Remove hardcoded paths in proteomics #206
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Signed-off-by: Josh Loecker <[email protected]>
Bumps [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) from 3 to 4. - [Release notes](https://github.com/astral-sh/setup-uv/releases) - [Commits](astral-sh/setup-uv@v3...v4) --- updated-dependencies: - dependency-name: astral-sh/setup-uv dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]>
Bumps [astral-sh/ruff-action](https://github.com/astral-sh/ruff-action) from 1 to 2. - [Release notes](https://github.com/astral-sh/ruff-action/releases) - [Changelog](https://github.com/astral-sh/ruff-action/blob/main/release-drafter.yml) - [Commits](astral-sh/ruff-action@v1...v2) --- updated-dependencies: - dependency-name: astral-sh/ruff-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[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]>
# Conflicts: # main/como/rnaseq.py
# Conflicts: # pyproject.toml
# Conflicts: # main/como/rnaseq_gen.py
Signed-off-by: Josh Loecker <[email protected]>
Signed-off-by: Josh Loecker <[email protected]>
Signed-off-by: Josh Loecker <[email protected]>
…-gen Remove hardcoded paths in RNA-seq Gen
…mics Remove hardcoded filepaths
…ed-paths/proteomics
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- tests/test_rnaseq_preprocess.py: Evaluated as low risk
- main/como/custom_types.py: Evaluated as low risk
- main/como/utils.py: Evaluated as low risk
- main/como/proteomics_gen.py: Evaluated as low risk
- main/como/proteomics_preprocessing.py: Evaluated as low risk
- main/como/types.py: Evaluated as low risk
- .pre-commit-config.yaml: Evaluated as low risk
- pyproject.toml: Evaluated as low risk
Comments skipped due to low confidence (4)
tests/unit/test_rnaseq_preprocess.py:12
- The class name
_STARinformationshould be renamed toSTARInformationto follow naming conventions.
_STARinformation
tests/unit/test_rnaseq_preprocess.py:43
- [nitpick] The error message could be more specific. Consider changing it to: 'Invalid file format: Building STAR information requires a .tab file'.
with pytest.raises(ValueError, match="Building STAR information requires a '.tab' file"):
tests/unit/test_rnaseq_preprocess.py:70
- The test
test_process_first_multirun_sampleshould check the content of the DataFrame, not just its structure.
result: pd.DataFrame = await _process_first_multirun_sample(strand_filepath, all_gene_count_filepaths)
tests/fixtures/collect_files.py:21
- [nitpick] The member name 'preparation_method' is inconsistent with the other member names. Consider renaming it to 'prep_method'.
preparation_method: Path
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