Merge pull request #354 from F2I-Consulting/dev

v2.12.0.0

Author: philippeVerney

.github/workflows/github-actions.yml

@@ -166,6 +166,40 @@ jobs:
         with:
           name: ubuntu-20.04-${{ matrix.cxx }}
           path: ${{ runner.temp }}/fesapi-install
+  build_wheels_windows:
+    name: Build wheels on windows-latest
+    runs-on: windows-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Stub `setup.py` check
+        # It will be generated during CMake run
+        # https://github.com/pypa/cibuildwheel/issues/1139
+        run: touch python/setup.py
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.21.3
+        env:
+          CIBW_BUILD: cp38-win_amd64 cp39-win_amd64 cp310-win_amd64 cp311-win_amd64 cp312-win_amd64 cp313-win_amd64
+          CIBW_ARCHS: auto64
+          CIBW_MANYLINUX_X86_64_IMAGE: manylinux_2_28
+          CIBW_BEFORE_ALL: >
+            %VCPKG_INSTALLATION_ROOT%\vcpkg install boost-uuid minizip hdf5[zlib] &&
+            cd ${{ runner.temp }} &&
+            mkdir fesapi-build &&
+            cd fesapi-build &&
+            cmake -DCMAKE_TOOLCHAIN_FILE=%VCPKG_INSTALLATION_ROOT%\scripts\buildsystems\vcpkg.cmake -G"Visual Studio 17 2022" -A x64 -T host=x64 -Wno-dev -Wno-deprecated -DWITH_PYTHON_WRAPPING=TRUE -DCMAKE_INSTALL_PREFIX=${{ runner.temp }}/fesapi-install ${{ github.workspace }} &&
+            cmake --build . --config Release -j2 &&
+            cmake --build . --config Release --target INSTALL &&
+            pip install delvewheel
+          CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: >
+            delvewheel repair --add-path ${{ runner.temp }}\fesapi-build\Release --namespace-pkg fesapi -w {dest_dir} {wheel}
+          CIBW_TEST_COMMAND: python ${{github.workspace}}\python\example\example.py
+        with:
+          package-dir: ./python
+          output-dir: wheelhouse
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-windows
+          path: ./wheelhouse/*.whl
   build_wheels_linux:
     name: Build wheels on ubuntu-latest
     runs-on: ubuntu-latest
@@ -176,28 +210,20 @@ jobs:
         # https://github.com/pypa/cibuildwheel/issues/1139
         run: touch python/setup.py
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.19.2
+        uses: pypa/cibuildwheel@v2.21.3
         env:
           CIBW_BUILD: cp38-manylinux_* cp39-manylinux_* cp310-manylinux_* cp311-manylinux_* cp312-manylinux_* cp313-manylinux_*
           CIBW_ARCHS: auto64
+          CIBW_MANYLINUX_X86_64_IMAGE: manylinux_2_28
           CIBW_BEFORE_ALL: >
-            yum install -y wget minizip-devel gcc-c++ boost-devel &&
+            yum install -y wget gcc-c++ boost-devel &&
             yum search epel-release &&
             yum info epel-release &&
             yum install -y epel-release &&
-            yum --enablerepo=epel install -y cmake3 &&
-            cd / &&
-            wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.3/src/hdf5-1.12.3.tar.gz &&
-            tar xf hdf5-1.12.3.tar.gz &&
-            mkdir hdf5-build &&
-            cd hdf5-build &&
-            cmake3 -G "Unix Makefiles" -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DBUILD_SHARED_LIBS:BOOL=OFF -DBUILD_TESTING:BOOL=OFF -DHDF5_BUILD_TOOLS:BOOL=OFF -DHDF5_BUILD_EXAMPLES:BOOL=OFF -DHDF5_BUILD_CPP_LIB:BOOL=OFF -DHDF5_BUILD_HL_LIB:BOOL=OFF -DCMAKE_INSTALL_PREFIX:STRING=/hdf5-install ../hdf5-1.12.3 &&
-            cmake3 --build . -j2 --config Release &&
-            cmake3 --install . &&
-            cd / &&
+            yum --enablerepo=epel install -y minizip1.2-devel hdf5-devel cmake3 &&
             mkdir build &&
             cd build &&
-            cmake3 -DCMAKE_BUILD_TYPE=Release -DHDF5_ROOT=/hdf5-install -DHDF5_USE_STATIC_LIBRARIES=TRUE -DWITH_PYTHON_WRAPPING=TRUE -DCMAKE_INSTALL_PREFIX:STRING=/fesapi-install {project} &&
+            cmake3 -DCMAKE_BUILD_TYPE=Release -DWITH_PYTHON_WRAPPING=TRUE -DCMAKE_INSTALL_PREFIX:STRING=/fesapi-install {project} &&
             cmake3 --build . -j2 --config Release &&
             cmake3 --install .
           CIBW_REPAIR_WHEEL_COMMAND_LINUX: >
@@ -209,7 +235,7 @@ jobs:
           output-dir: wheelhouse
       - uses: actions/upload-artifact@v4
         with:
-          name: cibw-wheels-ubuntu-latest
+          name: cibw-wheels-manylinux_2_28
           path: ./wheelhouse/*.whl
   build_wheels_mac:
     name: Build wheels on macos-14
@@ -221,10 +247,12 @@ jobs:
         # https://github.com/pypa/cibuildwheel/issues/1139
         run: touch python/setup.py
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.19.2
+        uses: pypa/cibuildwheel@v2.21.3
         env:
           CIBW_BUILD: cp38-macosx_* cp39-macosx_* cp310-macosx_* cp311-macosx_* cp312-macosx_* cp313-macosx_*
           CIBW_ARCHS: auto64
+          # See https://cibuildwheel.pypa.io/en/stable/cpp_standards/#macos-and-deployment-target-versions
+          MACOSX_DEPLOYMENT_TARGET: 10.14
           CIBW_BEFORE_ALL: >
             brew install boost swig &&
             git clone https://github.com/F2I-Consulting/Minizip.git ${{ github.workspace }}/../minizip &&
@@ -256,7 +284,7 @@ jobs:
           output-dir: wheelhouse
       - uses: actions/upload-artifact@v4
         with:
-          name: cibw-wheels-macos-14
+          name: cibw-wheels-macosx_arm64
           path: ./wheelhouse/*.whl
   ubuntu-20-mpi:
     runs-on: ubuntu-20.04    

CMakeLists.txt

@@ -12,7 +12,7 @@ set (FESAPI_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR})
 
 # version mechanism
 set (Fesapi_VERSION_MAJOR 2)
-set (Fesapi_VERSION_MINOR 11)
+set (Fesapi_VERSION_MINOR 12)
 set (Fesapi_VERSION_PATCH 0)
 set (Fesapi_VERSION_TWEAK 0)
 
@@ -31,7 +31,7 @@ IF (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
 ENDIF (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
 
 if (NOT DEFINED CMAKE_CXX_STANDARD)
-    set(CMAKE_CXX_STANDARD 11)
+    set(CMAKE_CXX_STANDARD 17)
 endif()
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
@@ -94,33 +94,8 @@ IF (NOT EXISTS ${SZIP_LIBRARY_DEBUG} AND WIN32 AND NOT ${HDF5_BUILT_AS_DYNAMIC_L
 	MESSAGE(WARNING "The Szip library (SZIP_LIBRARY_DEBUG variable) does not look to be a valid file. Please modify it.")
 ENDIF ()
 
-# Boost DEPENDENCY : Uuid (and potentially regex)
-unset(CAN_USE_STD_REGEX CACHE)
-include(CheckCXXSourceCompiles)
-check_cxx_source_compiles(
-   "#include <iostream>
-
-	//https://gcc.gnu.org/develop.html#timeline
-	int a =
-	#if !defined(__GLIBCXX__) || __GLIBCXX__ > 20150623 || __GLIBCXX__ == 20140422 || __GLIBCXX__ == 20140716 || __GLIBCXX__ == 20141030
-		1;
-	#else
-		fgsfds;
-	#endif
-
-    int main ()
-    {
-      return 0;
-
-    }"
-
-	CAN_USE_STD_REGEX
-)
-if (NOT CAN_USE_STD_REGEX)
-	find_package(Boost 1.44.0 REQUIRED regex) # 1.44 because we want boost::uuids::to_string method
-else ()
-	find_package(Boost 1.44.0 REQUIRED) # 1.44 because we want boost::uuids::to_string method
-endif()
+# Boost DEPENDENCY
+find_package(Boost 1.44.0 REQUIRED) # 1.44 because we want boost::uuids::to_string method
 
 # ============================================================================
 # some useful variables

README.md

@@ -7,16 +7,16 @@
 	 - build
 	 - fesapi (Git clone this repository into this folder "fesapi". You should then have a path fesapiEnv/fesapi/src)
 	 - dependencies 
-  - The following compilers are known to work (used in CI)
-    - gcc from version 4.8
-	- visual studio from version 2017
+  - The following compilers are known to work
+    - gcc from version 8
+	- visual studio from version 2019
 	- clang from version 5.0
 
 # Prepare the dependencies
 Download (build and install if necessary) third party libraries:
 - HDF5: Versions of 1.8.* (starting from 1.8.18), 1.10.* ([starting from 1.10.2](https://www.hdfgroup.org/2018/04/why-should-i-care-about-the-hdf5-1-10-2-release/)), all 1.12.* and all 1.14.* should be ok. https://support.hdfgroup.org/ftp/HDF5/releases/
 - MINIZIP : Version 1.1 is needed : it is the official version included in [current zlib distribution](https://www.zlib.net/) (look into "contrib" folder). You can directly install minizip development package on most of Linux distributions (https://packages.ubuntu.com/xenial/libminizip-dev). On Windows (or older Linux distributions), you can copy the CMakeLists.txt file from fesapi/cmake/minizip to the zlib minizip directory to help you to build minizip (we also provide a copy of minizip 1.1 with cmake files on github : https://github.com/F2I-Consulting/Minizip). It is also highly recommended to link minizip to the same zlib library than the one associated to your HDF5 library.
-- BOOST : Starting from version 1.44.0 (and at least 1.67.0 if you don't want to face [valgrid false positives](https://www.boost.org/doc/libs/1_66_0/libs/uuid/doc/uuid.html#Design%20notes)). FYI, on windows, boost uuid depends on bcrypt library.
+- BOOST (uuid) : Starting from version 1.44.0 (and at least 1.67.0 if you don't want to face [valgrid false positives](https://www.boost.org/doc/libs/1_66_0/libs/uuid/doc/uuid.html#Design%20notes)). FYI, on windows, boost uuid depends on bcrypt library.
 
 We advise you to install these third party libraries respectively into
 - fesapiEnv/dependencies/hdf5-particularVersion

cmake/pyproject.toml.in

@@ -0,0 +1,60 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = 'fesapi'
+version     = '${Fesapi_PYTHON_VERSION}'
+authors     = [
+    {name = "F2I-CONSULTING"},
+]
+maintainers = [
+    {name = "F2I-CONSULTING"},
+]
+description = "A library for using the Energistics data standards"
+readme      = "README.md"
+classifiers=[
+    'Development Status :: 5 - Production/Stable',
+    'Intended Audience :: Developers',
+    'License :: OSI Approved :: Apache Software License',
+    'Operating System :: Microsoft :: Windows',
+    'Operating System :: POSIX :: Linux',
+    'Operating System :: MacOS',
+    'Natural Language :: English',
+    'Programming Language :: Python :: 3',
+    'Programming Language :: Python :: 3.8',
+    'Programming Language :: Python :: 3.9',
+    'Programming Language :: Python :: 3.10',
+    'Programming Language :: Python :: 3.11',
+    'Programming Language :: Python :: 3.12',
+    'Topic :: Software Development',
+    'Topic :: Software Development :: Libraries',
+    'Topic :: Software Development :: Libraries :: Application Frameworks ',
+    'Topic :: File Formats',
+]
+keywords = [
+    "energistics",
+    "resqml",
+    "eml",
+    "witsml",
+    "prodml",
+    "osdu",
+    "rddms",
+]
+requires-python = ">=3.8"
+
+[project.urls]
+source = "https://github.com/F2I-Consulting/fesapi/issues"
+releasenotes = "https://github.com/F2I-Consulting/fesapi/releases"
+documentation = "https://www.f2i-consulting.com/fesapi/doxygen/"
+issues = "https://github.com/F2I-Consulting/fesapi/issues"
+
+[tool.setuptools]
+packages=['fesapi']
+package-dir={"fesapi" = "fesapi"}
+ext-modules = [
+    {name='fesapi._fesapi', sources=['swigGeneratedPythonWrapper.cpp'], library-dirs=['${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}'], libraries=['${ASSEMBLY_NAME}',], ${EXTRA_COMPILE_ARGS}}
+]
+
+[tool.setuptools.package-data]
+fesapi = ["*.dll", "*.so", "*.so.*"]

cmake/setup.py.in

@@ -2468,7 +2468,26 @@ bool serialize(const string& filePath)
 	EML2_NS::AbstractHdfProxy* hdfProxy = repo.createHdfProxy("", "Hdf Proxy", epcDoc.getStorageDirectory(), epcDoc.getName() + ".h5", COMMON_NS::DataObjectRepository::openingMode::OVERWRITE);
 	//hdfProxy->setCompressionLevel(6);
 
-	localTime3dCrs = repo.createLocalTime3dCrs("", "Default local time CRS", 1.0, 0.1, 15, .0, gsoap_resqml2_0_1::eml20__LengthUom::m, 23031, gsoap_resqml2_0_1::eml20__TimeUom::s, gsoap_resqml2_0_1::eml20__LengthUom::m, "Unknown", false); // CRS translation is just for testing;
+	localTime3dCrs = repo.createLocalTime3dCrs("", "Default local time CRS", 1.0, 0.1, 15, .0, gsoap_resqml2_0_1::eml20__LengthUom::m, 
+		"PROJCRS[\"ETRS89 Lambert Azimuthal Equal Area CRS\",  BASEGEODCRS[\"ETRS89\","
+			"DATUM[\"ETRS89\","
+			"ELLIPSOID[\"GRS 80\", 6378137, 298.257222101, LENGTHUNIT[\"metre\", 1.0]]]],"
+			"CONVERSION[\"LAEA\","
+			"METHOD[\"Lambert Azimuthal Equal Area\", ID[\"EPSG\", 9820]],"
+			"PARAMETER[\"Latitude of origin\", 52.0,"
+			"ANGLEUNIT[\"degree\", 0.0174532925199433]],"
+			"PARAMETER[\"Longitude of origin\", 10.0,"
+			"ANGLEUNIT[\"degree\", 0.0174532925199433]],"
+			"PARAMETER[\"False easting\", 4321000.0, LENGTHUNIT[\"metre\", 1.0]],"
+			"PARAMETER[\"False northing\", 3210000.0, LENGTHUNIT[\"metre\", 1.0]]],"
+			"CS[Cartesian, 2],"
+			"AXIS[\"(Y)\", north, ORDER[1]],"
+			"AXIS[\"(X)\", east, ORDER[2]],"
+			"LENGTHUNIT[\"metre\", 1.0],"
+			"SCOPE[\"Description of a purpose\"],"
+			"AREA[\"An area description\"],"
+			"ID[\"EuroGeographics\", \"ETRS-LAEA\"]]",
+		gsoap_resqml2_0_1::eml20__TimeUom::s, gsoap_resqml2_0_1::eml20__LengthUom::m, "Unknown", false); // CRS translation is just for testing;
 	local3dCrs = repo.createLocalDepth3dCrs("", "Default local CRS", .0, .0, .0, .0, gsoap_resqml2_0_1::eml20__LengthUom::m, 23031, gsoap_resqml2_0_1::eml20__LengthUom::m, "Unknown", false);
 	repo.setDefaultCrs(local3dCrs);
 
@@ -5114,11 +5133,15 @@ void deserialize(const string & inputFile)
 		cout << "Title is : " << crs->getTitle() << endl;
 		if (crs->isProjectedCrsDefinedWithEpsg())
 			cout << "Projected : EPSG " << crs->getProjectedCrsEpsgCode() << endl;
+		else if (crs->isProjectedCrsDefinedWithWkt())
+			cout << "Projected : WKT " << crs->getProjectedCrsWkt() << endl;
 		else if (crs->isProjectedCrsUnknown())
 			cout << "Projected : Unknown." << "Reason is:" << crs->getProjectedCrsUnknownReason() << endl;
 
 		if (crs->isVerticalCrsDefinedWithEpsg())
 			cout << "Vertical : EPSG one" << endl;
+		else if (crs->isVerticalCrsDefinedWithWkt())
+			cout << "Vertical : WKT " << crs->getVerticalCrsWkt() << endl;
 		else if (crs->isVerticalCrsUnknown())
 			cout << "Vertical : Unknown." << "Reason is:" << crs->getVerticalCrsUnknownReason() << endl;
 

example/example.cpp

@@ -1,5 +1,5 @@
 # ignore cmake and swig auto generated files
-setup.py
+pyproject.toml
 swigGeneratedPythonWrapper.cpp
 swigGeneratedPythonWrapper.h
 

python/.gitignore

@@ -0,0 +1,3 @@
+Enable CMake boolean variable SWIG_PYTHON_BUILTIN if you want more performance : read [SWIG documentation](http://swig.org/Doc4.0/SWIGDocumentation.html#Python_nn28) for more information about this "builtin" parameter. The main drawback of using such a parameter is that it will be harder/impossible for your Python IDE to enable autocompletion for your FESAPI python extension. The recommendation is to use SWIG_PYTHON_BUILTIN only in production.
+
+Please disable the SWIG_LINKED_TO_RELEASE cmake variable if you build FESAPI in Debug mode.

python/BUILD.md

@@ -28,11 +28,11 @@ else (WIN32)
 endif (WIN32)
 configure_file(${CMAKE_SOURCE_DIR}/cmake/swigPythonInclude.i.in ${CMAKE_SOURCE_DIR}/swig/swigPythonInclude.i) # Overwrite if different
 if (CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
-	set (EXTRA_COMPILE_ARGS "extra_compile_args=['/DSWIG_TYPE_TABLE=FESTAPI']")
+	set (EXTRA_COMPILE_ARGS "extra-compile-args=['/DSWIG_TYPE_TABLE=FESTAPI']")
 else ()
-	set (EXTRA_COMPILE_ARGS "extra_compile_args=['-DSWIG_TYPE_TABLE=FESTAPI', '-std=c++11']")
+	set (EXTRA_COMPILE_ARGS "extra-compile-args=['-DSWIG_TYPE_TABLE=FESTAPI', '-std=c++11']")
 endif()
-configure_file(${CMAKE_SOURCE_DIR}/cmake/setup.py.in ${CMAKE_SOURCE_DIR}/python/setup.py) # Overwrite if different
+configure_file(${CMAKE_SOURCE_DIR}/cmake/pyproject.toml.in ${CMAKE_SOURCE_DIR}/python/pyproject.toml) # Overwrite if different
 
 # SWIG execution
 message("Generating SWIG Python files...")

python/CMakeLists.txt

@@ -1,3 +1,15 @@
-Enable CMake boolean variable SWIG_PYTHON_BUILTIN if you want more performance : read [SWIG documentation](http://swig.org/Doc4.0/SWIGDocumentation.html#Python_nn28) for more information about this "builtin" parameter. The main drawback of using such a parameter is that it will be harder/impossible for your Python IDE to enable autocompletion for your FESAPI python extension. The recommendation is to use SWIG_PYTHON_BUILTIN only in production.
 
-Please disable the SWIG_LINKED_TO_RELEASE cmake variable if you build FESAPI in Debug mode.
+**FESAPI** is a library for Energistics data standards (mainly RESQML™)
+
+### Examples
+
+A Python script and a Jupyter Notebook are available [here](https://github.com/F2I-Consulting/fesapi/tree/master/python/example).
+
+### Credits
+This software was developed with :
+- the gSOAP toolkit from Genivia Inc
+- the date library from Howard Hinnant
+
+FESAPI Product incorporates RESQML™, WITSML™ and PRODML™ technology/standards provided by the Energistics Consortium, Inc.
+
+RESQML, WITSML and PRODML are trademarks or registered trademarks of Energistics Consortium, Inc.