Merge branch 'develop' of https://github.com/MHKiT-Software/MHKiT-Python

into fix_doc_warnings
MHKiT-Software · Dec 2, 2024 · 7bbc0ee · 7bbc0ee
2 parents 8a455e7 + 79f69ca
commit 7bbc0ee
Show file tree

Hide file tree

Showing 40 changed files with 2,565 additions and 1,823 deletions.
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