v1.0.0rc3

What's Changed

• Add tutorial for gget cellxgene module, edited by @pablo-gar in #450
• adds 'duplicate cells' notebooks by @pablo-gar in #448
• Pin tiledb version as work-around by @bkmartinjr in #454
• Incorporate comms changes by @pablo-gar in #456
• A few final edits to gget tutorial by @lauraluebbert in #451

New Contributors

• @lauraluebbert made their first contribution in #451

Full Changelog: v1.0.0rc2...v1.0.0rc3

v1.0.0

What's Changed

• update python package name python demonstration notebooks by @bkmartinjr in #350
• rerun notebooks for census build 2023-04-04 by @atolopko-czi in #353
• Builder: additional workflow steps by @bkmartinjr in #351
• [r] use new SOMATileDBContext$context() accessor by @mlin in #357
• census_dataset_presence.ipynb typo fix by @mlin in #352
• readthedocs setup by @ebezzi in #335
• Miscellaneous R doc changes by @ebezzi in #338
• Miscellaneous docs updates by @ebezzi in #365
• Update documentation link in README.md by @ebezzi in #367
• Adds Census FAQ by @pablo-gar in #362
• Add plausible to sphinx and pkgdown by @ebezzi in #366
• Update examples link in README.md by @ebezzi in #368
• Editorial changes to notebook comp_bio_data_integration_scvi.ipynb by @pablo-gar in #370
• Editorial changes to notebook census_axis_query.ipynb by @pablo-gar in #371
• Editorial changes to notebook comp_bio_census_info.ipynb by @pablo-gar in #369
• Fix naming and links and small editorial changes of documentation. by @pablo-gar in #373
• chore: fix link to tutorials in README by @pablo-gar in #375
• refractor get_seurat, update docs and tests by @pablo-gar in #381
• [r] add remaining API demo vignettes by @mlin in #358
• Use GET /datasets endpoint for builder by @ebezzi in #378
• New documentation pages by @ebezzi in #386
• Change template for docsite to look like cellxgene by @ebezzi in #385
• fix anchors in docs by @ebezzi in #387
• Audit notebook 4 by @pablo-gar in #377
• Updates schema to 1.0 by @pablo-gar in #374
• chore: pin uberon ontology version by @atolopko-czi in #388
• Make census builder adhere to census schema 1.0 by @ebezzi in #394
• [r] revise census_query_extract.Rmd by @mlin in #393
• Stable route for release.json by @ebezzi in #409
• Miscellaneous doc fixes by @ebezzi in #413
• Fix for Mac OSX certificate issue by @atolopko-czi in #416
• bump tiledbsoma to 1.2.2 by @atolopko-czi in #419
• Modify README.md to remove pre-release status by @ebezzi in #423
• Docsite GHA workflow by @ebezzi in #422
• Add Census link to docpage navbar by @ebezzi in #408
• Add missing docs dependency by @ebezzi in #425
• Incorporates comms edits and updates links to new landing site by @pablo-gar in #421
• Fix docsite build by @ebezzi in #431
• [doc-site] Small formatting nit fixes, removes one R example in quick start by @pablo-gar in #428
• Change plausible snippet to the new docsite by @ebezzi in #432
• Change plausible snippet to the new docsite for R by @ebezzi in #434
• open_soma() alias handling changes by @atolopko-czi in #435
• Updates cell number in docsite visual by @pablo-gar in #437
• Move release.json location by @ebezzi in #443
• Docsite favicon by @ebezzi in #442
• Add tutorial for gget cellxgene module, edited by @pablo-gar in #450
• adds 'duplicate cells' notebooks by @pablo-gar in #448
• Pin tiledb version as work-around by @bkmartinjr in #454
• Incorporate comms changes by @pablo-gar in #456
• A few final edits to gget tutorial by @lauraluebbert in #451
• revert R API release.json URL by @atolopko-czi in #458
• Fix docsite version and disable searchbar by @ebezzi in #460
• update release bootstrap URL to public permalink by @bkmartinjr in #459
• Remove pre-release from README.md by @ebezzi in #462

New Contributors

• @lauraluebbert made their first contribution in #451

Full Changelog: v0.13.0...v1.0.0

v1.0.0rc2

What's Changed

• Modify README.md to remove pre-release status by @ebezzi in #423
• Docsite GHA workflow by @ebezzi in #422
• Add Census link to docpage navbar by @ebezzi in #408
• Add missing docs dependency by @ebezzi in #425
• Incorporates comms edits and updates links to new landing site by @pablo-gar in #421
• Fix docsite build by @ebezzi in #431
• [doc-site] Small formatting nit fixes, removes one R example in quick start by @pablo-gar in #428
• Change plausible snippet to the new docsite by @ebezzi in #432
• Change plausible snippet to the new docsite for R by @ebezzi in #434
• open_soma() alias handling changes by @atolopko-czi in #435
• Updates cell number in docsite visual by @pablo-gar in #437
• Move release.json location by @ebezzi in #443
• Docsite favicon by @ebezzi in #442

Full Changelog: v1.0.0rc1...v1.0.0rc2

v1.0.0rc1

What's Changed

• update python package name python demonstration notebooks by @bkmartinjr in #350
• rerun notebooks for census build 2023-04-04 by @atolopko-czi in #353
• Builder: additional workflow steps by @bkmartinjr in #351
• [r] use new SOMATileDBContext$context() accessor by @mlin in #357
• census_dataset_presence.ipynb typo fix by @mlin in #352
• readthedocs setup by @ebezzi in #335
• Miscellaneous R doc changes by @ebezzi in #338
• Miscellaneous docs updates by @ebezzi in #365
• Update documentation link in README.md by @ebezzi in #367
• Adds Census FAQ by @pablo-gar in #362
• Add plausible to sphinx and pkgdown by @ebezzi in #366
• Update examples link in README.md by @ebezzi in #368
• Editorial changes to notebook comp_bio_data_integration_scvi.ipynb by @pablo-gar in #370
• Editorial changes to notebook census_axis_query.ipynb by @pablo-gar in #371
• Editorial changes to notebook comp_bio_census_info.ipynb by @pablo-gar in #369
• Fix naming and links and small editorial changes of documentation. by @pablo-gar in #373
• chore: fix link to tutorials in README by @pablo-gar in #375
• refractor get_seurat, update docs and tests by @pablo-gar in #381
• [r] add remaining API demo vignettes by @mlin in #358
• Use GET /datasets endpoint for builder by @ebezzi in #378
• New documentation pages by @ebezzi in #386
• Change template for docsite to look like cellxgene by @ebezzi in #385
• fix anchors in docs by @ebezzi in #387
• Audit notebook 4 by @pablo-gar in #377
• Updates schema to 1.0 by @pablo-gar in #374
• chore: pin uberon ontology version by @atolopko-czi in #388
• Make census builder adhere to census schema 1.0 by @ebezzi in #394
• [r] revise census_query_extract.Rmd by @mlin in #393
• Stable route for release.json by @ebezzi in #409
• Miscellaneous doc fixes by @ebezzi in #413
• Fix for Mac OSX certificate issue by @atolopko-czi in #416
• bump tiledbsoma to 1.2.2 by @atolopko-czi in #419

Full Changelog: v0.13.0...v1.0.0rc1

v0.13.0

What's Changed

Breaking changes:

• Python package name has changed to cellxgene_census.

Fixes:

• Fix Python package import error on Python 3.8

Summary of commits:

• acceptance test run by @bkmartinjr in #310
• Modify GHA to push builder Docker image by @ebezzi in #312
• Add requirements.txt for notebooks by @ebezzi in #308
• rename ECR repo by @ebezzi in #334
• clean up dependencies for cell_census by @bkmartinjr in #337
• Rename to CELLxGENE Discover Census in README.md by @ebezzi in #333
• Python API name changes by @ebezzi in #339
• Add builder sub-module for old build cleanup by @bkmartinjr in #331
• name migration for tools/builder by @bkmartinjr in #340
• package name changes in docstrings by @bkmartinjr in #343
• [r] rename CellCensus to cellxgene.census by @mlin in #344
• add old package name redirect by @bkmartinjr in #346
• Adds cell census release info and cleans up storage policy by @pablo-gar in #314
• Add notebook guidelines by @pablo-gar in #316
• update package metadata to tag maturity as beta by @bkmartinjr in #348
• update cell census name in docstrings/md files by @bkmartinjr in #347

Full Changelog: v0.12.0...v0.13.0

v0.12.0

What's Changed

Update package dependencies to specify tiledbsoma version 1.2.1.

• work-around and diagnostics for Ctx excess allocation bug by @bkmartinjr in #292
• [r] census_datasets vignette by @mlin in #252
• miscellaneous builder fixes / cleanup by @bkmartinjr in #298
• adds bug issue template by @pablo-gar in #303
• "acceptance" tests by @bkmartinjr in #305
• adds feature request template by @pablo-gar in #302
• [r] add get_seurat() by @mlin in #293

Full Changelog: v0.11.0...v0.12.0

v0.11.0

What's Changed

This release updates the cell census package to use tiledbsoma v1.1.1

• open_anndata unit test by @ebezzi in #254
• Unit tests for staging datasets by @ebezzi in #258
• Add validation data checks by @Bento007 in #243
• setup_module for multiprocessing tests (test_source_assets) by @ebezzi in #262
• assertion to confirm correct MP configuration by @bkmartinjr in #263
• [r] use SOMATileDBContext by @mlin in #256
• Util unit tests by @ebezzi in #261
• Update lifecycle annotations to be consistent with tiledbsoma by @ebezzi in #264
• Dockerfile for census builder by @ebezzi in #267
• [r] add get_presence_matrix by @mlin in #274
• Add note to tissue_mapper.py by @ebezzi in #276
• Adds text to README to indicate pre-release state by @pablo-gar in #273
• fix email address in Python package metadata by @bkmartinjr in #281
• Update readmes by @pablo-gar in #282
• improved build workflow by @bkmartinjr in #272
• Add nbqa to reformat notebooks by @ebezzi in #277
• update Python package dependency to tiledbsoma 1.1.1 by @bkmartinjr in #287

Full Changelog: v0.10.0...v0.11.0

v0.10.0

What's Changed

Updated package to use tiledbsoma version 1.0.0. There should be no breaking API changes.

• add unit tests for python cell_census package by @bkmartinjr in #244
• [ci] fix paths-ignore in workflow YMLs by @mlin in #251
• [r] add source h5ad accessor functions by @mlin in #250
• Update to tiledbsoma 1.0.0 by @bkmartinjr in #255

Full Changelog: v0.9.0...v0.10.0

v0.9.0

What's Changed

Updated package to use tiledbsoma version 1.0.0rc4. No significant changes to this package.

• [R] CellCensus package MVP by @mlin in #206
• rename CI workflows by @mlin in #232
• fix presence matrix wrong shape by @ebezzi in #236
• rerun notebooks for census build 2023-02-28 by @ebezzi in #234
• Change docstrings to use Google conventions by @ebezzi in #233
• R docs by @ebezzi in #226
• refactor ExperimentBuilder and validator for improved validator isolation by @bkmartinjr in #237
• update to tiledbsoma 1.0.0rc4 by @bkmartinjr in #239

New Contributors

• @mlin made their first contribution in #206

Full Changelog: v0.8.0...v0.9.0

v0.8.0

What's Changed

Update to tiledbsoma version 1.0.0rc2. No major changes to the cell-census package.

• Additional validation checks by @Bento007 in #204
• enable duplicates for performance by @bkmartinjr in #219
• Updates Readme by @pablo-gar in #212
• Notebook documentation by @ebezzi in #218
• Update python package and builder to tiledbsoma 1.0.0rc2 by @bkmartinjr in #227

Full Changelog: v0.7.0...v0.8.0