Remove zFPKM (#245)

* 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>

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Signed-off-by: Josh Loecker <joshloecker@icloud.com>

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Signed-off-by: Josh Loecker <joshloecker@icloud.com>

Author: JoshLoecker