Code

Ivirshup/census builder spatial#1245

Code

Draft

ivirshup wants to merge 73 commits intomainchanzuckerberg/cellxgene-census:mainfrom ivirshup/census-builder-spatialchanzuckerberg/cellxgene-census:ivirshup/census-builder-spatialCopy head branch name to clipboard

+8,310-89

Commits

Commits on Jun 7, 2024

• Add setup instructions to integrate soma spatial

  prathapsridharan

  committed
  56bd44b

• Install git in census builder docker container

  prathapsridharan

  committed
  76c2a8a

• Add back pyarrow pin on builder for testing

  prathapsridharan

  committed
  a38c215

• Modify builder pins to test builder unit tests on GH

  prathapsridharan

  committed
  8ae84af

• Remove cellxgene_census package dependency for testing

  prathapsridharan

  committed
  b330183

• Pin to tiledbsoma commit to test builder unit tests

  prathapsridharan

  committed
  6655196

• Pin to tiledbsoma git commit for 1.9.5 to test

  prathapsridharan

  committed
  e91b2fa

• Unpin pyarrow in builder to test builder unit tests

  prathapsridharan

  committed
  4115601

• Pin to tiledbsoma git commit for 1.10.2 to test

  prathapsridharan

  committed
  1c7f985

• Pin to tiledbsoma git commit for 1.11.1 to test

  prathapsridharan

  committed
  4aa689e

• Pin tiledbsoma to 16f481f - head of spatial branch

  prathapsridharan

  committed
  327cee6

• Pin pyarrow back to 15.0.2

  prathapsridharan

  committed
  97ef790

• Pin tiledbsoma to fc5f8e7 to fix census builder tests

  prathapsridharan

  committed
  3567dc7

• Add comments to notebook

  prathapsridharan

  committed
  ba5ac8f

• Create notebook to demo census object creation

  prathapsridharan

  committed
  b448027

• Use absolute file path for contents of manifest file

  prathapsridharan

  committed
  0f1f20a

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

  prathapsridharan

  committed
  5c81aaa

• Add comments for clarity in pyproject.toml

  prathapsridharan

  committed
  ce4b525

• Fix filepaths in notebook

  prathapsridharan

  committed
  1f654b6

• Make census builder run without errors on spatial datasets

  prathapsridharan

  committed
  4712e95

• Add census_data and census_spatial collections

  prathapsridharan

  committed
  e7e6b07

• Update notebook

  prathapsridharan

  committed
  44c1109

Commits on Jun 12, 2024

• Pin tiledbsoma to commit 5069714 for latest spatial

  prathapsridharan

  committed
  1854f41

• Update tiledbsoma spatial notebook

  prathapsridharan

  committed
  14d682e

• Update tiledbsoma spatial notebook

  prathapsridharan

  committed
  bf0fdea

• Update tiledbsoma spatial notebook

  prathapsridharan

  committed
  ebbe1b1

• Pin tiledbsoma to commit 69d699e for latest spatial

  prathapsridharan

  committed
  ff73498

Commits on Jun 13, 2024

• Pin tiledbsoma to commit 9eb540f for latest spatial

  prathapsridharan

  committed
  a5c21a1

Commits on Jun 14, 2024

• Update tiledbsoma spatial notebook

  prathapsridharan

  committed
  2cef2bb

Commits on Jul 12, 2024

• Use latest commit from tiledbsoma spatial branch

  ivirshup

  committed
  03afeb4

• get census spatial builder notebook running (i think)

  ivirshup

  committed
  f3b699b

Commits on Jul 17, 2024

• Update ingestion notebook

  ivirshup

  committed
  aca4bac

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

  ivirshup

  committed
  8b08ac8

• Fix typo

  ivirshup

  committed
  c10ac78

• Update source datasets to v5.1.0 versions

  ivirshup

  committed
  441fb64

• Update ingest notebook

  ivirshup

  committed
  62e3ae0

• First attempt at writing images, current in progress

  ivirshup

  committed
  e4d2bf2

Commits on Jul 18, 2024

• Fix up writing of images

  ivirshup

  committed
  229379c

Commits on Jul 24, 2024

• Start test suite

  ivirshup

  committed
  953b710

• Write locations

  ivirshup

  committed
  61b901e

• Write obs_scene

  ivirshup

  committed
  833260d

• silence mypy

  ivirshup

  committed
  48cd6e3

• sorta update test

  ivirshup

  committed
  8499603

• update notebooks

  ivirshup

  committed
  8f8adcd

• Fix builds on CI by using hatch as build tool

  ivirshup

  committed
  3e504de

Commits on Aug 1, 2024

• Get build running for visium

  ivirshup

  committed
  cf9be22

Commits on Aug 3, 2024

• Add tests for images and obs_scene

  ivirshup

  committed
  0a257f9

• add notebook so I can change branches

  ivirshup

  committed
  a6989f0

Commits on Aug 6, 2024

• Allow manifests to contain s3 uris, add manifest folder

  ivirshup

  committed
  cb891e8

Commits on Aug 7, 2024

• Add manifest for slideseq

  ivirshup

  committed
  f39300b

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

  ivirshup

  committed
  41c7c18

Commits on Aug 8, 2024

• Add slide-seqv2 to allowed assays

  ivirshup

  committed
  d33c7dd

Commits on Aug 9, 2024

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

  ivirshup

  committed
  9ca4327

Commits on Aug 16, 2024

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

  ivirshup

  committed
  07e6e30

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

  ivirshup

  authored
  d6a1ab6

• Add support for scene class

  ivirshup

  committed
  cd96482

Commits on Aug 28, 2024

• Bump to newer commit on tiledbsoma branch

  ivirshup

  committed
  4a4316d

Commits on Sep 4, 2024

• Update pinned tiledbsoma version (not quite working)

  ivirshup

  committed
  6c86a75

Commits on Sep 13, 2024

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

  ivirshup

  committed
  5b9f70a

Commits on Oct 22, 2024

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

  ivirshup

  committed
  8e6fa76

Commits on Oct 28, 2024

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

  ivirshup

  committed
  1058956

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

  ivirshup

  committed
  f9f72b8

Commits on Oct 29, 2024

• Working again! (mostly)

  ivirshup

  committed
  ef720da

• Add tiledb dep back

  ivirshup

  committed
  4241c9d

• update manifests

  ivirshup

  committed
  a4b34c1

Commits on Nov 18, 2024

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

  ivirshup

  committed
  5cf87f0

Commits on Nov 22, 2024

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

  ivirshup

  committed
  b06361f

Commits on Nov 23, 2024

• Bump to tiledbsoma==1.15.0rc4

  ivirshup

  committed
  4fb3198

Commits on Dec 6, 2024

• Update manifests

  ivirshup

  committed
  a75e510

Commits on Dec 13, 2024

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

  ivirshup

  committed
  39969f5

• Relax requirements

  ivirshup

  committed
  6a7c21d

• Account for differences in obs_spatial_presence

  ivirshup

  committed
  bbe7dbb

Commits on Dec 16, 2024

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

  ivirshup

  committed
  c2c2967