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Fix adata copy (coarse transition matrix) #1223

Merged
merged 35 commits into from
Sep 15, 2024
Merged

Fix adata copy (coarse transition matrix) #1223

merged 35 commits into from
Sep 15, 2024

Commits on Sep 5, 2024

  1. chore: bump ruff pre-commit hook version

    @afuetterer
    afuetterer committed Sep 5, 2024
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Commits on Sep 15, 2024

  1. Fix copy

    @michalk8
    michalk8 committed Sep 15, 2024
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  2. Fix some warnings

    @michalk8
    michalk8 committed Sep 15, 2024
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  3. Fix reading from adata

    @michalk8
    michalk8 committed Sep 15, 2024
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  4. Test on 3.12

    @michalk8
    michalk8 committed Sep 15, 2024
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  5. Update tox

    @michalk8
    michalk8 committed Sep 15, 2024
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  6. Use macos-14

    @michalk8
    michalk8 committed Sep 15, 2024
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  7. Drop 3.8 support

    @michalk8
    michalk8 committed Sep 15, 2024
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  8. Update pre-commits

    @michalk8
    michalk8 committed Sep 15, 2024
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  9. Update tests (pre-commit)

    @michalk8
    michalk8 committed Sep 15, 2024
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  10. Run more pre-commits

    @michalk8
    michalk8 committed Sep 15, 2024
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  11. Fix more pre-commits

    @michalk8
    michalk8 committed Sep 15, 2024
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  12. Switch mostly to np.random.default_rng

    @michalk8
    michalk8 committed Sep 15, 2024
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  13. Fix rest of the pre-commits

    @michalk8
    michalk8 committed Sep 15, 2024
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  14. Merge remote-tracking branch 'afut/ruff' into fix/adata-copy

    @michalk8
    michalk8 committed Sep 15, 2024
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  15. Update ruff version

    @michalk8
    michalk8 committed Sep 15, 2024
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  16. Use 3.9 type-hints

    @michalk8
    michalk8 committed Sep 15, 2024
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  17. Update black-docs

    @michalk8
    michalk8 committed Sep 15, 2024
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  18. Fix workflow Python version

    @michalk8
    michalk8 committed Sep 15, 2024
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  19. Try setting up conda on MacOS

    @michalk8
    michalk8 committed Sep 15, 2024
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  20. Fix if statement

    @michalk8
    michalk8 committed Sep 15, 2024
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  21. Use observed=False

    @michalk8
    michalk8 committed Sep 15, 2024
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  22. Update test figure

    @michalk8
    michalk8 committed Sep 15, 2024
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  23. Fix test on 3.12

    @michalk8
    michalk8 committed Sep 15, 2024
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  24. Unpin pytest version

    @michalk8
    michalk8 committed Sep 15, 2024
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  25. Remove worker_id

    @michalk8
    michalk8 committed Sep 15, 2024
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  26. Regenerate GT figures

    @michalk8
    michalk8 committed Sep 15, 2024
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  27. Regenerate rest of the figures

    @michalk8
    michalk8 committed Sep 15, 2024
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  28. Fix seeds in log_odds tests

    @michalk8
    michalk8 committed Sep 15, 2024
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  29. Update cluster_lineage figures

    @michalk8
    michalk8 committed Sep 15, 2024
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  30. Fix GAMR in failed model

    @michalk8
    michalk8 committed Sep 15, 2024
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  31. Reduce CI verbosity

    @michalk8
    michalk8 committed Sep 15, 2024
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  32. Run format-references

    @michalk8
    michalk8 committed Sep 15, 2024
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  33. Polish cite.rst

    @michalk8
    michalk8 committed Sep 15, 2024
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  34. Fix extra clustering_kwargs

    @michalk8
    michalk8 committed Sep 15, 2024
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