Tags: scverse/scirpy
Tags
Speed up clonotype distance calculation (#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>
PreviousNext