Merge pull request #33 from WISDEM/f/new_mod_options

F/new mod options

.github/workflows/CI_WEIS.yml

@@ -60,15 +60,14 @@ jobs:
       - name: Run parallel examples rotor optimization
         shell: pwsh
         run: |
-          cd examples/rotor_opt
+          cd examples/05_IEA-3.4-130-RWT
           mpirun -np 2 python weis_driver.py
       
       # Run scripts within control_opt folder, with and without MPI
       - name: Run examples control optimization
         shell: pwsh
         run: |
-          cd examples/control_opt
-          python runOptimization.py
+          cd examples/02_control_opt
           mpirun -np 2 python runOptimization.py
 
       # Run scripts within dac folder

.gitignore

@@ -1,3 +1,11 @@
+*.py[cod]
+
+# Emacs
+*~
+
+# pyMAP
+outlist.map.sum
+
 # Packages
 *.egg
 *.egg-info
@@ -6,7 +14,93 @@ build
 local
 .DS_Store
 __pycache__
+eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+
+# Output files
+outputs/
+*.out
+
+# Sphinx
+_build
+generated
+
+# XCode
+*.xcodeproj
+
+# C extensions
+*.so
+*.dSYM
+
+# Unit test / coverage reports
+.coverage
+.tox
+nosetests.xml
+
+# Translations
+*.mo
 
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# Compiled source #
+###################
+*.com
+*.class
+*.dll
+*.exe
+*.o
+*.so
+*.dylib
+
+# Packages #
+############
+# it's better to unpack these files and commit the raw source
+# git has its own built in compression methods
+*.7z
+*.dmg
+*.gz
+*.iso
+*.jar
+*.rar
+*.tar
+*.zip
+
+# Logs and databases #
+######################
+*.log
+*.sql
+*.sqlite
+
+# OS generated files #
+######################
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+Icon?
+ehthumbs.db
+Thumbs.db
+
+# Jupyter notebooks #
+#####################
+.ipynb_checkpoints
+
+# VSCode #
+##########
+.vscode/
+
+# IntelliJ Things #
+####################
+.idea/
 
 # Openfast
 *.outb
@@ -15,9 +109,6 @@ __pycache__
 *.ech
 *.dbg
 
-# vs code
-.vscode
-
 # Temp
 *Temp*
 *temp*

WISDEM/.flake8

@@ -0,0 +1,5 @@
+[flake8]
+ignore = E731,E402,F,W504,W503,E501,C901
+exclude = .git,__pycache__,docs/source/conf.py,old,build,dist
+max-complexity = 10
+max-line-length=120

WISDEM/.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
+- …

WISDEM/.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?

WISDEM/.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

WISDEM/.github/workflows/CI_WISDEM.yml

@@ -0,0 +1,68 @@
+name: CI_WISDEM
+
+# 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:
+    name: Build (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: true
+      matrix:
+        os: ["ubuntu-latest", "windows-latest"]
+        python-version: ["3.8"]
+
+    steps:
+      - uses: actions/checkout@v2
+      - 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
+
+      # Install dependencies of WEIS specific to ubuntu
+      - name: Add dependencies ubuntu specific
+        if: false == contains( matrix.os, 'windows')
+        #shell: pwsh # putting in a shell command makes for compile linking problems later
+        # (if you use the shell here, cannot use 'compiler' package)
+        run: |
+          conda install -y petsc4py mpi4py compilers
+      
+      # Install dependencies of WISDEM specific to windows
+      - name: Add dependencies windows specific
+        if: contains( matrix.os, 'windows')
+        run: |
+          conda install -y m2w64-toolchain libpython
+
+      # Debugging session
+      #- name: Setup tmate session
+      #  uses: mxschmitt/action-tmate@v3
+
+      # Install WISDEM
+      - name: Install WISDEM
+        shell: pwsh
+        run: |
+          python setup.py develop
+      
+      # Run all tests
+      - name: Run tests
+        if: contains( matrix.os, 'ubuntu')
+        shell: pwsh
+        run: |
+          pytest --cov-config=.coverageac --cov=wisdem 
+    
+      # Run coveralls
+      - name: Run coveralls
+        if: contains( matrix.os, 'ubuntu')
+        # This also works, https://github.com/AndreMiras/coveralls-python-action
+        #uses: AndreMiras/coveralls-python-action@develop
+        shell: pwsh
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          coveralls

WISDEM/.isort.cfg

@@ -0,0 +1,9 @@
+[settings]
+multi_line_output=3
+include_trailing_comma=True
+force_grid_wrap=0
+use_parentheses=True
+line_length=120
+sections=FUTURE,STDLIB,THIRDPARTY,FIRSTPARTY,LOCALFOLDER
+known_first_party=wisdem
+length_sort=1

WISDEM/.pre-commit-config.yaml

@@ -0,0 +1,31 @@
+repos:
+-   repo: https://github.com/timothycrosley/isort
+    rev: 4.3.21
+    hooks:
+        - id: isort
+          name: isort
+          stages: [commit]
+
+-   repo: https://github.com/psf/black
+    rev: stable
+    hooks:
+        - id: black
+          name: black
+          stages: [commit]
+          language_version: python3.8
+
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.3.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    # -   id: check-executables-have-shebangs
+    -   id: check-json
+    -   id: check-yaml
+    -   id: check-merge-conflict
+    -   id: check-symlinks
+    #-   id: flake8
+        exclude: ^docs/
+    -   id: mixed-line-ending
+    -   id: pretty-format-json
+        args: [--autofix]

WISDEM/README.md

@@ -59,6 +59,7 @@ The installation instructions below use the environment name, "wisdem-env," but
         conda remove --force wisdem
         conda install compilers     # (Mac / Linux only)
         conda install m2w64-toolchain libpython       # (Windows only)
+	pip install simpy marmot-agents
         git clone https://github.com/WISDEM/WISDEM.git
         cd WISDEM
         git checkout develop