Merge remote-tracking branch 'origin/develop' into DLC_RefactorCaseIn…

…puts

.github/workflows/CI_WEIS.yml

@@ -16,14 +16,10 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest", "macOS-latest", "windows-latest"]
-        python-version: ["3.9","3.10","3.11"]
+        os: ["ubuntu-latest", "macOS-13", "macOS-latest", "windows-latest"] # mac13 is intel, mac-14 arm
+        python-version: ["3.9","3.10","3.11","3.12"]
 
     steps:
-      #- name: Setup GNU Fortran
-      #  #  if: false == contains( matrix.os, 'windows')
-      #  uses: awvwgk/setup-fortran@main
-
       - uses: actions/checkout@v4
 
       - name: Install conda/mamba
@@ -38,6 +34,11 @@ jobs:
           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
 
       - name: Add dependencies ubuntu specific
         if: false == contains( matrix.os, 'windows')
@@ -46,7 +47,7 @@ jobs:
       
       - name: Add test packages
         run: |
-          conda install -y pytest pytest-cov coveralls
+          conda install -y pytest pytest-cov coveralls 
             
       - name: Show custom environment
         run: |
@@ -56,17 +57,29 @@ jobs:
       # Install WEIS
       - name: Install WEIS
         run: |
-          pip install -e . -v
+          python -m pip install --no-deps -e . -v
 
       # 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
-        run: |
-          pytest --collect-only weis 
+      #- name: List tests
+      #  run: |
+      #    pytest --collect-only weis 
 
       # Run all tests within WEIS, but not computationally expensive examples
       - name: Run tests within WEIS
@@ -76,10 +89,8 @@ jobs:
       # Run coveralls
       - name: Run coveralls
         if: contains( matrix.os, 'ubuntu') && contains( matrix.python-version, '3.11')
-        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
+        #uses: coverallsapp/github-action@v2
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          coveralls --service=github

.github/workflows/run_exhaustive_examples.yml

@@ -17,7 +17,7 @@ jobs:
       fail-fast: true
       matrix:
         os: ["ubuntu-latest"] #, "macOS-latest"]
-        python-version: ["3.9","3.10", "3.11"]
+        python-version: ["3.9","3.10", "3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v4
@@ -39,7 +39,11 @@ jobs:
       - name: Add dependencies ubuntu specific
         if: false == contains( matrix.os, 'windows')
         run: |
-          conda install -y petsc4py mpi4py openmpi
+          conda install -y petsc4py mpi4py openmpi pyoptsparse
+      
+      - name: Add test packages
+        run: |
+          conda install -y pytest pytest-cov coveralls treon 
 
       - name: Show custom environment
         run: |
@@ -53,7 +57,7 @@ jobs:
       # Install WEIS
       - name: Install WEIS
         run: |
-          pip install -e .
+          python -m pip install --no-deps -e . -v
 
       # Test walkthrough notebook
       - name: Test postprocessing notebooks

README.md

@@ -35,7 +35,7 @@ The core WEIS modules are:
 
 ## Installation
 
-On laptop and personal computers, 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.  WEIS 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 the [Miniforge3 distribution](https://github.com/conda-forge/miniforge?tab=readme-ov-file#miniforge3), which is much more lightweight and more easily solves for the package dependencies.  WEIS is currently supported on Linux, Mac, and Windows (natively or with the Linux sub-system (WSL)).
+On laptop and personal computers, 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.  WEIS 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 the [Miniforge3 distribution](https://github.com/conda-forge/miniforge?tab=readme-ov-file#miniforge3), which is much more lightweight and more easily solves for the package dependencies.  Sometimes, using `mamba` in place of `conda` with this distribution speeds up the installation process. WEIS is currently supported on Linux, MAC and Windows Sub-system for Linux (WSL). Installing WEIS on native Windows is not yet supported, but planned in 2024.
 
 The installation instructions below use the environment name, "weis-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`.
 
@@ -44,32 +44,35 @@ The installation instructions below use the environment name, "weis-env," but an
         module purge
         module load conda        
 
-1.  Setup and activate the Anaconda environment from a command prompt:
+1.  Setup and activate the Anaconda environment from a prompt (WSL terminal on Windows or Terminal.app on Mac)
 
         conda config --add channels conda-forge
-        conda env create --name weis-env -f https://raw.githubusercontent.com/WISDEM/WEIS/develop/environment.yml
+        conda install git
+        git clone https://github.com/WISDEM/WEIS.git
+        cd WEIS
+        git checkout branch_name                         # (Only if you want to switch branches, say "develop")
+        conda env create --name weis-env -f environment.yml
         conda activate weis-env                          # (if this does not work, try source activate weis-env)
-        conda install -y petsc4py mpi4py pyoptsparse     # (Mac / Linux only)   
 
 
-2. Clone the repository and install the software
+2. Add in final packages and install the software
 
-        git clone https://github.com/WISDEM/WEIS.git
-        cd WEIS
-        git checkout branch_name                         # (Only if you want to switch branches, say "develop")
+        conda install -y petsc4py mpi4py pyoptsparse     # (Mac / Linux only)
         pip install -e .
 
 3. Instructions specific for DOE HPC system Eagle.  Before executing the setup script, do:
 
         module load comp-intel intel-mpi mkl
         module unload gcc
-        pip install -e .
+        pip install --no-deps -e . -v
 
 **NOTE:** To use WEIS again after installation is complete, you will always need to activate the conda environment first with `conda activate weis-env` (or `source activate weis-env`). On Eagle, make sure to reload the necessary modules
 
+For Windows users, we recommend installing `git` and the `m264` packages in separate environments as some of the libraries appear to conflict such that WISDEM cannot be successfully built from source.  The `git` package is best installed in the `base` environment.
+
 ## Developer guide
 
-If you plan to contribute code to WEIS, please first consult the [developer guide](https://weis.readthedocs.io/en/latest/how_to_contribute_code.html).  You are also likely to want to install some of the compiled WEIS dependencies (OpenFAST or WISDEM or pyHAMS or ROSCO) from a local copy instead of relying on the conda packages.
+If you plan to contribute code to WEIS, please first consult the [developer guide](https://weis.readthedocs.io/en/latest/how_to_contribute_code.html).
 
 ## Feedback