v0.7.0

Breaking Changes

• cell_census Python package updated to utilize tiledbsoma 1.0.0rc1, which includes a small breaking change to SOMATileDBContext timestamp handling.

Known issues

• there is an errant debugging message which will be printed upon calling cell_census.open_soma(). It can be safely ignored.

What's Changed

• docs: Clarifies text for Feature Dataset Presence Matrix, rename schema file by @pablo-gar in #211
• Docsite by @ebezzi in #199
• feature: update builder tiledbsoma release by @atolopko-czi in #154
• Add SOMA page and links by @ebezzi in #217
• docs: fix header level of notebooks by @pablo-gar in #224
• add tests for builder arg parser by @Bento007 in #200
• Python package: update tiledbsoma dep to 1.0.0rc1 by @bkmartinjr in #225

Full Changelog: v0.6.0...v0.7.0

v0.6.0

Breaking Changes

• Updated to tiledbsoma version 1.0rc0

Improvements

• Fixed performance regression in open_soma

What's Changed

• Add codecov github action by @Bento007 in #178
• API cleanup by @bkmartinjr in #180
• Add validate to builder unit-test by @Bento007 in #147
• Allow default context to be use in open_soma by @Bento007 in #203
• update python package to tiledbsoma 1.0rc0 by @bkmartinjr in #209

Full Changelog: v0.5.0...v0.6.0

v0.5.0

What's Changed

No major changes. Update SOMA dependency to tiledbsoma==0.5.0a11.

• feature: builder census summary tweaks by @atolopko-czi in #171
• remove workaround for portal API gateway error bug by @bkmartinjr in #167
• update to mypy 1.0 by @bkmartinjr in #169
• lint in census_summary by @bkmartinjr in #175
• update cell_census python package dependency tiledbsoma 0.5.0a11 by @bkmartinjr in #176

Full Changelog: v0.4.0...v0.5.0

v0.4.0

Breaking Changes

• open_soma returns a handle which must be closed upon completion of census use. It is also a context operator, allowing the use of the with statement.
• get_anndata coords arguments take a single coordinate point list, slice or int, rather than a per-dimension tuple, as these dataframes are always one-dimensional, and indexed by their soma_joinid
• package now imports tiledbsoma==0.5.0a10 which has several breaking API changes.

Enhancements

• Python 3.7 support

What's Changed

• chore: Update license copyright year by @atolopko-czi in #118
• API cleanup by @bkmartinjr in #117
• Coords param change for get_anndata by @bkmartinjr in #122
• Add Python 3.7 support by @bkmartinjr in #121
• update installation docs to reflect publication of package on PyPi by @bkmartinjr in #153
• Port cell_census and notebooks to tiledbsoma 0.5.0a10 by @bkmartinjr in #132

New Contributors

• @ebezzi made their first contribution in #76
• @Bento007 made their first contribution in #115
• @metakuni made their first contribution in #127

Full Changelog: v0.3.0...v0.4.0

v0.3.0

Update to latest SOMA API, v0.5.0a8, including on-disk format change from TileDB v2.14. Includes breaking API changes from 0.2.0.

What's Changed

• update to tilebsoma 0.5.0a4 by @atolopko-czi in #77
• update to tiledbsoma 0.5.0a6 by @atolopko-czi in #82
• re-run comp_bio_explore_and_load_lung_data notebook by @atolopko-czi in #83
• builder fixes by @atolopko-czi in #84
• fix notebook import by @atolopko-czi in #90
• Improve notebook comp_bio_explore_and_load_lung_data.ipynb by @pablo-gar in #91
• Improve notebook comp_bio_data_integration_scvi.ipynb by @pablo-gar in #92
• tiledb version dependency fixes by @atolopko-czi in #95
• prep for 0.3.0 release by @bkmartinjr in #96

Full Changelog: v0.2.0...v0.3.0

v0.2.0

Support v0.2.0 of the Cell Census schema, which moves the location of the dataset presence matrix.

What's Changed

• feat: builder schema changes by @atolopko-czi in #66
• presence matrix location change in schema 0.2.0 by @bkmartinjr in #70
• fix cmd line example for builder by @atolopko-czi in #68
• docs: schema update presence matrix by @pablo-gar in #69
• atol/bump builder census schema version by @atolopko-czi in #71

Full Changelog: v0.1.0...v0.2.0

v0.1.0

What's Changed

• refinement of release process doc by @bkmartinjr in #51
• docs: Add comp bio notebooks by @pablo-gar in #45
• simplify get_anndata API by @bkmartinjr in #52
• docs: add integration notebook by @pablo-gar in #53
• docs: separates demonstration notebooks into two different folders by @pablo-gar in #54
• docs: add notebook to explain value_filter and column_selection by @pablo-gar in #55
• docs: update link to Discover API schema docs by @atolopko-czi in #58
• issue: 64 by @atolopko-czi in #65
• update cell_census package to use SOMA API 0.5.0a3 by @bkmartinjr in #63

Full Changelog: v0.0.1...v0.1.0

v0.0.1

Initial release.

What's Changed

• Preparations for making repo public by @bkmartinjr in #1
• initial commit of migrated source by @bkmartinjr in #2
• specification update wrt multi-species genes by @bkmartinjr in #19
• miscellaneous small fixes by @bkmartinjr in #27
• docs: add comp bio to notebook to learn about the census by @pablo-gar in #29
• fix query builder by @bkmartinjr in #33
• Add: schema doc and storage/release doc by @pablo-gar in #24
• schema performance tuning by @bkmartinjr in #28
• add get_experiment and get_presence_matrix by @bkmartinjr in #40
• Add unit tests by @bkmartinjr in #38
• doc typos & builder param tips by @atolopko-czi in #42
• accommodate SOMA API name changes by @bkmartinjr in #47
• build/packaging by @bkmartinjr in #41
• Refine unit test workflows by @bkmartinjr in #49
• Build and release refinement by @bkmartinjr in #50

New Contributors

• @bkmartinjr made their first contribution in #1
• @pablo-gar made their first contribution in #29

Full Changelog: https://github.com/chanzuckerberg/cell-census/commits/v0.0.1