Create release v0.5.0-rc.1.

.github/workflows/deploy-on-release.yml

@@ -43,7 +43,7 @@ jobs:
           endforeach()
         endif()
         message(STATUS "Setting binaries destination to '${_OUTPUT_LOCATION}'.")
-        message("::set-output name=BINARIES-DESTINATION::${_OUTPUT_LOCATION}")
+        file(APPEND $ENV{GITHUB_OUTPUT} "binaries-destination=${_OUTPUT_LOCATION}")
 
     - name: Determine next jobs
       id: do-jobs
@@ -67,7 +67,7 @@ jobs:
           endforeach()
         endif()
         message(STATUS "Setting allowed jobs to '${_ALLOWED_JOBS}'.")
-        message("::set-output name=allowed-jobs::${_ALLOWED_JOBS}")
+        file(APPEND $ENV{GITHUB_OUTPUT} "allowed-jobs=${_ALLOWED_JOBS}")
 
   os-binaries:
     needs: setup-jobs
@@ -99,19 +99,19 @@ jobs:
 
     steps:
     - name: Checkout libCellML
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         ref: ${{ github.event.release.tag_name }}
 
     - name: Checkout zlib
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         repository: OpenCMISS-Dependencies/zlib
         path: zlib
         ref: v1.2.3
 
     - name: Checkout LibXml2
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         repository: OpenCMISS-Dependencies/libxml2
         path: libxml2
@@ -257,8 +257,7 @@ jobs:
         # softprops action requires a list of newline separated files.
         # The %0A will be converted by GitHub actions into '\n'.
         string(REPLACE ";" "%0A" _DIST_FILES "${_DIST_FILES}")
-        execute_process(
-          COMMAND echo "::set-output name=files::${_DIST_FILES}")
+        file(APPEND $ENV{GITHUB_OUTPUT} "files=${_DIST_FILES}")
 
     - name: Publish libraries
       if: needs.setup-jobs.outputs.binaries-destination == 'Publish'
@@ -296,7 +295,7 @@ jobs:
 
     steps:
       - name: Check out libCellML
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           ref: ${{ github.event.release.tag_name }}
 
@@ -308,22 +307,21 @@ jobs:
           cp src/bindings/python/README.rst src/bindings/python/libcellml/README.rst
           mv src/bindings/python/cibuildwheel.setup.py src/bindings/python/setup.py
           v=${{ matrix.py }}
-          echo "Setting tag as: TAG=${GITHUB_REF#refs/tags/}"
-          echo ::set-output name=TAG::${GITHUB_REF#refs/tags/}
-          #echo ::set-output name=TAG::v0.2.0-dev.21
-          echo "Setting build as: BUILD=cp${v/./}-*"
-          echo ::set-output name=BUILD::cp${v/./}-*
+          echo "Setting tag as: tag=${GITHUB_REF#refs/tags/}"
+          echo "tag=${GITHUB_REF#refs/tags/}" >> $GITHUB_OUTPUT
+          echo "Setting build as: build=cp${v/./}-*"
+          echo "build=cp${v/./}-*" >> $GITHUB_OUTPUT
           if [[ "macOS" == "${{ matrix.name }}" ]]; then
             if [[ "${{ matrix.py }}" == "3.8" ]]; then
-              echo "Setting MACOS_ARCHS as: MACOS_ARCHS='x86_64'"
-              echo ::set-output name=MACOS_ARCHS::x86_64
+              echo "Setting macos_archs as: macos_archs='x86_64'"
+              echo "macos_archs=x86_64" >> $GITHUB_OUTPUT
             else
-              echo "Setting MACOS_ARCHS as: MACOS_ARCHS='x86_64 arm64'"
-              echo ::set-output name=MACOS_ARCHS::"x86_64 arm64"
+              echo "Setting macos_archs as: macos_archs='x86_64 arm64'"
+              echo 'MACOS_ARCHS="x86_64 arm64"' >> $GITHUB_OUTPUT
             fi
           else
-            echo "Setting MACOS_ARCHS as: MACOS_ARCHS='x86_64'"
-            echo ::set-output name=MACOS_ARCHS::x86_64
+            echo "Setting macos_archs as: macos_archs='x86_64'"
+            echo "macos_archs=x86_64" >> $GITHUB_OUTPUT
           fi
 
       - name: Configure MSVC
@@ -380,20 +378,20 @@ jobs:
     runs-on: macos-12
     steps:
       - name: Checkout libCellML
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           path: libcellml
           ref: ${{ github.event.release.tag_name }}
 
       - name: Checkout zlib
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           repository: OpenCMISS-Dependencies/zlib
           path: zlib
           ref: v1.2.3
 
       - name: Checkout LibXml2
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           repository: OpenCMISS-Dependencies/libxml2
           path: libxml2
@@ -435,7 +433,7 @@ jobs:
           cd build-libcellml-release/src/bindings/javascript
           npm pack
           package=`ls $PWD/libcellml.js-*.tgz`
-          echo "::set-output name=files::$package"
+          echo "files=$package" >> $GITHUB_OUTPUT
 
       - name: Upload libcellml.js as artifacts
         if: needs.setup-jobs.outputs.binaries-destination == 'Artifact'

CMakeLists.txt

@@ -14,10 +14,12 @@
 
 cmake_minimum_required(VERSION 3.18.0)
 
+set(CMAKE_OSX_DEPLOYMENT_TARGET 10.15 CACHE STRING "Minimum OS X deployment version.")
+
 set(PROJECT_NAME libCellML)
 set(PROJECT_URL https://libcellml.org)
-set(_PROJECT_VERSION 0.4.0)
-set(PROJECT_DEVELOPER_VERSION )
+set(_PROJECT_VERSION 0.5.0)
+set(PROJECT_DEVELOPER_VERSION -rc.1)
 project(${PROJECT_NAME} VERSION ${_PROJECT_VERSION} LANGUAGES CXX)
 
 # Set policies that affect the build.
@@ -105,7 +107,7 @@ set(_PARAM_ANNOTATION "Build Python wrappers.")
 if(BINDINGS_AVAILABLE AND PYTHON_BINDINGS_AVAILABLE)
   set(LIBCELLML_BINDINGS_PYTHON ON CACHE BOOL "${_PARAM_ANNOTATION}")
 endif()
-if(DEFINED BINDINGS_PYTHON AND BINDINGS_AVAILABLE AND Python_Development_FOUND)
+if(DEFINED BINDINGS_PYTHON AND BINDINGS_AVAILABLE AND PYTHON_BINDINGS_AVAILABLE)
   set(LIBCELLML_BINDINGS_PYTHON "${BINDINGS_PYTHON}" CACHE BOOL "${_PARAM_ANNOTATION}" FORCE)
 elseif(BINDINGS_PYTHON)
   message(WARNING "Python bindings requested but development files for Python or SWIG were not found!")
@@ -276,4 +278,3 @@ endif()
 # Add target to print out version
 add_custom_target(print_version
   COMMAND ${CMAKE_COMMAND} -E echo "version=v${PROJECT_VERSION}${PROJECT_DEVELOPER_VERSION}")
-

cmake/TestUndefinedSymbolsAllowed.cmake

@@ -26,6 +26,7 @@ function(Test_Undefined_Symbols_Allowed)
 
     file(WRITE "${test_project_dir}/CMakeLists.txt"
 "
+cmake_minimum_required(VERSION 3.18.0)
 project(undefined CXX)
 add_library(foo SHARED \"foo.cpp\")
 ")

cmake/environmentchecks.cmake

@@ -139,6 +139,8 @@ if(LibXml2_FOUND)
     set(LIBXML2_TARGET_NAME xml2)
   elseif(TARGET LibXml2)
     set(LIBXML2_TARGET_NAME LibXml2)
+  elseif(TARGET LibXml2::LibXml2)
+    set(LIBXML2_TARGET_NAME LibXml2::LibXml2)
   else()
     message(FATAL_ERROR "FindLibXml2: Found configuration file for LibXml2 but could not determine a target name from it.")
   endif()

cmake/utils/CMakeLists.txt

@@ -35,6 +35,7 @@ target_link_libraries(calculatesha1 PRIVATE cellml)
 add_custom_command(OUTPUT generatorprofilesha1values.cmake
   COMMENT "Updating SHA-1 values for C and Python generator profiles."
   WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+  DEPENDS calculatesha1
   COMMAND calculatesha1
   COMMAND ${CMAKE_COMMAND} -P "${PROJECT_SOURCE_DIR}/cmake/generateprofilesha1header.cmake")
 add_custom_target(update_generator_profile_sha1_values

docs/changelogs/changelog_v0.5.0-rc.1.rst

@@ -0,0 +1,100 @@
+libCellML v0.5.0-rc.1 Changelog
+===============================
+
+Analyser
+--------
+
+* Analyser: add support for unknown variables that have been marked as external by `@agarny <https://github.com/agarny>`_ [`#1184 <https://github.com/cellml/libcellml/pull/1184>`_].
+* Analyser: don't optimise the order of variables and equations by `@agarny <https://github.com/agarny>`_ [`#1090 <https://github.com/cellml/libcellml/pull/1090>`_].
+* Analyser: reworked the analysis of a model with external variables by `@agarny <https://github.com/agarny>`_ [`#1077 <https://github.com/cellml/libcellml/pull/1077>`_].
+* Analyser: allow for the unknown variable to be either on the LHS or RHS of an equation by `@agarny <https://github.com/agarny>`_ [`#1071 <https://github.com/cellml/libcellml/pull/1071>`_].
+
+Bug
+---
+
+* Fix flattening segfault by `@hsorby <https://github.com/hsorby>`_ [`#1179 <https://github.com/cellml/libcellml/pull/1179>`_].
+* Resolve imports by `@hsorby <https://github.com/hsorby>`_ [`#1177 <https://github.com/cellml/libcellml/pull/1177>`_].
+* Flattening is changing imported models by `@hsorby <https://github.com/hsorby>`_ [`#1175 <https://github.com/cellml/libcellml/pull/1175>`_].
+* Fix importing units from a common base model by `@hsorby <https://github.com/hsorby>`_ [`#1161 <https://github.com/cellml/libcellml/pull/1161>`_].
+* Fix importing in permissive mode by `@hsorby <https://github.com/hsorby>`_ [`#1157 <https://github.com/cellml/libcellml/pull/1157>`_].
+* Align assignAllIds with documentation by `@hsorby <https://github.com/hsorby>`_ [`#1151 <https://github.com/cellml/libcellml/pull/1151>`_].
+* Analyser/Generator: don't use weak pointers by `@agarny <https://github.com/agarny>`_ [`#1133 <https://github.com/cellml/libcellml/pull/1133>`_].
+* Fix an issue when initialising a state variable using a variable instead of a constant by `@agarny <https://github.com/agarny>`_ [`#1147 <https://github.com/cellml/libcellml/pull/1147>`_].
+* Fix segfault when using Units::equivalent/compatible API by `@hsorby <https://github.com/hsorby>`_ [`#1145 <https://github.com/cellml/libcellml/pull/1145>`_].
+* Fix parsing of CellML 1.X models with multiple math in a component by `@hsorby <https://github.com/hsorby>`_ [`#1146 <https://github.com/cellml/libcellml/pull/1146>`_].
+* Enable printer to print models that have multiple math documents in a single math container object by `@hsorby <https://github.com/hsorby>`_ [`#1142 <https://github.com/cellml/libcellml/pull/1142>`_].
+* Set minimum OSX deployment target that supports std::any by `@hsorby <https://github.com/hsorby>`_ [`#1111 <https://github.com/cellml/libcellml/pull/1111>`_].
+* Try using uLong for buffer size in uncompress by `@hsorby <https://github.com/hsorby>`_ [`#1110 <https://github.com/cellml/libcellml/pull/1110>`_].
+
+Coverage
+--------
+
+* Resolve branch coverage in validator.cpp by `@hsorby <https://github.com/hsorby>`_ [`#1128 <https://github.com/cellml/libcellml/pull/1128>`_].
+* Resolve branch coverage in annotator.cpp by `@hsorby <https://github.com/hsorby>`_ [`#1127 <https://github.com/cellml/libcellml/pull/1127>`_].
+* Resolve branch coverage in utilities.cpp by `@hsorby <https://github.com/hsorby>`_ [`#1126 <https://github.com/cellml/libcellml/pull/1126>`_].
+* Resolve branch coverage in units.cpp by `@hsorby <https://github.com/hsorby>`_ [`#1125 <https://github.com/cellml/libcellml/pull/1125>`_].
+* Resolve branch coverage in importer.cpp by `@hsorby <https://github.com/hsorby>`_ [`#1124 <https://github.com/cellml/libcellml/pull/1124>`_].
+* Resolve branch coverage in printer.cpp by `@hsorby <https://github.com/hsorby>`_ [`#1123 <https://github.com/cellml/libcellml/pull/1123>`_].
+* Resolve branch coverage in variable.cpp by `@hsorby <https://github.com/hsorby>`_ [`#1122 <https://github.com/cellml/libcellml/pull/1122>`_].
+* Resolve branch coverage in component.cpp by `@hsorby <https://github.com/hsorby>`_ [`#1116 <https://github.com/cellml/libcellml/pull/1116>`_].
+* Resolve branch coverage in reset.cpp by `@hsorby <https://github.com/hsorby>`_ [`#1120 <https://github.com/cellml/libcellml/pull/1120>`_].
+* Resolve branch coverage in model.cpp by `@hsorby <https://github.com/hsorby>`_ [`#1121 <https://github.com/cellml/libcellml/pull/1121>`_].
+* Resolve branch coverage in types.cpp by `@hsorby <https://github.com/hsorby>`_ [`#1119 <https://github.com/cellml/libcellml/pull/1119>`_].
+* Resolve branch coverage in logger.cpp by `@hsorby <https://github.com/hsorby>`_ [`#1118 <https://github.com/cellml/libcellml/pull/1118>`_].
+* Resolve branch coverage in importsource.cpp by `@hsorby <https://github.com/hsorby>`_ [`#1117 <https://github.com/cellml/libcellml/pull/1117>`_].
+* Resolve branch coverage in componententity.cpp by `@hsorby <https://github.com/hsorby>`_ [`#1115 <https://github.com/cellml/libcellml/pull/1115>`_].
+* Resolve branch coverage in xmlattribute.cpp by `@hsorby <https://github.com/hsorby>`_ [`#1114 <https://github.com/cellml/libcellml/pull/1114>`_].
+* Resolve branch coverage in xmlnode.cpp by `@hsorby <https://github.com/hsorby>`_ [`#1113 <https://github.com/cellml/libcellml/pull/1113>`_].
+* Resolve branch coverage in xmldoc.cpp by `@hsorby <https://github.com/hsorby>`_ [`#1112 <https://github.com/cellml/libcellml/pull/1112>`_].
+
+Generator
+---------
+
+* Generator: cast our malloc() calls by `@agarny <https://github.com/agarny>`_ [`#1076 <https://github.com/cellml/libcellml/pull/1076>`_].
+
+Imports
+-------
+
+* Flattening multiple equivalences by `@hsorby <https://github.com/hsorby>`_ [`#1170 <https://github.com/cellml/libcellml/pull/1170>`_].
+* Importing units with references to non-standard units by `@hsorby <https://github.com/hsorby>`_ [`#1167 <https://github.com/cellml/libcellml/pull/1167>`_].
+
+Infrastructure
+--------------
+
+* Set macOS 10.15 as the minimum deployment target for macOS by `@hsorby <https://github.com/hsorby>`_ [`#1181 <https://github.com/cellml/libcellml/pull/1181>`_].
+* GitHub Actions update by `@hsorby <https://github.com/hsorby>`_ [`#1154 <https://github.com/cellml/libcellml/pull/1154>`_].
+* CMake: fixed an issue with BINDINGS_PYTHON's value not being taken into account by `@agarny <https://github.com/agarny>`_ [`#1149 <https://github.com/cellml/libcellml/pull/1149>`_].
+* CMake: fixed a warning when running the `UNDEFINED_SYMBOLS_ALLOWED` test by `@agarny <https://github.com/agarny>`_ [`#1138 <https://github.com/cellml/libcellml/pull/1138>`_].
+* Analyser/Generator: cleaning up of code by `@agarny <https://github.com/agarny>`_ [`#1080 <https://github.com/cellml/libcellml/pull/1080>`_].
+* Fix for CI issues by `@hsorby <https://github.com/hsorby>`_ [`#1088 <https://github.com/cellml/libcellml/pull/1088>`_].
+* Update environmentchecks.cmake to handle newer LibXml2 CMake configuration by `@hsorby <https://github.com/hsorby>`_ [`#1085 <https://github.com/cellml/libcellml/pull/1085>`_].
+
+Miscellaneous
+-------------
+
+* Analyser/Generator: added some `xxxAsString()` methods by `@agarny <https://github.com/agarny>`_ [`#1131 <https://github.com/cellml/libcellml/pull/1131>`_].
+* Make gcc 11.3.0 happy on Ubuntu 22.04 LTS by `@agarny <https://github.com/agarny>`_ [`#1153 <https://github.com/cellml/libcellml/pull/1153>`_].
+* Analyser/Generator: replace if...else statements with switch ones wherever possible by `@agarny <https://github.com/agarny>`_ [`#1135 <https://github.com/cellml/libcellml/pull/1135>`_].
+* Tests: added support for libXml2 2.9.11+ by `@agarny <https://github.com/agarny>`_ [`#1069 <https://github.com/cellml/libcellml/pull/1069>`_].
+
+No category
+-----------
+
+* AnalyserVariable: hold onto the owning component reference by `@agarny <https://github.com/agarny>`_ [`#1185 <https://github.com/cellml/libcellml/pull/1185>`_].
+
+Validation
+----------
+
+* Improve MathML validation by `@agarny <https://github.com/agarny>`_ [`#1083 <https://github.com/cellml/libcellml/pull/1083>`_].
+
+Contributors
+------------
+
+.. image:: https://avatars.githubusercontent.com/u/778048?v=4
+   :target: https://github.com/hsorby
+   :height: 32
+   :width: 32
+.. image:: https://avatars.githubusercontent.com/u/602265?v=4
+   :target: https://github.com/agarny
+   :height: 32
+   :width: 32

docs/changelogs/index.rst

@@ -4,6 +4,7 @@ Changelogs
 
 .. toctree::
 
+   changelog_v0.5.0-rc.1
    changelog_v0.4.0
    changelog_v0.3.104
    changelog_v0.3.103

docs/coding_standards.rst

@@ -37,3 +37,8 @@ The following rules for naming of variables should be followed.
  * Class member variables: :code:`mMyClassMemberVariable`.
  * Function parameter variables: :code:`myFunctionParameterVariable`.
  * Local variables: :code:`myLocalVariable`.
+
+Weak pointers
+=============
+
+ * The return value of :code:`std::weak_ptr<T>::lock()` should only be tested if it may be equal to :code:`nullptr`.

docs/dev_building_web_assembly.rst

@@ -65,11 +65,11 @@ Start by making the current directory the parent of the zlib build directory::
 
 Then, as before, configure the library::
 
-  emcmake cmake -S libxml2 -B build-libxml2-release -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=usr/local -DZLIB_DIR=../usr/local/lib/cmake/ZLIB-1.2.3/ -DBUILD_SHARED_LIBS=OFF -DLIBXML2_WITH_ICONV=OFF -DLIBXML2_WITH_LZMA=OFF -DLIBXML2_WITH_PYTHON=OFF -DLIBXML2_WITH_TESTS=OFF -DLIBXML2_WITH_PROGRAMS=OFF
+  emcmake cmake -S libxml2 -B build-libxml2-release -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=usr/local -DZLIB_DIR=../usr/local/lib/cmake/ZLIB-1.2.12/ -DBUILD_SHARED_LIBS=OFF -DLIBXML2_WITH_ICONV=OFF -DLIBXML2_WITH_LZMA=OFF -DLIBXML2_WITH_PYTHON=OFF -DLIBXML2_WITH_TESTS=OFF -DLIBXML2_WITH_PROGRAMS=OFF
 
 There are seven additions to the configure command this time:
 
-1. We set :code:`ZLIB_DIR` to enable the configuration to find our *zlib* library we just installed, :code:`-DZLIB_DIR=../usr/local/lib/cmake/ZLIB-1.2.3/`.
+1. We set :code:`ZLIB_DIR` to enable the configuration to find our *zlib* library we just installed, :code:`-DZLIB_DIR=../usr/local/lib/cmake/ZLIB-1.2.12/`.
 2. We turn off building a shared *libxml2* library, -DBUILD_SHARED_LIBS=OFF.
 3. We turn off building *libxml2* with iconv, -DLIBXML2_WITH_ICONV=OFF.
 4. We turn off building *libxml2* with lzma compression, -DLIBXML2_WITH_LZMA=OFF.

docs/index.rst

@@ -39,6 +39,7 @@ Changelogs
 
 .. toctree::
 
+   changelogs/changelog_v0.5.0-rc.1
    changelogs/changelog_v0.4.0
    changelogs/changelog_v0.3.104
    changelogs/changelog_v0.3.103

src/CMakeLists.txt

@@ -33,15 +33,6 @@ configure_file(
   ${LIBCELLML_VERSIONCONFIG_H}
 )
 
-set(LIBCELLML_PRIVATECONFIG_IN_H "${CMAKE_CURRENT_SOURCE_DIR}/configure/libcellmlconfig_p.in.h")
-set(LIBCELLML_PRIVATECONFIG_H "${CMAKE_CURRENT_BINARY_DIR}/libcellmlconfig_p.h")
-if(MSVC)
-  set(UNCOMPRESS_SIZE_TYPE "unsigned long")
-else()
-  set(UNCOMPRESS_SIZE_TYPE "size_t")
-endif()
-configure_file(${LIBCELLML_PRIVATECONFIG_IN_H} ${LIBCELLML_PRIVATECONFIG_H})
-
 list(APPEND CLEAN_FILES ${LIBCELLML_VERSIONCONFIG_H} ${LIBCELLML_EXPORTDEFINITIONS_H})
 
 set(SOURCE_FILES
@@ -113,6 +104,7 @@ set(GIT_API_HEADER_FILES
   ${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/reset.h
   ${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/strict.h
   ${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/types.h
+  ${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/undefines.h
   ${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/units.h
   ${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/validator.h
   ${CMAKE_CURRENT_SOURCE_DIR}/api/libcellml/variable.h
@@ -163,7 +155,6 @@ set(GIT_HEADER_FILES
 
 set(HEADER_FILES
   ${GIT_HEADER_FILES}
-  ${LIBCELLML_PRIVATECONFIG_H}
   ${LIBCELLML_VERSIONCONFIG_H}
 )
 
@@ -243,6 +234,7 @@ target_include_directories(cellml_debug_utilities
 set_target_properties(cellml_debug_utilities PROPERTIES
   CXX_VISIBILITY_PRESET hidden
   DEBUG_POSTFIX d
+  POSITION_INDEPENDENT_CODE 1
   VISIBILITY_INLINES_HIDDEN 1
 )
 
@@ -383,7 +375,6 @@ set(API_HEADER_FILES ${GIT_API_HEADER_FILES} PARENT_SCOPE)
 set(MODULE_HEADER_FILES ${MODULE_HEADER_FILES} PARENT_SCOPE)
 set(HEADER_FILES ${GIT_HEADER_FILES} PARENT_SCOPE)
 set(GENERATED_HEADER_FILES
-  ${LIBCELLML_PRIVATECONFIG_H}
   ${LIBCELLML_VERSIONCONFIG_H}
   PARENT_SCOPE
 )