Merge pull request #33 from cokelaer/main

fix CI

Author: cokelaer

.github/workflows/main.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python: [ 3.8, 3.9, '3.10']
+        python: [ 3.9, '3.10', '3.11']
       fail-fast: false
 
 
@@ -31,10 +31,10 @@ jobs:
       uses: actions/checkout@v2
 
     - name: conda/mamba
-      uses: mamba-org/provision-with-micromamba@main
+      uses: mamba-org/setup-micromamba@v1
       with:
           environment-file: environment.yml
-          extra-specs: |
+          create-args: >-
             python=${{ matrix.python }}
 
     - name: install package itself

README.rst

@@ -172,14 +172,15 @@ Then follow the instructions (prepare and execute the pipeline).
 
 You should end up with a summary.hml report.
 
-You can brwose the different samples (only one in this example) and get a table with variant calls:
 
+You can browse the different samples (only one in this example) and get a table with variant calls:
 
-    table.png
+    https://raw.githubusercontent.com/sequana/variant_calling/refs/heads/main/doc/table.png
 
-If you set the coverage one, (not recommended for eukaryotes), you should see this kind of plots::
+If you set the coverage one, (not recommended for eukaryotes), you should see this kind of plots:
+
+    https://raw.githubusercontent.com/sequana/variant_calling/refs/heads/main/doc/coverage.png
 
-    coverage.png
 
 
 

test/test_main.py

@@ -71,9 +71,9 @@ def test_check_output_ref_annot():
 
         assert vv == {'alternative': 'T',
              'chr': 'JB409847',
-             'depth': 23,
+             'depth': 24,
              'type': 'snp',
-             'frequency': '0.261',
+             'frequency': '0.250',
              'position': 2221,
              'reference': 'C',
              'strand_balance': '0.333'}
@@ -107,10 +107,10 @@ def test_check_output_no_annotation():
         del vv['fisher_pvalue']
         assert vv == {'alternative': 'T',
              'chr': 'JB409847',
-             'depth': 23,
+             'depth': 24,
              #'freebayes_score': 2.78452e-14,
              'type': 'snp',
-             'frequency': '0.261',
+             'frequency': '0.250',   # freebayes 1.3.9 gives 0.250 previous version were giving 0.261...
              'position': 2221,
              'reference': 'C',
              'strand_balance': '0.333'}