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

.github/workflows/CI_WISDEM.yml

@@ -5,32 +5,31 @@ 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 -l {0}
-
+            shell: bash -el {0}
 
     strategy:
       fail-fast: False
       matrix:
-        os: [ubuntu-latest, windows-latest]
+        os: [ubuntu-latest, windows-latest] #macos-latest, 
         python-version: ["3.9", "3.10", "3.11"]
 
     steps:
       - name: checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
-      # Official way to do miniconda, but it messes with the worker environment and shell
-      - name: Install miniconda
+      - 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
@@ -41,49 +40,54 @@ jobs:
       - name: Add dependencies ubuntu specific
         if: false == contains( matrix.os, 'windows')
         run: |
-          conda install -y petsc4py mpi4py gfortran
-          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
         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')
-        run: |
-          rm -rf meson_build
-          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')
       #  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')
+        if: false == contains( matrix.os, 'windows')
         run: |
-          pytest --cov=wisdem
+          pytest -p no:warnings --disable-warnings --cov=wisdem
 
       # Run limited test on WINDOWS
-      - name: Add dependencies windows specific
+      - name: Limited Windows test
         if: contains( matrix.os, 'windows')
         run: |
           cd wisdem/test/test_gluecode
-          pytest test_g*
+          pytest  -p no:warnings --disable-warnings test_g*
 
       # Run coveralls
       - name: Run coveralls
@@ -94,3 +98,47 @@ jobs:
           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: |
+          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/

README.md

@@ -38,21 +38,29 @@ The core modules draw upon some utility packages, which are typically compiled c
 
 ## Installation
 
-Installation with [Anaconda](https://www.anaconda.com) is the recommended approach because of the ability to create self-contained environments suitable for testing and analysis.  WISDEM® requires [Anaconda 64-bit](https://www.anaconda.com/distribution/).
+Installation with [Anaconda](https://www.anaconda.com) is the recommended approach because of the ability to create self-contained environments suitable for testing and analysis.  WISDEM® requires [Anaconda 64-bit](https://www.anaconda.com/distribution/).  However, the `conda` command has begun to show its age and we now recommend the one-for-one replacement with `mamba` via the [Miniforge distribution](https://github.com/conda-forge/miniforge/releases), which is much more lightweight and more easily solves for the WISDEM package dependencies.
+
+### Installation as a "library"
+
+To use WISDEM's modules as a library for incorporation into other scripts or tools, WISDEM is available via `mamba install wisdem` or `pip install wisdem`, assuming that you have already setup your python environment.  Note that on Windows platforms, we suggest using `conda/mamba` exclusively.
+
+### Installation for direct use
+
+These instructions are for interaction with WISDEM directly, the use of its examples, and the direct inspection of its source code.
 
 The installation instructions below use the environment name, "wisdem-env," but any name is acceptable.  For those working behind company firewalls, you may have to change the conda authentication with `conda config --set ssl_verify no`.  Proxy servers can also be set with `conda config --set proxy_servers.http http://id:pw@address:port` and `conda config --set proxy_servers.https https://id:pw@address:port`. To setup an environment based on a different Github branch of WISDEM, simply substitute the branch name for `master` in the setup line.
 
 1.  Setup and activate the Anaconda environment from a prompt (Anaconda3 Power Shell on Windows or Terminal.app on Mac)
 
-        conda config --add channels conda-forge
-        conda env create --name wisdem-env -f https://raw.githubusercontent.com/WISDEM/WISDEM/master/environment.yml python=3.10
-        conda activate wisdem-env
+        mamba config --add channels conda-forge
+        mamba env create --name wisdem-env -f https://raw.githubusercontent.com/WISDEM/WISDEM/master/environment.yml python=3.10
+        mamba activate wisdem-env
 
 2.  In order to directly use the examples in the repository and peek at the code when necessary, we recommend all users install WISDEM in *developer / editable* mode using the instructions here.  If you really just want to use WISDEM as a library and lean on the documentation, you can always do `conda install wisdem` and be done.  Note the differences between Windows and Mac/Linux build systems. For Linux, we recommend using the native compilers (for example, gcc and gfortran in the default GNU suite).
 
-        conda install -y petsc4py mpi4py                 # (Mac / Linux only)
-        conda install -y gfortran                        # (Mac only without Homebrew or Macports compilers)
-        conda install -y m2w64-toolchain libpython       # (Windows only)
+        mamba install -y petsc4py mpi4py                 # (Mac / Linux only)
+        mamba install -y gfortran                        # (Mac only without Homebrew or Macports compilers)
+        mamba install -y m2w64-toolchain libpython       # (Windows only)
         git clone https://github.com/WISDEM/WISDEM.git
         cd WISDEM
         python setup.py develop				 # Currently more reliable than: pip install -e

docs/docstrings/var_guide_to_json.py

@@ -0,0 +1,43 @@
+#!/usr/bin/env python
+import sys
+import numpy as np
+import pandas as pd
+import json
+
+# these were spot checked, unclear if there's a better way to directly
+# obtain this mapping
+var_prefixes = {
+    'assembly': '*.', # scattered all over the place
+    'ccblade': 'rotorse.',
+    're': 'rotorse.',
+    'rp': 'rotorse.',
+    'rs': 'rotorse.',
+    'stall_check': 'rotorse.',
+    'wt_class': 'rotorse.',
+}
+
+# the variable guide in csv format is generated by get_omdao_vars.py
+tab = pd.read_csv('variable_guide.csv')
+if tab.iloc[-1]['Description'] == 'description':
+    # throw out footer
+    tab = tab.iloc[:-1]
+tab = tab.set_index('Variable')
+tab['Units'] = tab['Units'].replace(np.nan, '-')
+tab['Description'] = tab['Description'].replace(np.nan,'None')
+
+# convert to dict
+varsdict = {}
+for varn,info in tab.iterrows():
+    curlev = varsdict
+    varlevels = varn.split('.')
+    toplevel = varlevels[0]
+    for lev in varlevels[:-1]:
+        if lev not in curlev:
+            curlev[lev] = {}
+        curlev = curlev[lev]
+    curlev[varlevels[-1]] = info.to_dict() # Units, Description
+    curlev[varlevels[-1]]['Name'] = var_prefixes.get(toplevel,'') + varn
+
+# save
+with open('variable_guide.json','w') as f:
+    json.dump(varsdict, f, indent=2)