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mudata v0.3 #56

Merged
merged 65 commits into from
Jul 8, 2024
Merged

mudata v0.3 #56

merged 65 commits into from
Jul 8, 2024

Commits on Aug 15, 2023

  1. copy temp indexes when dealing with gene duplicates while reading zar… 

    …r file
    @mumichae
    mumichae authored Aug 15, 2023
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Commits on Sep 7, 2023

  1. Display (non-default) axis and fix dimensions for nested MuData

    @gtca
    gtca committed Sep 7, 2023
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Commits on Sep 8, 2023

  1. Implement modality structure representation 

    Resolves #44
    @gtca
    gtca committed Sep 8, 2023
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Commits on Sep 9, 2023

  1. Implement fsspec support for reading HDF5 files 

    Currently fsspec is not a dependency. However both
BufferedReader and OpenFile instances should be accepted
by the HDF5 reader functions.
    @gtca
    gtca committed Sep 9, 2023
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Commits on Sep 10, 2023

  1. Fix .uns slot for views

    @gtca
    gtca committed Sep 10, 2023
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  2. Drop 3.8 from dev CI following anndata

    @gtca
    gtca committed Sep 10, 2023
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  3. Use mod-order in read_zarr

    @gtca
    gtca committed Sep 10, 2023
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  4. Merge pull request #49 from mumichae/mumichae-patch-1 

    Fix #48
    @gtca
    gtca authored Sep 10, 2023
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  5. Drop dtype in AnnData constructors

    @gtca
    gtca committed Sep 10, 2023
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Commits on Sep 11, 2023

  1. With names intersecting between modalities, 

    avoid name (pandas index) sorting
when adding new modalities.

Resolves #46.
    @gtca
    gtca committed Sep 11, 2023
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  2. Implement to_anndata() and to_mudata() 

    Addresses #14.
    @gtca
    gtca committed Sep 11, 2023
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  3. Start the main branch for v0.3

    @gtca
    gtca committed Sep 11, 2023
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  4. Add a missing import

    @gtca
    gtca committed Sep 11, 2023
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  5. Fix an extra import

    @gtca
    gtca committed Sep 11, 2023
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  6. Fix code formatting

    @gtca
    gtca committed Sep 11, 2023
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  7. Drop 3.8 from dev CI following anndata

    @gtca
    gtca committed Sep 11, 2023
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  8. Fix code formatting

    @gtca
    gtca committed Sep 11, 2023
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  9. Coerce nullable boolean to bool when possible

    @gtca
    gtca committed Sep 11, 2023
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Commits on Sep 12, 2023

  1. Convert boolean to bool when possible during .update()

    @gtca
    gtca committed Sep 12, 2023
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  2. Add some tests for bool type coercion

    @gtca
    gtca committed Sep 12, 2023
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  3. Add tests for mod-order

    @gtca
    gtca committed Sep 12, 2023
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Commits on Sep 20, 2023

  1. Implement push/pull interface for annotations (obs/var)

    @gtca
    gtca committed Sep 20, 2023
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  2. Add .mod_names

    @gtca
    gtca committed Sep 20, 2023
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Commits on Sep 21, 2023

  1. Implement mudata.concat()

    @gtca
    gtca committed Sep 21, 2023
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  2. Add annotations management notebook (pull/push)

    @gtca
    gtca committed Sep 21, 2023
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Commits on Jun 30, 2024

  1. Merge concat interface and rebase on 0.2.4

    @gtca
    gtca committed Jun 30, 2024
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  2. Merge branch 'mudata-0.3-pull-push' into mudata-0.3

    @gtca
    gtca committed Jun 30, 2024
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  3. Merge branch 'mudata-0.3-to_' into mudata-0.3

    @gtca
    gtca committed Jun 30, 2024
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  4. Black formatting

    @gtca
    gtca committed Jun 30, 2024
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  5. Merge branch 'mudata-0.3-fixes' into mudata-0.3

    @gtca
    gtca committed Jun 30, 2024
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  6. Merge branch 'main' into mudata-0.3

    @gtca
    gtca authored Jun 30, 2024
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Commits on Jul 1, 2024

  1. Use Python >=3.10

    @gtca
    gtca committed Jul 1, 2024
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  2. Black formatting

    @gtca
    gtca committed Jul 1, 2024
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Commits on Jul 2, 2024

  1. Transition to the src layout

    @gtca
    gtca committed Jul 2, 2024
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  2. Update CI to use ruff and uv

    @gtca
    gtca committed Jul 2, 2024
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  3. Use pathlib in docs/source/conf.py

    @gtca
    gtca committed Jul 2, 2024
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  4. Improve code style for tests

    @gtca
    gtca committed Jul 2, 2024
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  5. Improve code style for src/

    @gtca
    gtca committed Jul 2, 2024
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  6. Add setuptools_scm to the dev install

    @gtca
    gtca committed Jul 2, 2024
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  7. Also use uv for coverage CI

    @gtca
    gtca committed Jul 2, 2024
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  8. Use venv for uv in CI

    @gtca
    gtca committed Jul 2, 2024
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  9. Use venv for all CI steps

    @gtca
    gtca committed Jul 2, 2024
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  10. Use venv for all CI steps

    @gtca
    gtca committed Jul 2, 2024
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  11. Ruff is not satisfied with _version.py by Hatch

    @gtca
    gtca committed Jul 2, 2024
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  12. Fix #52 and use DictView as in AnnData

    @gtca
    gtca committed Jul 2, 2024
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  13. Organize imports

    @gtca
    gtca committed Jul 2, 2024
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Commits on Jul 3, 2024

  1. Fix exports

    @gtca
    gtca committed Jul 3, 2024
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  2. Improve pull/push interfaces 

    - Add pull=True argument to the update functions
- Handle categorical data with different categories in _pull_attr
- Improve error messages for pull/push operations
    @gtca
    gtca committed Jul 3, 2024
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  3. Increase stacklevel of the DeprecationWarning

    @gtca
    gtca committed Jul 3, 2024
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  4. Roll out the new .update() that does not pull columns 

    - Introduce the new _update_attr() to make the default in later versions
- Use configuration to change pull behaviour on update
  (mudata.set_options(pull_on_update=False))
    @gtca
    gtca committed Jul 3, 2024
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  5. Keep columns hash but do not consider it in the new update

    @gtca
    gtca committed Jul 3, 2024
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  6. Update notebooks with the upcoming changes in v0.3

    @gtca
    gtca committed Jul 3, 2024
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  7. DeprecationWarning -> FutureWarning

    @gtca
    gtca committed Jul 3, 2024
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  8. Address pandas 3.0 FutureWarning

    @gtca
    gtca committed Jul 3, 2024
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  9. Update changelog

    @gtca
    gtca committed Jul 3, 2024
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  10. Add more new features to changelog

    @gtca
    gtca committed Jul 3, 2024
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  11. Keep hash and shrink attr on save as in v0.2 by default 

    Defaults will change in the next versions
    @gtca
    gtca committed Jul 3, 2024
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  12. Add coercion to bool or int when there are no NaNs

    @gtca
    gtca committed Jul 3, 2024
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  13. Fix a typo in ._update_attr()

    @gtca
    gtca committed Jul 3, 2024
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  14. Organize imports

    @gtca
    gtca committed Jul 3, 2024
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Commits on Jul 4, 2024

  1. Add information about axis to the spec

    @gtca
    gtca committed Jul 4, 2024
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  2. Update documentation according to the new default .update() behaviour

    @gtca
    gtca committed Jul 4, 2024
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  3. Improve visibility of changes to .update() on doc pages

    @gtca
    gtca committed Jul 4, 2024
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  4. Update year in the copyright

    @gtca
    gtca committed Jul 4, 2024
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  5. Add scverse core shield

    @gtca
    gtca committed Jul 4, 2024
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