Update pandocfilters requirement from >=1.5.0 to >=1.5.1 - #15
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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 [pandocfilters](https://github.com/jgm/pandocfilters) to permit the latest version. - [Release notes](https://github.com/jgm/pandocfilters/releases) - [Changelog](https://github.com/jgm/pandocfilters/blob/master/CHANGELOG.md) - [Commits](jgm/pandocfilters@1.5.0...1.5.1) --- updated-dependencies: - dependency-name: pandocfilters dependency-version: 1.5.1 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 pandocfilters to permit the latest version.
Release notes
Sourced from pandocfilters's releases.
Changelog
Sourced from pandocfilters's changelog.
Commits
1feb93eCI: remove python 2 (no longer supported in setup-python.1b3745aUpdate changelog.5839c04Bump verison to 1.5.14da2c73Fix possible TOCTOU issue in directory creation581dbd4Make temp directory creation more robust, log only on errors06f4db9fix typoDependabot 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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