Improved use of GitHub Actions + pandas warning fix

.github/workflows/python-app.yml

@@ -10,25 +10,38 @@ on:
     branches: [ master ]
 
 jobs:
+
   build:
-
-    runs-on: ubuntu-latest
-
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        version: ["3.8", "3.13"]
+    runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.8
+        python-version: ${{ matrix.version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - name: Lint with flake8
+        pip install .
+    - name: Test base functionality tool
       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
-
+        ena-upload-cli --help
+    - name: Create credentials file
+      run: |
+        echo "username: ${{ secrets.ENA_USERNAME }}" >> .secrets.yaml
+        echo "password: ${{ secrets.ENA_PASSWORD }}" >> .secrets.yml
+    - name: Test submission in --draft mode
+      run: |
+        ena-upload-cli --action add --draft --dev --center ${{ secrets.ENA_CENTER }} --data example_data/ENA_TEST1.R1.fastq.gz example_data/ENA_TEST2.R1.fastq.gz example_data/ENA_TEST2.R2.fastq.gz --checklist ERC000033 --secret .secret.yml --xlsx example_tables/ENA_excel_example_ERC000033.xlsx 
+    - name: Run Python to get temp directory
+      run: |
+        echo "TEMP_DIR=$(python -c 'import tempfile; print(tempfile.gettempdir())')" >> $GITHUB_ENV
+    - uses: actions/upload-artifact@v4
+      name: Output XMLs for ${{ matrix.os }} Python ${{ matrix.os }}
+      with:
+        name: ena-upload-cli_output_${{ matrix.os }}_python_${{ matrix.version }}
+        path: ${{ env.TEMP_DIR }}/*.xml

README.md

@@ -29,7 +29,7 @@ After a successful submission, new tsv tables will be generated with the ENA acc
 
 ## Tool dependencies
 
-* python 3.7+ including following packages:
+* python 3.8+ including following packages:
   * Genshi
   * lxml
   * pandas