diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs new file mode 100644 index 0000000..3c19dc1 --- /dev/null +++ b/.git-blame-ignore-revs @@ -0,0 +1,5 @@ +# This file is used to list commits which will be ignored by github to calculate git blame +# These are commits which modify multiple parts of the codebase, e.g formatting changes + +# Format Snakefile with snakefmt +684d582acdb8af4ae87911dc7eb747411ff30eaa diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index bce1441..5ff4bf9 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -49,11 +49,8 @@ jobs: run: pylint --rcfile=../pylint.cfg ./*.py - name: black - uses: psf/black@stable - with: - options: "--check --verbose --line-length=79 --required-version 24.1.1" - src: "./scripts" - + working-directory: ./scripts + run: black --check --verbose --line-length=79 ./*.py snakemake-format-graph-test: runs-on: ubuntu-latest diff --git a/environment.dev.yml b/environment.dev.yml index 4f7b611..ee918bc 100644 --- a/environment.dev.yml +++ b/environment.dev.yml @@ -3,6 +3,7 @@ channels: - conda-forge - bioconda dependencies: + - black>=24.1.1 - coverage>=7.3.2 - flake8>=6.1.0 - flake8-docstrings>=1.7.0 diff --git a/workflow/Snakefile b/workflow/Snakefile index 336d70b..8b3200c 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -107,8 +107,10 @@ rule finish: sample=pd.unique(samples_table.index.values), ), piles_design=expand( - PILEUP_DIR / "{condition}" / "check_file_{condition}.txt" - if config["lib_dict"] != None - else [], + ( + PILEUP_DIR / "{condition}" / "check_file_{condition}.txt" + if config["lib_dict"] != None + else [] + ), condition=list(config["lib_dict"].keys()), ),