feat: add tinit #215
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feat: add tinit #215
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This is functionally equivalent to the _read_counts_matrix function from rnaseq.py
Instead of checking if the stem of directories match, check that the same number of files are returned. Because the directories are sorted (and this comes from FastqToGeneCounts), they should always match
Removes an extra indentation
# Conflicts: # main/como/rnaseq.py
# Conflicts: # pyproject.toml
Signed-off-by: Josh Loecker <[email protected]>
Signed-off-by: Josh Loecker <[email protected]>
Signed-off-by: Josh Loecker <[email protected]>
Signed-off-by: Josh Loecker <[email protected]>
… fix/single-cell-processing
Signed-off-by: Josh Loecker <[email protected]>
Signed-off-by: Josh Loecker <[email protected]>
Signed-off-by: Josh Loecker <[email protected]>
Signed-off-by: Josh Loecker <[email protected]>
Signed-off-by: Josh Loecker <[email protected]>
Signed-off-by: Josh Loecker <[email protected]>
Signed-off-by: Josh Loecker <[email protected]>
Signed-off-by: Josh Loecker <[email protected]>
Signed-off-by: Josh Loecker <[email protected]>
Signed-off-by: Josh Loecker <[email protected]>
Signed-off-by: Josh Loecker <[email protected]>
Signed-off-by: Josh Loecker <[email protected]>
Signed-off-by: Josh Loecker <[email protected]>
Signed-off-by: Josh Loecker <[email protected]>
Signed-off-by: Josh Loecker <[email protected]>
Signed-off-by: Josh Loecker <[email protected]>
Signed-off-by: Josh Loecker <[email protected]>
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Copilot reviewed 13 out of 28 changed files in this pull request and generated 3 comments.
Files not reviewed (15)
- main/como/custom_types.py: Evaluated as low risk
- tests/test_rnaseq_preprocess.py: Evaluated as low risk
- main/como/proteomics_gen.py: Evaluated as low risk
- main/como/proteomics_preprocessing.py: Evaluated as low risk
- ruff.toml: Evaluated as low risk
- pyproject.toml: Evaluated as low risk
- main/como/utils.py: Evaluated as low risk
- main/como/graph/init.py: Evaluated as low risk
- main/como/proteomics/FTPManager.py: Evaluated as low risk
- main/como/proteomics/proteomics_preprocess.py: Evaluated as low risk
- main/como/cluster_rnaseq.py: Evaluated as low risk
- tests/test_proteomics.py: Evaluated as low risk
- .github/workflows/continuous_integration.yml: Evaluated as low risk
- main/como/init.py: Evaluated as low risk
- .pre-commit-config.yaml: Evaluated as low risk
Comments suppressed due to low confidence (6)
tests/unit/test_rnaseq_preprocess.py:70
- The test should validate the content of the DataFrame, not just the column names.
result: pd.DataFrame = await _process_first_multirun_sample(strand_filepath, all_gene_count_filepaths)
main/como/data_types.py:147
- [nitpick] The method
get_shorthandin the classCobraCompartmentsis inconsistent with the naming convention used in the rest of the codebase. It should be renamed togetto match the existing method names.
def get_shorthand(cls, longhand: str) -> str | None:
main/como/data_types.py:152
- [nitpick] The method
get_longhandin the classCobraCompartmentsis inconsistent with the naming convention used in the rest of the codebase. It should be renamed toget_longto match the existing method names.
def get_longhand(cls, shorthand: str) -> str | None:
main/como/data_types.py:82
- The
SourceTypesenum has a memberPROTEOMICS, but there is no corresponding logic or implementation for this source type in the codebase.
PROTEOMICS = "proteomics"
main/como/data_types.py:216
- The
_validate_attributemethod in the class_BaseDataTypeshould use the_log_and_raise_errorfunction for consistency.
def _validate_attribute(self, key):
tests/fixtures/collect_files.py:7
- [nitpick] The variable name
_fragment_size_filepathsis ambiguous. It should be renamed tofragment_size_filepaths.
_fragment_size_filepaths = list(Path("main/data/COMO_input").absolute().rglob("*fragment_size*.txt"))
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| def test_source_types(): | ||
| """Validate that source types always go in the order of 'trna', 'mrna', 'scrna', 'protemics'.""" |
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The word 'protemics' should be corrected to 'proteomics'.
Suggested change
| """Validate that source types always go in the order of 'trna', 'mrna', 'scrna', 'protemics'.""" | |
| """Validate that source types always go in the order of 'trna', 'mrna', 'scrna', 'proteomics'.""" |
Copilot is powered by AI, so mistakes are possible. Review output carefully before use.
| @pytest.mark.asyncio | ||
| async def test_build_from_tab_invalid_file(self): | ||
| """Validate error on invalid file.""" | ||
| with pytest.raises(ValueError, match="Building STAR information requires a '.tab' file"): |
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The word 'requires' should be 'require'.
Copilot is powered by AI, so mistakes are possible. Review output carefully before use.
| GIMME = "GIMME" | ||
| FASTCORE = "FASTCORE" | ||
| IMAT = "IMAT" | ||
| TINIT = "TINIT" |
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The enum Algorithm has a new member TINIT, but there is no corresponding logic or implementation for this algorithm in the codebase.
Copilot is powered by AI, so mistakes are possible. Review output carefully before use.
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Description
This pull request will add the t-INIT method from Troppo to the model-building options
create_context_specific_modelno longer acceptsoutput_model_filetypescreate_context_specific_modelparameteroutput_model_filepathsshould be a list of paths ending in.json,.mat,.xml, or.sbml, depending on the requested output type.