Split project tests

.github/workflows/ci_pipeline.yml

@@ -41,9 +41,10 @@ jobs:
     runs-on: ubuntu-latest
 
     strategy:
+      fail-fast: false
       matrix:
-        python: ['3.8', '3.9', '3.10']
         env: ['base', 'fenics', 'mpi4py', 'petsc']
+        python: ['3.8', '3.9', '3.10', '3.11', '3.12']
 
     defaults:
       run:
@@ -60,6 +61,10 @@ jobs:
           create-args: >-
               python=${{ matrix.python }}
 
+      - name: Install additional packages as needed
+        run: |
+          micromamba install -y --file etc/environment-tests.yml --freeze-installed
+
       - name: Run pytest for CPU stuff
         run: |
           echo "print('Loading sitecustomize.py...')
@@ -82,6 +87,77 @@ jobs:
             data_3.10
             coverage_${{ matrix.env }}_3.10.dat
 
+  project_cpu_tests_linux:
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        env: 
+          - AllenCahn_Bayreuth
+          - AsympConv
+          - DAE
+          - FastWaveSlowWave
+          # - GPU
+          - Hamiltonian
+          - matrixPFASST
+          - parallelSDC
+          - parallelSDC_reloaded
+          - PinTSimE
+          - RDC
+          - Resilience
+          - SDC_showdown
+          - Second_orderSDC
+          - soft_failure
+          - TOMS
+        python: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        exclude:
+          - env: parallelSDC
+            python: '3.11'
+          - env: parallelSDC
+            python: '3.12'
+
+    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/${{ matrix.env }}/environment.yml"
+          create-args: >-
+              python=${{ matrix.python }}
+
+      - name: Install additional packages as needed
+        run: |
+          micromamba install -y --file etc/environment-tests.yml --freeze-installed
+
+      - 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/projects/${{ matrix.env }}/tests
+
+      - name: Make coverage report
+        run: |
+          mv data data_${{ matrix.python }}
+          coverage combine
+          mv .coverage coverage_${{ matrix.env }}_${{ matrix.python }}.dat
+
+      - name: Uploading artifacts
+        uses: actions/upload-artifact@v3
+        if: matrix.python == '3.10'
+        with:
+          name: cpu-test-artifacts
+          path: |
+            data_3.10
+            coverage_${{ matrix.env }}_3.10.dat
+
   user_libpressio_tests:
     runs-on: ubuntu-latest
 
@@ -108,7 +184,7 @@ jobs:
           source /opt/spack/share/spack/setup-env.sh
           spack load libpressio
 
-          coverage run -m pytest --continue-on-collection-errors -v --durations=0 pySDC/tests -m libpressio
+          coverage run -m pytest --continue-on-collection-errors -v --durations=0 pySDC/projects/compression/tests -m libpressio
 
       - name: Make coverage report
         run: |
@@ -156,7 +232,7 @@ jobs:
           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
+          coverage run -m pytest --continue-on-collection-errors -v --durations=0 pySDC/projects/Monodomain/tests -m monodomain
 
       - name: Make coverage report
         run: |
@@ -215,6 +291,7 @@ jobs:
     needs:
       - lint
       - user_cpu_tests_linux
+      - project_cpu_tests_linux
       - user_libpressio_tests
       - user_monodomain_tests_linux
 #       - wait_for_gitlab
@@ -230,7 +307,7 @@ jobs:
       - name: Install Conda environment with Micromamba
         uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: "etc/environment-base.yml"
+          environment-file: "etc/environment-postprocess.yml"
 
       - name: Downloading artifacts
         uses: actions/download-artifact@v3

CONTRIBUTING.md

@@ -15,5 +15,6 @@ This follows a specific OOP framework, you can look at the page on [custom imple
 4. [Naming Conventions](./docs/contrib/03_naming_conventions.md)
 5. [Custom Implementations](./docs/contrib/04_custom_implementations.md)
 6. [Documenting Code](./docs/contrib/05_documenting_code.md)
+7. [Adding a project](./docs/contrib/06_new_project.md)
 
 :arrow_left: [Back to main page](./README.md)

docs/contrib/05_documenting_code.md

@@ -90,4 +90,4 @@ A more detailed example is given [here ...](https://sphinxcontrib-napoleon.readt
 
 :arrow_left: [Back to custom implementations](./04_custom_implementations.md) ---
 :arrow_up: [Contributing Summary](./../../CONTRIBUTING.md) ---
-:arrow_right: [Next to a cute picture of cat](https://www.vecteezy.com/photo/2098203-silver-tabby-cat-sitting-on-green-background)
+:arrow_right: [Next to Adding a new project](./06_new_project.md)

docs/contrib/06_new_project.md

@@ -0,0 +1,57 @@
+# Adding a project to pySDC (and automatic testing)
+
+When you do a project with pySDC we appreciate it if you merge it back to the main repository.
+We are committed to keeping your work reproducible and prevent it from fading into oblivion.
+To that end, please write extensive tests for your code and add them to the project.
+See the [contribution guide](./../../CONTRIBUTING.md) for general advice on testing etc.
+This guide will detail only how to add a project to pySDC.
+
+## Add a directory in 'pySDC/projects'
+
+First, create a new directory in `pySDC/projects` with the name of your project.
+The code of the new project should go into that newly created directory.
+
+## Add an environment-file
+
+The testing pipeline uses [micromamba](<https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html>)
+and requires an environment file for setup.
+This includes the dependencies that are required for your project to run.
+The file needs to be named `environment.yml` and needs to follow the structure shown below:
+
+```yaml
+name: pySDC
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - numpy
+```
+
+The list of dependencies can be extended as needed.
+The name should stay `pySDC`. The channels cover most of the usual packages.
+If a package is needed that cannot be found in those channels by conda (or mamba),
+please add the correct channel to the list.
+
+## Add tests to the project
+
+In order to automatically find the tests of your project, please add the tests to a subdirectory called `tests` in the directory of your project.
+Furthermore, the files should start with `test_` and the functions should also start with that.
+For more information see the documentation of pytest on [test discovery](<https://docs.pytest.org/en/8.2.x/explanation/goodpractices.html#tests-as-part-of-application-code>).
+
+## Add the project to the continuous integration pipeline
+
+To run the tests of all projects in parallel, the projects are explicitly mentioned in the CI-file.
+In order to run the tests of your project, please add the name of your project **as your directory is named**
+in the [CI-File](<https://github.com/Parallel-in-Time/pySDC/blob/master/.github/workflows/ci_pipeline.yml>)
+in the job `project_cpu_tests_linux` in the list `strategy/matrix/env`.
+
+## Getting a DOI of pySDC for publication
+
+If your project is published and you need a dedicated pySDC version with a DOI, please get in touch with us and/or open a new issue.
+We will help you with this as soon as possible.
+Note that a final DOI is usually only necessary once a paper is accepted and the final proofs are due.
+We strongly encourage to describe and cite the current version of pySDC already during initial submission, though.
+
+:arrow_left: [Back to Documenting Code](./05_documenting_code.md) ---
+:arrow_up: [Contributing Summary](./../../CONTRIBUTING.md) ---
+:arrow_right: [Next to a cute picture of cat](https://www.vecteezy.com/photo/2098203-silver-tabby-cat-sitting-on-green-background)

etc/environment-base.yml

@@ -9,9 +9,3 @@ dependencies:
   - sympy>=1.0
   - numba>=0.35
   - dill>=0.2.6
-  - pytest
-  - pytest-benchmark
-  - pytest-timeout
-  - pytest-order
-  - coverage[toml]
-  - sphinx

etc/environment-cupy.yml

@@ -7,8 +7,4 @@ dependencies:
   - scipy>=0.17.1
   - matplotlib>=3.0
   - dill>=0.2.6
-  - pytest
-  - pytest-cov
-  - pytest-timeout
-  - pytest-order
   - cupy

etc/environment-fenics.yml

@@ -9,7 +9,3 @@ dependencies:
   - dill>=0.2.6
   - fenics>=2019.1.0
   - mpi4py<=3.1.4
-  - pytest
-  - pytest-cov
-  - pytest-timeout
-  - pytest-order

etc/environment-mpi4py.yml

@@ -5,11 +5,8 @@ channels:
 dependencies:
   - numpy>=1.15.4
   - scipy>=0.17.1
-  - matplotlib>=3.0,<=3.5.3
+  - matplotlib>=3.0
   - dill>=0.2.6
   - mpich
   - mpi4py-fft>=2.0.2
   - mpi4py>=3.0.0
-  - pytest
-  - pytest-cov
-  - pytest-timeout

etc/environment-petsc.yml

@@ -10,7 +10,3 @@ dependencies:
   - mpich
   - petsc4py<3.20
   - mpi4py>=3.0.0
-  - pytest
-  - pytest-cov
-  - pytest-timeout
-  - pytest-order

etc/environment-postprocess.yml

@@ -0,0 +1,12 @@
+name: pySDC
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - coverage[toml]
+  - sphinx
+  - numpy
+  - scipy
+  - matplotlib
+  - dill
+  - numba

etc/environment-tests.yml

@@ -0,0 +1,10 @@
+name: pySDC
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - pytest
+  - pytest-benchmark
+  - pytest-timeout
+  - pytest-order
+  - coverage[toml]

pySDC/playgrounds/12th_PinT_Workshop/environment-tutorial.yml

@@ -5,7 +5,7 @@ channels:
 dependencies:
   - numpy>=1.15.4
   - scipy>=0.17.1
-  - matplotlib>=3.0,<=3.5.3
+  - matplotlib>=3.0
   - dill>=0.2.6
   - mpich
   - mpi4py>=3.0.0

pySDC/projects/AllenCahn_Bayreuth/environment.yml

@@ -0,0 +1,11 @@
+name: pySDC
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - mpi4py>=3.0.0
+  - mpi4py-fft>=2.0.2
+  - matplotlib>=3.0
+  - dill>=0.2.6
+  - scipy>=0.17.1
+

pySDC/projects/AsympConv/environment.yml

@@ -0,0 +1,8 @@
+name: pySDC
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - matplotlib>=3.0
+  - scipy>=0.17.1
+  - dill>=0.2.6

pySDC/projects/DAE/environment.yml

@@ -0,0 +1,8 @@
+name: pySDC
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - numpy
+  - scipy>=0.17.1
+  - dill>=0.2.6

pySDC/tests/test_projects/test_DAE/test_problems.py → pySDC/projects/DAE/tests/test_problems.py

@@ -612,6 +612,7 @@ def test_WSCC9_update_YBus():
     ), 'YBus after line outage does not match with the one it should supposed to!'
 
 
+@pytest.mark.timeout(360)
 @pytest.mark.base
 def test_WSCC9_SDC_detection():
     """

pySDC/projects/FastWaveSlowWave/environment.yml

@@ -0,0 +1,10 @@
+name: pySDC
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - numpy
+  - matplotlib>=3.0
+  - scipy>=0.17.1
+  - sympy>=1.0
+  - dill>=0.2.6

pySDC/projects/Hamiltonian/environment.yml

@@ -0,0 +1,9 @@
+name: pySDC
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - dill>=0.2.6
+  - numpy
+  - matplotlib>=3.0
+  - scipy>=0.17.1

pySDC/projects/PinTSimE/environment.yml

@@ -0,0 +1,9 @@
+name: pySDC
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - numpy
+  - scipy>=0.17.1
+  - dill>=0.2.6
+  - matplotlib>=3.0

pySDC/projects/RDC/environment.yml

@@ -0,0 +1,8 @@
+name: pySDC
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - numpy
+  - dill>=0.2.6
+  - scipy>=0.17.1

pySDC/projects/Resilience/environment.yml

@@ -0,0 +1,11 @@
+name: pySDC
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - mpi4py>=3.0.0
+  - mpi4py-fft>=2.0.2
+  - mpich
+  - matplotlib>=3.0
+  - dill>=0.2.6
+  - scipy>=0.17.1

pySDC/projects/SDC_showdown/environment.yml

@@ -0,0 +1,9 @@
+name: pySDC
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - petsc4py<3.20
+  - matplotlib>=3.0
+  - dill>=0.2.6
+  - scipy>=0.17.1