Update setuptools requirement from >=65.5.1 to >=84.0.0 - #20
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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.
Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 7. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v4...v7) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: '7' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [@openai/codex-sdk](https://github.com/openai/codex/tree/HEAD/sdk/typescript) from 0.116.0 to 0.146.0. - [Commits](https://github.com/openai/codex/commits/rust-v0.146.0/sdk/typescript) --- updated-dependencies: - dependency-name: "@openai/codex-sdk" dependency-version: 0.146.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>
Updates the requirements on [referencing](https://github.com/python-jsonschema/referencing) to permit the latest version. - [Release notes](https://github.com/python-jsonschema/referencing/releases) - [Changelog](https://github.com/python-jsonschema/referencing/blob/main/docs/changes.rst) - [Commits](python-jsonschema/referencing@v0.30.2...v0.37.0) --- updated-dependencies: - dependency-name: referencing dependency-version: 0.37.0 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>
A run costs roughly 80k prompt / 400k completion tokens plus 4-8 GPU-hours. Nothing in the repository showed what you get for that, so the decision to try CellForge had to be made blind. examples/outputs/adamson_crispri/ is a complete worked bundle laid out the way a run leaves one: task analysis report, research plan (md/json/mmd), and the generated training script with its metrics and verification output. On provenance, stated per file in PROVENANCE.md and in every README that points at the bundle. This was assembled without an LLM provider key, without the Codex CLI and without the dataset, so it is not the transcript of a live run: - task_analysis_report.md and research_plan.* are hand-written to match the schemas the code actually serialises, section for section (TaskAnalysisReport.to_markdown, refinement.py's five top-level plan keys) - result.py is real, working code. It passes the repository's own deterministic verifier: file, compile, --help, --selftest, and metrics.json structure - metrics.json and verification.json are the genuine output of really executing result.py and really running CodeGenerationVerifier, on synthetic data The synthetic numbers (pcc 0.618, pcc_de 0.218) are a smoke test and are not comparable to the paper's 0.9883 on real Adamson data. PROVENANCE.md says so, explains why genome-wide PCC is inflated on real data, why r2_de is legitimately negative, and notes that the synthetic generator is sympathetic to the architecture it demonstrates. result.py is not a sketch. It conditions the perturbation on the target gene's embedding tied to the decoder output weights, rather than a free lookup table, because held-out rows in a lookup table never receive gradient and the unseen-perturbation split is then unsolvable in principle. torch/numpy/anndata are imported lazily so --help and --selftest run in a bare interpreter. scripts/export_example_run.py packages a genuine run into this layout, scrubbing API keys, absolute paths, usernames and hostnames, and aborting rather than writing a file that still matches a credential pattern. A real bundle should replace this one; CONTRIBUTING.md now asks for exactly that. .gitignore needed an explicit !examples/outputs/ because `outputs/` matched it and git will not descend into an excluded directory. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
…ons/checkout-7 Bump actions/checkout from 4 to 7
…i/codex-sdk-0.146.0 Bump @openai/codex-sdk from 0.116.0 to 0.146.0
…e-0.37.0 Update referencing requirement from >=0.30.2 to >=0.37.0
Updates the requirements on [setuptools](https://github.com/pypa/setuptools) to permit the latest version. - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst) - [Commits](pypa/setuptools@v65.5.1...v84.0.0) --- updated-dependencies: - dependency-name: setuptools dependency-version: 84.0.0 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 setuptools to permit the latest version.
Changelog
Sourced from setuptools's changelog.
... (truncated)
Commits
72e919aMerge pull request #5293 from pypa/bugfix/integration-pip-flit-backend1b29701Select the top-level pyproject.toml when reading build requirementsbb1b381Bump version: 83.0.0 → 84.0.0ee6fdd7Sync with distutils @ e8eb87855 (#5292)2a4a9e4Merge remote-tracking branch 'origin/main' into distutils-e8eb87855cbd1195Merge https://github.com/jaraco/skeletonbd3594eMerge pull request #5287 from Avasam/Configuring-lint.flake8-comprehensions.a...f02e90aConfigure C408 to allow dict(a=1) rather than disabling itc55f52bConfiguring lint.flake8-comprehensions.allow-dict-calls-with-keyword-argument...e9904b0Match the distutils sdist base type for the user_options overrideDependabot 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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