Phase 2 Starting Point

.github/workflows/CI_WEIS.yml

@@ -24,18 +24,16 @@ jobs:
       #  #  if: false == contains( matrix.os, 'windows')
       #  uses: awvwgk/setup-fortran@main
 
-      - uses: actions/checkout@v3
+      - 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
+      - name: Install conda/mamba
+        uses: conda-incubator/setup-miniconda@v2
         # https://github.com/marketplace/actions/setup-miniconda
         with:
-          #miniconda-version: "latest"
-          #miniforge-version: "latest"
-          mamba-version: "*"
-          channels: conda-forge,defaults
-          channel-priority: true          
-          #auto-update-conda: true
+          # 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
@@ -45,26 +43,27 @@ jobs:
       - name: Add dependencies mac specific
         if: contains( matrix.os, 'mac')
         run: |
-            mamba install -y petsc4py mpi4py openmpi compilers
+            conda install -y petsc4py mpi4py openmpi compilers
 
       # Install dependencies of WISDEM specific to windows
       - name: Add dependencies windows specific
         if: contains( matrix.os, 'windows')
         run: |
-          mamba install -y m2w64-toolchain libpython
+          conda install -y m2w64-toolchain libpython
 
       # Install dependencies of WEIS specific to ubuntu
       - name: Add dependencies ubuntu specific
         if: contains( matrix.os, 'ubuntu')
         # (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: |
-          mamba install -y petsc4py mpi4py openmpi
+          conda install -y petsc4py mpi4py openmpi
           python -c "import platform; print(platform.node())"
 
       - name: Show custom environment
         run: |
-            mamba list
+            conda list
+            which -a gfortran
             printenv | sort
 
       # Debugging session
@@ -80,19 +79,21 @@ jobs:
       # List the collected tests for debugging purposes
       - name: List tests
         run: |
-          pytest weis --collect-only
+          pytest --collect-only weis 
 
       # Run all tests within WEIS, but not computationally expensive examples
       - name: Run tests within WEIS
         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
-        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

@@ -20,23 +20,47 @@ jobs:
         python-version: ["3.9","3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      # Even miniconda gets bogged down- try mamba
-      - name: Install Conda environment with Micromamba
-        uses: mamba-org/provision-with-micromamba@main
+      - name: Install conda/mamba
+        uses: conda-incubator/setup-miniconda@v2
+        # https://github.com/marketplace/actions/setup-miniconda
         with:
+          # To use mamba, uncomment here, comment out the miniforge line
+          #mamba-version: "*"
+          miniforge-version: "latest"
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
           environment-file: environment.yml
-          environment-name: test
-          channels: conda-forge
-          extra-specs: |
-            python=${{ matrix.python-version }}
-            mpi4py
-            petsc4py
-            openmpi
-            sel(osx): compilers
-            sel(win): m2w64-toolchain
-            sel(win): libpython`
+          activate-environment: test
+          auto-activate-base: false
+
+          #miniforge-variant: Mambaforge
+          #channels: conda-forge
+          #extra-specs: |
+          #  python=${{ matrix.python-version }}
+          #  mpi4py
+          #  petsc4py
+          #  openmpi
+          #  sel(osx): compilers
+          #  sel(win): m2w64-toolchain
+          #  sel(win): libpython`
+
+      # # Even miniconda gets bogged down- try mamba
+      # - name: Install Conda environment with Micromamba
+      #   uses: mamba-org/provision-with-micromamba@main
+      #   with:
+      #     environment-file: environment.yml
+      #     environment-name: test
+      #     channels: conda-forge
+      #     extra-specs: |
+      #       python=${{ matrix.python-version }}
+      #       mpi4py
+      #       petsc4py
+      #       openmpi
+      #       sel(osx): compilers
+      #       sel(win): m2w64-toolchain
+      #       sel(win): libpython`
 
       # 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
@@ -80,13 +104,13 @@ jobs:
       #    conda install -y m2w64-toolchain libpython
 
       # Install dependencies of WEIS specific to ubuntu
-      #- name: Add dependencies ubuntu specific
-      #  if: false == contains( matrix.os, 'windows')
-      #  # (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())"
+      - name: Add dependencies ubuntu specific
+        if: false == contains( matrix.os, 'windows')
+       # (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())"
 
       - name: Show custom environment
         run: |
@@ -105,7 +129,7 @@ jobs:
       - name: Test postprocessing notebooks
         run: |
           cd examples/16_postprocessing
-          gdown --no-check-certificate 1_FJaN-W1DoPNmO6YLSjnftvq6-7bn4VI
+          gdown --no-check-certificate 1AtLjjX5xpPqlHkfwDqeUj6VBMOYWcjmV
           unzip outputs
           treon plot_FAST.ipynb
           treon rev_DLCs_WEIS.ipynb
@@ -122,7 +146,7 @@ jobs:
       - name: Run parallel examples rotor optimization
         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
@@ -134,5 +158,5 @@ jobs:
       - name: Run examples design of experiments
         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

MoorPy/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,30 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+## Description
+_Describe the bug here_
+
+### Steps to reproduce issue
+_Please provide a minimum working example (MWE) if possible_
+
+1. …
+2. …
+3. …
+
+### Current behavior
+…
+
+### Expected behavior
+…
+
+
+### Code versions
+_List versions only if relevant_
+- Python
+- …

MoorPy/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,14 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+# Description of feature
+Describe the feature here and provide some context. Under what scenario would this be useful?
+
+# Potential solution
+Can you think of ways to implement this?

MoorPy/.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,28 @@
+Delete the text explanations below these headers and replace them with information about your PR.
+Please first consult the [developer guide](https://weis.readthedocs.io/en/latest/how_to_contribute_code.html) to make sure your PR follows all code, testing, and documentation conventions.
+
+## Purpose
+Explain the goal of this pull request. If it addresses an existing issue be sure to link to it. Describe the big picture of your changes here, perhaps using a bullet list if multiple changes are done to accomplish a single goal. If it accomplishes multiple goals, it may be best to create separate PR's for each. 
+
+## Type of change
+What types of change is it?
+_Select the appropriate type(s) that describe this PR_
+
+- [ ] Bugfix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (non-backwards-compatible fix or feature)
+- [ ] Code style update (formatting, renaming)
+- [ ] Refactoring (no functional changes, no API changes)
+- [ ] Documentation update
+- [ ] Maintenance update
+- [ ] Other (please describe)
+
+## Testing
+Explain the steps needed to test the new code to verify that it does indeed address the issue and produce the expected behavior.
+
+## Checklist
+_Put an `x` in the boxes that apply._
+
+- [ ] I have run existing tests which pass locally with my changes
+- [ ] I have added new tests or examples that prove my fix is effective or that my feature works
+- [ ] I have added necessary documentation

MoorPy/.github/workflows/CI_MoorPy.yml

@@ -0,0 +1,79 @@
+name: CI_MoorPy
+
+# We run CI on push commits and pull requests 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_pip:
+        name: Pip Build (${{ matrix.os }}) - ${{ matrix.python-version }}
+        runs-on: ${{ matrix.os }}
+        defaults:
+            run:
+                shell: bash -l {0}
+
+        strategy:
+            fail-fast: false #true
+            matrix:
+                os: ["ubuntu-latest", "macOS-latest", "windows-latest"]
+                python-version: ["3.9", "3.10", "3.11"]
+
+        steps:
+            - name: checkout repository
+              uses: actions/checkout@v3
+
+            - name: Set up Python ${{ matrix.python-version }}
+              uses: actions/setup-python@v4
+              id: cp
+              with:
+                  python-version: ${{ matrix.python-version }}
+                  update-environment: true
+
+            - name: Pip Install MoorPy
+              run: |
+                  '${{ steps.cp.outputs.python-path }}' -m pip install -vv -e .[test]
+
+            - name: Test run
+              run: |
+                  cd tests
+                  '${{ steps.cp.outputs.python-path }}' -m pytest .
+
+
+    build_conda:
+        name: Conda Build (${{ matrix.os }}) - ${{ matrix.python-version }}
+        runs-on: ${{ matrix.os }}
+        defaults:
+            run:
+                shell: bash -l {0}
+
+        strategy:
+            fail-fast: false
+            matrix:
+                os: ["ubuntu-latest", "macOS-latest", "windows-latest"]
+                python-version: ["3.9", "3.10", "3.11"]
+
+        steps:
+            - name: checkout repository
+              uses: actions/checkout@v3
+
+            - uses: conda-incubator/setup-miniconda@v2
+              # https://github.com/marketplace/actions/setup-miniconda
+              with:
+                  miniconda-version: "latest"
+                  auto-update-conda: true
+                  python-version: ${{ matrix.python-version }}
+                  environment-file: environment.yml
+                  channels: conda-forge
+                  activate-environment: test
+                  auto-activate-base: false
+
+            # Install 
+            - name: Conda Install MoorPy
+              run: |
+                  python -m pip install -e . -vv
+
+            - name: Test run
+              run: |
+                  cd tests
+                  pytest .
+

MoorPy/.github/workflows/Publish_MoorPy.yml

@@ -0,0 +1,44 @@
+name: Build and upload to PyPI
+
+# Build on every branch push, tag push, and pull request change:
+#on: [push, pull_request]
+# Alternatively, to publish when a (published) GitHub Release is created, use the following:
+on:
+    push:
+    pull_request:
+    release:
+        types:
+            - published
+
+jobs:
+    build_and_upload_pypi:
+        runs-on: ubuntu-latest
+
+        # upload to PyPI on every tag starting with 'v'
+        #if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+        # alternatively, to publish when a GitHub Release is created, use the following rule:
+        if: github.event_name == 'release' && github.event.action == 'published'
+        steps:
+            - name: checkout repository
+              uses: actions/checkout@v3
+
+            - name: Set up Python 
+              uses: actions/setup-python@v4
+              id: cp
+              with:
+                  python-version: "3.11"
+                  update-environment: true
+
+            - name: Install pypa/build
+              run: |
+                  python -m pip install build
+
+            - name: Build a binary wheel and a source tarball
+              run: |
+                  python -m build .
+
+            - uses: pypa/[email protected]
+              with:
+                  user: __token__
+                  password: ${{ secrets.pypi_password }}
+                  # To test: repository_url: https://test.pypi.org/legacy/