Merge remote-tracking branch 'upstream/develop' into ctopt

.github/ISSUE_TEMPLATE/bug_report.md

@@ -27,4 +27,4 @@ _Please provide a minimum working example (MWE) if possible_
 ### Code versions
 _List versions only if relevant_
 - Python
-- …
+- …

.github/ISSUE_TEMPLATE/feature_request.md

@@ -11,4 +11,4 @@ assignees: ''
 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?
+Can you think of ways to implement this?

.github/PULL_REQUEST_TEMPLATE.md

@@ -2,7 +2,7 @@ Delete the text explanations below these headers and replace them with informati
 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. 
+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?
@@ -25,4 +25,4 @@ _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
+- [ ] I have added necessary documentation

.github/workflows/CI_WISDEM.yml

@@ -5,87 +5,140 @@ 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 }}, Python ${{ matrix.python-version }})
+  build_conda:
+    name: Conda Build-Test (${{ matrix.os }} Python ${{ matrix.python-version }})
     runs-on: ${{ matrix.os }}
+
+    defaults:
+        run:
+            shell: bash -el {0}
+
     strategy:
       fail-fast: False
       matrix:
-        os: [ubuntu-latest, windows-latest]
-        python-version: [3.8, 3.9]
+        os: [ubuntu-latest, windows-latest] #macos-latest, 
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
+      - name: checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install conda/mamba
+        uses: conda-incubator/setup-miniconda@v2
         # https://github.com/marketplace/actions/setup-miniconda
         with:
-          miniconda-version: "latest"
-          channels: conda-forge
+          # 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')
-        # if you use the shell here, cannot use 'compiler' package due to linker conflicts
-        shell: bash -l {0}
-        #shell: pwsh
         run: |
-          conda install -y petsc4py mpi4py gfortran
-          conda init bash
-          conda info -e
+          conda install -y petsc4py gfortran
 
       # 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
+      - name: Debug config
+        run: |
+          conda list
+          which -a gfortran
+          which pip
 
       # Install WISDEM with setup
+      # Note: For some reason, pip --no-deps doesn't find conda packages and downloads everything
       - name: Install WISDEM with setup
-        shell: bash -l {0}
-        #shell: pwsh
         run: |
-          python setup.py develop
+          python setup.py install
 
       # Install WISDEM with pip
-      - name: Install WISDEM with pip for Unix
-        if: false == contains( matrix.os, 'windows')
-        shell: bash -l {0}
-        #shell: pwsh
-        run: |
-          pip install -vv --no-deps -e .
+      #- name: Install WISDEM with pip for Unix
+      #  if: false == contains( matrix.os, 'windows')
+      #  run: |
+      #    python setup.py install
 
       # Install WISDEM with pip
       #- name: Install WISDEM with pip for Windows
       #  if: contains( matrix.os, 'windows')
-      #  shell: bash -l {0}
-      #  shell: pwsh
       #  run: |
-      #    pip install -vv --no-deps --global-option --compiler=unix .
+      #      python setup.py install
+
+      # Debugging session
+      #- name: Setup tmate session
+      #  uses: mxschmitt/action-tmate@v3
 
       # Run all tests
       - name: Run tests
-        if: contains( matrix.os, 'ubuntu')
-        shell: bash -l {0}
-        #shell: pwsh
+        if: false == contains( matrix.os, 'windows')
+        run: |
+          pytest -p no:warnings --disable-warnings --cov=wisdem
+
+      # Run limited test on WINDOWS
+      - name: Limited Windows test
+        if: contains( matrix.os, 'windows')
         run: |
-          pytest --cov-config=.coverageac --cov=wisdem
+          cd wisdem/test/test_gluecode
+          pytest  -p no:warnings --disable-warnings test_g*
 
       # 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 -l {0}
-        #shell: pwsh
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        #env:
+        #  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        #run: |
+        #  coveralls --service=github
+
+  build_pip:
+    name: Pip Build-Test (${{ matrix.os }} Python ${{ matrix.python-version }})
+    runs-on: ${{ matrix.os }}
+
+    defaults:
+        run:
+            shell: bash -el {0}
+
+    strategy:
+      fail-fast: False
+      matrix:
+        os: [ubuntu-latest] #, windows-latest, macos-latest, 
+        python-version: ["3.10"]
+
+    steps:
+      - name: Setup GNU Fortran
+        uses: awvwgk/setup-fortran@v1
+        #with:
+        #    compiler: intel-classic
+
+      - name: checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        id: cp
+        with:
+            python-version: ${{ matrix.python-version }}
+            update-environment: true
+
+      # Install WISDEM with setup
+      # Note: For some reason, pip --no-deps doesn't find conda packages and downloads everything
+      - name: Install WISDEM with setup
+        run: |
+          '${{ steps.cp.outputs.python-path }}' -m pip install --upgrade pip install pytest
+          '${{ steps.cp.outputs.python-path }}' -m pip install -vv .
+
+      # Run limited tests
+      - name: Limited test
         run: |
-          coveralls --service=github
+          cd wisdem/test/test_gluecode
+          pytest -p no:warnings --disable-warnings test_g*

.github/workflows/Publish_WISDEM.yml

@@ -0,0 +1,66 @@
+name: Build and upload to PyPI
+# https://github.com/pypa/cibuildwheel/blob/main/examples/github-deploy.yml
+
+# 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:
+  release:
+    types:
+      - published
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
+    steps:
+      - name: Setup GNU Fortran
+        uses: awvwgk/setup-fortran@v1
+
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    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:
+      - uses: actions/download-artifact@v3
+        with:
+          # unpacks default artifact into dist/
+          # if `name: artifact` is omitted, the action will create extra parent dir
+          name: artifact
+          path: dist
+
+      - uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.pypi_password }}
+          # To test: repository_url: https://test.pypi.org/legacy/

.pre-commit-config.yaml

@@ -1,21 +1,21 @@
 repos:
--   repo: https://github.com/timothycrosley/isort
-    rev: 5.10.1
+-   repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
     hooks:
         - id: isort
           name: isort
           stages: [commit]
 
 -   repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 23.3.0
     hooks:
         - id: black
           name: black
           stages: [commit]
           language_version: python3
 
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.2.0
+    rev: v4.4.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer

.readthedocs.yaml

@@ -7,17 +7,32 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
-    python: "mambaforge-4.10"
-    # You can also specify other tool versions:
-    # nodejs: "16"
-    # rust: "1.55"
-    # golang: "1.17"
+    # This leads to "excessive memory use"
+    #python: "miniconda-latest"
+    python: "mambaforge-22.9"
+  apt_packages:
+      - snapd
+  jobs:
+    # Read the docs needs a couple packages not in the environment file
+    pre_install:
+      - conda install -y cmake compilers sphinx sphinxcontrib-bibtex
+      - conda install sphinx_rtd_theme>=1.3
+    pre_build:
+      - pwd
+      - wget https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64 -O yq && chmod +x yq
+      - ./yq -p yaml -o json wisdem/inputs/analysis_schema.yaml >| docs/schema/analysis_schema.json
+      - ./yq -p yaml -o json wisdem/inputs/modeling_schema.yaml >| docs/schema/modeling_schema.json
+      - sed -i -s '0,/properties/s//definitions/' docs/schema/modeling_schema.json
+      - sed -i -s '0,/properties/s//definitions/' docs/schema/analysis_schema.json
+      #- sed -i -s -e '/properties/{s//definitions/;:a' -e '$!N;$!ba' -e '}' docs/schema/modeling_schema.json
+      #- sed -i -s -e '/properties/{s//definitions/;:a' -e '$!N;$!ba' -e '}' docs/schema/analysis_schema.json
+
 
 # Shouldn't need conda for building the docs, but it is an option
 conda:
-  environment: docs/environment.yml
+  environment: environment.yml
 
 
 # Build documentation in the docs/ directory with Sphinx
@@ -31,7 +46,8 @@ sphinx:
 # Optionally declare the Python requirements required to build your docs
 python:
   install:
-    - requirements: docs/requirements.txt
     - method: pip
       path: .
-  system_packages: true
+      extra_requirements:
+        - docs
+#  system_packages: true

LICENSE

@@ -186,8 +186,6 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright 2012 NREL
-
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.
    You may obtain a copy of the License at

NOTICE

@@ -0,0 +1,12 @@
+Copyright 2014 Alliance for Sustainable Energy, LLC
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.