Fix workflow YAML syntax error

.github/workflows/_test-in-conda-env.yml

@@ -1,6 +1,6 @@
 name: Unit Test in NSLS-II Conda Environment
 
-on: 
+on:
   workflow_call:
     inputs:
       conda_env_name:
@@ -21,123 +21,120 @@ on:
         type: string
 
 jobs:
-
   test-in-conda-env:
-
     runs-on: ubuntu-latest
 
     defaults:
       run:
-        shell: bash -l {0}
+        shell: "bash -l {0}"
 
     steps:
+      - name: Set env vars
+        run: |
+          export REPOSITORY_NAME="${GITHUB_REPOSITORY#*/}"  # just the repo, as opposed to org/repo
+          echo "REPOSITORY_NAME=${REPOSITORY_NAME}" >> $GITHUB_ENV
+
+          export CONDA_ENV_NAME=${{ inputs.conda_env_name }}
+          echo "CONDA_ENV_NAME=${CONDA_ENV_NAME}" >> $GITHUB_ENV
+
+          export ZENODO_ID=${{ inputs.zenodo_id }}
+          echo "ZENODO_ID=${ZENODO_ID}" >> $GITHUB_ENV
+
+          export MD5_CHECKSUM=${{ inputs.md5_checksum }}
+          echo "MD5_CHECKSUM=${MD5_CHECKSUM}" >> $GITHUB_ENV
+
+          # Workaround for unset GDAL env variables used by newer conda envs
+          export GDAL_DATA="${GDAL_DATA-''}"
+          echo "GDAL_DATA=${GDAL_DATA}" >> $GITHUB_ENV
+          export GDAL_DRIVER_PATH="${GDAL_DRIVER_PATH-''}"
+          echo "GDAL_DRIVER_PATH=${GDAL_DRIVER_PATH}" >> $GITHUB_ENV
+          export GEOTIFF_CSV="${GEOTIFF_CSV-''}"
+          echo "GEOTIFF_CSV=${GEOTIFF_CSV}" >> $GITHUB_ENV
+
+          # Workaround for unset MKL env variables used by newer conda envs
+          export MKL_INTERFACE_LAYER="${MKL_INTERFACE_LAYER-''}"
+          echo "MKL_INTERFACE_LAYER=${MKL_INTERFACE_LAYER}" >> $GITHUB_ENV
+
+      - name: Check out the code repo
+        uses: actions/checkout@v4
+
+      - name: "Workaround: Fix .condarc MultipleKeysError"
+        run: |
+          sed -i '/auto_activate_base/d' /home/runner/.condarc || true
+          sed -i '/auto_activate:/d' /home/runner/.condarc || true
+
+      - name: Set up Python ${{ inputs.python-version }} with conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: ${{ env.REPOSITORY_NAME }}-py${{ inputs.python-version }}
+          auto-update-conda: true
+          miniconda-version: "latest"
+          python-version: ${{ inputs.python-version }}
+          mamba-version: "*"
+          channels: conda-forge
+
+      - name: Cache the archived conda environment
+        uses: actions/cache@v3
+        with:
+          path: ~/miniconda/envs/${{ env.CONDA_ENV_NAME }}
+          key: ${{ env.CONDA_ENV_NAME }}-${{ runner.os }}-${{ env.MD5_CHECKSUM }}-${{ env.CACHE_NUMBER }}
+        env:
+          # Increase this value to reset cache if ${CONDA_ENV_NAME}.tar.gz has not changed
+          CACHE_NUMBER: 0
+        id: cache-conda-archive
+
+      - name: Download and install the archived conda environment
+        if: steps.cache-conda-archive.outputs.cache-hit != 'true'
+        run: |
+          set -vxeuo pipefail
+          conda activate "${{ env.REPOSITORY_NAME }}-py${{ inputs.python-version }}"
+          url="https://zenodo.org/record/${ZENODO_ID}/files/${CONDA_ENV_NAME}.tar.gz?download=1"
+          wget --progress=dot:giga ${url} -O ${CONDA_ENV_NAME}.tar.gz
+          status=$?
+          if [ $status -gt 0 ]; then
+              echo "Cannot download from ${url}. Exit code: ${status}"
+              exit $status
+          fi
+          echo "${MD5_CHECKSUM} ${CONDA_ENV_NAME}.tar.gz" > checksum.txt
+          md5sum --check checksum.txt
+          mkdir -p $HOME/miniconda/envs/${CONDA_ENV_NAME}
+          tar -xf ${CONDA_ENV_NAME}.tar.gz -C $HOME/miniconda/envs/${CONDA_ENV_NAME}
+
+      - name: Activate and inspect the archived conda environment
+        run: |
+          set -vxeuo pipefail
+          conda activate $HOME/miniconda/envs/${CONDA_ENV_NAME}
+          conda unpack
+
+          conda info -a
+          conda env list
+          conda list
+          pip list
+
+      - name: Install the package and its dependencies
+        run: |
+          set -vxeuo pipefail
+          conda activate $HOME/miniconda/envs/${CONDA_ENV_NAME}
+          echo "Using conda environment at ${CONDA_PREFIX}"
+          pip install --upgrade pip setuptools wheel
+          pip uninstall -y backports || true
+          pip install backports.tarfile
+          pip install -r requirements-dev.txt
+          pip install -r requirements-extras.txt
+          pip install -e .
+          pip list
+
+      - name: Test with pytest
+        run: |
+          set -vxeuo pipefail
+          conda activate $HOME/miniconda/envs/${CONDA_ENV_NAME}
+          echo "Using conda environment at ${CONDA_PREFIX}"
+          coverage run --source=csxtools run_tests.py
+          coverage xml
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v2
+        with:
+          file: ./coverage.xml
+          flags: conda-env-unittests
 
-    - name: Set env vars
-      run: |
-        export REPOSITORY_NAME="${GITHUB_REPOSITORY#*/}"  # just the repo, as opposed to org/repo
-        echo "REPOSITORY_NAME=${REPOSITORY_NAME}" >> $GITHUB_ENV
-
-        export CONDA_ENV_NAME='${{ inputs.conda_env_name }}'
-        echo "CONDA_ENV_NAME=${CONDA_ENV_NAME}" >> $GITHUB_ENV
-
-        export ZENODO_ID='${{ inputs.zenodo_id }}'
-        echo "ZENODO_ID=${ZENODO_ID}" >> $GITHUB_ENV
-
-        export MD5_CHECKSUM='${{ inputs.md5_checksum }}'
-        echo "MD5_CHECKSUM=${MD5_CHECKSUM}" >> $GITHUB_ENV
-
-        # Workaround for unset GDAL env variables used by newer conda envs
-        export GDAL_DATA="${GDAL_DATA-''}"
-        echo "GDAL_DATA=${GDAL_DATA}" >> $GITHUB_ENV
-        export GDAL_DRIVER_PATH="${GDAL_DRIVER_PATH-''}"
-        echo "GDAL_DRIVER_PATH=${GDAL_DRIVER_PATH}" >> $GITHUB_ENV
-        export GEOTIFF_CSV="${GEOTIFF_CSV-''}"
-        echo "GEOTIFF_CSV=${GEOTIFF_CSV}" >> $GITHUB_ENV
-
-        # Workaround for unset MKL env variables used by newer conda envs
-        export MKL_INTERFACE_LAYER="${MKL_INTERFACE_LAYER-''}"
-        echo "MKL_INTERFACE_LAYER=${MKL_INTERFACE_LAYER}" >> $GITHUB_ENV
-
-    - name: Check out the code repo
-      uses: actions/checkout@v4
-
-    - name: Workaround: Fix .condarc MultipleKeysError
-      run: |
-        sed -i '/auto_activate_base/d' /home/runner/.condarc || true
-        sed -i '/auto_activate:/d' /home/runner/.condarc || true
-
-    - name: Set up Python ${{ inputs.python-version }} with conda
-      uses: conda-incubator/setup-miniconda@v3
-      with:
-        activate-environment: ${{ env.REPOSITORY_NAME }}-py${{ inputs.python-version }}
-        auto-update-conda: true
-        miniconda-version: "latest"
-        python-version: ${{ inputs.python-version }}
-        mamba-version: "*"
-        channels: conda-forge
-
-    - name: Cache the archived conda environment
-      uses: actions/cache@v3
-      with:
-        path: ~/miniconda/envs/${{ env.CONDA_ENV_NAME }}
-        key:
-          ${{ env.CONDA_ENV_NAME }}-${{ runner.os }}--${{ runner.arch }}-${{
-          env.MD5_CHECKSUM }}-${{ 
-          env.CACHE_NUMBER }}
-      env:
-        # Increase this value to reset cache if ${CONDA_ENV_NAME}.tar.gz has not changed
-        CACHE_NUMBER: 0
-      id: cache-conda-archive
-
-    - name: Download and install the archived conda environment
-      if: steps.cache-conda-archive.outputs.cache-hit != 'true'
-      run: |
-        set -vxeuo pipefail
-        conda activate "${{ env.REPOSITORY_NAME }}-py${{ inputs.python-version }}"
-        url="https://zenodo.org/record/${ZENODO_ID}/files/${CONDA_ENV_NAME}.tar.gz?download=1"
-        wget --progress=dot:giga ${url} -O ${CONDA_ENV_NAME}.tar.gz
-        status=$?
-        if [ $status -gt 0 ]; then
-            echo "Cannot download from ${url}. Exit code: ${status}"
-            exit $status
-        fi
-        echo "${MD5_CHECKSUM} ${CONDA_ENV_NAME}.tar.gz" > checksum.txt
-        md5sum --check checksum.txt
-        mkdir -p $HOME/miniconda/envs/${CONDA_ENV_NAME}
-        tar -xf ${CONDA_ENV_NAME}.tar.gz -C $HOME/miniconda/envs/${CONDA_ENV_NAME}
-
-    - name: Activate and inspect the archived conda environment
-      run: |
-        set -vxeuo pipefail
-        conda activate $HOME/miniconda/envs/${CONDA_ENV_NAME}
-        conda unpack
-
-        conda info -a
-        conda env list
-        conda list
-        pip list
-
-    - name: Install the package and its dependencies
-      run: |
-        set -vxeuo pipefail
-        conda activate $HOME/miniconda/envs/${CONDA_ENV_NAME}
-        echo "Using conda environment at ${CONDA_PREFIX}"
-        pip install --upgrade pip setuptools wheel
-        pip install -r requirements-dev.txt
-        pip install -r requirements-extras.txt
-        pip install -e .
-        pip list
-
-    - name: Test with pytest
-      run: |
-        set -vxeuo pipefail
-        conda activate $HOME/miniconda/envs/${CONDA_ENV_NAME}
-        echo "Using conda environment at ${CONDA_PREFIX}"
-        coverage run --source=csxtools run_tests.py
-        coverage xml
-
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v2
-      with:
-        file: ./coverage.xml 
-        flags: conda-env-unittests

.github/workflows/conda-env-tests.yml

@@ -1,29 +1,29 @@
-name: Unit Tests in NSLS-II Conda Environments
+name: Run tests in NSLS-II Conda Environments
 
-on: [push, pull_request, workflow_dispatch]
-
-env:
-  BRANCH_NAME: ${{ github.head_ref || github.ref_name }} 
+on:
+  push:
+    branches: [main]
+  pull_request:
 
 jobs:
-
+  # First prepare the matrix
   matrix_prep:
-
     uses: ./.github/workflows/_matrix_prep.yml
     with:
       config_prefix: recent
 
+  # Then run tests using that matrix
   test-in-conda-env:
-
     needs: matrix_prep
+    strategy:
+      max-parallel: 4
+      fail-fast: false
+      matrix:
+        include: ${{ fromJson(needs.matrix_prep.outputs.matrix_include) }}
+
     uses: ./.github/workflows/_test-in-conda-env.yml
     with:
       conda_env_name: ${{ matrix.conda_env_name }}
       zenodo_id: ${{ matrix.zenodo_id }}
       md5_checksum: ${{ matrix.md5_checksum }}
       python-version: ${{ matrix.python-version }}
-    strategy:
-      max-parallel: 4
-      matrix:
-        include: ${{ fromJson(needs.matrix_prep.outputs.matrix_include) }}
-      fail-fast: false

requirements-dev.txt

@@ -2,6 +2,6 @@ codecov
 coveralls
 flake8
 pytest
-pytest-pep8
+pytest-flake8
 sphinx
 sphinx-bootstrap-theme