From 30f9e20507be863bbfc730544d6560f6ee10b170 Mon Sep 17 00:00:00 2001 From: Lorena Pantano Date: Mon, 16 Sep 2024 16:46:39 +0000 Subject: [PATCH] add missing dep --- .github/workflows/python-package-conda.yml | 4 +++- environment.yml | 1 + 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml index 7c552f1..bb9e359 100644 --- a/.github/workflows/python-package-conda.yml +++ b/.github/workflows/python-package-conda.yml @@ -37,8 +37,10 @@ jobs: # stop the build if there are Python syntax errors or undefined names flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + #flake8 . --count --max-complexity=10 --max-line-length=127 --statistics - name: Test with pytest run: | conda install pytest + python setup.py develop pytest diff --git a/environment.yml b/environment.yml index 1baea78..01da3ea 100644 --- a/environment.yml +++ b/environment.yml @@ -2,5 +2,6 @@ dependencies: - python=3.11 - bioconda::pysam - bioconda::pybedtools + - bioconda::samtools=1.21 - conda-forge::pandas - conda-forge::biopython=1.83 \ No newline at end of file