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Update documentation, add CI/Docs GitHub Actions, and resolve type/lint errors - #4

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aarmey merged 5 commits into
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docs-and-ci
Aug 23, 2026
Merged

Update documentation, add CI/Docs GitHub Actions, and resolve type/lint errors#4
aarmey merged 5 commits into
mainfrom
docs-and-ci

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@aarmey

@aarmey aarmey commented Aug 23, 2026

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Description

This PR updates the project documentation to accurately reflect internal capabilities, fixes type check and linter errors, and adds GitHub Actions for continuous integration and documentation deployment.

Key Changes

  • README & Sphinx Documentation:
    • Added full documentation and examples for vcsc.load_and_normalize (fused loader and depth-normalization kernel for IVCSR files).
    • Clarified VCSCAnnData.raw_X property and its distinction from standard AnnData .raw.
    • Added coverage for matrix-matrix/vector products (x @ v, v @ B, B @ v), major-axis fast slicing (v[:, [1, 3, 5]]), array conversion utilities (to_csc, to_csr, toarray, from_scipy), and to_layer.
    • Documented Zarr persistence (write_zarr / read_zarr) and standard installation instructions.
    • Added load_and_normalize to Sphinx API reference (docs/api.md) and usage guide (docs/usage.md).
  • Typing & Linting Fixes:
    • Resolved ty check and ruff check diagnostics in src/vcsc/_rapid_load.py, src/vcsc/_ivcsc.py, src/vcsc/_compression.py, and tests/test_rapid_load.py.
  • GitHub Actions Workflows:
    • .github/workflows/ci.yml: Runs ruff check ., ty check, and pytest --cov across Python matrix (3.11, 3.12).
    • .github/workflows/docs.yml: Builds Sphinx HTML documentation on PRs and deploys to GitHub Pages on merges to main.
  • Git Configuration:
    • Added *.h5ad, *.zarr, and *.h5 to .gitignore to prevent accidental check-in of large dataset archives.

@aarmey
aarmey merged commit 5ada8d2 into main Aug 23, 2026
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@aarmey
aarmey deleted the docs-and-ci branch August 23, 2026 13:20
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