Merge pull request #176 from fbergmann/level1-version4

Merge l1v4 changes into l1v5

Author: fbergmann

.ci/checkout-submodules.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+git submodule update --init --remote
+
+pushd submodules/libSBML-dependencies
+
+# only checkout the expat submodule
+git submodule update --init --remote expat
+
+popd

.ci/create-sdist.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+
+# Create a source distribution
+cp src/bindings/python/setup.py .
+cp src/bindings/python/MANIFEST.in .
+python3 setup.py sdist

.github/workflows/cmake.yml

@@ -19,10 +19,14 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-    - uses: actions/checkout@v2
-
-    - name: Checkout submodules
-      run: git submodule update --init --recursive
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    
+    - name: checkout needed submodules
+      shell: bash
+      run: | 
+        ./.ci/checkout-submodules.sh
 
     - name: add SWIG to windows
       # this is separate from the SWIG download itself, because it needs to be added to the path also when SWIG is cached
@@ -163,7 +167,7 @@ jobs:
       run: cmake -E tar cvzf ../binaries_${{ matrix.os }}.tar.gz .
 
     - name: Upload
-      uses: actions/upload-artifact@v1
+      uses: actions/upload-artifact@v4
       with:
         path: ${{runner.workspace}}/build/binaries_${{ matrix.os }}.tar.gz
         name: binaries_${{ matrix.os }}.tar.gz

.github/workflows/wheels.yml

@@ -11,76 +11,113 @@ jobs:
     name: Make SDist
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
-        fetch-depth: 0  # Optional, use if you use setuptools_scm
-        submodules: recursive  # Optional, use if you have submodules
+        fetch-depth: 0
+    
+    - name: checkout needed submodules
+      run: | 
+        ./.ci/checkout-submodules.sh
 
     - name: Build SDist
       run: |
         cp src/bindings/python/setup.py .
         cp src/bindings/python/MANIFEST.in .
         pipx run build --sdist
 
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v4
       with:
         path: dist/*.tar.gz
         name: libSEDML-sdist
 
   build_wheels:
     name: Wheel on ${{ matrix.os }} for ${{ matrix.python_version }}
     runs-on: ${{ matrix.os }}
+    needs: [make_sdist]
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-20.04, windows-2019, macos-11]
-        python_version: ['cp37-*', 'cp38-*', 'cp39-*', 'cp310-*', 'cp311-*']
+        os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest, macos-13, macos-latest]
+        python_version: ['cp39-*', 'cp310-*', 'cp311-*', 'cp312-*', 'cp313-*']
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: seanmiddleditch/gha-setup-ninja@master
+
+    - name: Add msbuild to PATH (Windows)
+      if: matrix.os == 'windows-latest'
+      uses: ilammy/msvc-dev-cmd@v1
+
+    - name: Install cibuildwheel
+      run: |
+        python -m pip install cibuildwheel==2.23.2 swig==4.2.1 cmake==3.31.6
+
+        # print versions
+        python --version
+        cmake --version
+        swig -version
+
+    - name: Download sdist
+      uses: actions/download-artifact@v4
       with:
-        fetch-depth: 0  # Optional, use if you use setuptools_scm
-        submodules: recursive  # Optional, use if you have submodules
+        name: libSEDML-sdist
+        path: .
 
-    - name: Copy setup.py
+    - name: Unpack sdist
+      shell: bash
       run: |
-        cp src/bindings/python/setup.py .
+        ls -la
+        tar zxf python_libsedml-*.tar.gz
+        mv python_libsedml-*/* .
+        rm -rf python_libsedml-*
+        ls -la
+
 
-    - uses: pypa/[email protected]
+    - name: Build wheels
       env:
-          CIBW_BUILD: ${{ matrix.python_version }}
-          CIBW_ARCHS_MACOS: x86_64 arm64
+        CIBW_BUILD: ${{ matrix.python_version }}
+        CIBW_SKIP: "*-musllinux* cp36-* cp37-* cp38-* *-win32"
+      run: |
+        python -m cibuildwheel --output-dir wheelhouse
 
     - name: Upload wheels
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
         path: wheelhouse/*.whl
-        name: libSEDML-${{ matrix.os }}
-        
-  upload_all:
-    needs: [build_wheels, make_sdist]
+        name: libSEDML-${{ matrix.os }}-${{ strategy.job-index }}
+    
+  merge_wheels:
+    needs: [build_wheels]
     runs-on: ubuntu-latest
-    if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-    - uses: actions/download-artifact@v2
+    - uses: actions/download-artifact@v4
       with:
-        name: libSEDML-sdist
-        path: dist
-    - uses: actions/download-artifact@v2
-      with:
-        name: libSEDML-ubuntu-20.04
+        pattern: libSEDML-*
         path: dist
-    - uses: actions/download-artifact@v2
+    
+    - name: Move wheels from dist subfolder to dist folder
+      run: |
+        find dist -name "*.whl" -exec mv {} dist/ \;
+        find dist -name "*.tar.gz" -exec mv {} dist/ \;
+        find dist -type d -empty -delete
+
+    - uses: actions/upload-artifact@v4
       with:
-        name: libSEDML-macos-10.15
+        name: libSEDML-combined
         path: dist
-    - uses: actions/download-artifact@v2
+          
+
+  upload_all:
+    needs: [merge_wheels]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published'
+    steps:
+    - uses: actions/download-artifact@v4
       with:
-        name: libSEDML-windows-2019
+        name: libSEDML-combined
         path: dist
 
-    - uses: pypa/gh-action-pypi-publish@v1.4.2
+    - uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
         password: ${{ secrets.PYPI_API_TOKEN }}
-        skip_existing: true
+

.gitignore

@@ -173,3 +173,8 @@ libsedml/_*
 examples/python/*.xml
 dev/temp_deviser_file.xml
 setup.py
+MANIFEST.in
+
+# documentation
+/doc/html/
+Doxyfile

CMakeModules/FindEXPAT.cmake

@@ -48,11 +48,13 @@ find_path(EXPAT_INCLUDE_DIR expat.h
           /opt/csw/include   # Blastwave
           /opt/include
           /usr/freeware/include
-          NO_DEFAULT_PATH)
+          NO_DEFAULT_PATH
+          CMAKE_FIND_ROOT_PATH_BOTH)
 endif ()
 
 if (NOT EXPAT_INCLUDE_DIR)
-    find_path(EXPAT_INCLUDE_DIR expat.h)
+    find_path(EXPAT_INCLUDE_DIR expat.h
+    CMAKE_FIND_ROOT_PATH_BOTH)
 endif ()
 
 find_library(EXPAT_LIBRARY 
@@ -81,11 +83,13 @@ find_library(EXPAT_LIBRARY
           /opt/csw/lib   # Blastwave
           /opt/lib
           /usr/freeware/lib64
-          NO_DEFAULT_PATH)
+          NO_DEFAULT_PATH
+          CMAKE_FIND_ROOT_PATH_BOTH)
 endif()
 
 if (NOT EXPAT_LIBRARY)
-    find_library(EXPAT_LIBRARY NAMES libexpat expat)
+    find_library(EXPAT_LIBRARY NAMES libexpat expat
+    CMAKE_FIND_ROOT_PATH_BOTH )
 endif ()
 
 mark_as_advanced(EXPAT_INCLUDE_DIR EXPAT_LIBRARY)

CMakeModules/FindLIBNUML.cmake

@@ -34,6 +34,7 @@ if (NOT ${LIBNUML_LIBRARY_NAME}_FOUND)
           ${CONAN_LIB_DIRS_LIBNUML}/cmake
           ${${_PROJECT_DEPENDENCY_DIR}}/lib/cmake
           ${${_PROJECT_DEPENDENCY_DIR}}/lib64/cmake
+          CMAKE_FIND_ROOT_PATH_BOTH
   )
 endif()
 
@@ -90,7 +91,8 @@ find_path(LIBNUML_INCLUDE_DIR numl/NMBase.h
           /opt/csw/include   # Blastwave
           /opt/include
           /usr/freeware/include
-    NO_DEFAULT_PATH)
+    NO_DEFAULT_PATH
+    CMAKE_FIND_ROOT_PATH_BOTH)
 
 if (NOT LIBNUML_INCLUDE_DIR)
     find_path(LIBNUML_INCLUDE_DIR numl/NMBase.h)
@@ -117,7 +119,8 @@ find_library(LIBNUML_LIBRARY
           /opt/csw/lib   # Blastwave
           /opt/lib
           /usr/freeware/lib64
-    NO_DEFAULT_PATH)
+    NO_DEFAULT_PATH
+    CMAKE_FIND_ROOT_PATH_BOTH)
 
 if (NOT LIBNUML_LIBRARY)
     find_library(LIBNUML_LIBRARY 

CMakeModules/FindLIBSBML.cmake

@@ -1,4 +1,4 @@
-# Copyright (C) 2019 - 2022 by Pedro Mendes, Rector and Visitors of the 
+# Copyright (C) 2019 - 2023 by Pedro Mendes, Rector and Visitors of the 
 # University of Virginia, University of Heidelberg, and University 
 # of Connecticut School of Medicine. 
 # All rights reserved. 
@@ -33,11 +33,21 @@ endif()
 
 message (VERBOSE "Looking for ${LIBSBML_LIBRARY_NAME}")
 
-find_package(${LIBSBML_LIBRARY_NAME} CONFIG QUIET)
 
 string(TOUPPER ${PROJECT_NAME} _UPPER_PROJECT_NAME)
 set(_PROJECT_DEPENDENCY_DIR ${_UPPER_PROJECT_NAME}_DEPENDENCY_DIR)
 
+find_package(${LIBSBML_LIBRARY_NAME} CONFIG QUIET
+  PATHS ${${_PROJECT_DEPENDENCY_DIR}}/lib/cmake
+        ${${_PROJECT_DEPENDENCY_DIR}}/lib64/cmake
+        ${CONAN_LIB_DIRS_LIBSBML}/cmake
+        CMAKE_FIND_ROOT_PATH_BOTH
+        NO_DEFAULT_PATH)
+
+if (NOT ${LIBSBML_LIBRARY_NAME}_FOUND)        
+  find_package(${LIBSBML_LIBRARY_NAME} CONFIG QUIET)
+endif()
+
 if (NOT ${LIBSBML_LIBRARY_NAME}_FOUND)
   find_package(${LIBSBML_LIBRARY_NAME} CONFIG QUIET
     PATHS /usr/lib/cmake
@@ -48,6 +58,7 @@ if (NOT ${LIBSBML_LIBRARY_NAME}_FOUND)
           ${${_PROJECT_DEPENDENCY_DIR}}/lib/cmake
           ${${_PROJECT_DEPENDENCY_DIR}}/lib64/cmake
           ${CONAN_LIB_DIRS_LIBSBML}/cmake
+          CMAKE_FIND_ROOT_PATH_BOTH
   )
 endif()
 
@@ -111,6 +122,7 @@ find_path(LIBSBML_INCLUDE_DIR sbml/SBase.h
           /opt/csw/include   # Blastwave
           /opt/include
           /usr/freeware/include
+          CMAKE_FIND_ROOT_PATH_BOTH
     NO_DEFAULT_PATH)
 
 if (NOT LIBSBML_INCLUDE_DIR)
@@ -140,6 +152,7 @@ find_library(LIBSBML_LIBRARY
           /opt/csw/lib   # Blastwave
           /opt/lib
           /usr/freeware/lib64
+          CMAKE_FIND_ROOT_PATH_BOTH
     NO_DEFAULT_PATH)
 
 if (NOT LIBSBML_LIBRARY)

README.md

@@ -39,12 +39,23 @@ note the semicolon denoting the listing of several libraries. Of course you coul
 
 for linking against `expat` and indicating, that libSBML was compiled without compression.
 
+## Documentation
+API documentation is something to be added and pull requests are happily accepted to improve them. For now a basic doxygen file 
+is provided and documentation can be generated after checkout like so: 
+
+```bash
+PROJECT_NUMBER=2.0.32 doxygen -x libSEDML.doxyfile > Doxyfile && doxygen
+```
+
+This expands the version number in the doxygen file, creates a temporary `Doxyfile` and runs doxygen with it. After that the 
+generated documentation is available in the `./doc/html` folder.
+
 ## License
 
 This project is open source and freely available under the [Simplified BSD](http://opensource.org/licenses/BSD-2-Clause) license. Should that license not meet your needs, please contact me.
 
 
-Copyright (c) 2013-2021, Frank T. Bergmann  
+Copyright (c) 2013-2023, Frank T. Bergmann  
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

dev/create-source-package.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+# this script creates the python source package
+cp ./src/bindings/python/setup.py . 
+cp ./src/bindings/python/MANIFEST.in . 
+
+# remove old source packages
+rm ./dist/*.tar.gz
+
+# create the source package
+python3 setup.py sdist