Code

Ivirshup/census builder spatial#1245

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ivirshup wants to merge 96 commits intomainchanzuckerberg/cellxgene-census:mainfrom ivirshup/census-builder-spatialchanzuckerberg/cellxgene-census:ivirshup/census-builder-spatialCopy head branch name to clipboard

+9,058-215

Commits

Commits on Jun 7, 2024

• Add setup instructions to integrate soma spatial

  prathapsridharan

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  56bd44b

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• Install git in census builder docker container

  prathapsridharan

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  76c2a8a

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• Add back pyarrow pin on builder for testing

  prathapsridharan

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• Modify builder pins to test builder unit tests on GH

  prathapsridharan

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• Remove cellxgene_census package dependency for testing

  prathapsridharan

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• Pin to tiledbsoma commit to test builder unit tests

  prathapsridharan

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• Pin to tiledbsoma git commit for 1.9.5 to test

  prathapsridharan

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• Unpin pyarrow in builder to test builder unit tests

  prathapsridharan

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• Pin to tiledbsoma git commit for 1.10.2 to test

  prathapsridharan

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• Pin to tiledbsoma git commit for 1.11.1 to test

  prathapsridharan

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• Pin tiledbsoma to 16f481f - head of spatial branch

  prathapsridharan

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• Pin pyarrow back to 15.0.2

  prathapsridharan

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  97ef790

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• Pin tiledbsoma to fc5f8e7 to fix census builder tests

  prathapsridharan

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  3567dc7

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• Add comments to notebook

  prathapsridharan

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• Create notebook to demo census object creation

  prathapsridharan

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• Use absolute file path for contents of manifest file

  prathapsridharan

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• Add "EFO:0010961" to the list of allowed assays

  prathapsridharan

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• Add comments for clarity in pyproject.toml

  prathapsridharan

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• Fix filepaths in notebook

  prathapsridharan

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• Make census builder run without errors on spatial datasets

  prathapsridharan

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• Add census_data and census_spatial collections

  prathapsridharan

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  e7e6b07

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• Update notebook

  prathapsridharan

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Commits on Jun 12, 2024

• Pin tiledbsoma to commit 5069714 for latest spatial

  prathapsridharan

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• Update tiledbsoma spatial notebook

  prathapsridharan

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  14d682e

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• Update tiledbsoma spatial notebook

  prathapsridharan

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• Update tiledbsoma spatial notebook

  prathapsridharan

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• Pin tiledbsoma to commit 69d699e for latest spatial

  prathapsridharan

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Commits on Jun 13, 2024

• Pin tiledbsoma to commit 9eb540f for latest spatial

  prathapsridharan

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Commits on Jun 14, 2024

• Update tiledbsoma spatial notebook

  prathapsridharan

  committed
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Commits on Jul 12, 2024

• Use latest commit from tiledbsoma spatial branch

  ivirshup

  committed
  03afeb4

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• get census spatial builder notebook running (i think)

  ivirshup

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Commits on Jul 17, 2024

• Update ingestion notebook

  ivirshup

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  aca4bac

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• Merge branch 'main' into ivirshup/census-builder-spatial

  ivirshup

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  8b08ac8

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• Fix typo

  ivirshup

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• Update source datasets to v5.1.0 versions

  ivirshup

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• Update ingest notebook

  ivirshup

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• First attempt at writing images, current in progress

  ivirshup

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Commits on Jul 18, 2024

• Fix up writing of images

  ivirshup

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Commits on Jul 24, 2024

• Start test suite

  ivirshup

  committed
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• Write locations

  ivirshup

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• Write obs_scene

  ivirshup

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• silence mypy

  ivirshup

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  48cd6e3

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• sorta update test

  ivirshup

  committed
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• update notebooks

  ivirshup

  committed
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• Fix builds on CI by using hatch as build tool

  ivirshup

  committed
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Commits on Aug 1, 2024

• Get build running for visium

  ivirshup

  committed
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Commits on Aug 3, 2024

• Add tests for images and obs_scene

  ivirshup

  committed
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• add notebook so I can change branches

  ivirshup

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Commits on Aug 6, 2024

• Allow manifests to contain s3 uris, add manifest folder

  ivirshup

  committed
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Commits on Aug 7, 2024

• Add manifest for slideseq

  ivirshup

  committed
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• Merge branch 'main' into ivirshup/census-builder-spatial

  ivirshup

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Commits on Aug 8, 2024

• Add slide-seqv2 to allowed assays

  ivirshup

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Commits on Aug 9, 2024

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

  ivirshup

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Commits on Aug 16, 2024

• Use dask to write images + pin tiledbsoma to working commit

  ivirshup

  committed
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• Merge branch 'main' into ivirshup/census-builder-spatial

  ivirshup

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• Add support for scene class

  ivirshup

  committed
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Commits on Aug 28, 2024

• Bump to newer commit on tiledbsoma branch

  ivirshup

  committed
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Commits on Sep 4, 2024

• Update pinned tiledbsoma version (not quite working)

  ivirshup

  committed
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Commits on Sep 13, 2024

• Merge branch 'main' into ivirshup/census-builder-spatial

  ivirshup

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Commits on Oct 22, 2024

• Merge branch 'main' into ivirshup/census-builder-spatial, plus update test datasets

  ivirshup

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Commits on Oct 28, 2024

• Merge branch 'main' into ivirshup/census-builder-spatial

  ivirshup

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• Fix write_obs/var_dataframe for cases where that dataframe is None

  ivirshup

  committed
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Commits on Oct 29, 2024

• Working again! (mostly)

  ivirshup

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• Add tiledb dep back

  ivirshup

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• update manifests

  ivirshup

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Commits on Nov 18, 2024

• Merge branch 'main' into ivirshup/census-builder-spatial

  ivirshup

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Commits on Nov 22, 2024

• Bump tiledbsoma version. Temporarily turn off validation for testing.

  ivirshup

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Commits on Nov 23, 2024

• Bump to tiledbsoma==1.15.0rc4

  ivirshup

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Commits on Dec 6, 2024

• Update manifests

  ivirshup

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Commits on Dec 13, 2024

• Merge branch 'main' into ivirshup/census-builder-spatial

  ivirshup

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  39969f5

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• Relax requirements

  ivirshup

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  6a7c21d

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• Account for differences in obs_spatial_presence

  ivirshup

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Commits on Dec 16, 2024

• Get builds up to date (transforms are still broken)

  ivirshup

  committed
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Commits on Jan 9, 2025

• Bump tiledbsoma dep to include latest spatialdata exporter

  ivirshup

  committed
  3a6229d

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Commits on Jan 10, 2025

• Fix transformations

  ivirshup

  committed
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Commits on Jan 11, 2025

• Bump version of tiledbsoma used to 1.15.3

  ivirshup

  committed
  d4db232

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• Merge branch 'main' into ivirshup/census-builder-spatial

  ivirshup

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  f5efa68

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• Update required version of tiledbsoma for client

  ivirshup

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  8b54aea

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Commits on Jan 13, 2025

• Fix consolidation (#1329)

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  ebezzi

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• Merge branch 'main' into ivirshup/census-builder-spatial

  ivirshup

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  a37b74e

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• fix validation key (#1332)

  ebezzi

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  966d2e9

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• Merge branch 'main' into ivirshup/census-builder-spatial

  ivirshup

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Commits on Jan 15, 2025

• Only check files listed in manifest

  ivirshup

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  3b1d7ec

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Commits on Jan 17, 2025

• Add test for normalized matrix on spatial

  ivirshup

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Commits on Jan 21, 2025

• Merge branch 'ivirshup/census-builder-improved-test-cases' into ivirshup/census-builder-spatial

  ivirshup

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• Set name of visium/ slide-seq to census_spatial_sequencing

  ivirshup

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• Don't write a normalized layer for spatial sequencing experiments

  ivirshup

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• add pooch to deps (used in testing)

  ivirshup

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• Add pytest-xdist to builder test deps

  ivirshup

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• Remove alpha level from images

  ivirshup

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Commits on Jan 24, 2025

• Add minimum version bound to spatialdata dep

  ivirshup

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Commits on Jan 27, 2025

• Fix radius of visium spots

  ivirshup

  committed
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Commits on Jan 28, 2025

• Don't set coordinate space unit

  ivirshup

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• Better testing for coordinates

  ivirshup

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Commits on Jan 30, 2025

• Ivirshup/census builder spatial visium cols (#1344)

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  ivirshup

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• Merge branch 'main' into ivirshup/census-builder-spatial

  ivirshup

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