Fix Single Cell Processing

[JoshLoecker]

This pull request fixes errors found when running single-cell RNA sequencing data.

This comment will be updated with a list of breaking changes as they happen

• BREAKING CHANGE: Algorithms should be imported as como.Algorithm
• BREAKING CHANGE: Compartments should now be imported as como.CobraCompartments

[Copilot]

Copilot reviewed 10 out of 20 changed files in this pull request and generated 1 comment.

Files not reviewed (10)

• main/COMO.ipynb: Evaluated as low risk
• main/como/types.py: Evaluated as low risk
• main/como/proteomics/proteomics_preprocess.py: Evaluated as low risk
• main/como/cluster_rnaseq.py: Evaluated as low risk
• main/como/proteomics/FTPManager.py: Evaluated as low risk
• main/como/proteomics_gen.py: Evaluated as low risk
• .github/workflows/continuous_integration.yml: Evaluated as low risk
• ruff.toml: Evaluated as low risk
• main/como/rnaseq_preprocess.py: Evaluated as low risk
• main/como/init.py: Evaluated as low risk

Comments suppressed due to low confidence (6)

main/como/data_types.py:216

• [nitpick] The use of 'SourceTypes.member_map.values()' is unconventional and might be confusing. Consider using 'SourceTypes.members.values()' instead.

if key not in {i.value for i in SourceTypes._member_map_.values()}:

main/como/utils.py:130

• [nitpick] The variable name 'cohersion' might be a typo and should be 'coercion'.

return cohersion

main/como/utils.py:130

• The word 'cohersion' is misspelled; it should be 'coercion'.

return cohersion

main/como/utils.py:88

• The 'entrez_gene_id' column is cast to a string multiple times. This could be optimized.

single_gene_names = expression_data[~expression_data['entrez_gene_id'].astype(str).str.contains('//')]

main/como/utils.py:74

• The new behavior introduced by the 'entrez_as_index' parameter in 'split_gene_expression_data' should be covered by tests.

entrez_as_index: bool = True,

main/como/utils.py:260

• The '_log_and_raise_error' function should ensure that the 'level' parameter is either 'LogLevel.ERROR' or 'LogLevel.CRITICAL'.

case _: