Update gh actions and test

GillesFischerSorbonne · Oct 20, 2023 · 9126169 · 9126169
1 parent b414d26
commit 9126169
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Showing 2 changed files with 20 additions and 11 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -19,19 +19,28 @@ jobs:
       fail-fast: false
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.X
-      uses: actions/setup-python@v2
+    - uses: mamba-org/setup-micromamba@v1
       with:
-        python-version: ${{ matrix.python }}
-
-    - name: bedtools
-      run: |
-        sudo apt-get install -y bedtools
+          micromamba-version: '1.3.1-0'
+          cache-environment: true
+          environment-name: installation
+          condarc: |
+              channels:
+                  - conda-forge
+                  - bioconda
+                  - defaults
+          create-args: >-
+            python=${{ matrix.python }}
+            bedtools
+    - name: Checkout repo
+      uses: actions/checkout@v3
+
     - name: Install the package itself
-      run: |
-          pip install .
+      shell: bash -el {0}
+      run: pip install .
+
     - name: Test with pytest
+      shell: bash -el {0}
       run: |
         pip install pytest
         pip install pytest-cov

diff --git a/test/test_telomer.py b/test/test_telomer.py
@@ -6,4 +6,4 @@
 
 
 def test_run_on_single_fasta():
-    df = tf.run_on_single_fasta(filename, 0.8, 0.8, 8000, 1)
+    df = tf.run_on_single_fasta(filename, 0.8, 0.8, 8000, "both", 1)