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Ivirshup/census builder spatial #1245

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Ivirshup/census builder spatial #1245

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Commits on Jun 7, 2024

  1. Add setup instructions to integrate soma spatial

    @prathapsridharan
    prathapsridharan committed Jun 7, 2024
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  2. Install git in census builder docker container

    @prathapsridharan
    prathapsridharan committed Jun 7, 2024
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  3. Add back pyarrow pin on builder for testing

    @prathapsridharan
    prathapsridharan committed Jun 7, 2024
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  4. Modify builder pins to test builder unit tests on GH

    @prathapsridharan
    prathapsridharan committed Jun 7, 2024
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  5. Remove cellxgene_census package dependency for testing

    @prathapsridharan
    prathapsridharan committed Jun 7, 2024
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  6. Pin to tiledbsoma commit to test builder unit tests

    @prathapsridharan
    prathapsridharan committed Jun 7, 2024
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  7. Pin to tiledbsoma git commit for 1.9.5 to test

    @prathapsridharan
    prathapsridharan committed Jun 7, 2024
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  8. Unpin pyarrow in builder to test builder unit tests

    @prathapsridharan
    prathapsridharan committed Jun 7, 2024
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  9. Pin to tiledbsoma git commit for 1.10.2 to test

    @prathapsridharan
    prathapsridharan committed Jun 7, 2024
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  10. Pin to tiledbsoma git commit for 1.11.1 to test

    @prathapsridharan
    prathapsridharan committed Jun 7, 2024
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  11. Pin tiledbsoma to 16f481f - head of spatial branch

    @prathapsridharan
    prathapsridharan committed Jun 7, 2024
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  12. Pin pyarrow back to 15.0.2

    @prathapsridharan
    prathapsridharan committed Jun 7, 2024
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  13. Pin tiledbsoma to fc5f8e7 to fix census builder tests

    @prathapsridharan
    prathapsridharan committed Jun 7, 2024
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  14. Add comments to notebook

    @prathapsridharan
    prathapsridharan committed Jun 7, 2024
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  15. Create notebook to demo census object creation

    @prathapsridharan
    prathapsridharan committed Jun 7, 2024
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  16. Use absolute file path for contents of manifest file

    @prathapsridharan
    prathapsridharan committed Jun 7, 2024
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  17. Add "EFO:0010961" to the list of allowed assays

    @prathapsridharan
    prathapsridharan committed Jun 7, 2024
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  18. Add comments for clarity in pyproject.toml

    @prathapsridharan
    prathapsridharan committed Jun 7, 2024
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  19. Fix filepaths in notebook

    @prathapsridharan
    prathapsridharan committed Jun 7, 2024
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  20. Make census builder run without errors on spatial datasets

    @prathapsridharan
    prathapsridharan committed Jun 7, 2024
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  21. Add census_data and census_spatial collections

    @prathapsridharan
    prathapsridharan committed Jun 7, 2024
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  22. Update notebook

    @prathapsridharan
    prathapsridharan committed Jun 7, 2024
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Commits on Jun 12, 2024

  1. Pin tiledbsoma to commit 5069714 for latest spatial

    @prathapsridharan
    prathapsridharan committed Jun 12, 2024
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  2. Update tiledbsoma spatial notebook

    @prathapsridharan
    prathapsridharan committed Jun 12, 2024
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  3. Update tiledbsoma spatial notebook

    @prathapsridharan
    prathapsridharan committed Jun 12, 2024
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  4. Update tiledbsoma spatial notebook

    @prathapsridharan
    prathapsridharan committed Jun 12, 2024
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  5. Pin tiledbsoma to commit 69d699e for latest spatial

    @prathapsridharan
    prathapsridharan committed Jun 12, 2024
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Commits on Jun 13, 2024

  1. Pin tiledbsoma to commit 9eb540f for latest spatial

    @prathapsridharan
    prathapsridharan committed Jun 13, 2024
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Commits on Jun 14, 2024

  1. Update tiledbsoma spatial notebook

    @prathapsridharan
    prathapsridharan committed Jun 14, 2024
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Commits on Jul 12, 2024

  1. Use latest commit from tiledbsoma spatial branch

    @ivirshup
    ivirshup committed Jul 12, 2024
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  2. get census spatial builder notebook running (i think)

    @ivirshup
    ivirshup committed Jul 12, 2024
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Commits on Jul 17, 2024

  1. Update ingestion notebook

    @ivirshup
    ivirshup committed Jul 17, 2024
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  2. Merge branch 'main' into ivirshup/census-builder-spatial

    @ivirshup
    ivirshup committed Jul 17, 2024
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  3. Fix typo

    @ivirshup
    ivirshup committed Jul 17, 2024
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  4. Update source datasets to v5.1.0 versions

    @ivirshup
    ivirshup committed Jul 17, 2024
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  5. Update ingest notebook

    @ivirshup
    ivirshup committed Jul 17, 2024
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  6. First attempt at writing images, current in progress

    @ivirshup
    ivirshup committed Jul 17, 2024
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Commits on Jul 18, 2024

  1. Fix up writing of images

    @ivirshup
    ivirshup committed Jul 18, 2024
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Commits on Jul 24, 2024

  1. Start test suite

    @ivirshup
    ivirshup committed Jul 24, 2024
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  2. Write locations

    @ivirshup
    ivirshup committed Jul 24, 2024
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  3. Write obs_scene

    @ivirshup
    ivirshup committed Jul 24, 2024
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  4. silence mypy

    @ivirshup
    ivirshup committed Jul 24, 2024
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  5. sorta update test

    @ivirshup
    ivirshup committed Jul 24, 2024
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  6. update notebooks

    @ivirshup
    ivirshup committed Jul 24, 2024
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  7. Fix builds on CI by using hatch as build tool

    @ivirshup
    ivirshup committed Jul 24, 2024
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Commits on Aug 1, 2024

  1. Get build running for visium

    @ivirshup
    ivirshup committed Aug 1, 2024
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Commits on Aug 3, 2024

  1. Add tests for images and obs_scene

    @ivirshup
    ivirshup committed Aug 3, 2024
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  2. add notebook so I can change branches

    @ivirshup
    ivirshup committed Aug 3, 2024
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Commits on Aug 6, 2024

  1. Allow manifests to contain s3 uris, add manifest folder

    @ivirshup
    ivirshup committed Aug 6, 2024
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Commits on Aug 7, 2024

  1. Add manifest for slideseq

    @ivirshup
    ivirshup committed Aug 7, 2024
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  2. Merge branch 'main' into ivirshup/census-builder-spatial

    @ivirshup
    ivirshup committed Aug 7, 2024
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Commits on Aug 8, 2024

  1. Add slide-seqv2 to allowed assays

    @ivirshup
    ivirshup committed Aug 8, 2024
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Commits on Aug 9, 2024

  1. Branch to allow for datasets that don't have associated images

    @ivirshup
    ivirshup committed Aug 9, 2024
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Commits on Aug 16, 2024

  1. Use dask to write images + pin tiledbsoma to working commit

    @ivirshup
    ivirshup committed Aug 16, 2024
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  2. Merge branch 'main' into ivirshup/census-builder-spatial

    @ivirshup
    ivirshup authored Aug 16, 2024
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  3. Add support for scene class

    @ivirshup
    ivirshup committed Aug 16, 2024
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Commits on Aug 28, 2024

  1. Bump to newer commit on tiledbsoma branch

    @ivirshup
    ivirshup committed Aug 28, 2024
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Commits on Sep 4, 2024

  1. Update pinned tiledbsoma version (not quite working)

    @ivirshup
    ivirshup committed Sep 4, 2024
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Commits on Sep 13, 2024

  1. Merge branch 'main' into ivirshup/census-builder-spatial

    @ivirshup
    ivirshup committed Sep 13, 2024
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Commits on Oct 22, 2024

  1. Merge branch 'main' into ivirshup/census-builder-spatial, plus update… 

    … test datasets
    @ivirshup
    ivirshup committed Oct 22, 2024
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Commits on Oct 28, 2024

  1. Merge branch 'main' into ivirshup/census-builder-spatial

    @ivirshup
    ivirshup committed Oct 28, 2024
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  2. Fix write_obs/var_dataframe for cases where that dataframe is None

    @ivirshup
    ivirshup committed Oct 28, 2024
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Commits on Oct 29, 2024

  1. Working again! (mostly)

    @ivirshup
    ivirshup committed Oct 29, 2024
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  2. Add tiledb dep back

    @ivirshup
    ivirshup committed Oct 29, 2024
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  3. update manifests

    @ivirshup
    ivirshup committed Oct 29, 2024
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