Rely on conda package management to provide key elements of the WEIS stack

.github/workflows/CI_WEIS.yml

@@ -2,97 +2,101 @@ name: CI_WEIS
 
 # We run CI on push commits on all branches
 on: [push, pull_request]
-
+    
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   build:
-    name: Build (${{ matrix.os }})
+    name: Build (${{ matrix.os }} Python ${{ matrix.python-version }})
     runs-on: ${{ matrix.os }}
+
+    defaults:
+        run:
+            shell: bash -el {0}
+
     strategy:
-      fail-fast: true
+      fail-fast: false
       matrix:
-        os: ["ubuntu-latest"] #, "macOS-latest"]
-        python-version: ["3.8"]
+        os: ["ubuntu-latest", "macOS-latest"] #, "windows-latest"]
+        python-version: ["3.9","3.10","3.11"]
 
     steps:
-      - uses: actions/checkout@v2
-
-      # This is the more official way to do miniconda, but it messes with the GitHub worker environment and shell quite a bit
-      #- uses: conda-incubator/setup-miniconda@v2
-      #  # https://github.com/marketplace/actions/setup-miniconda
-      #  with:
-      #    #miniconda-version: "latest"
-      #    channels: conda-forge
-      #    auto-update-conda: true
-      #    python-version: 3.8
-      #    environment-file: environment.yml
+      #- name: Setup GNU Fortran
+      #  #  if: false == contains( matrix.os, 'windows')
+      #  uses: awvwgk/setup-fortran@main
 
-      # This is a less official, but more lightweight way to do miniconda
-      - uses: s-weigand/setup-conda@v1
-        # https://github.com/marketplace/actions/setup-conda
+      - uses: actions/checkout@v4
+
+      - name: Install conda/mamba
+        uses: conda-incubator/setup-miniconda@v2
+        # https://github.com/marketplace/actions/setup-miniconda
         with:
-          update-conda: true
-          python-version: 3.8
-          conda-channels: conda-forge
-          activate-conda: true
-      - run: conda env update --file environment.yml
-
-      #- name: Show custom environment
-      #  shell: bash
-      #  run: |
-      #      cat $GITHUB_ENV
-      #      printenv
+          # To use mamba, uncomment here, comment out the miniforge line
+          # mamba-version: "*"
+          miniforge-version: "latest"
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          environment-file: environment.yml
+          activate-environment: test
+          auto-activate-base: false
+
+      - name: Add dependencies windows specific
+        if: contains( matrix.os, 'windows')
+        run: |
+          conda install -y -c intel intel-openmp mkl
 
-      # Install dependencies of WEIS specific to ubuntu
       - name: Add dependencies ubuntu specific
         if: false == contains( matrix.os, 'windows')
-        shell: bash 
-        # (if you use the shell here, cannot use 'compiler' package otherwise get link problems to system libraries
-        # Mpi only seems to work with the shell command though, so instead rely on system compilers
         run: |
           conda install -y petsc4py mpi4py openmpi
-          python -c "import platform; print(platform.node())"
-
-      # Install dependencies of WISDEM specific to windows
-      - name: Add dependencies windows specific
-        if: contains( matrix.os, 'windows')
+
+      - name: Add test packages
         run: |
-          conda install -y m2w64-toolchain libpython
-
+          conda install -y pytest pytest-cov coveralls
+            
       - name: Show custom environment
-        shell: bash
         run: |
             conda list
-
-      # Debugging session
-      #- name: Setup tmate session
-      #  uses: mxschmitt/action-tmate@v3
+            printenv | sort
 
       # Install WEIS
       - name: Install WEIS
-        shell: bash
         run: |
-          python setup.py develop
+          pip install -e .
+
+      # Debugging session
+      #- name: Setup tmate session
+      #  if: contains( matrix.os, 'windows')
+      #  uses: mxschmitt/action-tmate@v3
+
+      #- name: Show openfast environment
+      #  run: |
+      #      which -a openfast
+      #      cd /c/Miniconda3/envs/test/Library/bin/
+      #      ls *fast*.exe
+      #      ls *fast*.dll
+      #      openfast -h
+      #      python -c "import ctypes; ctypes.cdll.LoadLibrary('openfastlib.dll')"
+      #      ls *fast*.dll
+      #      cd examples/03_NREL5MW_OC3_spar
+      #      python weis_driver.py
 
       # List the collected tests for debugging purposes
       - name: List tests
-        shell: bash
         run: |
-          pytest weis --collect-only
+          pytest --collect-only weis 
 
       # Run all tests within WEIS, but not computationally expensive examples
       - name: Run tests within WEIS
-        shell: bash
         run: |
-          pytest weis --cov-config=.coverageac --cov=weis
+          pytest --cov-config=.coverageac --cov=weis -p no:warnings --disable-warnings weis 
 
       # Run coveralls
       - name: Run coveralls
-        if: contains( matrix.os, 'ubuntu')
+        if: contains( matrix.os, 'ubuntu') && contains( matrix.python-version, '3.10')
+        uses: coverallsapp/github-action@v2
         # This also works, https://github.com/AndreMiras/coveralls-python-action
         #uses: AndreMiras/coveralls-python-action@develop
-        shell: bash
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          coveralls --service=github
+        #env:
+        #  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        #run: |
+        #  coveralls --service=github

.github/workflows/run_exhaustive_examples.yml

@@ -5,75 +5,62 @@ on: [pull_request]
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   build:
-    name: Build (${{ matrix.os }})
+    name: Build (${{ matrix.os }} Python ${{ matrix.python-version }})
     runs-on: ${{ matrix.os }}
     # if: "contains(github.event.head_commit.message, 'exhaustive_CI')"  # This line could be used to have commit-specific instructions
+
+    defaults:
+        run:
+            shell: bash -l {0}
+
     strategy:
       fail-fast: true
       matrix:
         os: ["ubuntu-latest"] #, "macOS-latest"]
-        python-version: ["3.8"]
+        python-version: ["3.9","3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      # This is the more official way to do miniconda, but it messes with the GitHub worker environment and shell quite a bit
-      #- uses: conda-incubator/setup-miniconda@v2
-      #  # https://github.com/marketplace/actions/setup-miniconda
-      #  with:
-      #    #miniconda-version: "latest"
-      #    channels: conda-forge
-      #    auto-update-conda: true
-      #    python-version: 3.8
-      #    environment-file: environment.yml
-
-      # This is a less official, but more lightweight way to do miniconda
-      - uses: s-weigand/setup-conda@v1
-        # https://github.com/marketplace/actions/setup-conda
+      - name: Install conda/mamba
+        uses: conda-incubator/setup-miniconda@v2
+        # https://github.com/marketplace/actions/setup-miniconda
         with:
-          update-conda: true
-          python-version: 3.8
-          conda-channels: conda-forge
-          activate-conda: true
-      - run: conda env update --file environment.yml
-
-      #- name: Show custom environment
-      #  shell: bash
-      #  run: |
-      #      cat $GITHUB_ENV
-      #      printenv
+          # To use mamba, uncomment here, comment out the miniforge line
+          #mamba-version: "*"
+          miniforge-version: "latest"
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          environment-file: environment.yml
+          activate-environment: test
+          auto-activate-base: false
 
       # Install dependencies of WEIS specific to ubuntu
       - name: Add dependencies ubuntu specific
         if: false == contains( matrix.os, 'windows')
-        shell: bash 
-        # (if you use the shell here, cannot use 'compiler' package otherwise get link problems to system libraries
-        # Mpi only seems to work with the shell command though, so instead rely on system compilers
         run: |
           conda install -y petsc4py mpi4py openmpi
-          python -c "import platform; print(platform.node())"
 
-      # Install dependencies of WISDEM specific to windows
-      - name: Add dependencies windows specific
-        if: contains( matrix.os, 'windows')
+      - name: Show custom environment
         run: |
-          conda install -y m2w64-toolchain libpython
+            conda list
+            printenv | sort
 
-      # Install WEIS
-      - name: Install WEIS
-        shell: bash
-        run: |
-          python setup.py develop
-
       # Debugging session
       #- name: Setup tmate session
       #  uses: mxschmitt/action-tmate@v3
+
+      # Install WEIS
+      - name: Install WEIS
+        run: |
+          pip install -e .
 
       # Test walkthrough notebook
       - name: Test postprocessing notebooks
         run: |
           cd examples/16_postprocessing
-          gdown --no-check-certificate 1_FJaN-W1DoPNmO6YLSjnftvq6-7bn4VI
+          pip install gdown
+          gdown --no-check-certificate 1AtLjjX5xpPqlHkfwDqeUj6VBMOYWcjmV
           unzip outputs
           treon plot_FAST.ipynb
           treon rev_DLCs_WEIS.ipynb
@@ -82,17 +69,15 @@ jobs:
 
       # Run all examples
       - name: Run tests within WEIS
-        shell: bash
         run: |
           cd weis/test
           python run_examples.py
 
       # Run scripts within rotor_opt folder with MPI
       - name: Run parallel examples rotor optimization
-        shell: bash
         run: |
           cd examples/05_IEA-3.4-130-RWT
-          mpirun -np 2 python weis_driver.py
+          mpiexec -np 2 python weis_driver.py
 
       # Run scripts within dac folder
       # - name: Run examples distributed aerodynamic control
@@ -102,8 +87,7 @@ jobs:
 
       # Run scripts within design of experiments folder
       - name: Run examples design of experiments
-        shell: bash
         run: |
           cd examples/09_design_of_experiments
-          mpirun -n 2 --bind-to core python DOE_openfast.py
+          mpiexec -n 2 --bind-to core python DOE_openfast.py
           python postprocess_results.py