc1..60fe097c 100644 --- a/packages/scLiTr/meta.yaml +++ b/packages/scLiTr/meta.yaml @@ -13,7 +13,8 @@ license: MIT publications: - 10.1101/2024.11.15.623687 version: v1.0.1 -authors: +contact: - serjisa test_command: | pip install . && pytest +category: ecosystem diff --git a/packages/scPRINT/meta.yaml b/packages/scPRINT/meta.yaml index 5fbf626a..ab50d3bf 100644 --- a/packages/scPRINT/meta.yaml +++ b/packages/scPRINT/meta.yaml @@ -21,6 +21,7 @@ tags: - lightning license: MIT version: v1.6.2 -authors: - - jkobject (jeremie kalfon) +contact: + - jkobject test_command: pip install . && make test +category: ecosystem diff --git a/packages/scXpand/meta.yaml b/packages/scXpand/meta.yaml new file mode 100644 index 00000000..b0665c65 --- /dev/null +++ b/packages/scXpand/meta.yaml @@ -0,0 +1,26 @@ +name: scXpand +description: | + scXpand is a machine learning framework for pan-cancer detection of T-cell clonal expansion + directly from single-cell RNA sequencing (scRNA-seq), without paired T-cell receptor (TCR) sequencing. +project_home: https://github.com/yizhak-lab-ccg/scXpand +documentation_home: https://scxpand.readthedocs.io/en/latest/ +tutorials_home: https://scxpand.readthedocs.io/en/latest/ +publications: + - 10.1101/2025.09.14.676069 +install: + pypi: scxpand +tags: + - cancer + - scRNA-seq + - scTCR-seq + - T-cell clonal expansion + - machine learning +license: MIT +version: v0.4.3 +contact: + - ronamit + - ofirshorer + - yizhak-lab-ccg +test_command: | + pip install -e ".[dev]" && pytest --cov=src.scxpand tests +category: ecosystem diff --git a/packages/scanpro/meta.yaml b/packages/scanpro/meta.yaml index 3fd3acdb..8aec480f 100644 --- a/packages/scanpro/meta.yaml +++ b/packages/scanpro/meta.yaml @@ -13,6 +13,8 @@ tags: - multi omics license: MIT version: 0.2.0 -authors: - - loosolab +contact: + - yalayoubi + - mlooso test_command: pip install . && pytest +category: ecosystem diff --git a/packages/schist/meta.yaml b/packages/schist/meta.yaml index 394cf32e..1f6a49eb 100644 --- a/packages/schist/meta.yaml +++ b/packages/schist/meta.yaml @@ -12,8 +12,9 @@ tags: publications: - 10.1186/s12859-021-04489-7 version: v0.8.1 -authors: +contact: - dawe - leomorelli test_command: | pytest conftest.py +category: ecosystem diff --git a/packages/scib/meta.yaml b/packages/scib/meta.yaml index 97c9df33..a470e0c5 100644 --- a/packages/scib/meta.yaml +++ b/packages/scib/meta.yaml @@ -13,9 +13,10 @@ tags: - data integration license: MIT version: v1.0.5 -authors: +contact: - mumichae - LuckyMD - danielStrobl - mbuttner test_command: pip install ".[test,rpy2,harmony,scvi,scanorama]" && pytest +category: ecosystem diff --git a/packages/scmcp/meta.yaml b/packages/scmcp/meta.yaml index fec5cc21..a4e5dfdc 100644 --- a/packages/scmcp/meta.yaml +++ b/packages/scmcp/meta.yaml @@ -11,6 +11,7 @@ tags: - AI license: BSD-3-Clause version: v0.2.2 -authors: +contact: - huangsh test_command: uv run --no-sync pytest +category: ecosystem diff --git a/packages/sctriangulate/meta.yaml b/packages/sctriangulate/meta.yaml index 3e5a582d..4ded158e 100644 --- a/packages/sctriangulate/meta.yaml +++ b/packages/sctriangulate/meta.yaml @@ -12,6 +12,7 @@ tags: - clustering license: MIT version: v0.12.0 -authors: +contact: - frankligy test_command: pip install "." && pytest +category: ecosystem diff --git a/packages/scvelo/meta.yaml b/packages/scvelo/meta.yaml index cc65b97b..a359f1d2 100644 --- a/packages/scvelo/meta.yaml +++ b/packages/scvelo/meta.yaml @@ -11,7 +11,8 @@ tags: - rna velocity license: BSD-3-Clause version: v0.2.5 -authors: +contact: - WeilerP - VolkerBergen test_command: pip install -e '.[dev]' && pytest +category: ecosystem diff --git a/packages/scxmatch/meta.yaml b/packages/scxmatch/meta.yaml index 42569afd..c599ad2b 100644 --- a/packages/scxmatch/meta.yaml +++ b/packages/scxmatch/meta.yaml @@ -19,8 +19,9 @@ tags: - condition license: MIT version: v0.1.0 -authors: +contact: - annmoel - dbblumenthal test_command: | conda install scxmatch -c conda-forge -c bioconda && git clone https://github.com/bionetslab/scxmatch.git && cd scxmatch/tests/ && python test_mwe.py +category: ecosystem diff --git a/packages/scyan/meta.yaml b/packages/scyan/meta.yaml index 12d2e442..1abe9a4c 100644 --- a/packages/scyan/meta.yaml +++ b/packages/scyan/meta.yaml @@ -17,6 +17,7 @@ tags: - debarcoding license: BSD-3-Clause version: v1.5.0 -authors: +contact: - quentinblampey test_command: pip install ".[dev]" && pytest +category: ecosystem diff --git a/packages/sfaira/meta.yaml b/packages/sfaira/meta.yaml index 3aeeab9c..62ad67bb 100644 --- a/packages/sfaira/meta.yaml +++ b/packages/sfaira/meta.yaml @@ -12,7 +12,7 @@ tags: - data repository license: BSD-3-Clause version: v0.3.12 -authors: +contact: - davidsebfischer - le-ander - Zethson @@ -27,3 +27,4 @@ authors: - giovp - Wang-Cankun test_command: null +category: ecosystem diff --git a/packages/sift-sc/meta.yaml b/packages/sift-sc/meta.yaml index 3746e31d..77af9977 100644 --- a/packages/sift-sc/meta.yaml +++ b/packages/sift-sc/meta.yaml @@ -13,7 +13,8 @@ tags: - filter license: BSD-3-Clause version: v0.1.0 -authors: +contact: - zoepiran test_command: | pip install ".[test]" && pytest +category: ecosystem diff --git a/packages/sobolev-alignment/meta.yaml b/packages/sobolev-alignment/meta.yaml index acbf8029..83055ce1 100644 --- a/packages/sobolev-alignment/meta.yaml +++ b/packages/sobolev-alignment/meta.yaml @@ -16,7 +16,8 @@ tags: - scrnaseq license: MIT version: 1.0.0 -authors: +contact: - saroudant test_command: | pip install ."[dev]" && pytest +category: ecosystem diff --git a/packages/sopa/meta.yaml b/packages/sopa/meta.yaml index c686735e..364a8f0d 100644 --- a/packages/sopa/meta.yaml +++ b/packages/sopa/meta.yaml @@ -17,6 +17,7 @@ tags: - pipeline license: BSD-3-Clause version: v1.0.0 -authors: +contact: - quentinblampey test_command: pip install ".[dev,cellpose]" && pytest +category: ecosystem diff --git a/packages/spatial-eggplant/meta.yaml b/packages/spatial-eggplant/meta.yaml index dba90c73..d09db477 100644 --- a/packages/spatial-eggplant/meta.yaml +++ b/packages/spatial-eggplant/meta.yaml @@ -13,6 +13,7 @@ tags: - spatial registration license: MIT version: v0.2.3 -authors: +contact: - almaan test_command: pip install "." && pytest +category: ecosystem diff --git a/packages/spatialproteomics/meta.yaml b/packages/spatialproteomics/meta.yaml index ab21ec6d..855ca35b 100644 --- a/packages/spatialproteomics/meta.yaml +++ b/packages/spatialproteomics/meta.yaml @@ -16,7 +16,8 @@ tags: - pipeline license: MIT version: v0.7.0 -authors: +contact: - MeyerBender - sagar87 test_command: pip install ".[all,dev]" && pytest +category: ecosystem diff --git a/packages/spatiomic/meta.yaml b/packages/spatiomic/meta.yaml index 80239330..809938b2 100644 --- a/packages/spatiomic/meta.yaml +++ b/packages/spatiomic/meta.yaml @@ -15,6 +15,7 @@ tags: - subcellular analysis license: GPL-3.0-only version: v0.5.0 -authors: +contact: - maltekuehl test_command: uv run pytest -m "not gpu" +category: ecosystem diff --git a/packages/symphonypy/meta.yaml b/packages/symphonypy/meta.yaml index cd06c0ed..9734db0b 100644 --- a/packages/symphonypy/meta.yaml +++ b/packages/symphonypy/meta.yaml @@ -10,8 +10,9 @@ tags: - label-transfer license: GPL-3.0-only version: v0.2.1 -authors: +contact: - serjisa - potulabe test_command: | pip install . && pytest +category: ecosystem diff --git a/packages/tangram/meta.yaml b/packages/tangram/meta.yaml index 91ffbc07..4a01dc5f 100644 --- a/packages/tangram/meta.yaml +++ b/packages/tangram/meta.yaml @@ -13,10 +13,11 @@ tags: - spatial mapping license: BSD-3-Clause version: v1.0.3 -authors: +contact: - ziqlu0722 - lewlin - gscalia - gaddamshreya - hejinhuang test_command: pip install "." && pytest +category: ecosystem diff --git a/packages/vitessce/meta.yaml b/packages/vitessce/meta.yaml index 875a9a81..9d3573a0 100644 --- a/packages/vitessce/meta.yaml +++ b/packages/vitessce/meta.yaml @@ -13,7 +13,7 @@ tags: - imaging license: MIT version: v3.5.7 -authors: +contact: - keller-mark - mccalluc - ilan-gold @@ -32,3 +32,4 @@ authors: - romanhaa - will-moore test_command: pip install "." && pytest +category: ecosystem diff --git a/packages/wsidata/meta.yaml b/packages/wsidata/meta.yaml index 9f1acfa4..cdddab0b 100644 --- a/packages/wsidata/meta.yaml +++ b/packages/wsidata/meta.yaml @@ -10,8 +10,9 @@ tags: - Whole Slide Imaging license: MIT version: v0.3.0 -authors: +contact: - Mr-Milk - eabila - afrendeiro test_command: uv run task test +category: ecosystem diff --git a/packages/zellkonverter/logo.svg b/packages/zellkonverter/logo.svg new file mode 100644 index 00000000..482b3e90 --- /dev/null +++ b/packages/zellkonverter/logo.svg @@ -0,0 +1,358 @@ + +image/svg+xmlPywww.bioconductor.orgwww.bioconductor.orgzellkonverterR diff --git a/packages/zellkonverter/meta.yaml b/packages/zellkonverter/meta.yaml new file mode 100644 index 00000000..653082e5 --- /dev/null +++ b/packages/zellkonverter/meta.yaml @@ -0,0 +1,21 @@ +name: zellkonverter +description: | + An Bioconductor R package that enables reading and writing of H5AD files + and conversion between AnnData and SingleCellExperiment objects by wrapping + the Python anndata package. +project_home: https://github.com/theislab/zellkonverter +documentation_home: https://bioconductor.org/packages/zellkonverter/ +tutorials_home: https://theislab.github.io/zellkonverter/ +install: + bioconductor: zellkonverter +license: MIT +tags: + - data structures + - interoperability + - R + - Bioconductor +version: 1.20.0 +contact: + - lazappi +logo: logo.svg +category: ecosystem diff --git a/scripts/README.md b/scripts/README.md new file mode 100644 index 00000000..9694f19c --- /dev/null +++ b/scripts/README.md @@ -0,0 +1,6 @@ +# Scripts + +To hack on the scripts, `cd` to this directory, then + +- Use `prek/pre-commit run -a jsonschema-gentypes` to generate types from schema initially +- Use `prek/pre-commit install` to so checks are automatically run on commit diff --git a/scripts/pyproject.toml b/scripts/pyproject.toml index abcb537d..77baf3bf 100644 --- a/scripts/pyproject.toml +++ b/scripts/pyproject.toml @@ -1,62 +1,79 @@ [build-system] -requires = ["hatchling", "hatch-vcs"] build-backend = "hatchling.build" +requires = [ "hatch-vcs", "hatchling" ] + [project] name = "ecosystem-scripts" -dynamic = ["version"] description = "scripts for ecosystem package data" readme = "../README.md" -requires-python = ">=3.11" license = "GPL-3.0" authors = [ - { name = "Philipp A.", email = "flying-sheep@web.de" }, + { name = "Philipp A.", email = "flying-sheep@web.de" }, + { name = "Gregor Sturm", email = "gregor.sturm@scverse.org" }, ] -urls.Documentation = "https://github.com/scverse/ecosystem-packages#readme" -urls.Issues = "https://github.com/scverse/ecosystem-packages/issues" -urls.Source = "https://github.com/scverse/ecosystem-packages" +requires-python = ">=3.12" +classifiers = [ + "Programming Language :: Python :: 3 :: Only", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", +] +dynamic = [ "version" ] dependencies = [ - "rich", - "PyGitHub", - "PyYAML", + "httpx", + "jsonschema>=4.25.1", + "pillow>=12", + "pygithub", + "pyyaml", + "rich", ] -[project.scripts] -register-template-repos = "ecosystem_scripts.template_repo_registry:main" +urls.Documentation = "https://github.com/scverse/ecosystem-packages#readme" +urls.Issues = "https://github.com/scverse/ecosystem-packages/issues" +urls.Source = "https://github.com/scverse/ecosystem-packages" +scripts.register-template-repos = "ecosystem_scripts.template_repo_registry:main" +scripts.validate-registry = "ecosystem_scripts.validate_registry:main" [tool.hatch.version] source = "vcs" fallback-version = "0.0" [tool.hatch.envs.default] -python = "3.11" +python = "3.13" [tool.ruff] line-length = 120 -select = [ - "A", - "ARG", - "B", - "C", - "DTZ", - "E", - "EM", - "F", - "FBT", - "I", - "ICN", - "ISC", - "N", - "PLC", - "PLE", - "PLR", - "PLW", - "RUF", - "S", - "T", - "TID", - "UP", - "W", - "YTT", +lint.select = [ + "A", + "ARG", + "B", + "C", + "DTZ", + "E", + "EM", + "F", + "FBT", + "I", + "ICN", + "ISC", + "N", + "PLC", + "PLE", + "PLR", + "PLW", + "RUF", + "S", + "T", + "TC", + "TID", + "UP", + "W", + "YTT", ] -ignore = [] +lint.ignore = [ ] + +[tool.mypy] +strict = true +explicit_package_bases = true +mypy_path = [ "$MYPY_CONFIG_FILE_DIR/typings", "$MYPY_CONFIG_FILE_DIR/src" ] diff --git a/scripts/src/ecosystem_scripts/_logging.py b/scripts/src/ecosystem_scripts/_logging.py new file mode 100644 index 00000000..1708184b --- /dev/null +++ b/scripts/src/ecosystem_scripts/_logging.py @@ -0,0 +1,13 @@ +from logging import basicConfig, getLogger + +from rich.logging import RichHandler + +log = getLogger(__name__) + + +def setup_logging() -> None: + """Set up logging and rich traceback.""" + basicConfig(level="INFO", handlers=[RichHandler()]) + + # Suppress httpx INFO logs to reduce verbosity + getLogger("httpx").setLevel("WARNING") diff --git a/schema.json b/scripts/src/ecosystem_scripts/schema.json similarity index 80% rename from schema.json rename to scripts/src/ecosystem_scripts/schema.json index f4774d30..af6e40b9 100644 --- a/schema.json +++ b/scripts/src/ecosystem_scripts/schema.json @@ -1,6 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/scverse/ecosystem-packages/main/schema.json", + "$id": "https://raw.githubusercontent.com/scverse/ecosystem-packages/main/scripts/src/ecosystem_scripts/schema.json", + "version": "2.0", "title": "Scverse Ecosystem Packages", "description": "An approved scverse ecosystem package that fulfils some minimal requirements", "type": "object", @@ -30,24 +31,26 @@ }, "install": { "type": "object", - "items": { - "properties": { - "pypi": { - "description": "PyPI identifier", - "type": "string" - }, - "conda": { - "description": "Conda identifier, including channel (e.g. conda-forge::scanpy)", - "type": "string", - "pattern": "(.*)::(.*)" - }, - "cran": { - "description": "CRAN identifier", - "type": "string" - } + "properties": { + "pypi": { + "description": "PyPI identifier", + "type": "string" + }, + "conda": { + "description": "Conda identifier, including channel (e.g. conda-forge::scanpy)", + "type": "string", + "pattern": "(.*)::(.*)" + }, + "cran": { + "description": "CRAN identifier", + "type": "string" + }, + "bioconductor": { + "description": "Bioconductor identifier", + "type": "string" } }, - "minItems": 1 + "minProperties": 1 }, "license": { "description": "The license of the code. Must be a OSI-approved SPDX license identifier (see https://spdx.org/licenses/)", @@ -205,8 +208,8 @@ "description": "The version of the package at the point when this entry was created or updated", "type": "string" }, - "authors": { - "description": "List of authors/maintainers of the package. Entries must be Github user IDs.", + "contact": { + "description": "Point of contact for this package. Does not need to be the full list of maintainers. Entries must be Github user IDs.", "type": "array", "items": { "type": "string" @@ -214,9 +217,24 @@ "minItems": 1, "uniqueItems": true }, + "logo": { + "description": "Path to the logo (relative to meta.yaml). Should be either logo.png, logo.webp, or logo.svg. In case of a PNG image, it must fit in a bounding box of 512x512px and one dimension must be exactly 512px.", + "type": "string", + "pattern": "logo\\.(svg|png|webp)" + }, "test_command": { "description": "A shell command to install the package and execute the tests, assuming you are inside a freshly cloned copy of the package repository. Often this will be `pip install \".[test]\" && pytest`", "type": ["string", "null"] + }, + "category": { + "type": "string", + "enum": [ + "core-framework", + "core-datastructure", + "core-infrastructure", + "ecosystem" + ], + "description": "Package category for the website and statistics." } }, "required": [ @@ -228,6 +246,7 @@ "license", "tags", "version", - "authors" + "category", + "contact" ] } diff --git a/scripts/src/ecosystem_scripts/template_repo_registry.py b/scripts/src/ecosystem_scripts/template_repo_registry.py index d329939f..c8bf3605 100644 --- a/scripts/src/ecosystem_scripts/template_repo_registry.py +++ b/scripts/src/ecosystem_scripts/template_repo_registry.py @@ -12,17 +12,16 @@ import os import sys -from collections.abc import Iterable -from logging import basicConfig, getLogger from pathlib import Path -from typing import NotRequired, TypedDict +from typing import TYPE_CHECKING, NotRequired, TypedDict, cast from github import Github -from rich.logging import RichHandler -from rich.traceback import install from yaml import safe_dump, safe_load -log = getLogger(__name__) +from ._logging import log, setup_logging + +if TYPE_CHECKING: + from collections.abc import Iterable, Sequence class Repo(TypedDict): @@ -35,7 +34,7 @@ def parse_repos(path: Path) -> list[Repo]: log.info(f"No existing file found at: {path}") return [] with path.open() as f: - repos = safe_load(f) + repos = cast("list[Repo]", safe_load(f)) log.info(f"Found {len(repos)} known repos in: {path}") return repos @@ -58,13 +57,8 @@ def merge_repos(known: Iterable[Repo], new: Iterable[str]) -> list[Repo]: return repos -def setup() -> None: - basicConfig(level="INFO", handlers=[RichHandler()]) - install(show_locals=True) - - -def main(args: Iterable[str] | None = None) -> None: - setup() +def main(args: Sequence[str] | None = None) -> None: + setup_logging() if args is None: args = sys.argv[1:] if len(args) != 1: diff --git a/scripts/src/ecosystem_scripts/validate_registry.py b/scripts/src/ecosystem_scripts/validate_registry.py new file mode 100644 index 00000000..0cd32f8b --- /dev/null +++ b/scripts/src/ecosystem_scripts/validate_registry.py @@ -0,0 +1,405 @@ +#!/usr/bin/env python +"""Validate packages' meta.yaml and generate an output directory with json/images to be uploaded on Github Pages""" + +from __future__ import annotations + +import argparse +import json +import os +import shutil +import sys +from collections import defaultdict +from importlib.resources import files +from pathlib import Path +from textwrap import dedent +from typing import TYPE_CHECKING, cast + +import httpx +import jsonschema +import yaml +from PIL import Image + +from ._logging import log, setup_logging + +if TYPE_CHECKING: + from collections.abc import Iterable, Mapping, Sequence + from importlib.resources.abc import Traversable + + from .schema import ScverseEcosystemPackages # pyright: ignore[reportMissingModuleSource] + + +# Constants +HERE = Path(__file__).parent +IMAGE_SIZE = 512 + + +class ValidationError(Exception): + pass + + +class ErrorList(list[Exception]): + """List of error messages. Ignores None objects, and logs an error when one gets added.""" + + def append(self, obj: Exception | None) -> None: + if obj is None: + return + log.error(f"Validation error: {obj}") + return super().append(obj) + + +class LinkChecker: + """Track known links and validate URLs.""" + + def __init__(self) -> None: + self.known_links: set[str] = set() + + def check_and_register(self, url: str, context: str) -> None | ValidationError: + """Check if URL is duplicate, validate it exists, and register it. + + Parameters + ---------- + url + The URL to check and register + context + Context information for error messages (e.g., file being validated) + """ + if url in self.known_links: + msg = f"{context}: Duplicate link: {url}" + return ValidationError(msg) + + response = httpx.head(url, follow_redirects=True) + if response.status_code != httpx.codes.OK: + msg = f"URL {url} is not reachable (error {response.status_code}). " + return ValidationError(msg) + + self.known_links.add(url) + return None + + +class GitHubUserValidator: + """Validate GitHub usernames using the GitHub API.""" + + def __init__(self, github_token: str | None = None) -> None: + self.github_token = github_token + self.validated_users: set[str] = set() + + def validate_usernames(self, usernames: Sequence[str], context: str) -> None | ValidationError: + """Validate that a GitHub username exists. + + Parameters + ---------- + username + The GitHub username to validate + context + Context information for error messages (e.g., file being validated) + """ + + if not (unvalidated := list(set(usernames) - self.validated_users)): + return None + + headers = {} + if self.github_token: + headers["Authorization"] = f"token {self.github_token}" + + q = "\n".join(f"user{i}: user(login: {json.dumps(name)}) {{ login }}" for i, name in enumerate(unvalidated)) + response = httpx.post("https://api.github.com/graphql", headers=headers, json={"query": f"query {{ {q} }}"}) + + if response.status_code != httpx.codes.OK: + msg = f"{context}: Failed to validate GitHub users {unvalidated!r} (error {response.status_code})" + return ValidationError(msg) + + gql_response = response.json() + if errors := gql_response.get("errors"): + error_msgs = "\n".join(f"- {error['message']}" for error in errors) + msg = f"{context}: Failed to validate GitHub users {unvalidated!r}:\n{error_msgs}" + return ValidationError(msg) + + self.validated_users |= set(unvalidated) + log.info(f"Validated GitHub users: {unvalidated!r}") + return None + + +class PyPIValidator: + """Validate PyPI package names against the PyPI API.""" + + def __init__(self) -> None: + self.validated_packages: set[str] = set() + + def validate_package(self, package_name: str, context: str) -> None | ValidationError: + """Validate that a PyPI package exists. + + Parameters + ---------- + package_name + The PyPI package name to validate + context + Context information for error messages (e.g., file being validated) + """ + if package_name in self.validated_packages: + return None + + response = httpx.head(f"https://pypi.org/pypi/{package_name}/json", follow_redirects=True) + + if response.status_code == httpx.codes.NOT_FOUND: + msg = f"{context}: PyPI package {package_name!r} does not exist" + return ValidationError(msg) + if response.status_code != httpx.codes.OK: + msg = f"{context}: Failed to validate PyPI package {package_name!r} (error {response.status_code})" + return ValidationError(msg) + + self.validated_packages.add(package_name) + log.info(f"Validated PyPI package: {package_name}") + return None + + +class CondaValidator: + """Validate Conda package identifiers using the Anaconda API.""" + + def __init__(self) -> None: + self.validated_packages: set[str] = set() + + def validate_package(self, package_spec: str, context: str) -> None | ValidationError: + """Validate that a Conda package exists. + + Parameters + ---------- + package_spec + The Conda package specification (e.g., "conda-forge::scanpy") + context + Context information for error messages (e.g., file being validated) + """ + if package_spec in self.validated_packages: + return None + + # Parse channel and package name + if "::" not in package_spec: + msg = f"{context}: Invalid Conda package spec {package_spec!r} (expected format: channel::package)" + return ValidationError(msg) + + channel, package_name = package_spec.split("::", 1) + + # Check package exists on the channel + response = httpx.head( + f"https://api.anaconda.org/package/{channel}/{package_name}", + follow_redirects=True, + ) + + if response.status_code == httpx.codes.NOT_FOUND: + msg = f"{context}: Conda package '{package_spec}' does not exist" + return ValidationError(msg) + if response.status_code != httpx.codes.OK: + msg = f"{context}: Failed to validate Conda package '{package_spec}' (error {response.status_code})" + return ValidationError(msg) + + self.validated_packages.add(package_spec) + log.info(f"Validated Conda package: {package_spec}") + return None + + +class CRANValidator: + """Validate CRAN package names using the CRAN API.""" + + def __init__(self) -> None: + self.validated_packages: set[str] = set() + + def validate_package(self, package_name: str, context: str) -> None | ValidationError: + """Validate that a CRAN package exists. + + Parameters + ---------- + package_name + The CRAN package name to validate + context + Context information for error messages (e.g., file being validated) + """ + if package_name in self.validated_packages: + return None + + # CRAN packages can be checked via the packages database + response = httpx.head( + f"https://crandb.r-pkg.org/{package_name}", + follow_redirects=True, + ) + + if response.status_code == httpx.codes.NOT_FOUND: + msg = f"{context}: CRAN package '{package_name}' does not exist" + return ValidationError(msg) + if response.status_code != httpx.codes.OK: + msg = f"{context}: Failed to validate CRAN package '{package_name}' (error {response.status_code})" + return ValidationError(msg) + + self.validated_packages.add(package_name) + log.info(f"Validated CRAN package: {package_name}") + return None + + +def check_image(img_path: Path) -> None | ValidationError: + """Validates that the image exists and that it is either a SVG or fits into the 512x512 bounding box.""" + if not img_path.exists(): + msg = f"Image does not exist: {img_path}" + return ValidationError(msg) + if img_path.suffix == ".svg": + return None + with Image.open(img_path) as img: + width, height = img.size + if not ((width == IMAGE_SIZE and height <= IMAGE_SIZE) or (width <= IMAGE_SIZE and height == IMAGE_SIZE)): + msg = dedent( + f"""\ + When validating {img_path}: Image must fit in a {IMAGE_SIZE}x{IMAGE_SIZE}px bounding box + and one dimension must be exactly {IMAGE_SIZE} px. + Actual dimensions (width, height): ({width}, ({height}))." + """ + ) + return ValidationError(msg) + return None + + +def validate_packages( + schema_file: Traversable, registry_dir: Path, github_token: str | None = None +) -> tuple[Mapping[str, Sequence[Exception]], Sequence[ScverseEcosystemPackages]]: + """Find all package `meta.yaml` files in the registry dir and yield package records.""" + schema = json.loads(schema_file.read_bytes()) + + # using different link checkers, + # because each of them may point to the same URL and this wouldn't qualify as duplicate + link_checker_home = LinkChecker() + link_checker_docs = LinkChecker() + link_checker_tutorials = LinkChecker() + + github_validator = GitHubUserValidator(github_token) + pypi_validator = PyPIValidator() + conda_validator = CondaValidator() + cran_validator = CRANValidator() + + errors: defaultdict[str, ErrorList] = defaultdict(ErrorList) + package_metadata: list[ScverseEcosystemPackages] = [] + + for tmp_meta_file in sorted(registry_dir.rglob("meta.yaml"), key=lambda x: x.parent.name): + pkg_id = tmp_meta_file.parent.name + pkg_errors = errors[pkg_id] + log.info(f"Validating {pkg_id}") + with tmp_meta_file.open() as f: + tmp_meta = cast("ScverseEcosystemPackages", yaml.load(f, yaml.SafeLoader)) + + try: + jsonschema.validate(tmp_meta, schema) + except jsonschema.ValidationError as e: + pkg_errors.append(e) + + # Check and register all links + pkg_errors.append(link_checker_home.check_and_register(tmp_meta["project_home"], pkg_id)) + pkg_errors.append(link_checker_docs.check_and_register(tmp_meta["documentation_home"], pkg_id)) + if url := tmp_meta.get("tutorials_home"): + pkg_errors.append(link_checker_tutorials.check_and_register(url, pkg_id)) + + # Validate GitHub usernames in contact field + if usernames := tmp_meta.get("contact"): + pkg_errors.append(github_validator.validate_usernames(usernames, pkg_id)) + + # Validate install packages + if install_info := tmp_meta.get("install"): + if pypi_name := install_info.get("pypi"): + pkg_errors.append(pypi_validator.validate_package(pypi_name, pkg_id)) + if conda_name := install_info.get("conda"): + pkg_errors.append(conda_validator.validate_package(conda_name, pkg_id)) + if cran_name := install_info.get("cran"): + pkg_errors.append(cran_validator.validate_package(cran_name, pkg_id)) + + # Check logo (if available) and make path relative to root of registry + if "logo" in tmp_meta: + img_path = registry_dir / pkg_id / tmp_meta["logo"] + pkg_errors.append(check_image(img_path)) + tmp_meta["logo"] = str(img_path) + + package_metadata.append(tmp_meta) + + return errors, package_metadata + + +def make_output( + packages: Iterable[ScverseEcosystemPackages], + *, + outdir: Path | None = None, +) -> None: + """Create the output directory. + + If outdir is not set, don't copy anything, just print the JSON to stdout + + Structure: + outdir + - ecosystem.json # contains package metadata + - packagexxx/icon.svg # original icon filenames under a folder for each package. + - packageyyy/icon.png + """ + packages_rel: list[ScverseEcosystemPackages] = [] + for pkg in packages: + pkg_rel = pkg.copy() + if logo := pkg.get("logo"): + img_srcpath = Path(logo) + img_localpath = Path(img_srcpath.parent.name) / img_srcpath.name + pkg_rel["logo"] = str(img_localpath) + if outdir: + img_outpath = outdir / img_localpath + img_outpath.parent.mkdir() + shutil.copy(img_srcpath, img_outpath) + packages_rel.append(pkg_rel) + + if outdir: + with (outdir / "packages.json").open("w") as f: + json.dump(packages_rel, f) + else: + json.dump(packages_rel, sys.stdout, indent=2) + + +class Args(argparse.Namespace): + registry_dir: Path + outdir: Path | None + + +def main(args: Sequence[str] | None = None) -> None: + """Main entry point for the validate-registry command.""" + setup_logging() + if args is None: + args = sys.argv[1:] + + parser = argparse.ArgumentParser( + prog="validate-registry", + description=( + "Validate packages' meta.yaml and generate an output directory " + "with json/images to be uploaded on github pages." + ), + ) + parser.add_argument( + "--registry-dir", + type=Path, + # HERE is /scripts/src/ecosystem_scripts/, so go up 3 levels + default=HERE.parent.parent.parent / "packages", + help="Path to the registry directory containing package meta.yaml files", + ) + parser.add_argument("--outdir", type=Path, help="outdir that will contain the data to be uploaded on github pages") + + parsed_args = parser.parse_args(args, Args()) + if not parsed_args.registry_dir.is_dir(): + msg = f"Invalid Registry directory: {parsed_args.registry_dir}" + raise ValueError(msg) + + schema_file = files("ecosystem_scripts").joinpath("schema.json") + github_token = os.environ.get("GITHUB_TOKEN") + if parsed_args.outdir is not None: + parsed_args.outdir.mkdir(parents=True) + + log.info("Starting validation") + errors, packages = validate_packages(schema_file, parsed_args.registry_dir, github_token) + + if any(errors.values()): + log.error("Validation error occured in at least one package. Exiting.") + sys.exit(1) + else: + make_output(packages, outdir=parsed_args.outdir) + + +if __name__ == "__main__": + try: + main() + except KeyboardInterrupt: + sys.exit(1) diff --git a/scripts/uv.lock b/scripts/uv.lock new file mode 100644 index 00000000..ece2aad7 --- /dev/null +++ b/scripts/uv.lock @@ -0,0 +1,765 @@ +version = 1 +revision = 3 +requires-python = ">=3.11" +resolution-markers = [ + "python_full_version >= '3.14' and platform_python_implementation != 'PyPy'", + "python_full_version < '3.14' and platform_python_implementation != 'PyPy'", + "platform_python_implementation == 'PyPy'", +] + +[[package]] +name = "anyio" +version = "4.11.0" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "idna" }, + { name = "sniffio" }, + { name = "typing-extensions", marker = "python_full_version < '3.13'" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/c6/78/7d432127c41b50bccba979505f272c16cbcadcc33645d5fa3a738110ae75/anyio-4.11.0.tar.gz", 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https://github.com/CompCy-lab/scHub - url: https://github.com/Computational-Morphogenomics-Group/Ladder - url: https://github.com/ComputationalBiomedicineGroup/Rectangle @@ -14,6 +16,7 @@ - url: https://github.com/Floto-Lab/BactGraph - url: https://github.com/FroeseLab/bulkpy - url: https://github.com/Gabriellvl/FlowSOM +- url: https://github.com/LiHongCSBLab/scMagnify - url: https://github.com/Lotfollahi-lab/mintflow - url: https://github.com/MannLabs/dvp-io - url: https://github.com/NKI-CCB/sobolev_alignment @@ -37,6 +40,7 @@ - url: https://github.com/adamgayoso/figmasvg - url: https://github.com/aertslab/CREsted - url: https://github.com/aertslab/EnhancerAI +- url: https://github.com/aertslab/TF-MINDI - url: https://github.com/aertslab/TF-MInDi - url: https://github.com/agerardy/myeditdistance - url: https://github.com/angelolab/Nimbus-Inference @@ -49,12 +53,16 @@ - url: https://github.com/bioFAM/prismo - url: https://github.com/bioFAM/scDoRI - url: 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https://github.com/theislab/cellflow_reproducibility +- url: https://github.com/theislab/cellink - url: https://github.com/theislab/devVI +- url: https://github.com/theislab/ehrapy - url: https://github.com/theislab/ehrdata - url: https://github.com/theislab/geome - url: https://github.com/theislab/mapqc @@ -141,4 +157,6 @@ - url: https://github.com/theislab/troutpy - url: https://github.com/timtreis/gefslim - url: https://github.com/vitkl/cell2module +- url: https://github.com/wangd12rpi/hescape_changed +- url: https://github.com/yizhak-lab-ccg/scXpand - url: https://github.com/zunderlab/eschr