Pytest integrated

.ci_fedora.sh

@@ -23,7 +23,7 @@ then
     test . != ".$2" && mpi="$2" || mpi=openmpi
     time $cmd pull ghcr.io/boutproject/bout-container-base:main
     time $cmd create --cap-add=SYS_PTRACE --security-opt seccomp=unconfined \
-	 --shm-size 256M \
+	 --shm-size 1G \
          --name mobydick ghcr.io/boutproject/bout-container-base:main \
 	     /tmp/BOUT-dev/.ci_fedora.sh $mpi
     time $cmd cp ${TRAVIS_BUILD_DIR:-$(pwd)} mobydick:/tmp/BOUT-dev
@@ -37,9 +37,15 @@ test . != ".$1" && mpi="$1" || mpi=openmpi
     cp -a /tmp/BOUT-dev /home/test/
     . /etc/profile.d/modules.sh
     module load mpi/${1}-x86_64
-    export OMPI_MCA_rmaps_base_oversubscribe=yes
+    sudo dnf install -y python3-pytest python3-pytest-xdist
+    # OpenMPI Oversubscription Overrides
+    export OMPI_MCA_rmaps_base_oversubscribe=1
+    export OMPI_MCA_hwloc_base_binding_policy=none
+    export OMPI_MCA_rmaps_base_mapping_policy=core:OVERSUBSCRIBE
+    export PRTE_MCA_rmaps_default_mapping_policy=core:OVERSUBSCRIBE
     export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe
     export TRAVIS=true
+    export CI=true
     # Try limiting openmp threads
     export FLEXIBLAS=NETLIB
     export MKL_NUM_THREADS=1

.ci_with_cmake.sh

@@ -13,7 +13,7 @@ fi
 
 cmake --build build --target build-check -j 2
 cd build
-ctest --output-on-failure --timeout 300
+cmake --build . --target check
 
 export LD_LIBRARY_PATH=/home/runner/local/lib:$LD_LIBRARY_PATH
 

.github/workflows/tests.yml

@@ -133,39 +133,48 @@ jobs:
           echo CMake options: ${{ matrix.config.cmake_options }}
 
       - name: Install dependencies
-        run: sudo apt update &&
-             sudo apt install -y
-                 libfftw3-dev
-                 libnetcdf-dev
-                 libnetcdf-c++4-dev
-                 netcdf-bin
-                 python3
-                 python3-pip
-                 python3-pytest
-                 python3-numpy
-                 python3-scipy
-                 lcov
-                 openmpi-bin
-                 libopenmpi-dev
-                 petsc-dev
-                 slepc-dev
-                 liblapack-dev
-                 libparpack2-dev
-                 libhypre-dev
+        run: |
+          sudo apt update
+          sudo apt install -y \
+              libfftw3-dev \
+              libnetcdf-dev \
+              libnetcdf-c++4-dev \
+              netcdf-bin \
+              lcov \
+              openmpi-bin \
+              libopenmpi-dev \
+              petsc-dev \
+              slepc-dev \
+              liblapack-dev \
+              libparpack2-dev \
+              libhypre-dev
 
       - uses: actions/checkout@v6
         with:
           submodules: true
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
       - uses: actions/setup-python@v6
         with:
           python-version: '3.x'
-          cache: 'pip'
 
-      - name: Install pip packages
+      - name: Setup virtual environment with uv
         run: |
-          python -m pip install --upgrade pip setuptools
-          python -m pip install -r requirements.txt
+          # uv sync automatically creates a .venv and installs the groups
+          uv sync --no-dev --group pytest --inexact
+
+          # Install the core requirements into the same venv
+          uv pip install -r requirements.txt
+
+          # Put the venv in the PATH
+          echo "$GITHUB_WORKSPACE/.venv/bin" >> $GITHUB_PATH
+
+          # Force CMake to recognize the virtual environment
+          echo "VIRTUAL_ENV=$GITHUB_WORKSPACE/.venv" >> $GITHUB_ENV
 
       - name: Cache Zenodo test data
         uses: actions/cache@v5
@@ -190,7 +199,9 @@ jobs:
         run: BUILD_ADIOS2=${{ matrix.config.build_adios2 }} ./.build_adios2_for_ci.sh
 
       - name: Build BOUT++
-        run: UNIT_ONLY=${{ matrix.config.unit_only }} ./.ci_with_cmake.sh ${{ matrix.config.cmake_options }}
+        run: |
+          UNIT_ONLY=${{ matrix.config.unit_only }} ./.ci_with_cmake.sh ${{ matrix.config.cmake_options }} \
+              -DPython3_EXECUTABLE=$GITHUB_WORKSPACE/.venv/bin/python
 
   Fedora:
     # This is its own job as it doesn't use most of the steps of the

CMakeLists.txt

@@ -750,6 +750,7 @@ option(
   OFF
 )
 if(BOUT_TESTS)
+  set(CMAKE_CTEST_ARGUMENTS "--output-on-failure" "--timeout" "300")
   enable_testing()
   # Targets for just building the tests
   # Tests need to add themselves as dependencies to these targets
@@ -777,7 +778,8 @@ if(BOUT_TESTS)
   endif()
 
   add_custom_target(
-    check-integrated-tests COMMAND ctest -R "test-" --output-on-failure
+    check-integrated-tests
+    COMMAND bash "${PROJECT_BINARY_DIR}/tests/run_integrated_tests.sh"
   )
   add_dependencies(check-integrated-tests build-check-integrated-tests)
 
@@ -791,6 +793,30 @@ if(BOUT_TESTS)
     add_dependencies(check check-unit-tests)
   endif()
 
+  # Copy the pytest config file
+  configure_file(
+    "${PROJECT_SOURCE_DIR}/tests/conftest.py"
+    "${PROJECT_BINARY_DIR}/tests/conftest.py"
+  )
+
+  # Copy the pyproject.toml file
+  configure_file(
+    "${PROJECT_SOURCE_DIR}/pyproject.toml"
+    "${PROJECT_BINARY_DIR}/pyproject.toml"
+  )
+
+  # Copy the pytest config file for the boutpp tests
+  configure_file(
+    "${PROJECT_SOURCE_DIR}/tests/integrated/test-boutpp/conftest.py"
+    "${PROJECT_BINARY_DIR}/tests/integrated/test-boutpp/conftest.py"
+  )
+
+  # Copy the pytest shell script
+  configure_file(
+    "${PROJECT_SOURCE_DIR}/tests/run_integrated_tests.sh"
+    "${PROJECT_BINARY_DIR}/tests/run_integrated_tests.sh" @ONLY
+  )
+
 endif()
 
 option(BOUT_BUILD_EXAMPLES "Build the examples" ON)

cmake/BOUT++functions.cmake

@@ -172,7 +172,9 @@ endfunction()
 #
 function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
   set(options USE_RUNTEST USE_DATA_BOUT_INP)
-  set(oneValueArgs EXECUTABLE_NAME PROCESSORS DOWNLOAD DOWNLOAD_NAME)
+  set(oneValueArgs EXECUTABLE_NAME PROCESSORS DOWNLOAD DOWNLOAD_NAME
+                   PYTHON_TEST_FILE
+  )
   set(multiValueArgs SOURCES EXTRA_FILES REQUIRES CONFLICTS TESTARGS
                      EXTRA_DEPENDS
   )
@@ -256,16 +258,29 @@ function(bout_add_integrated_or_mms_test BUILD_CHECK_TARGET TESTNAME)
 
   # Set the actual test command
   if(BOUT_TEST_OPTIONS_USE_RUNTEST)
-    add_test(NAME ${TESTNAME} COMMAND ./runtest ${BOUT_TEST_OPTIONS_TESTARGS})
+    if(BOUT_TEST_OPTIONS_PYTHON_TEST_FILE)
+      # It's an integrated test with a specific python file
+      add_test(NAME ${TESTNAME}
+               COMMAND pytest ${BOUT_TEST_OPTIONS_PYTHON_TEST_FILE}
+                       ${BOUT_TEST_OPTIONS_TESTARGS}
+      )
+    else()
+      # It's an MMS test still using the 'runtest' script
+      add_test(NAME ${TESTNAME} COMMAND ./runtest ${BOUT_TEST_OPTIONS_TESTARGS})
+    endif()
+
     set_tests_properties(
       ${TESTNAME} PROPERTIES ENVIRONMENT
                              PYTHONPATH=${BOUT_PYTHONPATH}:$ENV{PYTHONPATH}
     )
-    bout_copy_file(runtest)
   else()
     add_test(NAME ${TESTNAME} COMMAND ${TESTNAME} ${BOUT_TEST_OPTIONS_TESTARGS})
   endif()
 
+  if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/runtest)
+    bout_copy_file(runtest)
+  endif()
+
   set_tests_properties(
     ${TESTNAME} PROPERTIES PROCESSORS ${BOUT_TEST_OPTIONS_PROCESSORS}
                            PROCESSOR_AFFINITY ON
@@ -286,11 +301,23 @@ endfunction()
 
 # Add a new integrated test. See `bout_add_integrated_or_mms_test` for arguments
 function(bout_add_integrated_test TESTNAME)
+  # Construct the Python test filename
+  string(REGEX REPLACE "^(test-)?(.+)$" "test_\\2.py" TEST_FILENAME
+                       "${TESTNAME}"
+  )
+  string(REPLACE "-" "_" TEST_FILENAME "${TEST_FILENAME}")
+  string(REPLACE "test_test_" "test_" TEST_FILENAME "${TEST_FILENAME}")
+
   bout_add_integrated_or_mms_test(
-    build-check-integrated-tests ${TESTNAME} ${ARGV}
+    build-check-integrated-tests ${TESTNAME} PYTHON_TEST_FILE ${TEST_FILENAME}
+    ${ARGV}
   )
-endfunction()
 
+  # Only copy the file if the test wasn't skipped due to missing requirements
+  if(TARGET ${TESTNAME})
+    bout_copy_file(${TEST_FILENAME})
+  endif()
+endfunction()
 # Add a new MMS test. See `bout_add_integrated_or_mms_test` for arguments
 function(bout_add_mms_test TESTNAME)
   bout_add_integrated_or_mms_test(build-check-mms-tests ${TESTNAME} ${ARGV})

manual/sphinx/developer_docs/contributing.rst

@@ -196,6 +196,23 @@ formatters and run them according to the next section. Usually this is just:
 
 which will format just the parts of C++ files that have changed since ``next``.
 
+The "integrated" tests are run via pytest . To install the required packages using `uv
+<https://docs.astral.sh/uv/>`_ (from the top of your BOUT++ directory):
+
+.. code-block:: console
+
+    uv sync --group pytest --inexact
+
+They can be run via cmake in the same way as the other tests:
+
+.. code-block:: console
+
+    cmake --build build --target check-integrated-tests
+
+or directly, by running the script `tests/run_integrated_tests.sh`.
+
+For test isolation, pytest automatically copies each test to a temporary directory when running them.
+
 Formatting and Linters
 ~~~~~~~~~~~~~~~~~~~~~~
 

pyproject.toml

@@ -5,6 +5,9 @@ requires = []
 build-backend = "backend"
 backend-path = ["tools/pylib/_boutpp_build/"]
 
+[tool.pytest.ini_options]
+console_output_style = "plain"
+
 [dependency-groups]
 dev = [
      "cmake~=4.2",
@@ -19,6 +22,10 @@ dev = [
      "sphinx-lint~=1.0",
      "sync-with-uv~=0.5.0",
 ]
+pytest = [
+     "pytest~=8.4",
+     "pytest-xdist~=3.8",
+]
 maint = [
       "pygithub~=2.8",
       "ruamel-yaml~=0.19",

tests/conftest.py

@@ -0,0 +1,60 @@
+import pytest
+import shutil
+import os
+import subprocess
+import time
+from pathlib import Path
+
+
+def pytest_configure(config):
+    config.addinivalue_line(
+        "markers",
+        "serial: mark that the test should not be run concurrently with other. ",
+    )
+
+
+@pytest.fixture
+def test_dir(request) -> Path:
+    return Path(request.fspath).parent
+
+
+@pytest.fixture(scope="function", autouse=True)
+def copy_and_cwd_to_unique_tmp_dir(request, tmp_path_factory, monkeypatch):
+    """
+    For each test function, create a unique temporary copy of the test directory
+    and change cwd to it.
+    """
+
+    test_file_dir = Path(request.fspath).parent
+
+    if not test_file_dir.is_dir():
+        pytest.fail(f"Expected test directory '{test_file_dir}' not found")
+
+    # Create a unique temp dir for this test
+    run_dir = tmp_path_factory.mktemp(test_file_dir.name)
+
+    # Copy the original test directory into it
+    shutil.copytree(test_file_dir, run_dir, dirs_exist_ok=True)
+
+    # Change working directory to the copy
+    monkeypatch.chdir(run_dir)
+
+
+@pytest.fixture
+def assert_success_in_shell(test_dir):
+
+    def inner_function(command: str):
+        # MPI oversubscribe for communications test
+        os.environ["OMPI_MCA_rmaps_base_oversubscribe"] = "1"  # Allows 18 procs
+        start = time.time()
+        result = subprocess.run(
+            command, shell=True, capture_output=True, text=True, timeout=600
+        )
+        elapsed = time.time() - start
+        assert result.returncode == 0, (
+            f"Failed after {elapsed:.3f}s in {test_dir}\n"
+            f"Stderr: {result.stderr}\n"
+            f"Output: {result.stdout}"
+        )
+
+    return inner_function