Include gitlab-sync in master branch

.github/workflows/ci_pipeline.yml

@@ -37,30 +37,12 @@ jobs:
         run: |
           flakeheaven lint --benchmark pySDC
 
-#   mirror_to_gitlab:
-
-#     runs-on: ubuntu-latest
-
-#     steps:
-#       - name: Checkout
-#         uses: actions/checkout@v1
-
-#       - name: Mirror
-#         uses: jakob-fritz/github2lab_action@main
-#         env:
-#           MODE: 'mirror' # Either 'mirror', 'get_status', or 'both'
-#           GITLAB_TOKEN: ${{ secrets.GITLAB_SECRET_H }}
-#           FORCE_PUSH: "true"
-#           GITLAB_HOSTNAME: "codebase.helmholtz.cloud"
-#           GITLAB_PROJECT_ID: "3525"
-#           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
   user_cpu_tests_linux:
     runs-on: ubuntu-latest
 
     strategy:
       matrix:
-        python: ['3.7', '3.8', '3.9', '3.10']
+        python: ['3.8', '3.9', '3.10']
         env: ['base', 'fenics', 'mpi4py', 'petsc']
 
     defaults:
@@ -144,7 +126,53 @@ jobs:
           path: |
             data_libpressio
             coverage_libpressio_3.10.dat
-
+
+  user_monodomain_tests_linux:
+    runs-on: ubuntu-latest
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Install Conda environment with Micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: "pySDC/projects/Monodomain/etc/environment-monodomain.yml"
+          create-args: >-
+              python=3.10
+
+      - name: Compile C++ ionic models
+        env:
+          IONIC_MODELS_PATH: "pySDC/projects/Monodomain/problem_classes/ionicmodels/cpp"
+        run: |
+          c++ -O3 -Wall -shared -std=c++11 -fPIC -fvisibility=hidden $(python3 -m pybind11 --includes) ${IONIC_MODELS_PATH}/bindings_definitions.cpp -o ${IONIC_MODELS_PATH}/ionicmodels$(python3-config --extension-suffix)
+
+      - name: Run pytest for CPU stuff
+        run: |
+          echo "print('Loading sitecustomize.py...')
+          import coverage
+          coverage.process_startup() " > sitecustomize.py
+          coverage run -m pytest --continue-on-collection-errors -v --durations=0 pySDC/tests -m monodomain
+
+      - name: Make coverage report
+        run: |
+          mv data data_monodomain
+          coverage combine
+          mv .coverage coverage_monodomain_3.10.dat
+
+      - name: Uploading artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: cpu-test-artifacts
+          path: |
+            data_monodomain
+            coverage_monodomain_3.10.dat
+
+
 #  user_cpu_tests_macos:
 #    runs-on: macos-12
 #
@@ -169,24 +197,6 @@ jobs:
 #        run: |
 #          pytest --continue-on-collection-errors -v --durations=0 pySDC/tests -m ${{ matrix.env }}
 
-
-#   wait_for_gitlab:
-#     runs-on: ubuntu-latest
-
-#     needs:
-#       - mirror_to_gitlab
-
-#     steps:
-#       - name: Wait
-#         uses: jakob-fritz/github2lab_action@main
-#         env:
-#           MODE: 'get_status' # Either 'mirror', 'get_status', or 'both'
-#           GITLAB_TOKEN: ${{ secrets.GITLAB_SECRET_H }}
-#           FORCE_PUSH: "true"
-#           GITLAB_HOSTNAME: "codebase.helmholtz.cloud"
-#           GITLAB_PROJECT_ID: "3525"
-#           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
 # #      - name: Get and prepare artifacts
 # #        run: |
 # #          pipeline_id=$(curl --header "PRIVATE-TOKEN: ${{ secrets.GITLAB_SECRET_H }}" --silent "https://gitlab.hzdr.de/api/v4/projects/3525/repository/commits/${{ github.head_ref || github.ref_name }}" | jq '.last_pipeline.id')
@@ -206,6 +216,7 @@ jobs:
       - lint
       - user_cpu_tests_linux
       - user_libpressio_tests
+      - user_monodomain_tests_linux
 #       - wait_for_gitlab
 
     defaults:
@@ -346,4 +357,3 @@ jobs:
 #          rm -rf data
 #          unzip artifacts.zip
 #
-

.github/workflows/gitlab_ci.yml

@@ -0,0 +1,116 @@
+---
+
+name: Mirror to Gitlab to trigger CI
+
+on:
+  push:
+  pull_request_target:
+  schedule:
+    - cron: '1 5 2 * *'
+
+jobs:
+  check_permission:
+    runs-on: ubuntu-latest
+    if: >-
+        (github.repository_owner == 'Parallel-in-Time') &&
+        ((github.event_name == 'push') ||
+         (github.event_name == 'schedule') ||
+         ((github.event_name == 'pull_request_target') &&
+          (contains(github.event.pull_request.labels.*.name, 'gitlab-mirror'))
+         )
+        )
+    steps:
+      - name: Query permissions of triggering actor
+        id: query_permission_triggering_actor
+        if: github.event_name == 'pull_request_target'
+        uses: actions-cool/check-user-permission@v2
+        with:
+          username: ${{ github.triggering_actor }}
+          require: 'write'
+          token: ${{ secrets.GITHUB_TOKEN }}
+      - name: Interpret the queried result
+        if: github.event_name == 'pull_request_target'
+        run: |
+          echo "Current permission level is ${{ steps.query_permission_triggering_actor.outputs.user-permission }}"
+          echo "Job originally triggered by ${{ github.actor }}"
+          echo "Checking permission returned ${{ steps.query_permission_triggering_actor.outputs.require-result }}"
+          if ${{ steps.query_permission_triggering_actor.outputs.require-result }}
+            then
+              echo 'Permissions granted'
+              exit 0
+            else
+              echo 'Not enough permissions. Please ask a member of Parallel-in-Time to rerun the job.'
+              exit 1
+          fi
+      - name: Pass if workflow from push or schedule
+        if: >-
+          (github.event_name == 'push') ||
+          (github.event_name == 'schedule')
+        run: exit 0
+      # - name: Fail for other triggers
+      #   if: >-
+      #     (github.event_name != 'push') &&
+      #     (github.event_name != 'schedule') &&
+      #     (github.event_name != 'pull_request_target')
+      #   run: exit 1
+
+  mirror_to_gitlab:
+    runs-on: ubuntu-latest
+    if: >-
+        (github.repository_owner == 'Parallel-in-Time') &&
+        ((github.event_name == 'push') ||
+         (github.event_name == 'schedule') ||
+         ((github.event_name == 'pull_request_target') &&
+          (contains(github.event.pull_request.labels.*.name, 'gitlab-mirror'))
+         )
+        )
+    needs:
+      - check_permission
+    steps:
+      - name: set proper sha
+        run: |
+          echo "${{ github.event_name }}"
+          if [ "${{ github.event_name }}" == 'push' ] || [ "${{ github.event_name }}" == 'schedule' ]
+          then
+            echo "USED_SHA=${{ github.sha }}" >> "$GITHUB_ENV"
+          fi
+          if [ "${{ github.event_name }}" == 'pull_request_target' ]
+          then
+            echo "USED_SHA=${{ github.event.pull_request.head.sha }}" >> "$GITHUB_ENV"
+          fi
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          ref: "${{ env.USED_SHA }}"
+          persist-credentials: false
+      - name: check if merge is possible (merge is used for testing)
+        if: github.event_name == 'pull_request_target'
+        run: |
+          if $(git rev-parse --is-shallow-repository); then
+            git fetch --unshallow
+          else
+            git fetch
+          fi
+          echo "Checkout of ${{ github.base_ref }}"
+          git checkout "${{ github.base_ref }}"
+          echo "Git pull"
+          git pull
+          MIRROR_BRANCH="TEMPORARY_MERGE_PR_${{ github.event.number }}"
+          echo MIRROR_BRANCH="$MIRROR_BRANCH" >> $GITHUB_ENV
+          echo "Create new branch $MIRROR_BRANCH and check it out"
+          git checkout -b "$MIRROR_BRANCH"
+          echo "Setting git committer info, so that merge-commit can be created"
+          git config user.email "[email protected]"
+          git config user.name "Sync bot"
+          echo "Merge the two parts of the Merge-Request to test the resulting version"
+          git merge "${{ github.event.pull_request.head.sha }}"
+      - name: Mirror and wait for Gitlab-CI
+        uses: jakob-fritz/[email protected]
+        env:
+          MODE: 'all'  # Either 'mirror', 'get_status', 'get_artifact', or 'all'
+          GITLAB_TOKEN: ${{ secrets.GITLAB_SECRET }}
+          FORCE_PUSH: "true"
+          GITLAB_HOSTNAME: "gitlab.jsc.fz-juelich.de"
+          GITLAB_PROJECT_ID: "6029"
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          MIRROR_BRANCH: ${{ env.MIRROR_BRANCH }}

.gitignore

@@ -8,6 +8,8 @@ data/*
 step_*.png
 *.pkl
 *.swp
+*_data.json
+!_dataRef.json
 
 # Created by https://www.gitignore.io
 
@@ -158,3 +160,7 @@ Temporary Items
 .vscode
 *.cpp
 pySDC/playgrounds/FEniCS/jitfailure-dolfin_expression_fc28530d435fa2de045af3312fc07c3b/recompile.sh
+
+# videos
+*.mp4
+*.mkv

.gitlab-ci.yml

@@ -1,8 +1,84 @@
+---
+
 stages:
   - test
   - benchmark
   - upload
 
+
+variables:
+  JUWELS_ACCOUNT: "cstma"
+
+
+prepare_JUWELS:
+  stage: benchmark
+  rules:
+    - if: $CI_COMMIT_MESSAGE !~ /.*\[CI-no-benchmarks\]/
+  tags:
+    - jacamar
+    - juwels
+    - login
+    - shell
+  script:
+    - mkdir -p benchmarks
+    # load the latest Python module (currently 3.11)
+    - module --force purge
+    - module load Stages/2024
+    - module load GCC
+    - module load OpenMPI
+    - module load FFTW
+    - module load mpi4py
+    - module load SciPy-Stack
+    - module load CuPy
+    - pip install -e .
+    - pip install pytest-benchmark coverage
+
+
+test_JUWELS:
+  stage: benchmark
+  needs:
+    - prepare_JUWELS
+  rules:
+    - if: $CI_COMMIT_MESSAGE !~ /.*\[CI-no-benchmarks\]/
+  tags:
+    - jacamar
+    - juwels
+    - login
+    - shell
+  parallel:
+    matrix:
+      - SHELL_SCRIPT: ['benchmark', 'cupy']
+  artifacts:
+    when: always
+    paths:
+      - coverage_*.dat
+      - sbatch.err
+      - sbatch.out
+  before_script:
+    - mkdir -p benchmarks
+    # load the latest Python module (currently 3.11)
+    - module --force purge
+    - module load Stages/2024
+    - module load GCC
+    - module load OpenMPI
+    - module load FFTW
+    - module load mpi4py
+    - module load SciPy-Stack
+    - module load CuPy
+  script:
+    # - touch benchmarks/output.json
+    - echo $SYSTEMNAME
+    - sbatch --wait etc/juwels_${SHELL_SCRIPT}.sh
+    - touch .coverage.empty
+    - python -m coverage combine
+    - mv .coverage coverage_${SHELL_SCRIPT}.dat
+  after_script:
+    - echo "Following Errors occured:"
+    - cat sbatch.err
+    - echo "Following was written to stdout:"
+    - cat sbatch.out
+
+
 #test_kit:
 #  image: rcaspart/micromamba-cuda
 #  stage: benchmark
@@ -64,6 +140,9 @@ stages:
 benchmark:
   image: mambaorg/micromamba
   stage: benchmark
+  when: manual
+  tags:
+    - docker
   rules:
     - if: $CI_COMMIT_MESSAGE !~ /.*\[CI-no-benchmarks\]/
   artifacts:

CHANGELOG.md

@@ -2,6 +2,8 @@
 
 :arrow_left: [Back to main page](./README.md)
 
+-   January 24, 2024: Version 5.4.0 contains the code for the [second order SDC paper](https://arxiv.org/abs/2310.08352) by [\@ikrom96git](https://github.com/ikrom96git). It also has some changes to the FEniCS
+    part, including correct treatment of boundary conditions and first steps with FEniCS-x.
 -   July 28, 2023: For Version 5.3 a lot of pull requests got merged, thanks to [\@brownbaerchen](https://github.com/brownbaerchen),
     [\@tlunet](https://github.com/tlunet), [\@lisawim](https://github.com/lisawim), [\@ikrom96git](https://github.com/ikrom96git) for all the contributions.
     Besides the usual bugfixing and polishing, `pySDC` now comes with linear multistep methods, classical Runge Kutta methods, DAE sweepers, and more/improved projects.

CITATION.cff

@@ -21,9 +21,9 @@ authors:
     orcid: https://orcid.org/0000-0002-8869-0784
     affiliation: "Hamburg University of Technology, Institute of Mathematics, 21073 Hamburg, Germany"
 
-version: 5.3.0
+version: 5.4.3
 doi: 10.5281/zenodo.594191
-date-released: 2023-07-25
+date-released: 2024-03-27
 keywords: 
   - "parallel-in-time"
   - "spectral deferred corrections"