Purge fast_bioservices
#246
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Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
Signed-off-by: Josh Loecker <joshloecker@icloud.com>
JoshLoecker
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Feb 10, 2026
* fix(fpkm): update imports for zFPKM calculation improvements Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix(fpkm): use Salmon quantification instead of STAR quantification Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: ruff formatting Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: fill with integers for faster processing Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: remove unnecessary async function usage Signed-off-by: Josh Loecker <joshloecker@icloud.com> * fix: remove non existant genes from conversion Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: use more explicit (albeit longer) code to create gene_info dataframe object Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: import required modules Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: optional argument for fragment data Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: improve handling for single cell data Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: generalize data type input Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: ruff formatting Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: simplify FPKM/RPKM calculations; properly compute per-gene FPKM scores Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: move zfpkm calculation to external package Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: use np.bool for boolean array Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: ruff formatting Signed-off-by: Josh Loecker <joshloecker@icloud.com> * feat: allow setting negative zFPKM results to 0 Signed-off-by: Josh Loecker <joshloecker@icloud.com> * feat: simplification to use external zfpkm package Signed-off-by: Josh Loecker <joshloecker@icloud.com> * feat: allow providing the fragment size filepath (from rnaseq preprocessing) Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore(ruff): reduce max line length Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore(ruff): mark unsorted imports as fixable Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore(uv): lock pyproject file Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: remove zfpkm related code as it is now an external package Signed-off-by: Josh Loecker <joshloecker@icloud.com> * revert: remove local pyproject requirement Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: remove zfpkm testing files Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: force sync lock Signed-off-by: Josh Loecker <joshloecker@icloud.com> * Purge `fast_bioservices` (#246) * feat: use bioservice's `MyGeneInfo` Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: convert from fast_bioservices to COMO's built-in pipeline Signed-off-by: Josh Loecker <joshloecker@icloud.com> * refactor: remove fast-bioservices from pyproject Signed-off-by: Josh Loecker <joshloecker@icloud.com> * chore: use bioservices over fast_bioservices Signed-off-by: Josh Loecker <joshloecker@icloud.com> * feat(test): added unit tests for identifier conversion pipeline Signed-off-by: Josh Loecker <joshloecker@icloud.com> --------- Signed-off-by: Josh Loecker <joshloecker@icloud.com> --------- Signed-off-by: Josh Loecker <joshloecker@icloud.com>
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A dependency of the
fast_bioservicespackage (Hishel) has made significant changes in their v1.0 release, and it is too difficult to attempt to updatefast_bioservicesThis pull request implements an important data conversion pipeline using Bioservices's
MyGeneInfoobject, as it is much faster and more robust thanBioDBNetappears to be