Tags: alefrol638/scirpy
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Fix group_abundance (scverse#463) * Compute group abundance for all cells, not just those in .mod['airr'] * Add regression test for scverse#641 * Fix issue with group_abundance ... that occured when airr and gex modalities did not fully align. * Fix sort and normalize options * Fix group_abundance plot * Fix mudata test * Fix group abundance sort * Update CHANGELOG
[pre-commit.ci] pre-commit autoupdate (scverse#594) updates: - [github.com/astral-sh/ruff-pre-commit: v0.9.6 → v0.9.7](astral-sh/ruff-pre-commit@v0.9.6...v0.9.7) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Update pyproject.toml (scverse#589) * Update pyproject.toml * Update CHANGELOG.md
Fix incompatibility with latest vdjdb release (scverse#578) * Fix incompatibility with latest vdjdb release * Update changelog
Unpin anndata (scverse#551) * unpin anndata * Update CHANGELOG.md
Speed up clonotype distance calculation (scverse#470) * compute_distances new version added * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * data type for csr max computation set to int16 to allow negative values * data type also for csr_min set to int16 to allow negative values * raise AssertainError instead of assert False * matrix shape changed in lookup function * array size changed for v-gene and column matching * naming conventions * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * use self._chain_count2 for asymmetric matrix for filter_chain_count * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * reverse table assignment adjusted in lookup function * changed AssertionError to NotImplementedError * removed unnecessary for loop * refactored lookup function * refactored lookup function and added docstring * adapted docsting of lookup function * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * j_gene matching implemented * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixes typo in j_gene parameter * bind loop variables in function match_gene_segment * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * set datatypes of csr matrix arrays explicitely * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * docstring and data type checks added for csr_min and csr_max * Changed data types of indices and indptr arrays for the csr matrices in _dist_for_clonotype and lookup to int64 instead of int32. * Changed data type checks to max value checks * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * documentation adaptions * update pre-commit config * reformat * deleted print statement * Implemented allowing graph partitioning method "fastgreedy" * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * test case for j_gene added * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * refactored filter_chain_count and added documentation * documentation and refactoring * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Rerun tutorial * Update CHANGELOG * Attempt to fix conda CI * update conda CI * Fix python version conda ci * override python version --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Fix cpu count detection (scverse#527) * Update __init__.py * Update CHANGELOG.md
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