Merge branch 'rm-snakemake' into 'master'

Refactored Snakemake tests into pytest

See merge request ogs/ogs!5058

.pre-commit-config.yaml

@@ -80,7 +80,7 @@ repos:
       - id: vale
         args: [--output=line, --minAlertLevel=error]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.4.2"
+    rev: "v0.5.0"
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]
@@ -90,7 +90,7 @@ repos:
   # Run this hook (and all other manual hooks if any) with:
   # pre-commit run --hook-stage manual
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.4.2"
+    rev: "v0.5.0"
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]

Applications/Python/CMakeLists.txt

@@ -1,11 +1,58 @@
 # wheel: Install into Python module root dir (enables 'import ogs.simulator')
 set(_py_install_location ogs)
+set(_py_build_location ogs)
 if(NOT OGS_BUILD_WHEEL)
     set(_py_install_location
         "${CMAKE_INSTALL_LIBDIR}/python${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}/site-packages/ogs"
     )
+    set(_py_build_location "${PROJECT_BINARY_DIR}/site-packages/ogs")
 endif()
+
 add_subdirectory(ogs)
 add_subdirectory(ogs.simulator)
 add_subdirectory(ogs.mesh)
 add_subdirectory(ogs.callbacks)
+
+if(OGS_USE_PIP)
+    set_target_properties(
+        simulator mesh callbacks PROPERTIES LIBRARY_OUTPUT_DIRECTORY
+                                            ${_py_build_location}
+    )
+    file(
+        COPY ogs/.
+        DESTINATION ${_py_build_location}
+        PATTERN "__pycache__" EXCLUDE
+        PATTERN "CMakeLists.txt" EXCLUDE
+    )
+    # Fails with libGitInfoLib.so: undefined symbol: __asan_report_load8
+    if(NOT ENABLE_ASAN)
+        add_test(
+            NAME pytest
+            COMMAND
+                ${CMAKE_COMMAND} -DEXECUTABLE=pytest
+                "-DEXECUTABLE_ARGS=-c;${PROJECT_SOURCE_DIR}/pyproject.toml" # Quoted
+                                                                            # because
+                # passed as list see https://stackoverflow.com/a/33248574/80480
+                -DBINARY_PATH=${_binary_path}
+                -DWORKING_DIRECTORY=${PROJECT_SOURCE_DIR}
+                "-DLOG_ROOT=${PROJECT_BINARY_DIR}/logs"
+                "-DLOG_FILE_BASENAME=pytest.txt"
+                "-DTEST_COMMAND_IS_EXPECTED_TO_SUCCEED=TRUE" -P
+                ${PROJECT_SOURCE_DIR}/scripts/cmake/test/AddTestWrapper.cmake
+        )
+        set_tests_properties(
+            pytest PROPERTIES LABELS "default;python" COST 10
+        )
+
+        add_dependencies(
+            ctest
+            GMSH2OGS
+            Layers2Grid
+            AddFaultToVoxelGrid
+            ExtractBoundary
+            vtkdiff
+            generateStructuredMesh
+        )
+    endif()
+
+endif()

Applications/Python/ogs/CMakeLists.txt

@@ -1,3 +1,18 @@
+# cmake-lint: disable=E1126
+set(_config_content
+    "OGS_USE_PETSC = '@OGS_USE_PETSC@'" "OGS_VERSION = '@OGS_VERSION@'"
+    "OGS_USE_MKL = '@OGS_USE_MKL@'"
+)
+string(REPLACE ";" "\n" _config_content "${_config_content}")
+set(_config_file ${PROJECT_BINARY_DIR}/site-packages/ogs/config.py)
+file(CONFIGURE OUTPUT ${_config_file} CONTENT "${_config_content}")
+
+if(OGS_BUILD_WHEEL)
+    install(FILES ${_config_file} DESTINATION ${SKBUILD_PLATLIB_DIR}/ogs)
+else()
+    install(FILES ${_config_file} DESTINATION ${_py_install_location})
+endif()
+
 if(OGS_BUILD_WHEEL)
     return()
 endif()

Applications/Python/ogs/__init__.py

@@ -1 +1,13 @@
+import importlib.util
+import os
+
 from ._internal.wrap_cli_tools import cli  # noqa: F401
+
+if "PEP517_BUILD_BACKEND" in os.environ:
+    # on wheel build config.py is not generated at the beginning of the build
+    # but later after CMake has run
+    config_spec = importlib.util.find_spec(".config", package="ogs")
+    if config_spec is not None:
+        from .config import *  # noqa: F403
+else:
+    from .config import *  # noqa: F403

Applications/Python/ogs/_internal/provide_ogs_cli_tools_via_wheel.py

@@ -6,10 +6,6 @@
 
 from . import OGS_USE_PATH
 
-# Here, we assume that this script is installed, e.g., in a virtual environment
-# alongside a "bin" directory.
-OGS_BIN_DIR = Path(__file__).parent.parent.parent / "bin"
-
 binaries_list = [
     "addDataToRaster",
     "AddElementQuality",
@@ -112,14 +108,20 @@ def ogs_with_args(argv):
 
 
 if "PEP517_BUILD_BACKEND" not in os.environ:
+    # Here, we assume that this script is installed, e.g., in a virtual environment
+    # alongside a "bin" directory.
+    OGS_BIN_DIR = Path(__file__).parent.parent.parent / "bin"  # installed wheel
+    if not OGS_BIN_DIR.exists():
+        OGS_BIN_DIR = OGS_BIN_DIR.parent  # build directory
+
     if platform.system() == "Windows":
         os.add_dll_directory(OGS_BIN_DIR)
 
     def _program(name, args):
         exe = OGS_BIN_DIR / name
         if OGS_USE_PATH:
             exe = name
-        print(f"OGS_USE_PATH is true: {name} from $PATH is used!")
+            print(f"OGS_USE_PATH is true: {name} from $PATH is used!")
         return subprocess.run([exe] + args).returncode  # noqa: PLW1510
 
     FUNC_TEMPLATE = """def {0}(): raise SystemExit(_program("{0}", sys.argv[1:]))"""

Applications/Python/ogs/_internal/wrap_cli_tools.py

@@ -6,7 +6,9 @@
 
 # Here, we assume that this script is installed, e.g., in a virtual environment
 # alongside a "bin" directory.
-OGS_BIN_DIR = Path(__file__).parent.parent.parent / "bin"
+OGS_BIN_DIR = Path(__file__).parent.parent.parent / "bin"  # installed wheel
+if not OGS_BIN_DIR.exists():
+    OGS_BIN_DIR = OGS_BIN_DIR.parent  # build directory
 
 
 class CLI:
@@ -32,7 +34,7 @@ def ogs(self, *args, **kwargs):
         >>> cli = CLI()
         >>> cli.ogs("--help") # prints a help text
         ...
-        >>> cli.ogs(help=None) # special, does the same
+        >>> cli.ogs(help=True) # flags without any additional value can be set to True
         ...
 
         A more useful example. The following will create a line mesh:
@@ -52,12 +54,25 @@ def ogs(self, *args, **kwargs):
     @staticmethod
     def _format_kv(kwargs):
         for key, v in kwargs.items():
+            # Convert None to True
+            if v is None:
+                # TODO: Remove after 2025/08
+                print(
+                    f"Deprecation warning: Setting {v} to `None` is deprecated, set to `True` instead!"
+                )
+                v = True  # noqa: PLW2901
+
+            # If value is False then ignore
+            if isinstance(v, bool) and not v:
+                continue
+
             if len(key) == 1:
                 yield f"-{key}"
             else:
                 yield f"--{key}"
 
-            if v is not None:
+            # Pass value if not bool
+            if not isinstance(v, bool):
                 yield f"{v}"
 
     @staticmethod
@@ -74,6 +89,7 @@ def run_cmd(*args, **kwargs):
             cmdline = CLI._get_cmdline(cmd, *args, **kwargs)
             return subprocess.call(cmdline)
 
+        # TODO: Only arguments with underscores work. Arguments with dashes not.
         run_cmd.__doc__ = f"""
             This function wraps the commandline tool {attr} for easy use from Python.
 
@@ -89,7 +105,7 @@ def run_cmd(*args, **kwargs):
             >>> cli = CLI()
             >>> cli.{attr}("--help") # prints a help text
             ...
-            >>> cli.{attr}(help=None) # special, does the same
+            >>> cli.ogs(help=True) # flags without any additional value can be set to True
             ...
 
             A more useful example. The following will create a line mesh: