Use the GitHub container registry to store images

.github/actions/install/struphy_in_container/action.yml

@@ -0,0 +1,26 @@
+name: "Install Struphy in Container"
+
+runs:
+  using: composite
+  steps:
+    - name: Git branch name
+      id: git-branch-name
+      uses: EthanSK/git-branch-name-action@v1
+    - name: Echo the branch name
+      shell: bash
+      run: echo "Branch name ${GIT_BRANCH_NAME}"
+    - name: Install struphy
+      shell: bash
+      run: |
+          ls / -a
+          which python3
+          cd /struphy_c_
+          git status
+          git fetch origin
+          echo ${GIT_BRANCH_NAME}
+          git checkout ${GIT_BRANCH_NAME}
+          git pull
+          source env_c_/bin/activate
+          which python3
+          struphy -p
+          pip install -e ".[phys,mpi,doc]"

.github/workflows/reusable-testing.yml

@@ -0,0 +1,95 @@
+name: Testing
+
+on:
+  workflow_call:
+    inputs:
+      os:
+        required: true
+        type: string
+
+jobs:
+  test:
+    runs-on: ${{ inputs.os }}
+    env:
+      OMPI_MCA_rmaps_base_oversubscribe: 1 # Linux
+      PRRTE_MCA_rmaps_base_oversubscribe: 1 # MacOS
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+        compile-language: ["fortran", "c"]
+        test-type: ["unit", "model", "quickstart", "tutorials"]
+
+    steps:
+      # Checkout the repository
+      - name: Checkout code
+        uses: actions/checkout@v5
+
+      # https://docs.github.com/en/actions/tutorials/build-and-test-code/python
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # You can test your matrix by printing the current Python version
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+
+      # Cache pip dependencies
+      - name: Cache pip
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      # Install prereqs
+      # I don't think it's possible to use a single action for this because
+      # we can't use ${inputs.os} in an if statement, so we have to use two different actions.
+      - name: Install prerequisites (Ubuntu)
+        if: inputs.os == 'ubuntu-latest'
+        uses: ./.github/actions/install/ubuntu-latest
+
+      - name: Install prerequisites (macOS)
+        if: inputs.os == 'macos-latest'
+        uses: ./.github/actions/install/macos-latest
+
+      # Check that mpirun oversubscribing works, doesn't work unless OMPI_MCA_rmaps_base_oversubscribe==1
+      - name: Test mpirun
+        run: |
+          echo $OMPI_MCA_rmaps_base_oversubscribe
+          echo $PRRTE_MCA_rmaps_base_oversubscribe
+          pip install mpi4py -U
+          which mpirun
+          mpirun --version
+          mpirun --oversubscribe --report-bindings -n 4 python -c "from mpi4py import MPI; comm=MPI.COMM_WORLD; print(f'Hello from rank {comm.Get_rank()} of {comm.Get_size()}'); assert comm.Get_size()==4"
+
+      # Clone struphy-ci-testing
+      - name: Install struphy
+        uses: ./.github/actions/install/install-struphy
+        env:
+          FC: ${{ env.FC }}
+          CC: ${{ env.CC }}
+          CXX: ${{ env.CXX }}
+
+      # Compile
+      - name: Compile kernels
+        uses: ./.github/actions/compile
+
+      # Run tests
+      - name: Run unit tests
+        if: matrix.test-type == 'unit'
+        uses: ./.github/actions/tests/unit
+
+      - name: Run model tests
+        if: matrix.test-type == 'model'
+        uses: ./.github/actions/tests/models
+
+      - name: Run quickstart tests
+        if: matrix.test-type == 'quickstart'
+        uses: ./.github/actions/tests/quickstart
+
+      - name: Run tutorials
+        if: matrix.test-type == 'tutorials'
+        uses: ./.github/actions/tests/tutorials

.github/workflows/static_analysis.yml

@@ -121,15 +121,10 @@ jobs:
       - name: Checkout the code
         uses: actions/checkout@v4
 
-      # TODO: Remove --select I once all errors are fixed
-      - name: ruff check --select I
+      - name: Linting with ruff
         run: |
           pip install ruff
-          ruff check --select I
-
-      - name: ruff format --check
-        run: |
-          ruff format --check
+          ruff check --select I src/**/*.py
 
   # pylint:
   #   runs-on: ubuntu-latest

.github/workflows/test-PR-models.yml

@@ -0,0 +1,72 @@
+name: PR - model tests in Container
+
+on:
+  pull_request:
+    branches:
+      - main
+      - devel
+  workflow_dispatch:
+
+defaults:
+  run:
+    shell: bash
+
+permissions:
+  contents: read
+
+# concurrency:
+#   group: "pages"
+#   cancel-in-progress: false
+
+jobs:
+  model-tests-in-container-with-struphy:
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/struphy-hub/struphy/ubuntu-with-struphy:latest
+      credentials:
+        username: spossann
+        password: ${{ secrets.GHCR_TOKEN }}
+    steps:
+
+      - name: Check for dockerenv file
+        run: (ls /.dockerenv && echo Found dockerenv) || (echo No dockerenv)
+
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Install Struphy in Container
+        uses: ./.github/actions/install/struphy_in_container
+
+      - name: Compile Struphy
+        run: |
+          which python3
+          source /struphy_c_/env_c_/bin/activate
+          which python3
+          struphy compile --status
+          struphy compile
+
+      - name: Model tests
+        shell: bash
+        run: |
+          which python3
+          source /struphy_c_/env_c_/bin/activate
+          which python3
+          struphy compile --status
+          struphy test LinearMHD
+          struphy test toy
+          struphy test models 
+          struphy test verification 
+
+      - name: Model tests with  MPI
+        shell: bash
+        run: |
+          which python3
+          source /struphy_c_/env_c_/bin/activate
+          which python3
+          struphy compile --status
+          struphy test models 
+          struphy test models --mpi 2
+          struphy test verification --mpi 1
+          struphy test verification --mpi 4
+          struphy test verification --mpi 4 --nclones 2
+          struphy test VlasovAmpereOneSpecies --mpi 2 --nclones 2

.github/workflows/test-PR-unit.yml

@@ -0,0 +1,68 @@
+name: PR - unit tests in Container
+
+on:
+  pull_request:
+    branches:
+      - main
+      - devel
+  workflow_dispatch:
+
+defaults:
+  run:
+    shell: bash
+
+permissions:
+  contents: read
+
+# concurrency:
+#   group: "pages"
+#   cancel-in-progress: false
+
+jobs:
+  unit-tests-in-container-with-struphy:
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/struphy-hub/struphy/ubuntu-with-struphy:latest
+      credentials:
+        username: spossann
+        password: ${{ secrets.GHCR_TOKEN }}
+    steps:
+
+      - name: Check for dockerenv file
+        run: (ls /.dockerenv && echo Found dockerenv) || (echo No dockerenv)
+
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Install Struphy in Container
+        uses: ./.github/actions/install/struphy_in_container
+
+      - name: Compile Struphy
+        run: |
+          which python3
+          source /struphy_c_/env_c_/bin/activate
+          which python3
+          struphy compile --status
+          struphy compile
+
+      - name: Run unit tests with MPI
+        shell: bash
+        run: |
+          which python3
+          source /struphy_c_/env_c_/bin/activate
+          which python3
+          struphy compile --status
+          struphy --refresh-models
+          struphy test unit --mpi 2
+
+      - name: Run unit tests
+        shell: bash
+        run: |
+          which python3
+          source /struphy_c_/env_c_/bin/activate
+          which python3
+          struphy compile --status
+          struphy --refresh-models
+          pip show mpi4py
+          pip uninstall -y mpi4py
+          struphy test unit

.github/workflows/ubuntu-latest.yml

@@ -1,20 +1,11 @@
-name: Ubuntu
+name: Ubuntu latest - cronjob
 on:
-  push:
-    branches:
-      - main
-      - devel
-  pull_request:
-    branches:
-      - main
-      - devel
-
-# concurrency:
-#   group: ${{ github.ref }}
-#   cancel-in-progress: true
+  schedule:
+    # run at 1 a.m. on Sunday
+    - cron: "0 1 * * 0" 
 
 jobs:
   ubuntu-latest-build:
-    uses: ./.github/workflows/testing.yml
+    uses: ./.github/workflows/reusable-testing.yml
     with:
       os: ubuntu-latest

docker/almalinux-latest.dockerfile

@@ -1,12 +1,13 @@
-# Here is how to build the image and upload it to the mpcdf gitlab registry:
+# Here is how to build the image and upload it to the Github package registry:
 #
 # We suppose you are in the struphy repo directory. 
-# Start the docker engine and run "docker login" with the following token:
+# Start the docker engine and login to the Github package registry using a github personal acces token (classic):
 #
-# TOKEN=gldt-CgMRBMtePbSwdWTxKw4Q; echo "$TOKEN" | docker login gitlab-registry.mpcdf.mpg.de -u gitlab+deploy-token-162 --password-stdin
+# export CR_PAT=YOUR_TOKEN
+# echo $CR_PAT | docker login ghcr.io -u USERNAME --password-stdin
 # docker info
-# docker build -t gitlab-registry.mpcdf.mpg.de/struphy/struphy/almalinux-latest --provenance=false -f docker/almalinux-latest.dockerfile .
-# docker push gitlab-registry.mpcdf.mpg.de/struphy/struphy/almalinux-latest
+# docker build -t ghcr.io/struphy-hub/struphy/almalinux-with-reqs:latest --provenance=false -f docker/almalinux-latest.dockerfile .
+# docker push ghcr.io/struphy-hub/struphy/almalinux-with-reqs:latest
 
 FROM almalinux:latest
 
@@ -42,9 +43,6 @@ RUN echo "Installing additional tools..." \
     && export CC=`which gcc` \ 
     && export CXX=`which g++`
 
-# create new working dir
-WORKDIR /install_struphy_here/
-
 # allow mpirun as root
 ENV OMPI_ALLOW_RUN_AS_ROOT=1
 ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1

docker/fedora-latest.dockerfile

@@ -1,12 +1,13 @@
-# Here is how to build the image and upload it to the mpcdf gitlab registry:
+# Here is how to build the image and upload it to the Github package registry:
 #
 # We suppose you are in the struphy repo directory. 
-# Start the docker engine and run "docker login" with the following token:
+# Start the docker engine and login to the Github package registry using a github personal acces token (classic):
 #
-# TOKEN=gldt-CgMRBMtePbSwdWTxKw4Q; echo "$TOKEN" | docker login gitlab-registry.mpcdf.mpg.de -u gitlab+deploy-token-162 --password-stdin
+# export CR_PAT=YOUR_TOKEN
+# echo $CR_PAT | docker login ghcr.io -u USERNAME --password-stdin
 # docker info
-# docker build -t gitlab-registry.mpcdf.mpg.de/struphy/struphy/fedora-latest --provenance=false -f docker/fedora-latest.dockerfile .
-# docker push gitlab-registry.mpcdf.mpg.de/struphy/struphy/fedora-latest
+# docker build -t ghcr.io/struphy-hub/struphy/fedora-with-reqs:latest --provenance=false -f docker/fedora-latest.dockerfile .
+# docker push ghcr.io/struphy-hub/struphy/fedora-with-reqs:latest
 
 FROM fedora:latest
 
@@ -34,9 +35,6 @@ RUN echo "Installing additional tools..." \
     && export CC=`which gcc` \ 
     && export CXX=`which g++` 
 
-    # create new working dir
-WORKDIR /install_struphy_here/
-
 # allow mpirun as root
 ENV OMPI_ALLOW_RUN_AS_ROOT=1
 ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1