Set reaction arc line colors when setting line color of reaction.

.github/workflows/build-libsbmlnetworkjs.yml

@@ -0,0 +1,110 @@
+name: build-libsbmlnetwork-webassembly-github-actions
+run-name: Building libsbmlnetwork-webassembly
+on:
+  workflow_dispatch:
+    inputs:
+      sbmlnetwork_version:
+        description: 'SBMLNetwork version number'
+        required: true
+        default: '0.4.5'
+      libsbml_version:
+        description: 'LibSBML version number'
+        required: true
+        default: '5.20.0'
+jobs:
+  build-new-version-libsbmlnetwork-webassembly:
+    runs-on: ubuntu-latest
+    env:
+      EMSDK: emsdk
+      EMSCRIPTEN_VERS: '3.1.20'
+      EMSDK_NODE: emsdk/node/16.20.0_64bit/bin/node
+      SBML_VERS: ${{ inputs.libsbml_version }}
+      SBMLNETWORK_VERS: ${{ inputs.SBMLNETWORK_VERSion }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: get emscripten
+        run: git clone https://github.com/emscripten-core/emsdk.git
+      - name: change emsdk script permissions
+        run: chmod +x emsdk
+        working-directory: emsdk
+      - name: install emscripten sdk
+        run: ./emsdk install $EMSCRIPTEN_VERS
+        working-directory: emsdk
+      - name: activate emscripten
+        run: ./emsdk activate $EMSCRIPTEN_VERS
+        working-directory: emsdk
+      - run: echo "$GITHUB_WORKSPACE/emsdk/upstream/emscripten" >> $GITHUB_PATH
+      - run: echo "$GITHUB_WORKSPACE/emsdk" >> $GITHUB_PATH
+      - name: confirm emscripten works
+        run: emcc -v
+      - run: echo $PATH
+      - run: echo $EMSDK_NODE
+      - run: mkdir install
+      - run: wget https://github.com/libexpat/libexpat/releases/download/R_2_2_10/expat-2.2.10.tar.bz2
+      - run: tar -xf expat-2.2.10.tar.bz2
+      - run: mv expat-2.2.10 expat
+      - name: make expat build dir
+        run: mkdir build
+        working-directory: expat
+      - name: build expat lib
+        run: emcmake cmake .. -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/install/expat
+        working-directory: expat/build
+      - name: Compile expat lib
+        run: emmake make
+        working-directory: expat/build
+      - name: install expat lib
+        run: emmake make install
+        working-directory: expat/build
+      - name: Get libSBML
+        run: wget https://github.com/sbmlteam/libsbml/archive/refs/tags/v$SBML_VERS.zip
+      - run: unzip v$SBML_VERS.zip
+      - run: mv libsbml-$SBML_VERS libsbml
+      - name: make libsbml build dir
+        run: mkdir build
+        working-directory: libsbml
+      - name: build libsbml library
+        run: emcmake cmake .. -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/install/sbml -DCMAKE_BUILD_TYPE=Release -DWITH_CPP_NAMESPACE=ON -DWITH_EXPAT=ON -DWITH_LIBXML=OFF -DLIBSBML_SKIP_SHARED_LIBRARY=ON -DENABLE_LAYOUT=ON -DENABLE_RENDER=ON -DWITH_STABLE_PACKAGES=ON -DWITH_SWIG=OFF -DEXPAT_INCLUDE_DIR=$GITHUB_WORKSPACE/install/expat/include -DEXPAT_LIBRARY=$GITHUB_WORKSPACE/install/expat/lib/libexpat.a
+        working-directory: libsbml/build
+      - name: compile libsbml lib
+        run: emmake make
+        working-directory: libsbml/build
+      - name: install libsbml
+        run: emmake make install
+        working-directory: libsbml/build
+      - name: Get SBMLNetwork
+        run: wget https://github.com/sys-bio/SBMLNetwork/archive/refs/tags/v$SBMLNETWORK_VERS.zip
+      - run: unzip v$SBMLNETWORK_VERS.zip
+      - run: mv SBMLNetwork-$SBMLNETWORK_VERS/ SBMLNetwork
+      - name: make SBMLNetwork build dir
+        run: mkdir build
+        working-directory: SBMLNetwork
+      - name: Build SBMLNetwork library
+        run: emcmake cmake .. -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/install/SBMLNetwork -DCMAKE_BUILD_TYPE=Release -DEXPAT_INSTALL_PREFIX=$GITHUB_WORKSPACE/install/expat -DLIBEXPAT_LIBRARY=$GITHUB_WORKSPACE/install/expat/lib/libexpat.a -DLIBSBML_INSTALL_PREFIX=$GITHUB_WORKSPACE/install/sbml -DLIBSBML_LIBRARY=$GITHUB_WORKSPACE/install/sbml/lib/libsbml-static.a -DWITH_PYTHON=OFF
+        working-directory: SBMLNetwork/build
+      - name: Compile SBMLNetwork lib
+        run: emmake make
+        working-directory: SBMLNetwork/build
+      - name: Install SBMLNetwork lib
+        run: emmake make install
+        working-directory: SBMLNetwork/build
+      - name: Generate SBMLNetwork javascript and wasm files
+        run: em++ -I$GITHUB_WORKSPACE/install/SBMLNetwork/include -I$GITHUB_WORKSPACE/install/sbml/include -I$GITHUB_WORKSPACE/install/expat/include $GITHUB_WORKSPACE/install/SBMLNetwork/lib/libsbmlnetwork.a $GITHUB_WORKSPACE/install/sbml/lib/libsbml-static.a $GITHUB_WORKSPACE/install/expat/lib/libexpat.a -o libsbmlnetwork.js -s WASM=1 -s LINKABLE=1 -s EXPORT_ALL=1 -s MODULARIZE=1 -s EXPORT_ES6=1 -s EXPORTED_RUNTIME_METHODS='["ccall", "cwrap", "allocateUTF8", "UTF8ToString"]'
+        working-directory: install
+      - name: List build libsbmlnetwork-webassembly files
+        run: ls -l
+        working-directory: install
+      - name: Build output directory
+        run: |
+          mkdir -p $GITHUB_WORKSPACE/libsbmlnetwork-webassembly
+          echo "artifacts_path=$GITHUB_WORKSPACE/libsbmlnetwork-webassembly" >> "${GITHUB_ENV}"
+      - name: Copy libsbmlnetwork-webassembly files to the workspace
+        run: |
+          cp install/libsbmlnetwork.js $GITHUB_WORKSPACE/libsbmlnetwork-webassembly/
+          cp install/libsbmlnetwork.wasm $GITHUB_WORKSPACE/libsbmlnetwork-webassembly/
+      - name: Verify copied files
+        run: ls -l $GITHUB_WORKSPACE/libsbmlnetwork-webassembly
+      - name: Upload libsbmlnetwork-webassembly files
+        uses: actions/upload-artifact@v4
+        with:
+          name: libsbmlnetwork-webassembly
+          path: ${{env.artifacts_path}}

.github/workflows/build.yml

@@ -10,41 +10,41 @@ on:
 
 jobs:
   build_on_OSs:
-    name: Build RoadRunner on ${{ matrix.platform.name }}-python${{ matrix.python_version }}
+    name: Build SBMLNetwork on ${{ matrix.platform.name }}-python${{ matrix.python_version }}
     strategy:
       fail-fast: false
       matrix:
         platform:
-          - name: macos-12-release
+          - name: macos-15-intel-release
             os_type: macos
-            os_name: macos-12
+            os_name: macos-15-intel
             build_type: Release
             build_python: ON
-          - name: macos-12-debug
+          - name: macos-15-intel-debug
             os_type: macos
-            os_name: macos-12
+            os_name: macos-15-intel
             build_type: Debug
             build_python: ON
           - name: macos-latest-release
             os_type: macos
-            os_name: macos-latest
+            os_name: macos-14
             build_type: Release
             build_python: ON
           - name: macos-latest-debug
             os_type: macos
-            os_name: macos-latest
-            build_type: Debug
-            build_python: ON
-          - name: ubuntu-latest-release
-            os_type: ubuntu
-            os_name: ubuntu-latest
-            build_type: Release
-            build_python: ON
-          - name: ubuntu-latest-debug
-            os_type: ubuntu
-            os_name: ubuntu-latest
+            os_name: macos-14
             build_type: Debug
             build_python: ON
+#          - name: ubuntu-latest-release
+#            os_type: ubuntu
+#            os_name: ubuntu-latest
+#            build_type: Release
+#            build_python: ON
+#          - name: ubuntu-latest-debug
+#            os_type: ubuntu
+#            os_name: ubuntu-latest
+#            build_type: Debug
+#            build_python: ON
           - name: windows-latest-release
             os_type: windows
             os_name: windows-latest
@@ -70,7 +70,7 @@ jobs:
         libroadrunner_deps_owner: [ "sys-bio" ]
         libroadrunner_deps_repo: [ "libroadrunner-deps" ]
         libroadrunner_deps_name: [ "libroadrunner-deps" ]
-        libroadrunner_deps_release_version: [ "v2.1.2" ]
+        libroadrunner_deps_release_version: [ "v2.2.22" ]
         python_version: [ "3.11" ]
     runs-on: ${{ matrix.platform.os_name }}
     container:
@@ -241,14 +241,17 @@ jobs:
             python -m pip install pytest ipython setuptools wheel
             python -m pip install ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/libsbmlnetwork
             python -m pip install ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/sbmlnetwork
+            python -m pip install tellurium
           elif [ "${{ matrix.platform.os_type }}" == 'manylinux' ]; then
             python${{ matrix.python_version }} -m pip install --trusted-host pypi.org --trusted-host pypi.python.org --trusted-host files.pythonhosted.org pytest ipython setuptools wheel
             python${{ matrix.python_version }} -m pip install ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/libsbmlnetwork
             python${{ matrix.python_version }} -m pip install ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/sbmlnetwork
+            python${{ matrix.python_version }} -m pip install tellurium
           else
             python${{ matrix.python_version }} -m pip install pytest ipython setuptools wheel
             python${{ matrix.python_version }} -m pip install ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/libsbmlnetwork
             python${{ matrix.python_version }} -m pip install ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/sbmlnetwork
+            python${{ matrix.python_version }} -m pip install tellurium
           fi
 
       - name: Run libSBMLNetwork tests
@@ -259,7 +262,7 @@ jobs:
           if [ "${{ matrix.platform.os_type }}" == 'windows' ]; then
             python -m pytest -p no:cacheprovider
           else
-            python${{ matrix.python_version }} -m pytest -p no:cacheprovider
+            python${{ matrix.python_version }} -m pytest -v -p no:cacheprovider 
           fi
 
       - name: Set artifacts path and name
@@ -345,7 +348,7 @@ jobs:
           path: ${{env.libsbmlnetwork_python_wheel_artifacts_file}}
 
       - name: Upload SBMLNetwork Python wheel artifacts
-        if: matrix.platform.build_type == 'Release' && matrix.platform.build_python == 'ON' && matrix.platform.os_name == 'macos-latest'
+        if: matrix.platform.build_type == 'Release' && matrix.platform.build_python == 'ON' && matrix.platform.os_name == 'macos-14'
         uses: actions/upload-artifact@v4
         with:
           name: ${{env.sbmlnetwork_python_wheel_artifacts_name}}

.readthedocs.yaml

@@ -4,6 +4,8 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.12"
+  apt_packages:
+    - graphviz
   jobs:
     pre_build:
       - pip install -r docs/requirements.txt

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.6 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.10 FATAL_ERROR)
 
 project(libsbmlnetwork)
 add_definitions(-DLIBSBMLNETWORK_EXPORTS=true)
@@ -26,35 +26,51 @@ endif()
 
 add_definitions(-DLIBSBMLNETWORK_VERSION="${LIBSBMLNETWORK_DOTTED_VERSION}")
 
-## find dependency libraries
+## Dependency configuration
 set(DEPENDENCIES_INSTALL_PREFIX "" CACHE PATH "Path to the libsbml, libexpat, and libz installation directory")
-if(WIN32)
-	find_library(LIBSBML_LIBRARY NAMES libsbml-staticmd.lib libsbml-staticmdd.lib PATHS ${DEPENDENCIES_INSTALL_PREFIX}/lib REQUIRED)
-	if (NOT TARGET EXPAT::EXPAT)
-		find_library(LIBEXPAT_LIBRARY NAMES libexpatMD.lib libexpatdMD.lib PATHS ${DEPENDENCIES_INSTALL_PREFIX}/lib REQUIRED)
-	else ()
-		find_package(EXPAT REQUIRED)
-		set(LIBEXPAT_LIBRARY EXPAT::EXPAT)
-	endif ()
-	find_library(LIBZ_LIBRARY NAMES zlibstatic.lib zlibstaticd.lib PATHS ${DEPENDENCIES_INSTALL_PREFIX}/lib REQUIRED)
-elseif (APPLE)
-	find_library(LIBSBML_LIBRARY NAMES libsbml-static.a libsbml-staticd.a PATHS ${DEPENDENCIES_INSTALL_PREFIX}/lib REQUIRED)
-	find_library(LIBEXPAT_LIBRARY NAMES libexpat.a expat PATHS ${DEPENDENCIES_INSTALL_PREFIX}/lib REQUIRED)
-	find_library(LIBZ_LIBRARY NAMES libz.a PATHS ${DEPENDENCIES_INSTALL_PREFIX}/lib REQUIRED)
-elseif(UNIX)
-	find_library(LIBSBML_LIBRARY NAMES libsbml-static.a libsbml-staticd.a
-			PATHS ${DEPENDENCIES_INSTALL_PREFIX}/lib ${DEPENDENCIES_INSTALL_PREFIX}/lib64 REQUIRED)
-	find_library(LIBEXPAT_LIBRARY NAMES libexpat.a expat
-			PATHS ${DEPENDENCIES_INSTALL_PREFIX}/lib ${DEPENDENCIES_INSTALL_PREFIX}/lib64 REQUIRED)
-	find_library(LIBZ_LIBRARY NAMES libz.so
-			PATHS ${DEPENDENCIES_INSTALL_PREFIX}/lib ${DEPENDENCIES_INSTALL_PREFIX}/lib64 REQUIRED)
-endif()
 
-## set dependencies include directory if it is not set by a parent project
-if (NOT DEFINED DEPENDENCIES_INCLUDE_DIR)
-	set(DEPENDENCIES_INCLUDE_DIR ${DEPENDENCIES_INSTALL_PREFIX}/include)
+set(DEPENDENCY_CMAKE_CONFIG_PATHS
+		"${DEPENDENCIES_INSTALL_PREFIX}/cmake"
+		"${DEPENDENCIES_INSTALL_PREFIX}/lib/cmake"
+		"${DEPENDENCIES_INSTALL_PREFIX}/lib64/cmake"
+)
+set(CMAKE_PREFIX_PATH ${CMAKE_PREFIX_PATH} "${DEPENDENCY_CMAKE_CONFIG_PATHS}")
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${DEPENDENCY_CMAKE_CONFIG_PATHS}")
+
+message(STATUS "CMAKE_PREFIX_PATH: ${CMAKE_PREFIX_PATH}")
+
+## Set platform-specific libSBML target name
+if (WIN32)
+	set(SBML_TARGET_NAME "libsbml-static")
+else ()
+	set(SBML_TARGET_NAME "sbml-static")
 endif ()
 
+## Find ZLIB
+find_package(ZLIB CONFIG REQUIRED)
+set(LIBZ_LIBRARY ZLIB::ZLIBSTATIC)
+get_target_property(LIBZ_LIBRARY_LOCATION ZLIB::ZLIBSTATIC LOCATION)
+message(STATUS "ZLIB Library: ${LIBZ_LIBRARY_LOCATION}")
+set(ZLIB_LIBRARY "${LIBZ_LIBRARY_LOCATION}" CACHE FILEPATH "Path to zlib library" FORCE)
+set(ZLIB_INCLUDE_DIR "${DEPENDENCIES_INSTALL_PREFIX}/include" CACHE PATH "Path to zlib include directory" FORCE)
+set(ZLIB_FOUND TRUE CACHE BOOL "ZLIB found" FORCE)
+
+## Find expat
+find_package(expat CONFIG REQUIRED)
+set(EXPAT_LIBRARY expat::expat)
+get_target_property(EXPAT_LIBRARY_LOCATION expat::expat LOCATION)
+get_target_property(EXPAT_INCLUDE_DIR expat::expat INTERFACE_INCLUDE_DIRECTORIES)
+message(STATUS "Expat Library: ${EXPAT_LIBRARY_LOCATION}")
+message(STATUS "Expat Include: ${EXPAT_INCLUDE_DIR}")
+
+## Find libSBML
+find_package(${SBML_TARGET_NAME} CONFIG REQUIRED)
+set(LIBSBML_LIBRARY ${SBML_TARGET_NAME})
+message(STATUS "libSBML Target: ${LIBSBML_LIBRARY}")
+
+## Set dependencies include directory
+set(DEPENDENCIES_INCLUDE_DIR "${DEPENDENCIES_INSTALL_PREFIX}/include")
+
 ## whether to build the dynamic version of the library
 set(BUILD_SHARED_LIBS ON CACHE BOOL "Build the dynamic version of the library")