testing

.github/workflows/python-app.yml

@@ -1,43 +1,35 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-
-name: Python application
+name: Python application test with Conda
 
 on:
   push:
-    branches: [ "main" ]
+    branches:
+      - main
+      - master
   pull_request:
-    branches: [ "main" ]
-
-permissions:
-  contents: read
+    branches:
+      - main
+      - master
 
 jobs:
-  build:
-
+  test:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+    - name: Check out the code
+      uses: actions/checkout@v3
+
     - name: Set up Miniconda
       uses: conda-incubator/setup-miniconda@v2
       with:
         auto-update-conda: true
         python-version: 3.12.3   # Change this to your desired Python version
         environment-file: environment.yml
         activate-environment: protein-prediction  # Name of your conda environment as specified in environment.yml
+
     - name: Install dependencies
       run: conda env update --file environment.yml --name protein-prediction
-    - name: Set up Python 3.12.3 
-      uses: actions/setup-python@v3
-      with:
-        python-version: "3.12.3"
-    - name: Lint with flake8
-      run: |
-        # 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
-    - name: Test with pytest
+
+    - name: Run tests
       run: |
-        pytest
+        source activate myenv
+        pytest