From f223ce6c779fa42b8eeeeff4cd661448d20dca71 Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Mon, 5 Sep 2022 11:52:31 +0200
Subject: [PATCH 01/36] [py] Added scikit-build.

Build with:

```
pip install .
```
---
 .gitignore                         |  4 ++++
 pyproject.toml                     |  8 ++++++++
 scripts/cmake/packaging/Pack.cmake |  4 +++-
 setup.py                           | 14 ++++++++++++++
 4 files changed, 29 insertions(+), 1 deletion(-)
 create mode 100644 pyproject.toml
 create mode 100644 setup.py

diff --git a/.gitignore b/.gitignore
index 1c8d2d8653f..a023a253f49 100644
--- a/.gitignore
+++ b/.gitignore
@@ -38,4 +38,8 @@ CMakeUserPresets.json
 nohup.out
 
 /Documentation/.vale
+
+# Python build
+/_skbuild
+*.egg-info/
 .ipynb_checkpoints
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 00000000000..5c7d0579bbd
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,8 @@
+[build-system]
+requires = [
+  "setuptools>=42",
+  "scikit-build>=0.15.0",
+  "cmake>=3.22",
+  "ninja; platform_system!='Windows'",
+]
+build-backend = "setuptools.build_meta"
diff --git a/scripts/cmake/packaging/Pack.cmake b/scripts/cmake/packaging/Pack.cmake
index 8c1daaf61bc..33b91a33fc6 100644
--- a/scripts/cmake/packaging/Pack.cmake
+++ b/scripts/cmake/packaging/Pack.cmake
@@ -76,7 +76,9 @@ if(OGS_USE_PYTHON)
         install(FILES ${PYTHON_RUNTIME_LIBS} DESTINATION bin)
         file(COPY ${PYTHON_RUNTIME_LIBS} DESTINATION ${CMAKE_RUNTIME_OUTPUT_DIRECTORY})
     else()
-        install(FILES ${Python_LIBRARIES} DESTINATION bin)
+        file(INSTALL ${Python_LIBRARIES} DESTINATION ${CMAKE_INSTALL_LIBDIR}
+             FOLLOW_SYMLINK_CHAIN
+        )
     endif()
 endif()
 
diff --git a/setup.py b/setup.py
new file mode 100644
index 00000000000..58e18d9ad73
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,14 @@
+from skbuild import setup
+from setuptools import find_packages
+
+setup(
+    name="ogs",
+    version="6.4.2",
+    description="OpenGeoSys",
+    author="OpenGeoSys Community",
+    license="BSD-3-Clause",
+    packages=find_packages(where="."),
+    package_dir={"": "."},
+    cmake_args=["-DOGS_BUILD_PROCESSES=SteadyStateDiffusion", "-DOGS_BUILD_UTILS=OFF"],
+    python_requires=">=3.6",
+)

From 0abb165583580e2e3639571b41cccd911b2f64d7 Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Mon, 5 Sep 2022 13:58:39 +0200
Subject: [PATCH 02/36] [py] Module works.

```
pip install .
pytest
```
---
 .gitignore                                    |  1 +
 Applications/CLI/CMakeLists.txt               | 47 -------------------
 Applications/CLI/ogs_python_module.py         | 19 --------
 Applications/CMakeLists.txt                   |  4 ++
 Applications/Python/CMakeLists.txt            | 21 +++++++++
 Applications/Python/OpenGeoSys/__init__.py    |  1 +
 .../{CLI => Python}/ogs_python_module.cpp     |  2 +-
 Tests/Python/test_cli.py                      | 18 +++++++
 pyproject.toml                                | 16 +++++++
 .../cmake/DependenciesExternalProject.cmake   |  2 +-
 setup.py                                      | 19 ++++++--
 11 files changed, 78 insertions(+), 72 deletions(-)
 delete mode 100755 Applications/CLI/ogs_python_module.py
 create mode 100644 Applications/Python/CMakeLists.txt
 create mode 100644 Applications/Python/OpenGeoSys/__init__.py
 rename Applications/{CLI => Python}/ogs_python_module.cpp (99%)
 create mode 100644 Tests/Python/test_cli.py

diff --git a/.gitignore b/.gitignore
index a023a253f49..d3e5862f91c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -42,4 +42,5 @@ nohup.out
 # Python build
 /_skbuild
 *.egg-info/
+/wheelhouse
 .ipynb_checkpoints
diff --git a/Applications/CLI/CMakeLists.txt b/Applications/CLI/CMakeLists.txt
index 742e4be2a96..4d221c96d5d 100644
--- 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
deleted file mode 100755
index 8f553584fdd..00000000000
--- a/Applications/CLI/ogs_python_module.py
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env python3
-
-# The OpenGeoSys python library will be created in the lib folder of the build
-# directory
-## export PYTHONPATH=$PYTHONPATH:your-build_directory-here/lib
-
-import sys
-import tempfile
-import OpenGeoSys
-
-arguments = ["", sys.argv[1], "-o " + tempfile.mkdtemp()]
-
-print("Python OpenGeoSys.init ...")
-OpenGeoSys.initialize(arguments)
-print("Python OpenGeoSys.executeSimulation ...")
-OpenGeoSys.executeSimulation()
-print("Python OpenGeoSys.finalize() ...")
-OpenGeoSys.finalize()
-print("Python world.")
diff --git a/Applications/CMakeLists.txt b/Applications/CMakeLists.txt
index 386e8b3f40d..ce44d2681a9 100644
--- a/Applications/CMakeLists.txt
+++ b/Applications/CMakeLists.txt
@@ -19,3 +19,7 @@ endif() # OGS_BUILD_CLI
 if(OGS_USE_INSITU)
     add_subdirectory(InSituLib)
 endif()
+
+if(OGS_BUILD_PYTHON_MODULE)
+    add_subdirectory(Python)
+endif()
diff --git a/Applications/Python/CMakeLists.txt b/Applications/Python/CMakeLists.txt
new file mode 100644
index 00000000000..0d6bb59652c
--- /dev/null
+++ b/Applications/Python/CMakeLists.txt
@@ -0,0 +1,21 @@
+# Create OpenGeoSys python module
+# https://pybind11.readthedocs.io/en/stable/compiling.html#building-with-cmake
+pybind11_add_module(
+    _cli MODULE ogs_python_module.cpp ../CLI/CommandLineArgumentParser.cpp
+)
+
+# lld linker strips out PyInit_OpenGeoSys symbol. Use standard linker.
+get_target_property(_link_options _cli LINK_OPTIONS)
+if(_link_options)
+    list(REMOVE_ITEM _link_options -fuse-ld=lld)
+    set_target_properties(_cli PROPERTIES LINK_OPTIONS "${_link_options}")
+endif()
+
+target_link_libraries(_cli PRIVATE ApplicationsLib BaseLib GitInfoLib tclap)
+target_include_directories(_cli PRIVATE ../CLI)
+
+set(_cli_dest ${CMAKE_INSTALL_LIBDIR})
+if(SKBUILD)
+    set(_cli_dest .)
+endif()
+install(TARGETS _cli LIBRARY DESTINATION ${_cli_dest})
diff --git a/Applications/Python/OpenGeoSys/__init__.py b/Applications/Python/OpenGeoSys/__init__.py
new file mode 100644
index 00000000000..2ad97321e99
--- /dev/null
+++ b/Applications/Python/OpenGeoSys/__init__.py
@@ -0,0 +1 @@
+from ._cli import *
diff --git a/Applications/CLI/ogs_python_module.cpp b/Applications/Python/ogs_python_module.cpp
similarity index 99%
rename from Applications/CLI/ogs_python_module.cpp
rename to Applications/Python/ogs_python_module.cpp
index 9abbe7a727d..c3e6f190a87 100644
--- a/Applications/CLI/ogs_python_module.cpp
+++ b/Applications/Python/ogs_python_module.cpp
@@ -122,7 +122,7 @@ void finalize()
 }
 
 /// python module name is OpenGeoSys
-PYBIND11_MODULE(OpenGeoSys, m)
+PYBIND11_MODULE(_cli, m)
 {
     m.doc() = "pybind11 ogs example plugin";
     m.def("initialize", &initOGS, "init OGS");
diff --git a/Tests/Python/test_cli.py b/Tests/Python/test_cli.py
new file mode 100644
index 00000000000..7517dfa739b
--- /dev/null
+++ b/Tests/Python/test_cli.py
@@ -0,0 +1,18 @@
+import OpenGeoSys
+import tempfile
+import os
+
+
+def test_init():
+    arguments = [
+        "",
+        f"{os.path.abspath(os.path.dirname(__file__))}/../Data/Parabolic/LiquidFlow/Flux/cube_1e3_calculatesurfaceflux.prj",
+        "-o " + tempfile.mkdtemp(),
+    ]
+
+    print("Python OpenGeoSys.init ...")
+    OpenGeoSys.initialize(arguments)
+    print("Python OpenGeoSys.executeSimulation ...")
+    OpenGeoSys.executeSimulation()
+    print("Python OpenGeoSys.finalize() ...")
+    OpenGeoSys.finalize()
diff --git a/pyproject.toml b/pyproject.toml
index 5c7d0579bbd..754315d212c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,3 +6,19 @@ requires = [
   "ninja; platform_system!='Windows'",
 ]
 build-backend = "setuptools.build_meta"
+
+[tool.pytest.ini_options]
+testpaths = ["Tests"]
+norecursedirs = ["Tests/Data"]
+
+[tool.cibuildwheel]
+archs = "auto64"
+build = "cp310-*"
+skip = "*musllinux*"
+test-extras = "test"
+test-command = "pytest {project}/Tests/Python"
+build-verbosity = "1"
+
+[tool.cibuildwheel.linux]
+manylinux-x86_64-image = "manylinux2014"
+manylinux-aarch64-image = "manylinux2014"
diff --git a/scripts/cmake/DependenciesExternalProject.cmake b/scripts/cmake/DependenciesExternalProject.cmake
index ec14fe15943..5a9c922131b 100644
--- a/scripts/cmake/DependenciesExternalProject.cmake
+++ b/scripts/cmake/DependenciesExternalProject.cmake
@@ -202,7 +202,7 @@ if(OGS_USE_MPI)
     set(HDF5_PREFER_PARALLEL ON)
     list(APPEND _hdf5_options "-DHDF5_ENABLE_PARALLEL=ON")
 endif()
-if(WIN32)
+if(WIN32 OR HDF5_USE_STATIC_LIBRARIES)
     set(HDF5_USE_STATIC_LIBRARIES ON)
     list(APPEND _hdf5_options "-DBUILD_SHARED_LIBS=OFF")
 endif()
diff --git a/setup.py b/setup.py
index 58e18d9ad73..f709460ae90 100644
--- a/setup.py
+++ b/setup.py
@@ -2,13 +2,24 @@
 from setuptools import find_packages
 
 setup(
-    name="ogs",
+    name="OpenGeoSys",
     version="6.4.2",
     description="OpenGeoSys",
     author="OpenGeoSys Community",
     license="BSD-3-Clause",
-    packages=find_packages(where="."),
-    package_dir={"": "."},
-    cmake_args=["-DOGS_BUILD_PROCESSES=SteadyStateDiffusion", "-DOGS_BUILD_UTILS=OFF"],
+    packages=find_packages(where="Applications/Python"),
+    package_dir={"": "Applications/Python"},
+    cmake_install_dir="Applications/Python/OpenGeoSys",
+    extras_require={"test": ["pytest"]},
+    cmake_args=[
+        "-DOGS_BUILD_PROCESSES=LiquidFlow",
+        "-DOGS_BUILD_UTILS=OFF",
+        "-DHDF5_USE_STATIC_LIBRARIES=ON",
+        "-DOGS_BUILD_HDF5=ON",
+        "-DOGS_USE_PYTHON=OFF",  # not possible because manylinux does not provide libpythonX.Y.so
+        "-DOGS_BUILD_PYTHON_MODULE=ON",
+        "-DOGS_BUILD_TESTING=OFF",
+        "-DOGS_INSTALL_DEPENDENCIES=OFF",  # otherwise auditwheel fails
+    ],
     python_requires=">=3.6",
 )

From 85385aae8ecb2bca288ae10379f0625d78695fb3 Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Tue, 6 Sep 2022 17:26:30 +0200
Subject: [PATCH 03/36] [cmake] OGS_BUILD_PYTHON_MODULE is now an independent
 option.

Was coupled to OGS_USE_PYTHON before.
---
 CMakeLists.txt                   | 7 ++-----
 scripts/cmake/Dependencies.cmake | 2 +-
 scripts/cmake/PythonSetup.cmake  | 8 +++++++-
 3 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 7c4027cd17f..556122f6a8b 100644
--- 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/scripts/cmake/Dependencies.cmake b/scripts/cmake/Dependencies.cmake
index 5c174b73f02..16e59865072 100644
--- a/scripts/cmake/Dependencies.cmake
+++ b/scripts/cmake/Dependencies.cmake
@@ -87,7 +87,7 @@ if(tetgen_ADDED)
     list(APPEND DISABLE_WARNINGS_TARGETS tet tetgen)
 endif()
 
-if(OGS_USE_PYTHON)
+if(OGS_USE_PYTHON OR OGS_BUILD_PYTHON_MODULE)
     CPMAddPackage(
         NAME pybind11 GITHUB_REPOSITORY pybind/pybind11
         GIT_TAG f1abf5d9159b805674197f6bc443592e631c9130
diff --git a/scripts/cmake/PythonSetup.cmake b/scripts/cmake/PythonSetup.cmake
index 833bb5718ca..14ac317021d 100644
--- a/scripts/cmake/PythonSetup.cmake
+++ b/scripts/cmake/PythonSetup.cmake
@@ -38,9 +38,15 @@ endif()
 
 set(_python_componets Interpreter)
 if(OGS_USE_PYTHON)
+    list(APPEND _python_componets Development.Embed)
+endif()
+if(OGS_BUILD_PYTHON_MODULE)
+    list(APPEND _python_componets Development.Module)
+endif()
+if(OGS_USE_PYTHON OR OGS_BUILD_PYTHON_MODULE)
     set(CMAKE_REQUIRE_FIND_PACKAGE_Python TRUE)
-    list(APPEND _python_componets Development)
 endif()
+
 find_package(
     Python ${ogs.minimum_version.python}${_python_version_max}
     COMPONENTS ${_python_componets}

From 61b1a2a6f82d5923bb7a2c9314a5594fa473dc1f Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Wed, 7 Sep 2022 08:56:30 +0200
Subject: [PATCH 04/36] [wheel] Moved CMake options to preset.

---
 CMakePresets.json | 14 ++++++++++++++
 setup.py          | 11 +----------
 2 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/CMakePresets.json b/CMakePresets.json
index 703fc056a2c..7bb0e9709bd 100644
--- a/CMakePresets.json
+++ b/CMakePresets.json
@@ -187,6 +187,20 @@
         "OGS_USE_PYTHON": "OFF",
         "OGS_USE_UNITY_BUILDS": "OFF"
       }
+    },
+    {
+      "name": "wheel",
+      "inherits": "release",
+      "cacheVariables": {
+        "OGS_BUILD_PROCESSES": "LiquidFlow",
+        "OGS_BUILD_UTILS": "OFF",
+        "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"
+      }
     }
   ],
   "buildPresets": [
diff --git a/setup.py b/setup.py
index f709460ae90..59908b1de0b 100644
--- a/setup.py
+++ b/setup.py
@@ -11,15 +11,6 @@
     package_dir={"": "Applications/Python"},
     cmake_install_dir="Applications/Python/OpenGeoSys",
     extras_require={"test": ["pytest"]},
-    cmake_args=[
-        "-DOGS_BUILD_PROCESSES=LiquidFlow",
-        "-DOGS_BUILD_UTILS=OFF",
-        "-DHDF5_USE_STATIC_LIBRARIES=ON",
-        "-DOGS_BUILD_HDF5=ON",
-        "-DOGS_USE_PYTHON=OFF",  # not possible because manylinux does not provide libpythonX.Y.so
-        "-DOGS_BUILD_PYTHON_MODULE=ON",
-        "-DOGS_BUILD_TESTING=OFF",
-        "-DOGS_INSTALL_DEPENDENCIES=OFF",  # otherwise auditwheel fails
-    ],
+    cmake_args=["--preset wheel"],
     python_requires=">=3.6",
 )

From 0566d251e99910e71ade90c766227b884f54c8db Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Wed, 7 Sep 2022 10:50:12 +0200
Subject: [PATCH 05/36] [wheel] Added ogs binary entrypoint.

Implementation from
https://github.com/scikit-build/cmake-python-distributions
---
 Applications/Python/OpenGeoSys/__init__.py | 14 ++++++++++++++
 CMakePresets.json                          |  4 ++++
 Tests/Python/__init__.py                   | 11 +++++++++++
 Tests/Python/test_cli.py                   | 22 ++++++++++++++++++++--
 setup.py                                   |  7 ++++++-
 5 files changed, 55 insertions(+), 3 deletions(-)
 create mode 100644 Tests/Python/__init__.py

diff --git a/Applications/Python/OpenGeoSys/__init__.py b/Applications/Python/OpenGeoSys/__init__.py
index 2ad97321e99..7631e8c3369 100644
--- a/Applications/Python/OpenGeoSys/__init__.py
+++ b/Applications/Python/OpenGeoSys/__init__.py
@@ -1 +1,15 @@
+import os
+import subprocess
+import sys
+
 from ._cli import *
+
+OGS_BIN_DIR = os.path.join(os.path.join(os.path.dirname(__file__), "bin"))
+
+
+def _program(name, args):
+    return subprocess.call([os.path.join(OGS_BIN_DIR, name)] + args)
+
+
+def ogs():
+    raise SystemExit(_program("ogs", sys.argv[1:]))
diff --git a/CMakePresets.json b/CMakePresets.json
index 7bb0e9709bd..3b710a650c6 100644
--- a/CMakePresets.json
+++ b/CMakePresets.json
@@ -284,6 +284,10 @@
     {
       "name": "ci-no-unity",
       "configurePreset": "ci-no-unity"
+    },
+    {
+      "name": "wheel",
+      "configurePreset": "wheel"
     }
   ],
   "testPresets": [
diff --git a/Tests/Python/__init__.py b/Tests/Python/__init__.py
new file mode 100644
index 00000000000..fd1659acb19
--- /dev/null
+++ b/Tests/Python/__init__.py
@@ -0,0 +1,11 @@
+import sys
+
+from contextlib import contextmanager
+
+
+@contextmanager
+def push_argv(argv):
+    old_argv = sys.argv
+    sys.argv = argv
+    yield
+    sys.argv = old_argv
diff --git a/Tests/Python/test_cli.py b/Tests/Python/test_cli.py
index 7517dfa739b..7f6c624269d 100644
--- a/Tests/Python/test_cli.py
+++ b/Tests/Python/test_cli.py
@@ -1,9 +1,12 @@
-import OpenGeoSys
 import tempfile
 import os
 
+import pytest
+
+import OpenGeoSys
 
-def test_init():
+
+def test_module():
     arguments = [
         "",
         f"{os.path.abspath(os.path.dirname(__file__))}/../Data/Parabolic/LiquidFlow/Flux/cube_1e3_calculatesurfaceflux.prj",
@@ -16,3 +19,18 @@ def test_init():
     OpenGeoSys.executeSimulation()
     print("Python OpenGeoSys.finalize() ...")
     OpenGeoSys.finalize()
+
+
+from . import push_argv
+
+
+def _run(program, args):
+    func = getattr(OpenGeoSys, program)
+    args = ["%s.py" % program] + args
+    with push_argv(args), pytest.raises(SystemExit) as excinfo:
+        func()
+    assert 0 == excinfo.value.code
+
+
+def test_binaries():
+    _run("ogs", ["--version"])
diff --git a/setup.py b/setup.py
index 59908b1de0b..eaa57d94967 100644
--- a/setup.py
+++ b/setup.py
@@ -11,6 +11,11 @@
     package_dir={"": "Applications/Python"},
     cmake_install_dir="Applications/Python/OpenGeoSys",
     extras_require={"test": ["pytest"]},
-    cmake_args=["--preset wheel"],
+    cmake_args=["--preset wheel", "-B ."],
     python_requires=">=3.6",
+    entry_points={
+        "console_scripts": [
+            "ogs=OpenGeoSys:ogs",
+        ]
+    },
 )

From 39ce500aed533f6fc2ef1ff67c95449bfe9eaff1 Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Wed, 7 Sep 2022 11:25:52 +0200
Subject: [PATCH 06/36] [ci] Added job build wheels linux.

---
 .gitlab-ci.yml                   | 1 +
 scripts/ci/jobs/build-wheels.yml | 9 +++++++++
 2 files changed, 10 insertions(+)
 create mode 100644 scripts/ci/jobs/build-wheels.yml

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index e4fe9bb3d18..b92c02dcc36 100644
--- 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/scripts/ci/jobs/build-wheels.yml b/scripts/ci/jobs/build-wheels.yml
new file mode 100644
index 00000000000..0c29c74387e
--- /dev/null
+++ b/scripts/ci/jobs/build-wheels.yml
@@ -0,0 +1,9 @@
+build wheels linux:
+  stage: build
+  needs: [meta]
+  tags: [envinf3-shell]
+  script:
+    - pipx run cibuildwheel
+  artifacts:
+    paths:
+      - wheelhouse/

From 791ae864b7135917e53cc0aa6766ca9a9ba3e91b Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Wed, 7 Sep 2022 14:20:14 +0200
Subject: [PATCH 07/36] [wheel] Get ogs version from env or git.

[ci] Upload wheel to GitLab registry.
---
 Applications/Python/OpenGeoSys/__init__.py |  1 +
 pyproject.toml                             |  1 +
 scripts/ci/jobs/build-wheels.yml           |  6 ++++
 setup.py                                   | 32 +++++++++++++++++++++-
 4 files changed, 39 insertions(+), 1 deletion(-)

diff --git a/Applications/Python/OpenGeoSys/__init__.py b/Applications/Python/OpenGeoSys/__init__.py
index 7631e8c3369..628678b353d 100644
--- a/Applications/Python/OpenGeoSys/__init__.py
+++ b/Applications/Python/OpenGeoSys/__init__.py
@@ -11,5 +11,6 @@ def _program(name, args):
     return subprocess.call([os.path.join(OGS_BIN_DIR, name)] + args)
 
 
+# Binary entrypoints
 def ogs():
     raise SystemExit(_program("ogs", sys.argv[1:]))
diff --git a/pyproject.toml b/pyproject.toml
index 754315d212c..9c3d7b3b2c7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,3 +22,4 @@ build-verbosity = "1"
 [tool.cibuildwheel.linux]
 manylinux-x86_64-image = "manylinux2014"
 manylinux-aarch64-image = "manylinux2014"
+environment-pass = ["OGS_VERSION"]
diff --git a/scripts/ci/jobs/build-wheels.yml b/scripts/ci/jobs/build-wheels.yml
index 0c29c74387e..6bcab571755 100644
--- a/scripts/ci/jobs/build-wheels.yml
+++ b/scripts/ci/jobs/build-wheels.yml
@@ -4,6 +4,12 @@ build wheels linux:
   tags: [envinf3-shell]
   script:
     - pipx run cibuildwheel
+    - >
+      pipx run twine upload
+      --repository-url https://gitlab.opengeosys.org/api/v4/projects/${CI_PROJECT_ID}/packages/pypi
+      --username gitlab-ci-token
+      --password ${CI_JOB_TOKEN}
+      wheelhouse/*
   artifacts:
     paths:
       - wheelhouse/
diff --git a/setup.py b/setup.py
index eaa57d94967..f95e450d35f 100644
--- a/setup.py
+++ b/setup.py
@@ -1,9 +1,39 @@
 from skbuild import setup
 from setuptools import find_packages
 
+import os
+import re
+import subprocess
+
+
+def get_version():
+    git_version = ""
+    if "OGS_VERSION" in os.environ:
+        git_version = os.environ["OGS_VERSION"]
+    else:
+        git_version = subprocess.run(
+            ["git describe --tags"],
+            capture_output=True,
+            text=True,
+            shell=True,
+        ).stdout.strip()
+
+    if re.match("\d+\.\d+\.\d+-\d+-g\w+", git_version):
+        # Make it PEP 440 compliant
+        # e.g. 6.4.2-1140-g85bbc8b4e1 -> 6.4.2.dev1140
+        m = re.match(".+?(?=-g[\w]*$)", git_version)  # strip out commit hash
+        if m:
+            return m.group(0).replace("-", ".dev")  # insert dev
+        else:
+            print("WARNING: Could not get ogs version!")
+            exit(1)
+    else:
+        return git_version
+
+
 setup(
     name="OpenGeoSys",
-    version="6.4.2",
+    version=get_version(),
     description="OpenGeoSys",
     author="OpenGeoSys Community",
     license="BSD-3-Clause",

From 850d10ae840349994917762e01359bc2fb3b6e67 Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Thu, 8 Sep 2022 13:16:43 +0200
Subject: [PATCH 08/36] [wheel] Enabled MFront and optimized size with shared
 libs.

---
 Applications/Python/CMakeLists.txt         | 6 +-----
 Applications/Python/OpenGeoSys/__init__.py | 8 +++++++-
 CMakePresets.json                          | 5 ++++-
 3 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/Applications/Python/CMakeLists.txt b/Applications/Python/CMakeLists.txt
index 0d6bb59652c..98801e4cf44 100644
--- a/Applications/Python/CMakeLists.txt
+++ b/Applications/Python/CMakeLists.txt
@@ -14,8 +14,4 @@ endif()
 target_link_libraries(_cli PRIVATE ApplicationsLib BaseLib GitInfoLib tclap)
 target_include_directories(_cli PRIVATE ../CLI)
 
-set(_cli_dest ${CMAKE_INSTALL_LIBDIR})
-if(SKBUILD)
-    set(_cli_dest .)
-endif()
-install(TARGETS _cli LIBRARY DESTINATION ${_cli_dest})
+install(TARGETS _cli LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
diff --git a/Applications/Python/OpenGeoSys/__init__.py b/Applications/Python/OpenGeoSys/__init__.py
index 628678b353d..d25cddd08e7 100644
--- a/Applications/Python/OpenGeoSys/__init__.py
+++ b/Applications/Python/OpenGeoSys/__init__.py
@@ -2,7 +2,13 @@
 import subprocess
 import sys
 
-from ._cli import *
+try:
+    from .lib64._cli import *
+except ImportError:
+    try:
+        from .lib._cli import *
+    except ImportError:
+        print("ERROR: could not import OpenGeoSys Python module!")
 
 OGS_BIN_DIR = os.path.join(os.path.join(os.path.dirname(__file__), "bin"))
 
diff --git a/CMakePresets.json b/CMakePresets.json
index 3b710a650c6..517f699d1b3 100644
--- a/CMakePresets.json
+++ b/CMakePresets.json
@@ -199,7 +199,10 @@
         "OGS_USE_PYTHON": "OFF",
         "OGS_BUILD_PYTHON_MODULE": "ON",
         "OGS_BUILD_TESTING": "OFF",
-        "OGS_INSTALL_DEPENDENCIES": "OFF"
+        "OGS_INSTALL_DEPENDENCIES": "OFF",
+        "OGS_USE_PIP": "OFF",
+        "OGS_USE_MFRONT": "ON",
+        "BUILD_SHARED_LIBS": "ON"
       }
     }
   ],

From 34d166828092a68223837e0b3780e8165c1503b8 Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Thu, 8 Sep 2022 15:09:32 +0200
Subject: [PATCH 09/36] [T] Fixed tclap exceptions due to duplicate flags.

---
 Applications/Utils/MeshEdit/appendLinesAlongPolyline.cpp        | 2 +-
 .../MeshGeoTools/computeSurfaceNodeIDsInPolygonalRegion.cpp     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Applications/Utils/MeshEdit/appendLinesAlongPolyline.cpp b/Applications/Utils/MeshEdit/appendLinesAlongPolyline.cpp
index 0774cc64529..1b6625b70fe 100644
--- 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
index b628eceb948..355c00e3269 100644
--- 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);

From ca159582aae6f95be5820f8f3e9377981cab7870 Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Thu, 8 Sep 2022 15:10:08 +0200
Subject: [PATCH 10/36] [T] Added correct --version information.

---
 Applications/Utils/GeoTools/addDataToRaster.cpp | 10 +++++++++-
 Applications/Utils/GeoTools/createRaster.cpp    | 11 +++++++++--
 2 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/Applications/Utils/GeoTools/addDataToRaster.cpp b/Applications/Utils/GeoTools/addDataToRaster.cpp
index f21fc93f952..92e3ef9d337 100644
--- 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
index d58e7c29036..c9a521c53d5 100644
--- 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)",

From 26e78e47aa6f3c9b33fb9df663e4198a11932c71 Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Thu, 8 Sep 2022 15:10:42 +0200
Subject: [PATCH 11/36] [wheel] Added missing binary entry points for all
 tools.

---
 Applications/Python/OpenGeoSys/__init__.py | 69 +++++++++++++++++++++-
 CMakePresets.json                          |  1 -
 Tests/Python/test_cli.py                   |  5 +-
 setup.py                                   | 14 +++--
 4 files changed, 79 insertions(+), 10 deletions(-)

diff --git a/Applications/Python/OpenGeoSys/__init__.py b/Applications/Python/OpenGeoSys/__init__.py
index d25cddd08e7..120592366f0 100644
--- a/Applications/Python/OpenGeoSys/__init__.py
+++ b/Applications/Python/OpenGeoSys/__init__.py
@@ -12,11 +12,74 @@
 
 OGS_BIN_DIR = os.path.join(os.path.join(os.path.dirname(__file__), "bin"))
 
+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",
+]
+
 
 def _program(name, args):
     return subprocess.call([os.path.join(OGS_BIN_DIR, name)] + args)
 
 
-# Binary entrypoints
-def ogs():
-    raise SystemExit(_program("ogs", sys.argv[1:]))
+FUNC_TEMPLATE = """def {0}(): raise SystemExit(_program("{0}", sys.argv[1:]))"""
+for f in binaries_list:
+    exec(FUNC_TEMPLATE.format(f))
diff --git a/CMakePresets.json b/CMakePresets.json
index 517f699d1b3..5eabcc4085b 100644
--- a/CMakePresets.json
+++ b/CMakePresets.json
@@ -193,7 +193,6 @@
       "inherits": "release",
       "cacheVariables": {
         "OGS_BUILD_PROCESSES": "LiquidFlow",
-        "OGS_BUILD_UTILS": "OFF",
         "HDF5_USE_STATIC_LIBRARIES": "ON",
         "OGS_BUILD_HDF5": "ON",
         "OGS_USE_PYTHON": "OFF",
diff --git a/Tests/Python/test_cli.py b/Tests/Python/test_cli.py
index 7f6c624269d..e2b60fc4fd4 100644
--- a/Tests/Python/test_cli.py
+++ b/Tests/Python/test_cli.py
@@ -33,4 +33,7 @@ def _run(program, args):
 
 
 def test_binaries():
-    _run("ogs", ["--version"])
+    ignore_list = ["moveMeshNodes", "mpmetis", "tetgen"]  # have no --version cli flag
+    for f in OpenGeoSys.binaries_list:
+        if f not in ignore_list:
+            _run(f, ["--version"])
diff --git a/setup.py b/setup.py
index f95e450d35f..2cb3ad792f5 100644
--- a/setup.py
+++ b/setup.py
@@ -4,6 +4,7 @@
 import os
 import re
 import subprocess
+import sys
 
 
 def get_version():
@@ -31,6 +32,13 @@ def get_version():
         return git_version
 
 
+sys.path.append("Applications/Python")
+from OpenGeoSys import binaries_list
+
+console_scripts = []
+for b in binaries_list:
+    console_scripts.append(f"{b}=OpenGeoSys:{b}")
+
 setup(
     name="OpenGeoSys",
     version=get_version(),
@@ -43,9 +51,5 @@ def get_version():
     extras_require={"test": ["pytest"]},
     cmake_args=["--preset wheel", "-B ."],
     python_requires=">=3.6",
-    entry_points={
-        "console_scripts": [
-            "ogs=OpenGeoSys:ogs",
-        ]
-    },
+    entry_points={"console_scripts": console_scripts},
 )

From 3dded39521aa5ac2d1d67562344df1b8afeaf17a Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Thu, 8 Sep 2022 15:14:27 +0200
Subject: [PATCH 12/36] [ci] Added mac jobs for wheels.

---
 scripts/ci/jobs/build-wheels.yml | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/scripts/ci/jobs/build-wheels.yml b/scripts/ci/jobs/build-wheels.yml
index 6bcab571755..b08f6981978 100644
--- a/scripts/ci/jobs/build-wheels.yml
+++ b/scripts/ci/jobs/build-wheels.yml
@@ -13,3 +13,24 @@ build wheels linux:
   artifacts:
     paths:
       - wheelhouse/
+
+build wheels mac:
+  stage: build
+  needs: [meta]
+  tags:
+    - mac
+    - ${ARCHITECTURE}
+  script:
+    - CMAKE_OSX_DEPLOYMENT_TARGET=10.15 pipx run cibuildwheel
+    - >
+      pipx run twine upload
+      --repository-url https://gitlab.opengeosys.org/api/v4/projects/${CI_PROJECT_ID}/packages/pypi
+      --username gitlab-ci-token
+      --password ${CI_JOB_TOKEN}
+      wheelhouse/*
+  artifacts:
+    paths:
+      - wheelhouse/
+  parallel:
+    matrix:
+      - ARCHITECTURE: ["amd64", "arm64"]

From 7957a454206767ac60ec8305d478a38e47d8457a Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Thu, 8 Sep 2022 15:52:33 +0200
Subject: [PATCH 13/36] [wheel] Build for different Python versions.

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 9c3d7b3b2c7..e9b2b352a81 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,7 +13,7 @@ norecursedirs = ["Tests/Data"]
 
 [tool.cibuildwheel]
 archs = "auto64"
-build = "cp310-*"
+build = "cp3*"
 skip = "*musllinux*"
 test-extras = "test"
 test-command = "pytest {project}/Tests/Python"

From 71b9cac855f02b3e0b734d9d5ae8201d2a2bd428 Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Thu, 8 Sep 2022 20:34:26 +0200
Subject: [PATCH 14/36] [cmake] Bump pybind11 to 2.10.0.

---
 scripts/cmake/Dependencies.cmake | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/scripts/cmake/Dependencies.cmake b/scripts/cmake/Dependencies.cmake
index 16e59865072..5a37639f28a 100644
--- a/scripts/cmake/Dependencies.cmake
+++ b/scripts/cmake/Dependencies.cmake
@@ -89,8 +89,7 @@ endif()
 
 if(OGS_USE_PYTHON OR OGS_BUILD_PYTHON_MODULE)
     CPMAddPackage(
-        NAME pybind11 GITHUB_REPOSITORY pybind/pybind11
-        GIT_TAG f1abf5d9159b805674197f6bc443592e631c9130
+        NAME pybind11 GITHUB_REPOSITORY pybind/pybind11 VERSION 2.10.0
     )
 endif()
 

From 6c5d4aebbb5b41dcd1705482058881e90b8d931d Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Thu, 8 Sep 2022 22:15:55 +0200
Subject: [PATCH 15/36] [wheel] Dont' build 3.6 and 3.7 wheels on macOS.

Is not supported for CMAKE_OSX_DEPLOYMENT_TARGET=10.15
---
 pyproject.toml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index e9b2b352a81..69021cbd4a1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -23,3 +23,6 @@ build-verbosity = "1"
 manylinux-x86_64-image = "manylinux2014"
 manylinux-aarch64-image = "manylinux2014"
 environment-pass = ["OGS_VERSION"]
+
+[tool.cibuildwheel.macos]
+skip = ["cp36-*", "cp37-*", "cp38-*x86_64"]

From 91ed5d1650f0ae91c71877c8f1fa536b0e2921c6 Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Fri, 9 Sep 2022 13:16:32 +0200
Subject: [PATCH 16/36] [cmake] Added missing dependency in Python _cli module.

---
 Applications/Python/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Applications/Python/CMakeLists.txt b/Applications/Python/CMakeLists.txt
index 98801e4cf44..ef45e964522 100644
--- a/Applications/Python/CMakeLists.txt
+++ b/Applications/Python/CMakeLists.txt
@@ -11,7 +11,7 @@ if(_link_options)
     set_target_properties(_cli PROPERTIES LINK_OPTIONS "${_link_options}")
 endif()
 
-target_link_libraries(_cli PRIVATE ApplicationsLib BaseLib GitInfoLib tclap)
+target_link_libraries(_cli PRIVATE ApplicationsLib BaseLib CMakeInfoLib GitInfoLib tclap)
 target_include_directories(_cli PRIVATE ../CLI)
 
 install(TARGETS _cli LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})

From ac90b262a93eeb49787489353bb381348464ab6c Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Fri, 9 Sep 2022 13:18:58 +0200
Subject: [PATCH 17/36] [cmake] Enable BUILD_SHARED_LIBS=ON on Windows.

---
 scripts/cmake/Dependencies.cmake | 1 +
 scripts/cmake/MetisSetup.cmake   | 5 ++++-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/scripts/cmake/Dependencies.cmake b/scripts/cmake/Dependencies.cmake
index 5a37639f28a..f891daaf0e8 100644
--- a/scripts/cmake/Dependencies.cmake
+++ b/scripts/cmake/Dependencies.cmake
@@ -181,6 +181,7 @@ if(OGS_BUILD_SWMM)
     CPMAddPackage(
         NAME SWMMInterface GITHUB_REPOSITORY ufz/SwmmInterface
         GIT_TAG 141e05ae1f419918799d7bf9178ebcd97feb1ed3
+        OPTIONS "BUILD_SHARED_LIBS OFF"
     )
     if(SWMMInterface_ADDED)
         target_include_directories(
diff --git a/scripts/cmake/MetisSetup.cmake b/scripts/cmake/MetisSetup.cmake
index 6c6fde90cae..73131168b26 100644
--- a/scripts/cmake/MetisSetup.cmake
+++ b/scripts/cmake/MetisSetup.cmake
@@ -10,7 +10,10 @@ include(${GKLIB_PATH}/GKlibSystem.cmake)
 
 # Metis library
 file(GLOB _metis_sources ${metis_SOURCE_DIR}/libmetis/*.c)
-ogs_add_library(ogs_metis ${GKlib_sources} ${_metis_sources})
+if(WIN32)
+    set(_metis_static STATIC)
+endif()
+ogs_add_library(ogs_metis ${_metis_static} ${GKlib_sources} ${_metis_sources})
 target_compile_definitions(ogs_metis PUBLIC USE_GKREGEX)
 target_include_directories(
     ogs_metis PUBLIC ${metis_SOURCE_DIR}/GKlib ${metis_SOURCE_DIR}/include

From 7512578a23f6103eb3e847a9e9ef72f1ada3b786 Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Fri, 9 Sep 2022 21:51:16 +0200
Subject: [PATCH 18/36] [wheel] Win builds.

---
 Applications/Python/OpenGeoSys/__init__.py | 36 +++++++++++++---------
 CMakePresets.json                          | 21 +++++++++++++
 pyproject.toml                             |  9 ++++--
 setup.py                                   | 11 +++++--
 4 files changed, 57 insertions(+), 20 deletions(-)

diff --git a/Applications/Python/OpenGeoSys/__init__.py b/Applications/Python/OpenGeoSys/__init__.py
index 120592366f0..d4b704a8f3e 100644
--- a/Applications/Python/OpenGeoSys/__init__.py
+++ b/Applications/Python/OpenGeoSys/__init__.py
@@ -1,17 +1,8 @@
 import os
+import platform
 import subprocess
 import sys
 
-try:
-    from .lib64._cli import *
-except ImportError:
-    try:
-        from .lib._cli import *
-    except ImportError:
-        print("ERROR: could not import OpenGeoSys Python module!")
-
-OGS_BIN_DIR = os.path.join(os.path.join(os.path.dirname(__file__), "bin"))
-
 binaries_list = [
     "addDataToRaster",
     "AddElementQuality",
@@ -75,11 +66,26 @@
     "Vtu2Grid",
 ]
 
+if "PEP517_BUILD_BACKEND" not in os.environ:
+    if platform.system() == "Windows":
+        os.add_dll_directory(os.path.join(os.path.dirname(__file__), "bin"))
+        from .lib._cli import *
+    else:
+        try:
+            from .lib64._cli import *
+        except ImportError:
+            try:
+                from .lib._cli import *
+            except ImportError:
+                print("ERROR: could not import OpenGeoSys Python module!")
+
+    OGS_BIN_DIR = os.path.join(os.path.join(os.path.dirname(__file__), "bin"))
+
 
-def _program(name, args):
-    return subprocess.call([os.path.join(OGS_BIN_DIR, name)] + args)
+    def _program(name, args):
+        return subprocess.call([os.path.join(OGS_BIN_DIR, name)] + args)
 
 
-FUNC_TEMPLATE = """def {0}(): raise SystemExit(_program("{0}", sys.argv[1:]))"""
-for f in binaries_list:
-    exec(FUNC_TEMPLATE.format(f))
+    FUNC_TEMPLATE = """def {0}(): raise SystemExit(_program("{0}", sys.argv[1:]))"""
+    for f in binaries_list:
+        exec(FUNC_TEMPLATE.format(f))
diff --git a/CMakePresets.json b/CMakePresets.json
index 5eabcc4085b..500fcc83850 100644
--- a/CMakePresets.json
+++ b/CMakePresets.json
@@ -202,6 +202,23 @@
         "OGS_USE_PIP": "OFF",
         "OGS_USE_MFRONT": "ON",
         "BUILD_SHARED_LIBS": "ON"
+      },
+      "condition": {
+        "type": "notEquals",
+        "lhs": "${hostSystemName}",
+        "rhs": "Windows"
+      }
+    },
+    {
+      "name": "wheel-win",
+      "inherits": "wheel",
+      "cacheVariables": {
+        "OGS_USE_MFRONT": "OFF"
+      },
+      "condition": {
+        "type": "equals",
+        "lhs": "${hostSystemName}",
+        "rhs": "Windows"
       }
     }
   ],
@@ -290,6 +307,10 @@
     {
       "name": "wheel",
       "configurePreset": "wheel"
+    },
+    {
+      "name": "wheel-win",
+      "configurePreset": "wheel-win"
     }
   ],
   "testPresets": [
diff --git a/pyproject.toml b/pyproject.toml
index 69021cbd4a1..768f363e681 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,9 +1,10 @@
 [build-system]
 requires = [
   "setuptools>=42",
-  "scikit-build>=0.15.0",
+  "scikit-build @ git+https://github.com/bilke/scikit-build/@disable-cmake-install-check#egg=scikit-build ; platform_system == 'Windows'",
+  "scikit-build>=0.15.0 ; platform_system != 'Windows'",
   "cmake>=3.22",
-  "ninja; platform_system!='Windows'",
+  "ninja ; platform_system != 'Windows'",
 ]
 build-backend = "setuptools.build_meta"
 
@@ -17,6 +18,7 @@ build = "cp3*"
 skip = "*musllinux*"
 test-extras = "test"
 test-command = "pytest {project}/Tests/Python"
+# test-command = ""
 build-verbosity = "1"
 
 [tool.cibuildwheel.linux]
@@ -26,3 +28,6 @@ environment-pass = ["OGS_VERSION"]
 
 [tool.cibuildwheel.macos]
 skip = ["cp36-*", "cp37-*", "cp38-*x86_64"]
+
+[tool.cibuildwheel.windows]
+skip = ["cp36-*", "cp37-*"]
diff --git a/setup.py b/setup.py
index 2cb3ad792f5..e5a8c44f2da 100644
--- a/setup.py
+++ b/setup.py
@@ -13,7 +13,7 @@ def get_version():
         git_version = os.environ["OGS_VERSION"]
     else:
         git_version = subprocess.run(
-            ["git describe --tags"],
+            ["git", "describe", "--tags"],
             capture_output=True,
             text=True,
             shell=True,
@@ -32,13 +32,18 @@ def get_version():
         return git_version
 
 
-sys.path.append("Applications/Python")
+sys.path.append(os.path.join("Applications", "Python"))
 from OpenGeoSys import binaries_list
 
 console_scripts = []
 for b in binaries_list:
     console_scripts.append(f"{b}=OpenGeoSys:{b}")
 
+import platform
+cmake_preset = "wheel"
+if platform.system() == "Windows":
+    cmake_preset += "-win"
+
 setup(
     name="OpenGeoSys",
     version=get_version(),
@@ -49,7 +54,7 @@ def get_version():
     package_dir={"": "Applications/Python"},
     cmake_install_dir="Applications/Python/OpenGeoSys",
     extras_require={"test": ["pytest"]},
-    cmake_args=["--preset wheel", "-B ."],
+    cmake_args=[f"--preset {cmake_preset}", "-B ."],
     python_requires=">=3.6",
     entry_points={"console_scripts": console_scripts},
 )

From 7e96be7e88a8e8424531bb1c209686c525b77ac6 Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Fri, 9 Sep 2022 21:53:32 +0200
Subject: [PATCH 19/36] [ci] Added build wheels win job.

---
 CMakePresets.json                |  3 ++-
 scripts/ci/jobs/build-wheels.yml | 19 +++++++++++++++++++
 2 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/CMakePresets.json b/CMakePresets.json
index 500fcc83850..3f2871df967 100644
--- a/CMakePresets.json
+++ b/CMakePresets.json
@@ -213,7 +213,8 @@
       "name": "wheel-win",
       "inherits": "wheel",
       "cacheVariables": {
-        "OGS_USE_MFRONT": "OFF"
+        "OGS_USE_MFRONT": "OFF",
+        "OGS_BUILD_PROCESS_TH2M": "OFF"
       },
       "condition": {
         "type": "equals",
diff --git a/scripts/ci/jobs/build-wheels.yml b/scripts/ci/jobs/build-wheels.yml
index b08f6981978..213db165ae9 100644
--- a/scripts/ci/jobs/build-wheels.yml
+++ b/scripts/ci/jobs/build-wheels.yml
@@ -34,3 +34,22 @@ build wheels mac:
   parallel:
     matrix:
       - ARCHITECTURE: ["amd64", "arm64"]
+
+build wheels win:
+    stage: build
+    needs: [meta]
+    tags:
+      - windows
+    extends:
+      - .vs2019-environment
+    script:
+      - pipx run cibuildwheel
+      - >
+        pipx run twine upload
+        --repository-url https://gitlab.opengeosys.org/api/v4/projects/${CI_PROJECT_ID}/packages/pypi
+        --username gitlab-ci-token
+        --password ${CI_JOB_TOKEN}
+        wheelhouse/*
+    artifacts:
+      paths:
+        - wheelhouse/

From c925801e332dff9e23967d8c90b55227e7b03afb Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Tue, 13 Sep 2022 08:41:36 +0200
Subject: [PATCH 20/36] [cmake] Allow Python 3.11 wheel builds.

---
 pyproject.toml                  | 2 +-
 scripts/cmake/PythonSetup.cmake | 5 ++++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 768f363e681..acb60b62466 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,7 +15,7 @@ norecursedirs = ["Tests/Data"]
 [tool.cibuildwheel]
 archs = "auto64"
 build = "cp3*"
-skip = "*musllinux*"
+skip = ["*musllinux*"]
 test-extras = "test"
 test-command = "pytest {project}/Tests/Python"
 # test-command = ""
diff --git a/scripts/cmake/PythonSetup.cmake b/scripts/cmake/PythonSetup.cmake
index 14ac317021d..ef6be751483 100644
--- a/scripts/cmake/PythonSetup.cmake
+++ b/scripts/cmake/PythonSetup.cmake
@@ -1,6 +1,9 @@
 # cmake-lint: disable=C0103
 
-set(_python_version_max "...<3.11")
+if(OGS_USE_PYTHON)
+    set(_python_version_max "...<3.11")
+endif()
+
 if(OGS_USE_PIP)
     set(Python_ROOT_DIR ${PROJECT_BINARY_DIR}/.venv)
     set(CMAKE_REQUIRE_FIND_PACKAGE_Python TRUE)

From 4f5d8a36a229f1b7545f134326794e64d497f071 Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Tue, 13 Sep 2022 14:38:26 +0200
Subject: [PATCH 21/36] [py] Renamed wheels package to ogs and coupling module
 to ogs.simulator.

---
 Applications/Python/CMakeLists.txt            | 18 +--------------
 .../Python/ogs.simulator/CMakeLists.txt       | 21 ++++++++++++++++++
 .../{ => ogs.simulator}/ogs_python_module.cpp |  3 ++-
 .../Python/{OpenGeoSys => ogs}/__init__.py    | 11 ----------
 Tests/Python/test_cli.py                      | 22 +++----------------
 Tests/Python/test_simlator.py                 | 20 +++++++++++++++++
 pyproject.toml                                |  3 +--
 scripts/cmake/ProjectSetup.cmake              |  8 +++++--
 setup.py                                      | 19 +++++++++-------
 9 files changed, 65 insertions(+), 60 deletions(-)
 create mode 100644 Applications/Python/ogs.simulator/CMakeLists.txt
 rename Applications/Python/{ => ogs.simulator}/ogs_python_module.cpp (98%)
 rename Applications/Python/{OpenGeoSys => ogs}/__init__.py (87%)
 create mode 100644 Tests/Python/test_simlator.py

diff --git a/Applications/Python/CMakeLists.txt b/Applications/Python/CMakeLists.txt
index ef45e964522..667d1aff703 100644
--- a/Applications/Python/CMakeLists.txt
+++ b/Applications/Python/CMakeLists.txt
@@ -1,17 +1 @@
-# Create OpenGeoSys python module
-# https://pybind11.readthedocs.io/en/stable/compiling.html#building-with-cmake
-pybind11_add_module(
-    _cli MODULE ogs_python_module.cpp ../CLI/CommandLineArgumentParser.cpp
-)
-
-# lld linker strips out PyInit_OpenGeoSys symbol. Use standard linker.
-get_target_property(_link_options _cli LINK_OPTIONS)
-if(_link_options)
-    list(REMOVE_ITEM _link_options -fuse-ld=lld)
-    set_target_properties(_cli PROPERTIES LINK_OPTIONS "${_link_options}")
-endif()
-
-target_link_libraries(_cli PRIVATE ApplicationsLib BaseLib CMakeInfoLib GitInfoLib tclap)
-target_include_directories(_cli PRIVATE ../CLI)
-
-install(TARGETS _cli LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
+add_subdirectory(ogs.simulator)
diff --git a/Applications/Python/ogs.simulator/CMakeLists.txt b/Applications/Python/ogs.simulator/CMakeLists.txt
new file mode 100644
index 00000000000..dce167cd59f
--- /dev/null
+++ b/Applications/Python/ogs.simulator/CMakeLists.txt
@@ -0,0 +1,21 @@
+# Create OpenGeoSys python module
+# https://pybind11.readthedocs.io/en/stable/compiling.html#building-with-cmake
+pybind11_add_module(
+    simulator MODULE ogs_python_module.cpp
+    ../../CLI/CommandLineArgumentParser.cpp
+)
+
+# lld linker strips out PyInit_OpenGeoSys symbol. Use standard linker.
+get_target_property(_link_options simulator LINK_OPTIONS)
+if(_link_options)
+    list(REMOVE_ITEM _link_options -fuse-ld=lld)
+    set_target_properties(simulator PROPERTIES LINK_OPTIONS "${_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/Python/ogs_python_module.cpp b/Applications/Python/ogs.simulator/ogs_python_module.cpp
similarity index 98%
rename from Applications/Python/ogs_python_module.cpp
rename to Applications/Python/ogs.simulator/ogs_python_module.cpp
index c3e6f190a87..ab4103c7c65 100644
--- a/Applications/Python/ogs_python_module.cpp
+++ b/Applications/Python/ogs.simulator/ogs_python_module.cpp
@@ -122,8 +122,9 @@ void finalize()
 }
 
 /// python module name is OpenGeoSys
-PYBIND11_MODULE(_cli, 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/OpenGeoSys/__init__.py b/Applications/Python/ogs/__init__.py
similarity index 87%
rename from Applications/Python/OpenGeoSys/__init__.py
rename to Applications/Python/ogs/__init__.py
index d4b704a8f3e..2aca7ae9d52 100644
--- a/Applications/Python/OpenGeoSys/__init__.py
+++ b/Applications/Python/ogs/__init__.py
@@ -69,23 +69,12 @@
 if "PEP517_BUILD_BACKEND" not in os.environ:
     if platform.system() == "Windows":
         os.add_dll_directory(os.path.join(os.path.dirname(__file__), "bin"))
-        from .lib._cli import *
-    else:
-        try:
-            from .lib64._cli import *
-        except ImportError:
-            try:
-                from .lib._cli import *
-            except ImportError:
-                print("ERROR: could not import OpenGeoSys Python module!")
 
     OGS_BIN_DIR = os.path.join(os.path.join(os.path.dirname(__file__), "bin"))
 
-
     def _program(name, args):
         return subprocess.call([os.path.join(OGS_BIN_DIR, name)] + args)
 
-
     FUNC_TEMPLATE = """def {0}(): raise SystemExit(_program("{0}", sys.argv[1:]))"""
     for f in binaries_list:
         exec(FUNC_TEMPLATE.format(f))
diff --git a/Tests/Python/test_cli.py b/Tests/Python/test_cli.py
index e2b60fc4fd4..52a50e2acb6 100644
--- a/Tests/Python/test_cli.py
+++ b/Tests/Python/test_cli.py
@@ -3,29 +3,13 @@
 
 import pytest
 
-import OpenGeoSys
-
-
-def test_module():
-    arguments = [
-        "",
-        f"{os.path.abspath(os.path.dirname(__file__))}/../Data/Parabolic/LiquidFlow/Flux/cube_1e3_calculatesurfaceflux.prj",
-        "-o " + tempfile.mkdtemp(),
-    ]
-
-    print("Python OpenGeoSys.init ...")
-    OpenGeoSys.initialize(arguments)
-    print("Python OpenGeoSys.executeSimulation ...")
-    OpenGeoSys.executeSimulation()
-    print("Python OpenGeoSys.finalize() ...")
-    OpenGeoSys.finalize()
-
+import ogs
 
 from . import push_argv
 
 
 def _run(program, args):
-    func = getattr(OpenGeoSys, program)
+    func = getattr(ogs, program)
     args = ["%s.py" % program] + args
     with push_argv(args), pytest.raises(SystemExit) as excinfo:
         func()
@@ -34,6 +18,6 @@ def _run(program, args):
 
 def test_binaries():
     ignore_list = ["moveMeshNodes", "mpmetis", "tetgen"]  # have no --version cli flag
-    for f in OpenGeoSys.binaries_list:
+    for f in ogs.binaries_list:
         if f not in ignore_list:
             _run(f, ["--version"])
diff --git a/Tests/Python/test_simlator.py b/Tests/Python/test_simlator.py
new file mode 100644
index 00000000000..bb41cad5e08
--- /dev/null
+++ b/Tests/Python/test_simlator.py
@@ -0,0 +1,20 @@
+import tempfile
+import os
+
+import pytest
+import ogs.simulator as sim
+
+
+def test_simulator():
+    arguments = [
+        "",
+        f"{os.path.abspath(os.path.dirname(__file__))}/../Data/Parabolic/LiquidFlow/Flux/cube_1e3_calculatesurfaceflux.prj",
+        "-o " + tempfile.mkdtemp(),
+    ]
+
+    print("Python OpenGeoSys.init ...")
+    sim.initialize(arguments)
+    print("Python OpenGeoSys.executeSimulation ...")
+    sim.executeSimulation()
+    print("Python OpenGeoSys.finalize() ...")
+    sim.finalize()
diff --git a/pyproject.toml b/pyproject.toml
index acb60b62466..5dc4a1ce709 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,13 +15,12 @@ norecursedirs = ["Tests/Data"]
 [tool.cibuildwheel]
 archs = "auto64"
 build = "cp3*"
-skip = ["*musllinux*"]
 test-extras = "test"
 test-command = "pytest {project}/Tests/Python"
-# test-command = ""
 build-verbosity = "1"
 
 [tool.cibuildwheel.linux]
+skip = ["*musllinux*", "cp36-*"]
 manylinux-x86_64-image = "manylinux2014"
 manylinux-aarch64-image = "manylinux2014"
 environment-pass = ["OGS_VERSION"]
diff --git a/scripts/cmake/ProjectSetup.cmake b/scripts/cmake/ProjectSetup.cmake
index 597971cecf2..16bd5894c4d 100644
--- a/scripts/cmake/ProjectSetup.cmake
+++ b/scripts/cmake/ProjectSetup.cmake
@@ -40,8 +40,12 @@ endif()
 file(RELATIVE_PATH relDir ${CMAKE_CURRENT_BINARY_DIR}/${CMAKE_INSTALL_BINDIR}
      ${CMAKE_CURRENT_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR}
 )
-list(APPEND CMAKE_INSTALL_RPATH ${BASEPOINT} ${BASEPOINT}/${relDir})
-list(APPEND CMAKE_BUILD_RPATH ${BASEPOINT} ${BASEPOINT}/${relDir})
+list(APPEND CMAKE_INSTALL_RPATH ${BASEPOINT} ${BASEPOINT}/${relDir}
+     ${BASEPOINT}/${CMAKE_INSTALL_LIBDIR} # Python modules
+)
+list(APPEND CMAKE_BUILD_RPATH ${BASEPOINT} ${BASEPOINT}/${relDir}
+     ${BASEPOINT}/${CMAKE_INSTALL_LIBDIR} # Python modules
+)
 
 # Some external dependencies always use lib instead of lib64, Fix for
 # lib64-based systems, e.g. OpenSUSE:
diff --git a/setup.py b/setup.py
index e5a8c44f2da..93a30713680 100644
--- a/setup.py
+++ b/setup.py
@@ -2,6 +2,7 @@
 from setuptools import find_packages
 
 import os
+import platform
 import re
 import subprocess
 import sys
@@ -12,8 +13,11 @@ def get_version():
     if "OGS_VERSION" in os.environ:
         git_version = os.environ["OGS_VERSION"]
     else:
+        git_describe_cmd = ["git describe --tags"]
+        if platform.system() == "Windows":
+            git_describe_cmd = ["git", "describe", "--tags"]
         git_version = subprocess.run(
-            ["git", "describe", "--tags"],
+            git_describe_cmd,
             capture_output=True,
             text=True,
             shell=True,
@@ -33,28 +37,27 @@ def get_version():
 
 
 sys.path.append(os.path.join("Applications", "Python"))
-from OpenGeoSys import binaries_list
+from ogs import binaries_list
 
 console_scripts = []
 for b in binaries_list:
-    console_scripts.append(f"{b}=OpenGeoSys:{b}")
+    console_scripts.append(f"{b}=ogs:{b}")
 
-import platform
 cmake_preset = "wheel"
 if platform.system() == "Windows":
     cmake_preset += "-win"
 
 setup(
-    name="OpenGeoSys",
+    name="ogs",
     version=get_version(),
-    description="OpenGeoSys",
+    description="OpenGeoSys Python Module",
     author="OpenGeoSys Community",
     license="BSD-3-Clause",
     packages=find_packages(where="Applications/Python"),
     package_dir={"": "Applications/Python"},
-    cmake_install_dir="Applications/Python/OpenGeoSys",
+    cmake_install_dir="Applications/Python/ogs",
     extras_require={"test": ["pytest"]},
     cmake_args=[f"--preset {cmake_preset}", "-B ."],
-    python_requires=">=3.6",
+    python_requires=">=3.7",
     entry_points={"console_scripts": console_scripts},
 )

From 3469b061d5e3022ef09093b4ba3b656e8073bfb3 Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Tue, 13 Sep 2022 14:57:02 +0200
Subject: [PATCH 22/36] [ci] Upload release wheels.

---
 scripts/ci/jobs/release.yml | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/scripts/ci/jobs/release.yml b/scripts/ci/jobs/release.yml
index 81bba47813a..bb2581ec1ca 100644
--- a/scripts/ci/jobs/release.yml
+++ b/scripts/ci/jobs/release.yml
@@ -9,3 +9,24 @@ release:
   release:
     tag_name: "$CI_COMMIT_TAG"
     description: "Created using the GitLab release-cli."
+
+publish wheels:
+  stage: release
+  needs: ["build wheels linux", "build wheels mac", "build wheels win"]
+  tags: [envinf, shell]
+  rules:
+    - if: $CI_COMMIT_REF_NAME == $CI_DEFAULT_BRANCH
+      variables:
+        PYPI_PASSWORD: "${TEST_PYPI_TOKEN}"
+        PYPI_REPO: testpypi
+    - if: $CI_COMMIT_TAG
+      variables:
+        PYPI_PASSWORD: "${PYPI_TOKEN}"
+        PYPI_REPO: pypi
+  script:
+    - >
+      pipx run twine upload
+      --repository ${PYPI_REPO}
+      --username __token__
+      --password ${PYPI_PASSWORD}
+      wheelhouse/*

From a563fa8d3121be89f5bb2541788a27e6387fc333 Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Tue, 13 Sep 2022 15:37:15 +0200
Subject: [PATCH 23/36] [wheel] Enable all processes.

---
 CMakePresets.json | 1 -
 1 file changed, 1 deletion(-)

diff --git a/CMakePresets.json b/CMakePresets.json
index 3f2871df967..583bde18d31 100644
--- a/CMakePresets.json
+++ b/CMakePresets.json
@@ -192,7 +192,6 @@
       "name": "wheel",
       "inherits": "release",
       "cacheVariables": {
-        "OGS_BUILD_PROCESSES": "LiquidFlow",
         "HDF5_USE_STATIC_LIBRARIES": "ON",
         "OGS_BUILD_HDF5": "ON",
         "OGS_USE_PYTHON": "OFF",

From c286aa7931ce32935f51a7ee1c015370e4754ca2 Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Tue, 13 Sep 2022 22:26:44 +0200
Subject: [PATCH 24/36] [ML] Fixed linking issue under macOS when
 BUILD_SHARED_LIBS=ON.

Linker error was:

Undefined symbols for architecture arm64:
  "MaterialLib::Solids::Ehlers::StateVariables<2>::getEquivalentPlasticStrain() const", referenced from:
      vtable for MaterialLib::Solids::Ehlers::StateVariables<2> in unity_0_cxx.cxx.o
  "MaterialLib::Solids::Ehlers::StateVariables<3>::getEquivalentPlasticStrain() const", referenced from:
      vtable for MaterialLib::Solids::Ehlers::StateVariables<3> in
      unity_0_cxx.cxx.o
---
 MaterialLib/SolidModels/Ehlers.cpp |  3 +++
 MaterialLib/SolidModels/Ehlers.h   | 10 ++++++----
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/MaterialLib/SolidModels/Ehlers.cpp b/MaterialLib/SolidModels/Ehlers.cpp
index 28adfbd6cae..83995b28955 100644
--- 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
index 9c9d3ec2bfb..d984878cf13 100644
--- 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

From 81c35a6fd128eee0ee196de9e3292b5e9e0dcba2 Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Tue, 13 Sep 2022 22:35:49 +0200
Subject: [PATCH 25/36] [wheel] Include README.

---
 setup.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/setup.py b/setup.py
index 93a30713680..a9cd2b4b9f7 100644
--- a/setup.py
+++ b/setup.py
@@ -47,10 +47,17 @@ def get_version():
 if platform.system() == "Windows":
     cmake_preset += "-win"
 
+from pathlib import Path
+
+this_directory = Path(__file__).parent
+long_description = (this_directory / "README.md").read_text()
+
 setup(
     name="ogs",
     version=get_version(),
     description="OpenGeoSys Python Module",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
     author="OpenGeoSys Community",
     license="BSD-3-Clause",
     packages=find_packages(where="Applications/Python"),

From f9c6e4e17e2407c021885a6b6d8a611a5cc6aadb Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Wed, 14 Sep 2022 12:56:58 +0200
Subject: [PATCH 26/36] [ci] Refactor wheel jobs to use template.

---
 scripts/ci/jobs/build-wheels.yml | 53 +++++++++-----------------------
 1 file changed, 15 insertions(+), 38 deletions(-)

diff --git a/scripts/ci/jobs/build-wheels.yml b/scripts/ci/jobs/build-wheels.yml
index 213db165ae9..b43eb0402b7 100644
--- a/scripts/ci/jobs/build-wheels.yml
+++ b/scripts/ci/jobs/build-wheels.yml
@@ -1,55 +1,32 @@
-build wheels linux:
+.wheels_template: &wheels_template
   stage: build
   needs: [meta]
-  tags: [envinf3-shell]
   script:
     - pipx run cibuildwheel
-    - >
-      pipx run twine upload
-      --repository-url https://gitlab.opengeosys.org/api/v4/projects/${CI_PROJECT_ID}/packages/pypi
-      --username gitlab-ci-token
-      --password ${CI_JOB_TOKEN}
-      wheelhouse/*
+  rules:
+    - if: $CI_COMMIT_REF_NAME == $CI_DEFAULT_BRANCH
+    - if: $CI_COMMIT_TAG
   artifacts:
     paths:
       - wheelhouse/
 
+build wheels linux:
+  tags: [envinf3-shell]
+  <<: *wheels_template
+
 build wheels mac:
-  stage: build
-  needs: [meta]
   tags:
     - mac
     - ${ARCHITECTURE}
-  script:
-    - CMAKE_OSX_DEPLOYMENT_TARGET=10.15 pipx run cibuildwheel
-    - >
-      pipx run twine upload
-      --repository-url https://gitlab.opengeosys.org/api/v4/projects/${CI_PROJECT_ID}/packages/pypi
-      --username gitlab-ci-token
-      --password ${CI_JOB_TOKEN}
-      wheelhouse/*
-  artifacts:
-    paths:
-      - wheelhouse/
+  variables:
+    CMAKE_OSX_DEPLOYMENT_TARGET: "10.15"
   parallel:
     matrix:
       - ARCHITECTURE: ["amd64", "arm64"]
+  <<: *wheels_template
 
 build wheels win:
-    stage: build
-    needs: [meta]
-    tags:
-      - windows
-    extends:
-      - .vs2019-environment
-    script:
-      - pipx run cibuildwheel
-      - >
-        pipx run twine upload
-        --repository-url https://gitlab.opengeosys.org/api/v4/projects/${CI_PROJECT_ID}/packages/pypi
-        --username gitlab-ci-token
-        --password ${CI_JOB_TOKEN}
-        wheelhouse/*
-    artifacts:
-      paths:
-        - wheelhouse/
+  tags: [windows]
+  extends:
+    - .vs2019-environment
+  <<: *wheels_template

From dd0afe59f0172629b0856745f6702de91f810bb2 Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Wed, 14 Sep 2022 20:17:06 +0200
Subject: [PATCH 27/36] [ci] Run jupyter job on envinf2 and envinf3.

---
 scripts/ci/jobs/jupyter.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/ci/jobs/jupyter.yml b/scripts/ci/jobs/jupyter.yml
index 875e30ff859..039cd85185c 100644
--- a/scripts/ci/jobs/jupyter.yml
+++ b/scripts/ci/jobs/jupyter.yml
@@ -1,7 +1,7 @@
 # Built for Sandy Bridge (envinf1) and newer
 build jupyter:
   stage: build
-  tags: [envinf, shell]
+  tags: [envinf23, shell]
   needs: [meta]
   extends:
     - .container-maker-setup

From a06d04465eece7fde3c61867e433f25a8213dc83 Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Wed, 14 Sep 2022 20:17:08 +0200
Subject: [PATCH 28/36] [ci] Run clang-format only on .h and .cpp files.

---
 scripts/ci/jobs/pre-commit.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/ci/jobs/pre-commit.yml b/scripts/ci/jobs/pre-commit.yml
index 292e826aeab..10672766a16 100644
--- a/scripts/ci/jobs/pre-commit.yml
+++ b/scripts/ci/jobs/pre-commit.yml
@@ -20,7 +20,7 @@ clang-format:
   needs: [ci_images]
   allow_failure: true
   script:
-    - git clang-format ${CI_MERGE_REQUEST_TARGET_BRANCH_SHA}
+    - git clang-format --extensions "h,cpp" ${CI_MERGE_REQUEST_TARGET_BRANCH_SHA}
     - if [[ $(git diff) ]]; then exit 1; fi
   after_script:
     - git diff

From d65f121aed9079fd6d91e3656b6a7e2474e04ad9 Mon Sep 17 00:00:00 2001
From: GitLab Runner <ci@opengeosys.org>
Date: Wed, 14 Sep 2022 20:44:20 +0200
Subject: [PATCH 29/36] [versions] Updated cpm cache info.

---
 web/data/versions.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/web/data/versions.json b/web/data/versions.json
index d064e9cdf8d..45f0d34dee4 100644
--- a/web/data/versions.json
+++ b/web/data/versions.json
@@ -71,8 +71,8 @@
     }
   },
   "cpm": {
-    "package_file_id": 119,
-    "package_file_sha256": "7d98b148e6d24acd72d17d2503f3ce3bab74029da5b3328788b2d4c379e9dcac"
+    "package_file_id": 182,
+    "package_file_sha256": "00d7dea24754ad415e7003535b36a7d5b4e7224701341f5ca587f93e42b63563"
   },
   "ext": {
     "cache_hash": "e6f3f1f4c29c6c5f096f89785e6e245bdf39ac1a"

From eec595dec3e655566c236ecb28c32a8f225dae27 Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Thu, 15 Sep 2022 09:05:01 +0200
Subject: [PATCH 30/36] [wheel] Removed unnecessary else statements.

---
 setup.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/setup.py b/setup.py
index a9cd2b4b9f7..e607d50f4a5 100644
--- a/setup.py
+++ b/setup.py
@@ -29,11 +29,10 @@ def get_version():
         m = re.match(".+?(?=-g[\w]*$)", git_version)  # strip out commit hash
         if m:
             return m.group(0).replace("-", ".dev")  # insert dev
-        else:
-            print("WARNING: Could not get ogs version!")
-            exit(1)
-    else:
-        return git_version
+        print("ERROR: Could not get ogs version!")
+        exit(1)
+
+    return git_version
 
 
 sys.path.append(os.path.join("Applications", "Python"))

From b28f26aefec5529cb7e37b38de3212c2d665a486 Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Thu, 15 Sep 2022 17:41:11 +0200
Subject: [PATCH 31/36] [web] Added docs on pip install usage and wheel
 development.

---
 .../devguide/advanced/python-wheel/index.md   | 75 +++++++++++++++++++
 .../userguide/basics/introduction/index.md    | 52 ++++++++++++-
 2 files changed, 124 insertions(+), 3 deletions(-)
 create mode 100644 web/content/docs/devguide/advanced/python-wheel/index.md

diff --git a/web/content/docs/devguide/advanced/python-wheel/index.md b/web/content/docs/devguide/advanced/python-wheel/index.md
new file mode 100644
index 00000000000..91154b43ab4
--- /dev/null
+++ b/web/content/docs/devguide/advanced/python-wheel/index.md
@@ -0,0 +1,75 @@
++++
+date = "2022-02-09T11:00:13+01:00"
+title = "Python wheel development"
+author = "Lars Bilke"
+weight = 1068
+
+[menu]
+  [menu.devguide]
+    parent = "advanced"
++++
+
+## Local setup
+
+Python wheel builds are driven by [scikit-build](https://scikit-build.readthedocs.io/en/latest/) which basically is a `setuptools`-wrapper for CMake-based projects.
+
+The entrypoint is `setup.py` in the root directory. It uses the `wheel` CMake preset (or `wheel-win` on Windows).
+
+You can locally develop and test with the following setup:
+
+```bash
+# Create a virtual environment inside your source directory
+python3 -m venv .venv
+# Activate the environment
+source .venv/bin/activate
+# Install (build) the local Python project
+pip install -v .[test]
+...
+Successfully installed ogs-6.4.2.dev1207
+```
+
+The `pip install`-step starts a new CMake-based ogs build in `_skbuild`-subdirectory (inside the source code) using the `wheel`-preset. When the CMake build is done it installs the wheel into the activated virtual environment and you can interact with it, e.g.:
+
+```bash
+# Run python tests
+pytest
+============================================== test session starts ===============================================
+platform darwin -- Python 3.10.6, pytest-7.1.3, pluggy-1.0.0
+rootdir: ~/code/ogs/ogs, configfile: pyproject.toml, testpaths: Tests
+collected 2 items
+
+Tests/Python/test_cli.py .                                                                                 [ 50%]
+Tests/Python/test_simlator.py .                                                                            [100%]
+
+=============================================== 2 passed in 0.55s ================================================
+
+# Start the python interpreter
+python3
+>>> import ogs.simulator as sim
+>>> sim.initialize(["", "--help"])
+```
+
+If you make modifications you need to run `pip install .[test]` again (or for temporary modifications you can directly edit inside the virtual environment, e.g. in `.venv/lib/python3.10/site-packages/ogs`).
+
+The contents of `_skbuild/[platform-specific]/cmake-install` will make up the wheel.
+
+## CI
+
+For generating the various wheels for different Python versions and platforms [`cibuildwheel`](https://cibuildwheel.readthedocs.io/en/stable/) is used.
+
+You can test it locally with, e.g. only building for Python 3.10:
+
+```bash
+CIBW_BUILD="cp310*" pipx run cibuildwheel
+```
+
+Please note that on Linux `cibuildwheel` runs the builds inside [manylinux](https://github.com/pypa/manylinux) Docker containers. On other platforms the build happens with native tools. See the [cibuildwheel docs](https://cibuildwheel.readthedocs.io/en/stable/#how-it-works) for more information.
+
+Wheels are generated in the `wheelhouse/`-folder.
+
+`cibuildwheel` is configured in `pyproject.toml`:
+
+```toml
+[tool.cibuildwheel]
+...
+```
diff --git a/web/content/docs/userguide/basics/introduction/index.md b/web/content/docs/userguide/basics/introduction/index.md
index 208d6437359..d808b4c07ce 100644
--- a/web/content/docs/userguide/basics/introduction/index.md
+++ b/web/content/docs/userguide/basics/introduction/index.md
@@ -15,14 +15,60 @@ weight = 1
 post = "Download, install and run an OGS benchmark in 5 minutes! No development setup required."
 +++
 
-## Download
+## Installation
 
-Download the latest release of OpenGeoSys from the [Releases](/releases)-page. Be sure to pick the correct file for your operating system.
+<div class='win'>
 
-## Installation
+Download the latest release of OpenGeoSys from the [Releases](/releases)-page. Be sure to pick the correct file for your operating system.
 
 OGS itself is a simple executable file so you can put it anywhere you like. For convenience you may put into a location which is in your `PATH`-environment variable which allows you to start the executable without specifying its full file path.
 
+<div class="note">
+
+### Alternative: Install via `pip`
+
+You can also install ogs via Python's [`pip`-tool](https://packaging.python.org/en/latest/tutorials/installing-packages/):
+
+```bat
+pip install ogs
+```
+
+If you install into an activated [virtual environment](https://docs.python.org/3/library/venv.html) then ogs and its tools are automatically also in the `PATH`. Otherwise `pip` will print instructions which directory needs to be added to the `PATH`.
+
+</div>
+
+</div>
+
+<div class='linux'>
+
+Install via Python's [`pip`-tool](https://packaging.python.org/en/latest/tutorials/installing-packages/):
+
+```bash
+pip install ogs
+```
+
+You may want to set up and activate a [virtual environment](https://docs.python.org/3/library/venv.html) before.
+
+You could also use [`pipx`](https://pypa.github.io/pipx/) to install into an isolated environment.
+
+</div>
+
+<div class='mac'>
+
+See Linux tab!
+
+</div>
+
+<div class="note">
+
+### Limitations of the `pip`-based installation
+
+- Serial config only! For PETSc-support please use a [Singularity container]({{< relref "container" >}}).
+- No embedded Python interpreter, i.e. no Python boundary conditions!
+- A Python (3.8 - 3.11) installation with `pip` is required.
+
+</div>
+
 ## Download benchmarks
 
 You can download the latest benchmark files from GitLab:

From ce05ebb88786da9b2a737c89ba16e23a5b25f346 Mon Sep 17 00:00:00 2001
From: Christoph Lehmann <christoph.lehmann@ufz.de>
Date: Fri, 16 Sep 2022 07:48:53 +0200
Subject: [PATCH 32/36] [App] Moved Python code for CLI tools

---
 Applications/Python/ogs/__init__.py           | 80 -------------------
 Applications/Python/ogs/_internal/__init__.py |  0
 .../provide_ogs_cli_tools_via_wheel.py        | 80 +++++++++++++++++++
 3 files changed, 80 insertions(+), 80 deletions(-)
 create mode 100644 Applications/Python/ogs/_internal/__init__.py
 create mode 100644 Applications/Python/ogs/_internal/provide_ogs_cli_tools_via_wheel.py

diff --git a/Applications/Python/ogs/__init__.py b/Applications/Python/ogs/__init__.py
index 2aca7ae9d52..e69de29bb2d 100644
--- a/Applications/Python/ogs/__init__.py
+++ b/Applications/Python/ogs/__init__.py
@@ -1,80 +0,0 @@
-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:
-    if platform.system() == "Windows":
-        os.add_dll_directory(os.path.join(os.path.dirname(__file__), "bin"))
-
-    OGS_BIN_DIR = os.path.join(os.path.join(os.path.dirname(__file__), "bin"))
-
-    def _program(name, args):
-        return subprocess.call([os.path.join(OGS_BIN_DIR, name)] + args)
-
-    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/Python/ogs/_internal/__init__.py b/Applications/Python/ogs/_internal/__init__.py
new file mode 100644
index 00000000000..e69de29bb2d
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
new file mode 100644
index 00000000000..2aca7ae9d52
--- /dev/null
+++ 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:
+    if platform.system() == "Windows":
+        os.add_dll_directory(os.path.join(os.path.dirname(__file__), "bin"))
+
+    OGS_BIN_DIR = os.path.join(os.path.join(os.path.dirname(__file__), "bin"))
+
+    def _program(name, args):
+        return subprocess.call([os.path.join(OGS_BIN_DIR, name)] + args)
+
+    FUNC_TEMPLATE = """def {0}(): raise SystemExit(_program("{0}", sys.argv[1:]))"""
+    for f in binaries_list:
+        exec(FUNC_TEMPLATE.format(f))

From ccf3ea0bb124bbf303bec82b17f3c3c0c308b2a7 Mon Sep 17 00:00:00 2001
From: Christoph Lehmann <christoph.lehmann@ufz.de>
Date: Fri, 16 Sep 2022 07:50:36 +0200
Subject: [PATCH 33/36] [App] Use recommended subprocess method

---
 .../Python/ogs/_internal/provide_ogs_cli_tools_via_wheel.py     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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
index 2aca7ae9d52..6399fd881b7 100644
--- a/Applications/Python/ogs/_internal/provide_ogs_cli_tools_via_wheel.py
+++ b/Applications/Python/ogs/_internal/provide_ogs_cli_tools_via_wheel.py
@@ -73,7 +73,7 @@
     OGS_BIN_DIR = os.path.join(os.path.join(os.path.dirname(__file__), "bin"))
 
     def _program(name, args):
-        return subprocess.call([os.path.join(OGS_BIN_DIR, 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:

From f86edadd20be2ebbb466450faee14eaab4998c32 Mon Sep 17 00:00:00 2001
From: Christoph Lehmann <christoph.lehmann@ufz.de>
Date: Fri, 16 Sep 2022 10:56:10 +0200
Subject: [PATCH 34/36] Reflect moved Python code in setup.py

---
 setup.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index e607d50f4a5..177b162c830 100644
--- a/setup.py
+++ b/setup.py
@@ -36,11 +36,11 @@ def get_version():
 
 
 sys.path.append(os.path.join("Applications", "Python"))
-from ogs import binaries_list
+from ogs._internal.provide_ogs_cli_tools_via_wheel import binaries_list
 
 console_scripts = []
 for b in binaries_list:
-    console_scripts.append(f"{b}=ogs:{b}")
+    console_scripts.append(f"{b}=ogs._internal.provide_ogs_cli_tools_via_wheel:{b}")
 
 cmake_preset = "wheel"
 if platform.system() == "Windows":

From fb2d813a6c01f9ef702b129052da215b1c7ac52f Mon Sep 17 00:00:00 2001
From: Christoph Lehmann <christoph.lehmann@ufz.de>
Date: Fri, 16 Sep 2022 13:01:28 +0200
Subject: [PATCH 35/36] [T] Adjusted Python CLI tool test.

---
 Tests/Python/test_cli.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Tests/Python/test_cli.py b/Tests/Python/test_cli.py
index 52a50e2acb6..c9d23bb8d79 100644
--- a/Tests/Python/test_cli.py
+++ b/Tests/Python/test_cli.py
@@ -3,13 +3,13 @@
 
 import pytest
 
-import ogs
+import ogs._internal.provide_ogs_cli_tools_via_wheel as ogs_cli_wheel
 
 from . import push_argv
 
 
 def _run(program, args):
-    func = getattr(ogs, program)
+    func = getattr(ogs_cli_wheel, program)
     args = ["%s.py" % program] + args
     with push_argv(args), pytest.raises(SystemExit) as excinfo:
         func()
@@ -18,6 +18,6 @@ def _run(program, args):
 
 def test_binaries():
     ignore_list = ["moveMeshNodes", "mpmetis", "tetgen"]  # have no --version cli flag
-    for f in ogs.binaries_list:
+    for f in ogs_cli_wheel.binaries_list:
         if f not in ignore_list:
             _run(f, ["--version"])

From dfd918f52122657424d0664e38c856e98fa0b53b Mon Sep 17 00:00:00 2001
From: Christoph Lehmann <christoph.lehmann@ufz.de>
Date: Mon, 19 Sep 2022 08:10:39 +0200
Subject: [PATCH 36/36] [App] Corrected OGS_BIN_DIR

---
 .../Python/ogs/_internal/provide_ogs_cli_tools_via_wheel.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

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
index 6399fd881b7..ea18d343753 100644
--- a/Applications/Python/ogs/_internal/provide_ogs_cli_tools_via_wheel.py
+++ b/Applications/Python/ogs/_internal/provide_ogs_cli_tools_via_wheel.py
@@ -67,10 +67,10 @@
 ]
 
 if "PEP517_BUILD_BACKEND" not in os.environ:
-    if platform.system() == "Windows":
-        os.add_dll_directory(os.path.join(os.path.dirname(__file__), "bin"))
+    OGS_BIN_DIR = os.path.join(os.path.join(os.path.dirname(__file__), "..", "bin"))
 
-    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