Add AnnData support in Landscape widget #131
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cornhundred
merged commit cdc5fbf
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DEGA-68-parquet-for-Landscape-traitlet-data-transfer
cornhundred
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Jul 17, 2025
* renaming class * clustergram registry * linting fixes * removed print statement * removed name logic * Add Parquet export support for Clustergram widget (#111) * manually bringing in parquet processing * big int * fixing bug with parquet matrix processing * fix index parsing bug * removed print and console logs * added mat as kwarg * Update src/celldega/viz/widget.py Co-authored-by: Copilot <[email protected]> * Update js/read_parquet/network_from_parquet.js Co-authored-by: Copilot <[email protected]> * implemnting astype change --------- Co-authored-by: Copilot <[email protected]> * Update src/celldega/clust/matrix.py more efficient hash for sparse data Co-authored-by: Copilot <[email protected]> * ruff fix * docs: add parquet_data usage (#117) * Add Clustergram parquet widget tests (#116) * upadted test * fixed test lint * ruff format * format JS * Refine Landscape metadata handling * feat(viz): support AnnData in Landscape (#131) * adding print statement * getting single-cell metadata to transfer * making column for meta_cluster * cleaning console logs * working on parsing parquet to objects * meta_cell working * parsing meta_cell_attr * setting up multiple attr support for cells * getting multiple attr working for meta_clust * meta_cluster and meta_cell starting to work * working on cell_attr * format * cleaning * Update js/read_parquet/objects_from_parquet.js Co-authored-by: Copilot <[email protected]> * Update src/celldega/viz/widget.py Co-authored-by: Copilot <[email protected]> * Update js/widget.js Co-authored-by: Copilot <[email protected]> * added example notebook * cleaning * ordered imports * Handle Leiden colors when not precomputed (#157) * fix(viz): generate leiden colors via scanpy * added color generation if not available * ruff * added fix for cell_id not being index in AnnData * ruff * Update src/celldega/viz/widget.py Co-authored-by: Copilot <[email protected]> * Update src/celldega/viz/widget.py Co-authored-by: Copilot <[email protected]> * Update js/viz/landscape_ist.js Co-authored-by: Copilot <[email protected]> * Update js/viz/landscape_ist.js Co-authored-by: Copilot <[email protected]> * Update js/widget.js Co-authored-by: Copilot <[email protected]> * Update js/widget.js Co-authored-by: Copilot <[email protected]> * Update js/widget.js Co-authored-by: Copilot <[email protected]> * Update js/widget.js Co-authored-by: Copilot <[email protected]> * Update src/celldega/viz/widget.py Co-authored-by: Copilot <[email protected]> * Update src/celldega/viz/widget.py Co-authored-by: Copilot <[email protected]> * added default to prevent failure with no AnnDAta --------- Co-authored-by: Copilot <[email protected]>
cornhundred
added a commit
that referenced
this pull request
Jul 17, 2025
* renaming class * clustergram registry * linting fixes * removed print statement * removed name logic * Add Parquet export support for Clustergram widget (#111) * manually bringing in parquet processing * big int * fixing bug with parquet matrix processing * fix index parsing bug * removed print and console logs * added mat as kwarg * Update src/celldega/viz/widget.py Co-authored-by: Copilot <[email protected]> * Update js/read_parquet/network_from_parquet.js Co-authored-by: Copilot <[email protected]> * implemnting astype change --------- Co-authored-by: Copilot <[email protected]> * Update src/celldega/clust/matrix.py more efficient hash for sparse data Co-authored-by: Copilot <[email protected]> * ruff fix * docs: add parquet_data usage (#117) * Add Clustergram parquet widget tests (#116) * upadted test * fixed test lint * ruff format * format JS * Refine Landscape metadata handling * feat(viz): support AnnData in Landscape (#131) * adding print statement * getting single-cell metadata to transfer * making column for meta_cluster * cleaning console logs * working on parsing parquet to objects * meta_cell working * parsing meta_cell_attr * setting up multiple attr support for cells * getting multiple attr working for meta_clust * meta_cluster and meta_cell starting to work * working on cell_attr * format * cleaning * Update js/read_parquet/objects_from_parquet.js Co-authored-by: Copilot <[email protected]> * Update src/celldega/viz/widget.py Co-authored-by: Copilot <[email protected]> * Update js/widget.js Co-authored-by: Copilot <[email protected]> * added example notebook * cleaning * Add Parquet traitlet support for neighborhoods --------- Co-authored-by: Copilot <[email protected]>
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Summary
AnnDatakwarg inLandscapewidgetTesting
pre-commit run --files src/celldega/viz/widget.py README.md(fails: command not found)pytest -q(fails: unrecognized arguments)https://chatgpt.com/codex/tasks/task_b_686feee1e4e0832aafa6af0dc6327223