test unit and integrations tests in CI

Computational-Plant-Science · Jan 9, 2022 · 1be38a3 · 1be38a3
1 parent fa3bab6
commit 1be38a3
Showing 1 changed file with 58 additions and 58 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -42,13 +42,13 @@ jobs:
           # source ~/.profile
           
           # install singularity
-          wget https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-ce-${SINGULARITY_VERSION}.tar.gz
-          tar -xzf singularity-ce-${SINGULARITY_VERSION}.tar.gz
-          cd singularity-ce-${SINGULARITY_VERSION}
-          ./mconfig
-          make -C builddir
-          sudo make -C builddir install
-          cd ..
+          # wget https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-ce-${SINGULARITY_VERSION}.tar.gz
+          # tar -xzf singularity-ce-${SINGULARITY_VERSION}.tar.gz
+          # cd singularity-ce-${SINGULARITY_VERSION}
+          # ./mconfig
+          # make -C builddir
+          # sudo make -C builddir install
+          # cd ..
       - name: Lint
         run: |
           # stop the build if there are Python syntax errors or undefined names
@@ -67,58 +67,58 @@ jobs:
         run: |
           mkdir -p /opt/plantit-cli/runs/
           python -m pytest /home/runner/work/plantit-cli/plantit-cli/plantit_cli/tests/unit -s
-  # integration-tests:
-  #   runs-on: ubuntu-latest
-  #   strategy:
-  #     max-parallel: 1
-  #     matrix:
-  #       python-version: [3.6]
-  #   steps:
-  #     - uses: actions/checkout@v2
-  #     - name: Set up Python ${{ matrix.python-version }}
-  #       uses: actions/setup-python@v2
-  #       with:
-  #         python-version: ${{ matrix.python-version }}
-  #     - name: Install dependencies
-  #       env:
-  #         SINGULARITY_VERSION: ${{ secrets.SINGULARITY_VERSION }}
-  #       run: |
-  #         # python
-  #         python -m pip install --upgrade pip
-  #         pip install flake8 pytest coveralls setuptools wheel twine
-  #         pip install -e .
+  integration-tests:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 1
+      matrix:
+        python-version: [3.6]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        env:
+          SINGULARITY_VERSION: ${{ secrets.SINGULARITY_VERSION }}
+        run: |
+          # python
+          python -m pip install --upgrade pip
+          pip install flake8 pytest coveralls setuptools wheel twine
+          pip install -e .
 
-  #         # singularity
-  #         wget https://github.com/sylabs/singularity/releases/download/v3.8.0/singularity-ce-3.8.0.tar.gz
-  #         tar -xzf singularity-ce-3.8.0.tar.gz
-  #         cd singularity-ce-3.8.0
-  #         ./mconfig
-  #         make -C builddir
-  #         sudo make -C builddir install
-  #     - name: Lint
-  #       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
-  #       env:
-  #         TEST_DIRECTORY: ${{ secrets.TEST_DIRECTORY }}
-  #         CYVERSE_USERNAME: ${{ secrets.CYVERSE_USERNAME }}
-  #         CYVERSE_PASSWORD: ${{ secrets.CYVERSE_PASSWORD }}
-  #         COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
-  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  #         COVERALLS_FLAG_NAME: ${{ matrix.python-version }}
-  #         COVERALLS_PARALLEL: true
-  #       run: |
-  #         mkdir -p /opt/plantit-cli/runs/
-  #         coverage run --source=plantit_cli -m pytest /home/runner/work/plantit-cli/plantit-cli/plantit_cli/tests/integration -s
-  #         coveralls
-  #     - name: Update Coveralls
-  #       run: |
-  #         coveralls --finish
-  #       env:
-  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          # singularity
+          # wget https://github.com/sylabs/singularity/releases/download/v3.8.0/singularity-ce-3.8.0.tar.gz
+          # tar -xzf singularity-ce-3.8.0.tar.gz
+          # cd singularity-ce-3.8.0
+          # ./mconfig
+          # make -C builddir
+          # sudo make -C builddir install
+      - name: Lint
+        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
+        env:
+          TEST_DIRECTORY: ${{ secrets.TEST_DIRECTORY }}
+          CYVERSE_USERNAME: ${{ secrets.CYVERSE_USERNAME }}
+          CYVERSE_PASSWORD: ${{ secrets.CYVERSE_PASSWORD }}
+          COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COVERALLS_FLAG_NAME: ${{ matrix.python-version }}
+          COVERALLS_PARALLEL: true
+        run: |
+          mkdir -p /opt/plantit-cli/runs/
+          coverage run --source=plantit_cli -m pytest /home/runner/work/plantit-cli/plantit-cli/plantit_cli/tests/integration -s
+          coveralls
+      - name: Update Coveralls
+        run: |
+          coveralls --finish
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   publish:
     needs: [unit-tests]
     runs-on: ubuntu-latest