Hindcast Test: Conda python version (#318)

- Uses python version correctly
- Installs MHKiT dependencies in conda build 
- Use coverage actions instead of coverage CLI 
- Uses an updated coverage version with lcov support
- Adds an `environment.yaml` file for conda environment install 
- Special case for MacOS-latest (macos 14)  and Py 3.8
- CI test job `set-os` logic modified to now run all OS on push to `develop`

Author: ssolson

.github/workflows/main.yml

@@ -17,8 +17,8 @@ jobs:
     steps:
       - id: set-matrix
         run: |
-          if [[ "${{ github.base_ref }}" == "develop" ]]; then
-            echo "matrix_os=[\"ubuntu-latest\"]" >> $GITHUB_OUTPUT          
+          if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "develop" ]]; then
+            echo "matrix_os=[\"ubuntu-latest\"]" >> $GITHUB_OUTPUT
           else
             echo "matrix_os=[\"windows-latest\", \"ubuntu-latest\", \"macos-latest\"]" >> $GITHUB_OUTPUT
           fi
@@ -107,14 +107,14 @@ jobs:
           miniconda-version: 'latest'
           auto-update-conda: true
           activate-environment: TEST
-          python-version: ${{ matrix.python-version }}
+          python-version: ${{ env.PYTHON_VER }}
           use-only-tar-bz2: true
 
       - name: Setup Conda environment
         shell: bash -l {0}
         run: |
           conda install numpy cython pip pytest hdf5 libnetcdf cftime netcdf4 coverage --strict-channel-priority
-          pip install -e . --no-deps --force-reinstall
+          pip install -e . --force-reinstall
 
       - name: Install dependencies
         shell: bash -l {0}
@@ -149,7 +149,7 @@ jobs:
           miniconda-version: 'latest'
           auto-update-conda: true
           activate-environment: TEST
-          python-version: ${{ matrix.python-version }}
+          python-version: ${{ env.PYTHON_VER }}
           use-only-tar-bz2: true
 
       - name: Setup Conda environment
@@ -195,41 +195,36 @@ jobs:
         with:
           miniconda-version: 'latest'
           auto-update-conda: true
+          environment-file: environment.yml
           activate-environment: TEST
           python-version: ${{ matrix.python-version }}
-          use-only-tar-bz2: true
+          use-only-tar-bz2: false
 
       - name: Create and setup Conda environment
         shell: bash -l {0}
         run: |
-          conda install numpy cython pip hdf5 libnetcdf cftime netcdf4 --strict-channel-priority
-          pip install -e . --no-deps --force-reinstall
-
-      - name: Install dependencies
-        shell: bash -l {0}
-        run: |
-          python -m pip install --upgrade pip wheel
-          pip install coverage pytest coveralls .
+          conda install -c conda-forge pytest coverage=7.5.0 coveralls --strict-channel-priority
+          pip install -e . --force-reinstall
 
       - name: Download data from artifact
         uses: actions/download-artifact@v4
         with:
           name: data
           path: ~/.cache/mhkit
 
-      - name: Run pytest
+      - name: Run pytest & generate coverage report
         shell: bash -l {0}
         run: |
           coverage run --rcfile=.github/workflows/.coveragerc --source=./mhkit/ -m pytest -c .github/workflows/pytest.ini
+          coverage lcov
 
       - name: Upload coverage data to coveralls.io
-        shell: bash -l {0}
-        run: |
-          coveralls --service=github
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COVERALLS_FLAG_NAME: ${{ matrix.python-version }}
-          COVERALLS_PARALLEL: true
+        uses: coverallsapp/github-action@master
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          flag-name: ${{ matrix.python-version }}
+          parallel: true
+          path-to-lcov: ./coverage.lcov
 
   pip-build:
     name: pip-${{ matrix.os }}/${{ matrix.python-version }}
@@ -249,6 +244,21 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
+      - name: Install HDF5 (macOS with Python 3.8)
+        if: startsWith(runner.os, 'macOS') && matrix.python-version == '3.8'
+        run: brew install hdf5
+
+      - name: Install NetCDF (macOS with Python 3.8)
+        if: startsWith(runner.os, 'macOS') && matrix.python-version == '3.8'
+        run: brew install netcdf
+
+      - name: Set environment variables (macOS with Python 3.8)
+        if: startsWith(runner.os, 'macOS') && matrix.python-version == '3.8'
+        run: |
+          echo "HDF5_DIR=$(brew --prefix hdf5)" >> $GITHUB_ENV
+          echo "NETCDF4_DIR=$(brew --prefix netcdf)" >> $GITHUB_ENV
+          echo "PKG_CONFIG_PATH=$(brew --prefix hdf5)/lib/pkgconfig:$(brew --prefix netcdf)/lib/pkgconfig:$PKG_CONFIG_PATH" >> $GITHUB_ENV
+
       - name: Set up Git repository
         uses: actions/checkout@v4
 
@@ -264,17 +274,19 @@ jobs:
           python -m pip install --upgrade pip wheel
           pip install coverage pytest coveralls .
 
-      - name: Run pytest
+      - name: Run pytest & generate coverage report
         shell: bash -l {0}
         run: |
-          coverage run --rcfile=.github/workflows/.coveragerc --source=./mhkit/  -m pytest -c .github/workflows/pytest.ini
+          coverage run --rcfile=.github/workflows/.coveragerc --source=./mhkit/ -m pytest -c .github/workflows/pytest.ini
+          coverage lcov
 
       - name: Upload coverage data to coveralls.io
-        run: coveralls --service=github
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COVERALLS_FLAG_NAME: ${{ matrix.python-version }}
-          COVERALLS_PARALLEL: true
+        uses: coverallsapp/github-action@master
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          flag-name: ${{ matrix.python-version }}
+          parallel: true
+          path-to-lcov: ./coverage.lcov
 
   hindcast-calls:
     name: hindcast-${{ matrix.os }}/${{ matrix.python-version }}
@@ -338,15 +350,15 @@ jobs:
           python -m pip install --upgrade pip wheel
           pip install coveralls .
           coverage run --rcfile=.github/workflows/.coveragehindcastrc -m pytest -c .github/workflows/pytest-hindcast.ini
+          coverage lcov
 
       - name: Upload coverage data to coveralls.io
-        shell: bash -l {0}
-        run: |
-          coveralls --service=github
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COVERALLS_FLAG_NAME: ${{ matrix.python-version }}
-          COVERALLS_PARALLEL: true
+        uses: coverallsapp/github-action@master
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          flag-name: ${{ matrix.python-version }}
+          parallel: true
+          path-to-lcov: ./coverage.lcov
 
   coveralls:
     name: Indicate completion to coveralls.io

environment.yml

@@ -0,0 +1,25 @@
+name: myenv
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python>=3.8
+  - pandas>=1.0.0
+  - numpy>=1.21.0
+  - scipy
+  - matplotlib
+  - requests
+  - lxml
+  - scikit-learn
+  - statsmodels
+  - bottleneck
+  - beautifulsoup4
+  - xarray
+  - h5py>=3.6.0
+  - netcdf4>=1.5.8
+  - pip:
+      - pecos>=0.3.0
+      - fatpack
+      - NREL-rex>=0.2.63
+      - h5pyd>=0.7.0
+      - six>=1.13.0