Merge branch 'refactor-py-module' into 'master'

Python wheels for module and ogs binaries See merge request ogs/ogs!4263
ufz · Sep 19, 2022 · 5d0ac0c · 5d0ac0c
2 parents 93bb8a9 + dfd918f
commit 5d0ac0c
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Showing 37 changed files with 550 additions and 98 deletions.
diff --git a/.gitignore b/.gitignore
@@ -38,4 +38,9 @@ CMakeUserPresets.json
 nohup.out
 
 /Documentation/.vale
+
+# Python build
+/_skbuild
+*.egg-info/
+/wheelhouse
 .ipynb_checkpoints
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -37,6 +37,7 @@ include:
   - local: "/scripts/ci/jobs/build-win.yml"
   - local: "/scripts/ci/jobs/build-mac.yml"
   - local: "/scripts/ci/jobs/build-container.yml"
+  - local: "/scripts/ci/jobs/build-wheels.yml"
   - local: "/scripts/ci/jobs/jupyter.yml"
   - local: "/scripts/ci/jobs/code-quality.yml"
   - local: "/scripts/ci/jobs/code-coverage.yml"

diff --git a/Applications/CLI/CMakeLists.txt b/Applications/CLI/CMakeLists.txt
@@ -45,31 +45,6 @@ if(OGS_USE_PYTHON)
                $<$<BOOL:${BUILD_SHARED_LIBS}>:PRIVATE
                OGS_BUILD_SHARED_LIBS>
     )
-
-    # Create OpenGeoSys python module
-    # https://pybind11.readthedocs.io/en/stable/compiling.html#building-with-cmake
-    if(OGS_BUILD_PYTHON_MODULE)
-        pybind11_add_module(
-            OpenGeoSys MODULE ogs_python_module.cpp
-            CommandLineArgumentParser.cpp
-        )
-
-        # lld linker strips out PyInit_OpenGeoSys symbol. Use standard linker.
-        get_target_property(_link_options OpenGeoSys LINK_OPTIONS)
-        if(_link_options)
-            list(REMOVE_ITEM _link_options -fuse-ld=lld)
-            set_target_properties(
-                OpenGeoSys PROPERTIES LINK_OPTIONS "${_link_options}"
-            )
-        endif()
-
-        target_link_libraries(
-            OpenGeoSys PRIVATE ApplicationsLib BaseLib GitInfoLib tclap
-                               pybind11::pybind11
-        )
-
-        install(TARGETS OpenGeoSys LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
-    endif()
 endif()
 
 ogs_add_executable(ogs ogs.cpp CommandLineArgumentParser.cpp)
@@ -94,28 +69,6 @@ target_link_libraries(
 add_test(NAME ogs_no_args COMMAND ogs)
 set_tests_properties(ogs_no_args PROPERTIES WILL_FAIL TRUE LABELS "default")
 
-if(OGS_BUILD_PYTHON_MODULE AND NOT (WIN32 AND "${CMAKE_BUILD_TYPE}" STREQUAL
-                                              "Release")
-)
-    # TODO: does not work on Windows Release
-    add_test(
-        NAME ogs_python_module
-        COMMAND
-            ${Python_EXECUTABLE}
-            ${CMAKE_CURRENT_SOURCE_DIR}/ogs_python_module.py
-            ${CMAKE_SOURCE_DIR}/Tests/Data/Parabolic/LiquidFlow/Flux/cube_1e3_calculatesurfaceflux.prj
-    )
-    set_tests_properties(
-        ogs_python_module
-        PROPERTIES
-            LABELS
-            "default"
-            ENVIRONMENT_MODIFICATION
-            PYTHONPATH=path_list_append:$<TARGET_FILE_DIR:OpenGeoSys>:${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}
-            DISABLED
-            $<NOT:$<TARGET_EXISTS:LiquidFlow>>
-    )
-endif()
 # ---- Installation ----
 install(TARGETS ogs RUNTIME DESTINATION bin)
 

diff --git a/Applications/CLI/ogs_python_module.py b/Applications/CLI/ogs_python_module.py
diff --git a/Applications/CMakeLists.txt b/Applications/CMakeLists.txt
@@ -19,3 +19,7 @@ endif() # OGS_BUILD_CLI
 if(OGS_USE_INSITU)
     add_subdirectory(InSituLib)
 endif()
+
+if(OGS_BUILD_PYTHON_MODULE)
+    add_subdirectory(Python)
+endif()
diff --git a/Applications/Python/CMakeLists.txt b/Applications/Python/CMakeLists.txt
@@ -0,0 +1 @@
+add_subdirectory(ogs.simulator)
diff --git a/Applications/Python/ogs.simulator/CMakeLists.txt b/Applications/Python/ogs.simulator/CMakeLists.txt
@@ -0,0 +1,21 @@
+# Create OpenGeoSys python module
+# https://pybind11.readthedocs.io/en/stable/compiling.html#building-with-cmake
+pybind11_add_module(
+    simulator MODULE ogs_python_module.cpp
+    ../../CLI/CommandLineArgumentParser.cpp
+)
+
+# lld linker strips out PyInit_OpenGeoSys symbol. Use standard linker.
+get_target_property(_link_options simulator LINK_OPTIONS)
+if(_link_options)
+    list(REMOVE_ITEM _link_options -fuse-ld=lld)
+    set_target_properties(simulator PROPERTIES LINK_OPTIONS "${_link_options}")
+endif()
+
+target_link_libraries(
+    simulator PRIVATE ApplicationsLib BaseLib CMakeInfoLib GitInfoLib tclap
+)
+target_include_directories(simulator PRIVATE ../../CLI)
+
+# Install into root dir (in Python module, enables 'import ogs.simulator')
+install(TARGETS simulator LIBRARY DESTINATION .)
diff --git a/Applications/CLI/ogs_python_module.cpp → ...ython/ogs.simulator/ogs_python_module.cpp b/Applications/CLI/ogs_python_module.cpp → ...ython/ogs.simulator/ogs_python_module.cpp
@@ -122,8 +122,9 @@ void finalize()
 }
 
 /// python module name is OpenGeoSys
-PYBIND11_MODULE(OpenGeoSys, m)
+PYBIND11_MODULE(simulator, m)
 {
+    m.attr("__name__") = "ogs.simulator";
     m.doc() = "pybind11 ogs example plugin";
     m.def("initialize", &initOGS, "init OGS");
     m.def("currentTime", &currentTime, "get current OGS time");

diff --git a/Applications/Python/ogs/__init__.py b/Applications/Python/ogs/__init__.py
diff --git a/Applications/Python/ogs/_internal/__init__.py b/Applications/Python/ogs/_internal/__init__.py
diff --git a/Applications/Python/ogs/_internal/provide_ogs_cli_tools_via_wheel.py b/Applications/Python/ogs/_internal/provide_ogs_cli_tools_via_wheel.py
@@ -0,0 +1,80 @@
+import os
+import platform
+import subprocess
+import sys
+
+binaries_list = [
+    "addDataToRaster",
+    "AddElementQuality",
+    "AddFaultToVoxelGrid",
+    "AddLayer",
+    "appendLinesAlongPolyline",
+    "AssignRasterDataToMesh",
+    "checkMesh",
+    "ComputeNodeAreasFromSurfaceMesh",
+    "computeSurfaceNodeIDsInPolygonalRegion",
+    "constructMeshesFromGeometry",
+    "convertGEO",
+    "convertToLinearMesh",
+    "convertVtkDataArrayToVtkDataArray",
+    "CreateBoundaryConditionsAlongPolylines",
+    "createIntermediateRasters",
+    "createLayeredMeshFromRasters",
+    "createMeshElemPropertiesFromASCRaster",
+    "createNeumannBc",
+    "createQuadraticMesh",
+    "createRaster",
+    "editMaterialID",
+    "ExtractBoundary",
+    "ExtractMaterials",
+    "ExtractSurface",
+    "generateGeometry",
+    "generateMatPropsFromMatID",
+    "generateStructuredMesh",
+    "geometryToGmshGeo",
+    "GMSH2OGS",
+    "GocadSGridReader",
+    "GocadTSurfaceReader",
+    "identifySubdomains",
+    "IntegrateBoreholesIntoMesh",
+    "Layers2Grid",
+    "MapGeometryToMeshSurface",
+    "Mesh2Raster",
+    "MoveGeometry",
+    "MoveMesh",
+    "moveMeshNodes",
+    "mpmetis",
+    "NodeReordering",
+    "ogs",
+    "OGS2VTK",
+    "partmesh",
+    "PVD2XDMF",
+    "queryMesh",
+    "Raster2Mesh",
+    "RemoveGhostData",
+    "removeMeshElements",
+    "ResetPropertiesInPolygonalRegion",
+    "reviseMesh",
+    "scaleProperty",
+    "swapNodeCoordinateAxes",
+    "TecPlotTools",
+    "tetgen",
+    "TIN2VTK",
+    "VTK2OGS",
+    "VTK2TIN",
+    "vtkdiff",
+    "Vtu2Grid",
+]
+
+if "PEP517_BUILD_BACKEND" not in os.environ:
+    OGS_BIN_DIR = os.path.join(os.path.join(os.path.dirname(__file__), "..", "bin"))
+
+    if platform.system() == "Windows":
+        os.add_dll_directory(OGS_BIN_DIR)
+
+    def _program(name, args):
+        return subprocess.run([os.path.join(OGS_BIN_DIR, name)] + args).returncode
+
+    FUNC_TEMPLATE = """def {0}(): raise SystemExit(_program("{0}", sys.argv[1:]))"""
+    for f in binaries_list:
+        exec(FUNC_TEMPLATE.format(f))
diff --git a/Applications/Utils/GeoTools/addDataToRaster.cpp b/Applications/Utils/GeoTools/addDataToRaster.cpp
@@ -24,6 +24,7 @@
 #include "GeoLib/AABB.h"
 #include "GeoLib/Point.h"
 #include "GeoLib/Raster.h"
+#include "InfoLib/GitInfo.h"
 
 double compute2DGaussBellCurveValues(GeoLib::Point const& point,
                                      GeoLib::AABB const& aabb)
@@ -51,7 +52,14 @@ double computeSinXSinY(GeoLib::Point const& point, GeoLib::AABB const& aabb)
 
 int main(int argc, char* argv[])
 {
-    TCLAP::CmdLine cmd("Add values to raster.", ' ', "0.1");
+    TCLAP::CmdLine cmd(
+        "Add values to raster.\n\n"
+        "OpenGeoSys-6 software, version " +
+            GitInfoLib::GitInfo::ogs_version +
+            ".\n"
+            "Copyright (c) 2012-2022, OpenGeoSys Community "
+            "(http://www.opengeosys.org)",
+        ' ', GitInfoLib::GitInfo::ogs_version);
 
     TCLAP::ValueArg<std::string> out_raster_arg(
         "o",

diff --git a/Applications/Utils/GeoTools/createRaster.cpp b/Applications/Utils/GeoTools/createRaster.cpp
@@ -20,11 +20,18 @@
 #include "GeoLib/AABB.h"
 #include "GeoLib/Point.h"
 #include "GeoLib/Raster.h"
+#include "InfoLib/GitInfo.h"
 
 int main(int argc, char* argv[])
 {
-    TCLAP::CmdLine cmd("Create a raster where every pixel is zero.", ' ',
-                       "0.1");
+    TCLAP::CmdLine cmd(
+        "computeSurfaceNodeIDsInPolygonalRegion\n\n"
+        "OpenGeoSys-6 software, version " +
+            GitInfoLib::GitInfo::ogs_version +
+            ".\n"
+            "Copyright (c) 2012-2022, OpenGeoSys Community "
+            "(http://www.opengeosys.org)",
+        ' ', GitInfoLib::GitInfo::ogs_version);
 
     TCLAP::ValueArg<std::string> output_arg("o", "output",
                                             "Name of the output raster (*.asc)",

diff --git a/Applications/Utils/MeshEdit/appendLinesAlongPolyline.cpp b/Applications/Utils/MeshEdit/appendLinesAlongPolyline.cpp
@@ -50,7 +50,7 @@ int main(int argc, char* argv[])
         "the name of the geometry file");
     cmd.add(geoFileArg);
 
-    TCLAP::ValueArg<std::string> gmsh_path_arg("g", "gmsh-path",
+    TCLAP::ValueArg<std::string> gmsh_path_arg("", "gmsh-path",
                                                "the path to the gmsh binary",
                                                false, "", "path as string");
     cmd.add(gmsh_path_arg);

diff --git a/Applications/Utils/MeshGeoTools/computeSurfaceNodeIDsInPolygonalRegion.cpp b/Applications/Utils/MeshGeoTools/computeSurfaceNodeIDsInPolygonalRegion.cpp
@@ -94,7 +94,7 @@ int main(int argc, char* argv[])
         true, "", "file name of input geometry");
     cmd.add(geo_in);
 
-    TCLAP::ValueArg<std::string> gmsh_path_arg("g", "gmsh-path",
+    TCLAP::ValueArg<std::string> gmsh_path_arg("", "gmsh-path",
                                                "the path to the gmsh binary",
                                                false, "", "path as string");
     cmd.add(gmsh_path_arg);

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -4,12 +4,9 @@ cmake_minimum_required(VERSION 3.22)
 project(OGS-6)
 
 option(OGS_USE_PYTHON "Interface with Python" ON)
-include(CMakeDependentOption)
-cmake_dependent_option(
-    OGS_BUILD_PYTHON_MODULE "Should the OGS Python module be built?" ON
-    "OGS_USE_PYTHON" OFF
-)
+option(OGS_BUILD_PYTHON_MODULE "Should the OGS Python module be built?" ON)
 
+include(CMakeDependentOption)
 include(scripts/cmake/DownloadCpmCache.cmake)
 include(scripts/cmake/CPM.cmake)
 include(scripts/cmake/CMakeSetup.cmake)

diff --git a/CMakePresets.json b/CMakePresets.json
@@ -187,6 +187,39 @@
         "OGS_USE_PYTHON": "OFF",
         "OGS_USE_UNITY_BUILDS": "OFF"
       }
+    },
+    {
+      "name": "wheel",
+      "inherits": "release",
+      "cacheVariables": {
+        "HDF5_USE_STATIC_LIBRARIES": "ON",
+        "OGS_BUILD_HDF5": "ON",
+        "OGS_USE_PYTHON": "OFF",
+        "OGS_BUILD_PYTHON_MODULE": "ON",
+        "OGS_BUILD_TESTING": "OFF",
+        "OGS_INSTALL_DEPENDENCIES": "OFF",
+        "OGS_USE_PIP": "OFF",
+        "OGS_USE_MFRONT": "ON",
+        "BUILD_SHARED_LIBS": "ON"
+      },
+      "condition": {
+        "type": "notEquals",
+        "lhs": "${hostSystemName}",
+        "rhs": "Windows"
+      }
+    },
+    {
+      "name": "wheel-win",
+      "inherits": "wheel",
+      "cacheVariables": {
+        "OGS_USE_MFRONT": "OFF",
+        "OGS_BUILD_PROCESS_TH2M": "OFF"
+      },
+      "condition": {
+        "type": "equals",
+        "lhs": "${hostSystemName}",
+        "rhs": "Windows"
+      }
     }
   ],
   "buildPresets": [
@@ -270,6 +303,14 @@
     {
       "name": "ci-no-unity",
       "configurePreset": "ci-no-unity"
+    },
+    {
+      "name": "wheel",
+      "configurePreset": "wheel"
+    },
+    {
+      "name": "wheel-win",
+      "configurePreset": "wheel-win"
     }
   ],
   "testPresets": [

diff --git a/MaterialLib/SolidModels/Ehlers.cpp b/MaterialLib/SolidModels/Ehlers.cpp
@@ -842,6 +842,9 @@ SolidEhlers<DisplacementDim>::getInternalVariables() const
 template class SolidEhlers<2>;
 template class SolidEhlers<3>;
 
+template struct StateVariables<2>;
+template struct StateVariables<3>;
+
 template <>
 MathLib::KelvinVector::KelvinMatrixType<3> sOdotS<3>(
     MathLib::KelvinVector::KelvinVectorType<3> const& v)

diff --git a/MaterialLib/SolidModels/Ehlers.h b/MaterialLib/SolidModels/Ehlers.h
@@ -24,11 +24,10 @@
 
 #include "BaseLib/Error.h"
 #include "MathLib/KelvinVector.h"
+#include "MechanicsBase.h"
 #include "NumLib/NewtonRaphson.h"
 #include "ParameterLib/Parameter.h"
 
-#include "MechanicsBase.h"
-
 namespace MaterialLib
 {
 namespace Solids
@@ -250,8 +249,8 @@ struct StateVariables
     Damage damage_prev;                      ///< \copydoc damage
 
 #ifndef NDEBUG
-    friend std::ostream& operator<<(
-        std::ostream& os, StateVariables<DisplacementDim> const& m)
+    friend std::ostream& operator<<(std::ostream& os,
+                                    StateVariables<DisplacementDim> const& m)
     {
         os << "State:\n"
            << "eps_p_D: " << m.eps_p.D << "\n"
@@ -358,6 +357,9 @@ class SolidEhlers final : public MechanicsBase<DisplacementDim>
 
 extern template class SolidEhlers<2>;
 extern template class SolidEhlers<3>;
+
+extern template struct StateVariables<2>;
+extern template struct StateVariables<3>;
 }  // namespace Ehlers
 }  // namespace Solids
 }  // namespace MaterialLib