Merge dev to dev-unstable after 3.5.3 updates

.dockerignore

@@ -0,0 +1,26 @@
+# System, cache and editor files
+**/__pycache__
+**/.DS_Store
+
+.editorconfig
+.idea
+.git
+.github
+.gitignore
+.pytest_cache
+.pre-commit-config.yaml
+.readthedocs.yml
+.coverage
+Procfile
+README.md
+
+# Never bake in environment variables
+.env
+.env*
+google_credentials.json
+# See: https://github.com/google-github-actions/auth/issues/123
+gha-creds-*.json
+gcp-creds-*.json
+
+.devcontainer/.zsh_history
+share/docker

.github/workflows/automated-dev-tests.yml

@@ -50,8 +50,7 @@ jobs:
           products: Simulink
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install numpy "Bokeh>=2.4,!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3"
+          pip install -r requirements.txt
           sudo apt-get update -y
           sudo apt-get install -y libopenblas-dev libopenblas-openmp-dev
       - name: Setup workspace
@@ -137,8 +136,7 @@ jobs:
           cache: 'pip'
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install numpy "Bokeh>=2.4,!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3"
+          pip install -r requirements.txt
           sudo apt-get update -y
           sudo apt-get install -y libopenblas-dev libopenblas-openmp-dev
       - name: Setup workspace
@@ -187,8 +185,7 @@ jobs:
           products: Simulink
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install numpy "Bokeh>=2.4,!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3"
+          pip install -r requirements.txt
           sudo apt-get update -y
           sudo apt-get install -y libopenblas-dev libopenblas-openmp-dev
           sudo apt-get install -y libhdf5-dev libnetcdf-dev libopenmpi-dev libyaml-cpp-dev  # gcovr
@@ -242,8 +239,7 @@ jobs:
           cache: 'pip'
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install numpy "Bokeh>=2.4,!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3"
+          pip install -r requirements.txt
           sudo apt-get update -y
           sudo apt-get install -y libopenblas-dev libopenblas-openmp-dev
           sudo apt-get install -y libhdf5-dev libnetcdf-dev libopenmpi-dev libyaml-cpp-dev
@@ -280,8 +276,7 @@ jobs:
           cache: 'pip'
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install numpy "Bokeh>=2.4,!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3"
+          pip install -r requirements.txt
           sudo apt-get update -y
           sudo apt-get install -y libopenblas-dev libopenblas-openmp-dev
           sudo apt-get install -y libhdf5-dev libnetcdf-dev libopenmpi-dev libyaml-cpp-dev
@@ -318,8 +313,7 @@ jobs:
           cache: 'pip'
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install numpy "Bokeh>=2.4,!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3"
+          pip install -r requirements.txt
           sudo apt-get update -y
           sudo apt-get install -y libopenblas-dev libopenblas-openmp-dev
           sudo apt-get install -y libhdf5-dev libnetcdf-dev libopenmpi-dev libyaml-cpp-dev
@@ -344,7 +338,7 @@ jobs:
   ### BUILD AND TEST JOBS
 
   build-test-uadriver-debug:
-    # UA driver requires -DUA_OUTS, cannot be compiled with other
+    # UA driver used to require -DUA_OUTS
     runs-on: ubuntu-22.04
     steps:
       - name: Checkout
@@ -358,8 +352,7 @@ jobs:
           cache: 'pip'
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install numpy "Bokeh>=2.4,!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3"
+          pip install -r requirements.txt
           sudo apt-get update -y
           sudo apt-get install -y libopenblas-dev
       - name: Setup workspace
@@ -379,7 +372,6 @@ jobs:
             -DVARIABLE_TRACKING=OFF \
             -DBUILD_TESTING:BOOL=ON \
             -DCTEST_PLOT_ERRORS:BOOL=ON \
-            -DCMAKE_Fortran_FLAGS="-DUA_OUTS=ON" \
             ${GITHUB_WORKSPACE}
       - name: Build all
         working-directory: ${{runner.workspace}}/openfast/build
@@ -420,8 +412,7 @@ jobs:
           cache: 'pip'
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install numpy "Bokeh>=2.4,!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3"
+          pip install -r requirements.txt
           sudo apt-get update -y
           sudo apt-get install -y libopenblas-dev libopenblas-openmp-dev
           sudo apt-get install -y libhdf5-dev libnetcdf-dev libopenmpi-dev libyaml-cpp-dev
@@ -478,8 +469,7 @@ jobs:
           cache: 'pip'
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install numpy "Bokeh>=2.4,!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3"
+          pip install -r requirements.txt
           sudo apt-get update -y
           sudo apt-get install -y libopenblas-dev libopenblas-openmp-dev
           sudo apt-get install -y libhdf5-dev libnetcdf-dev libopenmpi-dev libyaml-cpp-dev
@@ -539,8 +529,7 @@ jobs:
           cache: 'pip'
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install numpy "Bokeh>=2.4,!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3" vtk
+          pip install -r requirements.txt
           sudo apt-get update -y
           sudo apt-get install -y libopenblas-dev libopenblas-openmp-dev
           sudo apt-get install -y libhdf5-dev libnetcdf-dev libopenmpi-dev libyaml-cpp-dev
@@ -587,8 +576,7 @@ jobs:
           cache: 'pip'
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install numpy "Bokeh>=2.4,!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3"
+          pip install -r requirements.txt
           sudo apt-get update -y
           sudo apt-get install -y libopenblas-dev libopenblas-openmp-dev
           sudo apt-get install -y libhdf5-dev libnetcdf-dev libopenmpi-dev libyaml-cpp-dev
@@ -721,8 +709,7 @@ jobs:
           cache: 'pip'
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install numpy "Bokeh>=2.4,!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3"
+          pip install -r requirements.txt
           sudo apt-get update -y
           sudo apt-get install -y libopenblas-dev libopenblas-openmp-dev
           sudo apt-get install -y libhdf5-dev libnetcdf-dev libopenmpi-dev libyaml-cpp-dev
@@ -771,8 +758,7 @@ jobs:
           cache: 'pip'
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install numpy "Bokeh>=2.4,!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3"
+          pip install -r requirements.txt
           sudo apt-get update -y
           sudo apt-get install -y libopenblas-dev libopenblas-openmp-dev
           sudo apt-get install -y libhdf5-dev libnetcdf-dev libopenmpi-dev libyaml-cpp-dev
@@ -821,8 +807,7 @@ jobs:
           cache: 'pip'
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install numpy "Bokeh>=2.4,!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3"
+          pip install -r requirements.txt
           sudo apt-get update -y
           sudo apt-get install -y libopenblas-dev libopenblas-openmp-dev
           sudo apt-get install -y libhdf5-dev libnetcdf-dev libopenmpi-dev libyaml-cpp-dev
@@ -871,8 +856,7 @@ jobs:
           cache: 'pip'
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install numpy "Bokeh>=2.4,!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3"
+          pip install -r requirements.txt
           sudo apt-get update -y
           sudo apt-get install -y libopenblas-dev libopenblas-openmp-dev
           sudo apt-get install -y libhdf5-dev libnetcdf-dev libopenmpi-dev libyaml-cpp-dev
@@ -921,8 +905,7 @@ jobs:
           cache: 'pip'
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install numpy "Bokeh>=2.4,!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3"
+          pip install -r requirements.txt
           sudo apt-get update -y
           sudo apt-get install -y libopenblas-dev libopenblas-openmp-dev
           sudo apt-get install -y libhdf5-dev libnetcdf-dev libopenmpi-dev libyaml-cpp-dev
@@ -971,8 +954,7 @@ jobs:
           cache: 'pip'
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install numpy "Bokeh>=2.4,!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3"
+          pip install -r requirements.txt
           sudo apt-get update -y
           sudo apt-get install -y libopenblas-dev libopenblas-openmp-dev
           sudo apt-get install -y libhdf5-dev libnetcdf-dev libopenmpi-dev libyaml-cpp-dev
@@ -1020,8 +1002,7 @@ jobs:
           cache: 'pip'
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install numpy "Bokeh>=2.4,!=3.0.0,!=3.0.1,!=3.0.2,!=3.0.3"
+          pip install -r requirements.txt
           sudo apt-get update -y
           sudo apt-get install -y libopenblas-dev libopenblas-openmp-dev
           sudo apt-get install -y libhdf5-dev libnetcdf-dev libopenmpi-dev libyaml-cpp-dev

.github/workflows/build-docker-image-automatic.yml

@@ -0,0 +1,59 @@
+# This workflow builds an OpenFAST docker image for the linux/amd64 and linux/aarch64 architectures on merge into
+# `main` from a release candidate branch. The image is tagged both with "latest" and the version extracted from the
+# release candidate branch's name (e.g. "rc-3.5.3") before being pushed to the `nrel/openfast` repository. The build
+# cache is stored in GitHub actions.
+name: build-docker-image-automatic
+
+on:
+  release:
+    types:
+      - released
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    timeout-minutes: 300
+    env:
+      DOCKERFILE_PATH: share/docker/Dockerfile
+      DOCKERHUB_REPOSITORY: nrel/openfast
+      GH_REGISTRY: ghcr.io/OpenFAST/openfast
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      # Commenting out until we get the NREL DockerHub credentials
+      # - name: Log in to DockerHub
+      #   uses: docker/login-action@v3
+      #   with:
+      #     username: ${{ secrets.DOCKERHUB_USERNAME }}
+      #     password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.GH_REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract tag from release candidate branch name
+        id: extract-tag
+        run: echo "openfast-tag=$(expr substr "${{ github.head_ref }}" 4 100)" >> $GITHUB_OUTPUT
+
+      - name: Build and push to registry
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: ${{ env.DOCKERFILE_PATH }}
+          platforms: linux/amd64,linux/aarch64
+          tags: |
+            ${{ env.GH_REGISTRY }}:${{ steps.extract-tag.outputs.openfast-tag }},${{ env.DOCKERHUB_REPOSITORY }}:latest
+# ${{ env.DOCKERHUB_REPOSITORY }}:${{ steps.extract-tag.outputs.openfast-tag }},${{ env.DOCKERHUB_REPOSITORY }}:latest
+          push: true
+          cache-from: type=gha
+          cache-to: type=gha,mode=max

.github/workflows/build-docker-image-manual.yml

@@ -0,0 +1,72 @@
+# This manually-triggered workflow builds OpenFAST docker images for the linux/amd64 and linux/aarch64 architectures for
+# the specified git ref (this can be a branch, tag, or commit hash). The image is tagged with the given tag and pushed
+# to the `nrel/openfast` repository. The build cache is stored in GitHub actions.
+name: build-docker-image-manual
+
+on:
+  workflow_dispatch:
+    inputs:
+      tag:
+        description: 'Tag for Docker image (excluding the "v" prefix e.g. 3.5.3)'
+        required: true
+      ref:
+        description: 'Branch, tag, or commit SHA to build from'
+        required: true
+        default: main
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    timeout-minutes: 300
+    env:
+      DOCKERFILE_PATH: share/docker/Dockerfile
+      DOCKERFILE_PERMALINK: https://raw.githubusercontent.com/OpenFAST/openfast/main/share/docker/Dockerfile
+      DOCKERHUB_REPOSITORY: nrel/openfast
+      GH_REGISTRY: ghcr.io/OpenFAST/openfast
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.inputs.ref }}
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      # Commenting out until we get the NREL DockerHub credentials
+      # - name: Log in to DockerHub
+      #   uses: docker/login-action@v3
+      #   with:
+      #     username: ${{ secrets.DOCKERHUB_USERNAME }}
+      #     password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.GH_REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # The updated Dockerfile is only available in the repository at the tag v3.5.3 and above. To build versions of
+      # OpenFAST that are below this version, the updated Dockerfile from that tag of the repository has to be acquired
+      # before building. For versions >= v3.5.3, the Dockerfile is already there so this step does nothing.
+      - name: Get Dockerfile for versions < 3.5.3
+        run: |
+          if [ ! -f ${{ env.DOCKERFILE_PATH }} ]; \
+          then wget -O ${{ env.DOCKERFILE_PATH }} ${{ env.DOCKERFILE_PERMALINK }}; \
+          fi
+
+      - name: Build and push to registry
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: ${{ env.DOCKERFILE_PATH }}
+          platforms: linux/amd64,linux/aarch64
+          tags: |
+            ${{ env.GH_REGISTRY }}:${{ github.event.inputs.tag }}
+# ${{ env.DOCKERHUB_REPOSITORY }}:${{ github.event.inputs.tag }}
+          push: true
+          cache-from: type=gha
+          cache-to: type=gha,mode=max

.github/workflows/test-build-docker-image.yml

@@ -0,0 +1,38 @@
+# This workflow tests building an OpenFAST docker image for the linux/amd64 architecture on push to a release candidate
+# branch. The build cache is stored in GitHub actions.
+name: test-build-docker-image
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  test-build:
+    if: startsWith(github.head_ref, 'rc-')
+    runs-on: ubuntu-latest
+    timeout-minutes: 300
+    env:
+      DOCKERFILE_PATH: share/docker/Dockerfile
+      DOCKERHUB_REPOSITORY: nrel/openfast
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Extract tag from release candidate branch name
+        id: extract-tag
+        run: echo "openfast-tag=$(expr substr "${{ github.head_ref }}" 4 100)" >> $GITHUB_OUTPUT
+
+      - name: Test building docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: ${{ env.DOCKERFILE_PATH }}
+          platforms: linux/amd64
+          tags: ${{ env.DOCKERHUB_REPOSITORY }}:${{ steps.extract-tag.outputs.openfast-tag }}
+          push: false
+          cache-from: type=gha
+          cache-to: type=gha,mode=max