Update black requirement from >=23.1.0 to >=26.5.1 - #13
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dependabot[bot] wants to merge 41 commits into
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dependabot[bot] wants to merge 41 commits into
dependabot[bot] wants to merge 41 commits into
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The repo documented the CLI but never said what CellForge is for or what it achieved. This makes the paper's contribution legible from the front page and adds the project infrastructure a research tool needs to take contributions. README - Lead with the result: PCC 0.9883 on Adamson, MSE_DE 0.1736 on Norman, first in 14/15 blinded judge comparisons, 6 datasets across 3 modalities. - Map the three paper stages (Formulation/Ideation/Execution) onto the package layout, and document the coordination score and its convergence criterion. - Summarise the six generated architectures, the benchmark datasets with GEO accessions, per-run token and GPU cost, and the measured failure-mode distribution. - State the weak results (0.535 DEG recall, 0.420 protein recall) rather than omit them. docs/ - QUICKSTART, ARCHITECTURE, RESULTS, MODELS, DATASETS, FAQ, ROADMAP. Infrastructure - CI: pytest on Python 3.9-3.12, lint, sdist/wheel build, CITATION.cff validation, secret scan. requirements-ci.txt carries the minimal set the 43 tests actually need, so CI skips the full scientific stack. - Issue templates (bug, bad research plan, feature), PR template, dependabot. - CONTRIBUTING, CODE_OF_CONDUCT, SECURITY, CHANGELOG. - pyproject.toml for the build backend and black/isort/ruff/mypy/pytest config. Package metadata stays in setup.py to avoid a second source of truth for dependencies. Data and examples - scripts/download_datasets.py fetches all six benchmark datasets from the scPerturb Zenodo records with md5 verification. Filenames, sizes, and checksums were read from the live Zenodo API; one download was verified end to end. - examples/ carries a task description per benchmark. CITATION.cff listed "CellForge authors" and no paper. It now carries the full author roster and arXiv:2508.02276 as the preferred citation. Verified: 43/43 tests pass, twine check passes, CITATION.cff validates against schema 1.2.0, all .github YAML parses, no broken relative links across the 15 markdown files.
Updates the requirements on [black](https://github.com/psf/black) to permit the latest version. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](psf/black@23.1.0...26.5.1) --- updated-dependencies: - dependency-name: black dependency-version: 26.5.1 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>
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OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting If you change your mind, just re-open this PR and I'll resolve any conflicts on it. |
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Updates the requirements on black to permit the latest version.
Release notes
Sourced from black's releases.
Changelog
Sourced from black's changelog.
... (truncated)
Commits
87928e6Prepare release 26.5.1 (#5140)c970a49Preserve comments before fmt: skip lines (#5139)5809338Preserve inline comments inside annotation subscripts (#5130)61361b7docs: add Neovim integration guide and fix http link (#5124)ebe6018CI Hotfixes (#5136)9cbd95fFix publish binaries again on Windows (#5134)3dc8e6cAdd new changelog (#5132)6d0fff0Fix publish binaries workflow (#5133)d2490e2Prepare release 26.5.0 (#5131)2b13ea7Preserve multiline headers with fmt skip (#5117)Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting
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