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Fix TSV formatting so GitHub's file preview works (#233) #325
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,40 +1,55 @@ | ||
| files: src/python | ||
| repos: | ||
| - repo: https://github.com/pre-commit/pre-commit-hooks | ||
| rev: v4.6.0 | ||
| hooks: | ||
| - id: check-yaml | ||
| description: Check yaml files for parseable syntax | ||
| files: ^src/python/ | ||
| - id: check-added-large-files | ||
| description: Prevent large files from being committed | ||
| files: ^src/python/ | ||
| - id: check-merge-conflict | ||
| description: Check for files that contain merge conflict strings | ||
| files: ^src/python/ | ||
| - id: check-symlinks | ||
| description: Check for symlinks which do not point to anything | ||
| files: ^src/python/ | ||
| - id: check-executables-have-shebangs | ||
| description: Check that (non-binary) executables have shebangs | ||
| files: ^src/python/ | ||
| - id: detect-private-key | ||
| description: Detects the presence of private keys | ||
| files: ^src/python/ | ||
| - id: end-of-file-fixer | ||
| description: Fix empty lines at ends of files | ||
| # also cover the PEtab TSV data files, not just src/python | ||
| files: (^src/python/|\.tsv$) | ||
| - id: mixed-line-ending | ||
| description: Replace or check mixed line endings | ||
| args: [--fix=lf] | ||
| files: (^src/python/|\.tsv$) | ||
| - id: trailing-whitespace | ||
| description: Trim trailing whitespaces | ||
| # not extended to *.tsv: a trailing tab there is a legitimate empty | ||
| # last field, not whitespace to strip (checked by bmp-check-tsv-format | ||
| # instead, which is field-aware) | ||
| files: ^src/python/ | ||
|
|
||
| - repo: https://github.com/astral-sh/ruff-pre-commit | ||
| # Ruff version. | ||
| rev: v0.6.7 | ||
| hooks: | ||
| # Run the linter. | ||
| - id: ruff | ||
| files: ^src/python/ | ||
| args: | ||
| - --fix | ||
| - --config | ||
| - src/python/pyproject.toml | ||
|
|
||
| # Run the formatter. | ||
| - id: ruff-format | ||
| files: ^src/python/ | ||
| args: | ||
| - --config | ||
| - src/python/pyproject.toml | ||
42 changes: 21 additions & 21 deletions
42
Benchmark-Models/Alkan_SciSignal2018/visualizationSpecification_Alkan_SciSignal2018.tsv
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6 changes: 3 additions & 3 deletions
6
...k-Models/Armistead_CellDeathDis2024/experimentalConditions_Armistead_CellDeathDis2024.tsv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,3 @@ | ||
| conditionId conditionName S_on Cer Sphinga Sphingo S1P | ||
| wild_type wild-type 1 0.988 0.000732 0.000395 1.551 | ||
| mutant Hai1a deletion mutant 0 0.822 0.000795 0.000364 2.07 | ||
| conditionId conditionName S_on Cer Sphinga Sphingo S1P | ||
| wild_type wild-type 1 0.988 0.000732 0.000395 1.551 | ||
| mutant Hai1a deletion mutant 0 0.822 0.000795 0.000364 2.07 |
10 changes: 5 additions & 5 deletions
10
Benchmark-Models/Armistead_CellDeathDis2024/observables_Armistead_CellDeathDis2024.tsv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,5 @@ | ||
| observableId observableName observableFormula noiseFormula noiseDistribution | ||
| Sphinga_obs Sphinganine concentration [area ratio/Protein] - indication of Cer de novo production Sphinga noiseParameter1_Sphinga_obs*Sphinga normal | ||
| Cer_obs Ceramide concentration [area ratio/Protein] Cer noiseParameter1_Cer_obs*Cer normal | ||
| Sphingo_obs Sphingosine concentration [area ratio/Protein] Sphingo noiseParameter1_Sphingo_obs*Sphingo normal | ||
| S1P_obs Sphingosine-1-phosphate indirect measurement S1P noiseParameter1_S1P_obs*S1P normal | ||
| observableId observableName observableFormula noiseFormula noiseDistribution | ||
| Sphinga_obs Sphinganine concentration [area ratio/Protein] - indication of Cer de novo production Sphinga noiseParameter1_Sphinga_obs*Sphinga normal | ||
| Cer_obs Ceramide concentration [area ratio/Protein] Cer noiseParameter1_Cer_obs*Cer normal | ||
| Sphingo_obs Sphingosine concentration [area ratio/Protein] Sphingo noiseParameter1_Sphingo_obs*Sphingo normal | ||
| S1P_obs Sphingosine-1-phosphate indirect measurement S1P noiseParameter1_S1P_obs*S1P normal |
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Unfortunate that it doesn't look easy to have separate pre-commit configs for the Python code and the PEtab problems.
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I didn't find a more convenient option either, but I think it's quite manageable...