Lint: Utils module (#350)

1. This PR makes the utils module PyLint compatible and enforces this compatibility through GitHub Actions. 2. Updates the GitHub Actions testing environment to use the conda environment.yml file for consistency. 3. Updates the folium map calls in the Pacwave example to align with the latest folium API changes.
MHKiT-Software · Nov 27, 2024 · 27114e7 · 27114e7
1 parent ca9709f
commit 27114e7
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -65,23 +65,30 @@ jobs:
           auto-update-conda: true
           python-version: ${{ env.PYTHON_VER }}
           activate-environment: TESTconda
-          use-only-tar-bz2: true
+          use-only-tar-bz2: false
 
-      - name: Setup Conda environment
+      - name: Create MHKiT Conda environment
         shell: bash -l {0}
         run: |
-          conda install numpy cython pip hdf5 libnetcdf cftime netcdf4 --strict-channel-priority
-          pip install -e . --force-reinstall
+          conda env create -f environment.yml
+          conda activate mhkit-env
 
-      - name: Install dependencies
+      - name: Install testing dependencies
         shell: bash -l {0}
         run: |
-          python -m pip install --upgrade pip wheel
-          pip install coverage pytest coveralls .
+          conda activate mhkit-env
+          conda install -y pytest coverage coveralls
+
+      - name: Install mhkit
+        shell: bash -l {0}
+        run: |
+          conda activate mhkit-env
+          pip install -e . --no-deps
 
       - name: Prepare non-hindcast API data
         shell: bash -l {0}
         run: |
+          conda activate mhkit-env
           pytest mhkit/tests/river/test_io_usgs.py
           pytest mhkit/tests/tidal/test_io.py
           pytest mhkit/tests/wave/io/test_cdip.py
@@ -109,23 +116,30 @@ jobs:
           auto-update-conda: true
           activate-environment: TEST
           python-version: ${{ env.PYTHON_VER }}
-          use-only-tar-bz2: true
+          use-only-tar-bz2: false
 
-      - name: Setup Conda environment
+      - name: Create MHKiT Conda environment
         shell: bash -l {0}
         run: |
-          conda install numpy cython pip pytest hdf5 libnetcdf cftime netcdf4 coverage --strict-channel-priority
-          pip install -e . --force-reinstall
+          conda env create -f environment.yml
+          conda activate mhkit-env
 
-      - name: Install dependencies
+      - name: Install testing dependencies
         shell: bash -l {0}
         run: |
-          python -m pip install --upgrade pip wheel
-          pip install coverage pytest coveralls .
+          conda activate mhkit-env
+          conda install -y pytest coverage coveralls
+
+      - name: Install mhkit
+        shell: bash -l {0}
+        run: |
+          conda activate mhkit-env
+          pip install -e . --no-deps
 
       - name: Prepare Wave Hindcast data
         shell: bash -l {0}
         run: |
+          conda activate mhkit-env
           pytest mhkit/tests/wave/io/hindcast/test_hindcast.py
 
       - name: Upload Wave Hindcast data as artifact
@@ -151,23 +165,30 @@ jobs:
           auto-update-conda: true
           activate-environment: TEST
           python-version: ${{ env.PYTHON_VER }}
-          use-only-tar-bz2: true
+          use-only-tar-bz2: false
 
-      - name: Setup Conda environment
+      - name: Create MHKiT 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
+          conda env create -f environment.yml
+          conda activate mhkit-env
 
-      - name: Install dependencies
+      - name: Install testing dependencies
         shell: bash -l {0}
         run: |
-          python -m pip install --upgrade pip wheel
-          pip install coverage pytest coveralls .
+          conda activate mhkit-env
+          conda install -y pytest coverage coveralls
+
+      - name: Install mhkit
+        shell: bash -l {0}
+        run: |
+          conda activate mhkit-env
+          pip install -e . --no-deps
 
       - name: Prepare Wind Hindcast data
         shell: bash -l {0}
         run: |
+          conda activate mhkit-env
           pytest mhkit/tests/wave/io/hindcast/test_wind_toolkit.py
 
       - name: Upload Wind Hindcast data as artifact
@@ -201,21 +222,28 @@ jobs:
           python-version: ${{ matrix.python-version }}
           use-only-tar-bz2: false
 
-      - name: Create and setup Conda environment
+      - name: Create MHKiT Conda environment
         shell: bash -l {0}
         run: |
-          conda install -c conda-forge pytest coverage=7.5.0 coveralls --strict-channel-priority
-          pip install -e . --force-reinstall
+          conda env create -f environment.yml
+          conda activate mhkit-env
 
-      - name: Download data from artifact
-        uses: actions/download-artifact@v4
-        with:
-          name: data
-          path: ~/.cache/mhkit
+      - name: Install testing dependencies
+        shell: bash -l {0}
+        run: |
+          conda activate mhkit-env
+          conda install -y pytest coverage coveralls
+
+      - name: Install mhkit
+        shell: bash -l {0}
+        run: |
+          conda activate mhkit-env
+          pip install -e . --no-deps
 
       - name: Run pytest & generate coverage report
         shell: bash -l {0}
         run: |
+          conda activate mhkit-env
           coverage run --rcfile=.github/workflows/.coveragerc --source=./mhkit/ -m pytest -c .github/workflows/pytest.ini
           coverage lcov
 
@@ -310,11 +338,23 @@ jobs:
           python-version: ${{ matrix.python-version }}
           use-only-tar-bz2: false
 
-      - name: Setup Conda environment
+      - name: Create MHKiT Conda environment
         shell: bash -l {0}
         run: |
-          conda install -c conda-forge pytest coverage=7.5.0 coveralls --strict-channel-priority
-          pip install -e . --force-reinstall
+          conda env create -f environment.yml
+          conda activate mhkit-env
+
+      - name: Install testing dependencies
+        shell: bash -l {0}
+        run: |
+          conda activate mhkit-env
+          conda install -y pytest coverage coveralls
+
+      - name: Install mhkit
+        shell: bash -l {0}
+        run: |
+          conda activate mhkit-env
+          pip install -e . --no-deps
 
       - name: Download Wave Hindcast data from artifact
         uses: actions/download-artifact@v4
@@ -335,9 +375,10 @@ jobs:
           mv ~/.cache/mhkit/wind-hindcast/hindcast/* ~/.cache/mhkit/hindcast/
         shell: bash
 
-      - name: Install MHKiT and run pytest
+      - name: Run hindcast pytest
         shell: bash -l {0}
         run: |
+          conda activate mhkit-env
           coverage run --rcfile=.github/workflows/.coveragehindcastrc -m pytest -c .github/workflows/pytest-hindcast.ini
           coverage lcov
 
@@ -416,23 +457,25 @@ jobs:
           auto-update-conda: true
           python-version: '3.11'
           activate-environment: TESTconda
-          use-only-tar-bz2: true
+          use-only-tar-bz2: false
 
-      - name: Install dependencies
+      - name: Create MHKiT Conda environment
         shell: bash -l {0}
         run: |
-          conda install numpy cython pip hdf5 libnetcdf cftime netcdf4 --strict-channel-priority
-          pip install -e . --force-reinstall
-          python -m pip install --upgrade pip wheel
-          pip install nbval jupyter
-          pip install utm folium
+          conda env create -f environment.yml
+          conda activate mhkit-env
+
+      - name: Install notebook testing dependencies
+        shell: bash -l {0}
+        run: |
+          conda activate mhkit-env
+          conda install -y pytest coverage coveralls nbval jupyter utm folium
 
-      - name: Ensure Conda environment is activated
+      - name: Install mhkit
         shell: bash -l {0}
         run: |
-          echo "source ~/miniconda3/etc/profile.d/conda.sh" >> ~/.bashrc
-          echo "conda activate TESTconda" >> ~/.bashrc
-          source ~/.bashrc
+          conda activate mhkit-env
+          pip install -e . --no-deps
 
       - name: Download non-hindcast data
         uses: actions/download-artifact@v4
@@ -470,6 +513,7 @@ jobs:
       - name: Run notebook
         shell: bash -l {0}
         run: |
+          conda activate mhkit-env
           if [[ "${{ matrix.notebook }}" == "examples/metocean_example.ipynb" || "${{ matrix.notebook }}" == "examples/WPTO_hindcast_example.ipynb" ]]; then
             if [[ "${{ needs.check-changes.outputs.should-run-hindcast }}" == 'true' ]]; then
               jupyter nbconvert --to notebook --execute --inplace --ExecutePreprocessor.timeout=${{ matrix.timeout }} "${{ matrix.notebook }}"

diff --git a/.github/workflows/pylint.yml b/.github/workflows/pylint.yml
@@ -29,6 +29,10 @@ jobs:
         run: |
           pylint mhkit/power/
 
+      - name: Run Pylint on mhkit/utils/
+        run: |
+          pylint mhkit/utils/
+
       - name: Run Pylint on mhkit/acoustics/
         run: |
           pylint mhkit/acoustics/
diff --git a/environment.yml b/environment.yml
@@ -1,4 +1,4 @@
-name: myenv
+name: mhkit-env
 channels:
   - conda-forge
   - defaults
@@ -12,16 +12,16 @@ dependencies:
   - scikit-learn>=1.5.1
   - h5py>=3.11.0
   - h5pyd>=0.18.0
+  - netCDF4>=1.6.5
+  - hdf5>=1.14.3,<1.14.5.0a0
   - statsmodels>=0.14.2
   - requests
   - beautifulsoup4
   - numexpr>=2.10.0
   - lxml
   - bottleneck
-  - pip:
-      - netCDF4>=1.7.1.post1
-      - matplotlib>=3.9.1
-      - pecos>=0.3.0
-      - fatpack
-      - NREL-rex>=0.2.63
-      - notebook
+  - pecos>=0.3.0
+  - notebook
+  - matplotlib>=3.9.1
+  - fatpack
+  - nrel-rex