use cond envs

.github/workflows/test-snake.yml

@@ -51,15 +51,8 @@ jobs:
         with:
           directory: '.test'
           snakefile: 'workflow/Snakefile'
-          args: '--cores 1 --use-conda --conda-cleanup-pkgs cache'
+          args: '--cores 1 --use-conda --conda-frontend mamba --conda-cleanup-pkgs cache'
           stagein: |
-            source $GITHUB_WORKSPACE/.venv/bin/activate
-            export PYTHONPATH="${PYTHONPATH}:$GITHUB_WORKSPACE:$GITHUB_WORKSPACE/src"
+            export PYTHONPATH="${PYTHONPATH}:/github/workspace:/github/workspace/src"
             echo $PYTHONPATH
-            which python
-            python --version
-            pip list
-            python -c "import sys; print(sys.path)"
-            python -c "import usefulgnom; print(usefulgnom.__file__)"
-            python -c "import snakemake; print(snakemake.__file__)"
           show-disk-usage-on-error: true

environment.yml

@@ -9,4 +9,10 @@ channels:
 dependencies:
   - python=3.11.2
   - snakemake=8.18.2
-  - poetry=1.8.3
+  - poetry=1.8.3
+  - matplotlib=3.9.2
+  - pandas=2.2.2
+  - seaborn=0.13.2
+  - pip
+  - pip:
+    - -e .

src/usefulgnom/analyze/basecnt_coverage.py

@@ -1,4 +1,5 @@
-"""Implements the read coverage analysis.
+"""
+    Implements the read coverage analysis.
 
     Credits:
         - core code: @AugusteRi ([email protected])

workflow/Snakefile

@@ -5,6 +5,9 @@ configfile: "../config/config.yaml"
 include: "rules/base_coverage.smk"
 include: "rules/smk_testing.smk"
 
+conda:
+        "../environment.yml"
+
 rule all:
     input:
         "../results/statistics.csv"