From 5febd95cbf9e58e1bafbeda56cb4984e617362d9 Mon Sep 17 00:00:00 2001
From: Alan Garny <agarny@hellix.com>
Date: Wed, 16 Oct 2024 09:46:14 +1300
Subject: [PATCH 01/12] CI: added some "basic" GitHub Actions.

---
 .github/workflows/ci.yml | 111 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 111 insertions(+)
 create mode 100644 .github/workflows/ci.yml

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 0000000000..b279063427
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,111 @@
+name: CI
+
+on:
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+
+env:
+  BUILDCACHE_ACCURACY: STRICT
+  BUILDCACHE_COMPRESS_FORMAT: ZSTD
+  BUILDCACHE_DEBUG: -1
+  BUILDCACHE_LOG_FILE: ""
+
+jobs:
+  cpp_python:
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: 'Windows static (BPT)'
+            os: windows-latest
+            bindings_python: ON
+            build_shared: OFF
+            unit_tests: ON
+            set_path: $env:Path="C:\libxml2\bin;C:\zlib\bin;"+$env:Path
+            additional_cmake_options: -DLIBXML2_INCLUDE_DIR="C:\libxml2\include\libxml2" -DLIBXML2_LIBRARY="C:\libxml2\lib\libxml2.lib" -DZLIB_INCLUDE_DIR="C:\zlib\include" -DZLIB_LIBRARY="C:\zlib\lib\z_dll.lib"
+          - name: 'Windows shared (BPT)'
+            os: windows-latest
+            bindings_python: ON
+            build_shared: ON
+            unit_tests: ON
+            set_path: $env:Path="C:\libxml2\bin;C:\zlib\bin;"+$env:Path
+            additional_cmake_options: -DLIBXML2_INCLUDE_DIR="C:\libxml2\include\libxml2" -DLIBXML2_LIBRARY="C:\libxml2\lib\libxml2.lib" -DZLIB_INCLUDE_DIR="C:\zlib\include" -DZLIB_LIBRARY="C:\zlib\lib\z_dll.lib"
+          - name: 'Linux static (B)'
+            os: ubuntu-latest
+            bindings_python: OFF
+            build_shared: OFF
+            unit_tests: OFF
+          - name: 'Linux shared (BPT)'
+            os: ubuntu-latest
+            bindings_python: ON
+            build_shared: ON
+            unit_tests: ON
+          - name: 'macOS static (Intel) (BT)'
+            os: macos-13
+            bindings_python: OFF
+            build_shared: OFF
+            unit_tests: ON
+          - name: 'macOS shared (Intel) (BPT)'
+            os: macos-13
+            bindings_python: ON
+            build_shared: ON
+            unit_tests: ON
+          - name: 'macOS static (ARM) (BT)'
+            os: macos-latest
+            bindings_python: OFF
+            build_shared: OFF
+            unit_tests: ON
+          - name: 'macOS shared (ARM) (BPT)'
+            os: macos-latest
+            bindings_python: ON
+            build_shared: ON
+            unit_tests: ON
+    steps:
+      - name: Check out libCellML
+        uses: actions/checkout@v4
+      - name: Install Python (if needed)
+        if: ${{ matrix.bindings_python == 'ON' }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+      - name: Install CMake and Ninja
+        uses: lukka/get-cmake@latest
+      - name: Install buildcache
+        uses: mikehardy/buildcache-action@v2
+        with:
+          cache_key: ${{ matrix.os }}-${{ matrix.build_shared }}
+      - name: Configure MSVC (Windows only)
+        if: ${{ runner.os == 'Windows' }}
+        uses: ilammy/msvc-dev-cmd@v1
+      - name: Install libxml2 (Windows only)
+        if: ${{ runner.os == 'Windows' }}
+        run: |
+          Invoke-WebRequest -UseBasicParsing https://github.com/cellml/gha/releases/download/gha/libxml2.zip -OutFile libxml2.zip
+          Expand-Archive -LiteralPath libxml2.zip -DestinationPath C:\
+      - name: Install SWIG (macOS only and if needed)
+        if: ${{ runner.os == 'macOS' && matrix.bindings_python == 'ON' }}
+        run: |
+          brew install swig
+      - name: Install zlib (Windows only)
+        if: ${{ runner.os == 'Windows' }}
+        run: |
+          Invoke-WebRequest -UseBasicParsing https://github.com/cellml/gha/releases/download/gha/zlib.zip -OutFile zlib.zip
+          Expand-Archive -LiteralPath zlib.zip -DestinationPath C:\
+      - name: Configure libCellML
+        run: |
+          mkdir build
+          cd build
+          ${{ matrix.set_path }}
+          cmake -G Ninja -DBINDINGS_PYTHON=${{ matrix.bindings_python }} -DBUILD_SHARED=${{ matrix.build_shared }} -DCOVERAGE=OFF -DLLVM_COVERAGE=OFF -DMEMCHECK=OFF -DUNIT_TESTS=${{ matrix.unit_tests }} ${{ matrix.additional_cmake_options }} ..
+      - name: Build libCellML
+        run: |
+          cd build
+          ninja
+      - name: Unit testing
+        if: ${{ matrix.unit_tests == 'ON' }}
+        run: |
+          cd build
+          ninja test

From cf90c3bd3deeb7818375112e078b4d3aeeb18488 Mon Sep 17 00:00:00 2001
From: Alan Garny <agarny@hellix.com>
Date: Wed, 16 Oct 2024 13:41:15 +1300
Subject: [PATCH 02/12] CI: added some "basic" GitHub Actions.

---
 .github/workflows/ci.yml | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b279063427..8ef4447caf 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -109,3 +109,26 @@ jobs:
         run: |
           cd build
           ninja test
+  code_formatting:
+    name: Code formatting
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    steps:
+      - name: Check out libCellML
+        uses: actions/checkout@v4
+      - name: Install ClangFormat
+        run: |
+          sudo apt update
+          sudo apt install clang-format
+      - name: Install CMake and Ninja
+        uses: lukka/get-cmake@latest
+      - name: Configure libCellML
+        run: |
+          mkdir build
+          cd build
+          cmake -G Ninja ..
+      - name: Code formatting
+        run: |
+          cd build
+          ninja test_clang_format

From 96877a67512dfa4547d9fe1f63827d28949ce4af Mon Sep 17 00:00:00 2001
From: Alan Garny <agarny@hellix.com>
Date: Wed, 16 Oct 2024 14:00:00 +1300
Subject: [PATCH 03/12] CI: added some "basic" GitHub Actions.

---
 .github/workflows/ci.yml             | 32 ++++++++++++++
 cmake/environmentchecks.cmake        |  2 +
 docs/CMakeLists.txt                  |  5 +--
 docs/conf.in.py                      | 66 ++++++++++++++--------------
 src/api/libcellml/generatorprofile.h |  2 +-
 5 files changed, 70 insertions(+), 37 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8ef4447caf..067e470736 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -132,3 +132,35 @@ jobs:
         run: |
           cd build
           ninja test_clang_format
+  documentation:
+    name: Documentation
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    steps:
+      - name: Check out libCellML
+        uses: actions/checkout@v4
+      - name: Install CMake and Ninja
+        uses: lukka/get-cmake@latest
+      - name: Install buildcache
+        uses: mikehardy/buildcache-action@v2
+      - name: Install dot
+        run: |
+          sudo apt update
+          sudo apt install graphviz
+      - name: Install Doxygen
+        run: |
+          sudo apt update
+          sudo apt install doxygen
+      - name: Install Sphinx
+        run: |
+          pip3 install sphinx
+      - name: Configure libCellML
+        run: |
+          mkdir build
+          cd build
+          cmake -G Ninja -DBINDINGS_PYTHON=OFF ..
+      - name: Documentation
+        run: |
+          cd build
+          ninja docs
diff --git a/cmake/environmentchecks.cmake b/cmake/environmentchecks.cmake
index 071e33682c..59c61a3baf 100644
--- a/cmake/environmentchecks.cmake
+++ b/cmake/environmentchecks.cmake
@@ -45,6 +45,7 @@ else ()
   endif()
   find_program(CLANG_FORMAT_EXE NAMES ${PREFERRED_CLANG_FORMAT_NAMES} clang-format)
   find_program(CLANG_TIDY_EXE NAMES ${PREFERRED_CLANG_TIDY_NAMES} clang-tidy)
+  find_program(DOT_EXE NAMES ${PREFERRED_FIND_NAMES} dot)
   find_program(FIND_EXE NAMES ${PREFERRED_FIND_NAMES} find)
   find_program(GCOV_EXE NAMES ${PREFERRED_GCOV_NAMES} gcov)
   find_program(LLVM_COV_EXE NAMES ${PREFERRED_LLVM_COV_NAMES} llvm-cov HINTS ${LLVM_BIN_DIR} /Library/Developer/CommandLineTools/usr/bin/)
@@ -93,6 +94,7 @@ else ()
     BUILDCACHE_EXE
     CLANG_TIDY_EXE
     CLANG_FORMAT_EXE
+    DOT_EXE
     FIND_EXE
     GCC_COVERAGE_COMPILER_FLAGS_OK
     GCOV_EXE
diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
index 6795596e50..8498fc7b4a 100644
--- a/docs/CMakeLists.txt
+++ b/docs/CMakeLists.txt
@@ -49,7 +49,7 @@ if(SPHINX_FOUND)
     COMMENT "Building HTML documentation with Sphinx")
 endif()
 
-if(DOXYGEN_FOUND)
+if(DOXYGEN_FOUND AND DOT_EXE)
   set(DOXYGEN_DOCS_TARGET api_docs)
   configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in.config ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
   add_custom_target(${DOXYGEN_DOCS_TARGET}
@@ -76,7 +76,7 @@ if(LIBCELLML_COVERAGE)
     COMMENT "Running coverage tests with html output")
 endif()
 
-if(SPHINX_FOUND OR DOXYGEN_FOUND OR LIBCELLML_COVERAGE)
+if(SPHINX_FOUND AND DOXYGEN_FOUND AND LIBCELLML_COVERAGE)
   add_custom_target(docs
     DEPENDS ${SPHINX_DOCS_TARGET} ${DOXYGEN_DOCS_TARGET} ${COVERAGE_DOCS_TARGET} ${DOXYGEN_API_XML_DOCS_TARGET}
     COMMENT "Generating documentation")
@@ -86,4 +86,3 @@ if(SPHINX_FOUND OR DOXYGEN_FOUND OR LIBCELLML_COVERAGE)
     COMMAND ${CMAKE_COMMAND} -E remove_directory ${CMAKE_CURRENT_BINARY_DIR}/_doctrees
     COMMENT "Cleaning documentation")
 endif()
-
diff --git a/docs/conf.in.py b/docs/conf.in.py
index 1fad261573..b671f63111 100644
--- a/docs/conf.in.py
+++ b/docs/conf.in.py
@@ -47,42 +47,42 @@
 # These are the shorthand for external links.  Use them in the other pages as:
 #   :shortcut:`Shortcut text <extra string if needed>` NB space before <
 # Declare below as:
-#   'shortcut': ('http://linkhere/%s',''), NB have to put the string insertion %s to make it work
+#   'shortcut': ('http://linkhere/%s', None), NB have to put the string insertion %s to make it work
 extlinks = {
     # NB for deployment outside of the libcellml.org domain, you will need to include the root of the href for the
     # :api: shortcut here.  This only works internally.
-    'api': ('/documentation/latest/api/classlibcellml_1_1%s', ''),
-    'buildbot': ('https://buildbot.net/%s',''),
-    'cellml': ('https://www.cellml.org/%s',''),
-    'cellml2spec': ('https://www.cellml.org/specifications/cellml_2.0%s', ''),
-    'clang': ('https://clang.llvm.org/%s',''),
-    'cmake': ('https://cmake.org/%s',''),
-    'doxygen': ('http://www.doxygen.nl/%s',''),
-    'forcescheduler': ('http://docs.buildbot.net/latest/developer/cls-forcesched.html%s',''),
-    'gcc': ('https://gcc.gnu.org/%s',''),
-    'gcovr': ('https://gcovr.com/%s',''),
-    'git': ('https://git-scm.com/%s',''),
-    'github': ('https://github.com/%s',''),
-    'github_desktop': ('https://desktop.github.com/%s',''),
-    'github_help': ('https://help.github.com%s',''),
-    'github_rtd': ('https://github.com/rtfd/readthedocs.org/issues%s',''),
-    'google_style_guide': ('https://google.github.io/styleguide/cppguide.html%s',''),
-    'graphviz': ('http://graphviz.org%s',''),
-    'htpasswd': ('https://httpd.apache.org/docs/current/programs/htpasswd.html%s',''),
-    'libcellml_repo': ('https://github.com/cellml/libcellml/%s',''),
-    'libcellml_buildbot': ('https://autotest.bioeng.auckland.ac.nz/buildbot/libcellml/#/builders%s',''),
-    'libxml2': ('http://xmlsoft.org/%s',''),
-    'mathml': ('https://www.w3.org/Math/%s',''),
-    'msvs': ('https://visualstudio.microsoft.com%s',''),
-    'opencmiss_libxml2_repo': ('https://github.com/OpenCMISS-Dependencies/libxml2/releases%s',''),
-    'opencmiss_zlib_repo': ('https://github.com/OpenCMISS-Dependencies/zlib/releases%s',''),
-    'python': ('https://www.python.org/%s',''),
-    'sphinx': ('http://www.sphinx-doc.org/en/master/%s',''),
-    'swig':('http://swig.org%s',''),
-    'swigwin_download': ('https://sourceforge.net/projects/swig/files/swigwin/%s',''),
-    'wikipedia': ('https://en.wikipedia.org/wiki%s',''),
-    'xml': ('https://www.w3.org/XML/%s',''),
-    'zlib': ('https://www.zlib.net/%s',''),
+    'api': ('/documentation/latest/api/classlibcellml_1_1%s', None),
+    'buildbot': ('https://buildbot.net/%s', None),
+    'cellml': ('https://www.cellml.org/%s', None),
+    'cellml2spec': ('https://www.cellml.org/specifications/cellml_2.0%s', None),
+    'clang': ('https://clang.llvm.org/%s', None),
+    'cmake': ('https://cmake.org/%s', None),
+    'doxygen': ('http://www.doxygen.nl/%s', None),
+    'forcescheduler': ('http://docs.buildbot.net/latest/developer/cls-forcesched.html%s', None),
+    'gcc': ('https://gcc.gnu.org/%s', None),
+    'gcovr': ('https://gcovr.com/%s', None),
+    'git': ('https://git-scm.com/%s', None),
+    'github': ('https://github.com/%s', None),
+    'github_desktop': ('https://desktop.github.com/%s', None),
+    'github_help': ('https://help.github.com%s', None),
+    'github_rtd': ('https://github.com/rtfd/readthedocs.org/issues%s', None),
+    'google_style_guide': ('https://google.github.io/styleguide/cppguide.html%s', None),
+    'graphviz': ('http://graphviz.org%s', None),
+    'htpasswd': ('https://httpd.apache.org/docs/current/programs/htpasswd.html%s', None),
+    'libcellml_repo': ('https://github.com/cellml/libcellml/%s', None),
+    'libcellml_buildbot': ('https://autotest.bioeng.auckland.ac.nz/buildbot/libcellml/#/builders%s', None),
+    'libxml2': ('http://xmlsoft.org/%s', None),
+    'mathml': ('https://www.w3.org/Math/%s', None),
+    'msvs': ('https://visualstudio.microsoft.com%s', None),
+    'opencmiss_libxml2_repo': ('https://github.com/OpenCMISS-Dependencies/libxml2/releases%s', None),
+    'opencmiss_zlib_repo': ('https://github.com/OpenCMISS-Dependencies/zlib/releases%s', None),
+    'python': ('https://www.python.org/%s', None),
+    'sphinx': ('http://www.sphinx-doc.org/en/master/%s', None),
+    'swig':('http://swig.org%s', None),
+    'swigwin_download': ('https://sourceforge.net/projects/swig/files/swigwin/%s', None),
+    'wikipedia': ('https://en.wikipedia.org/wiki%s', None),
+    'xml': ('https://www.w3.org/XML/%s', None),
+    'zlib': ('https://www.zlib.net/%s', None),
 }
 
 # The master toctree document.
diff --git a/src/api/libcellml/generatorprofile.h b/src/api/libcellml/generatorprofile.h
index 10335d24d8..fb9c90510c 100644
--- a/src/api/libcellml/generatorprofile.h
+++ b/src/api/libcellml/generatorprofile.h
@@ -2587,7 +2587,7 @@ class LIBCELLML_EXPORT GeneratorProfile
      * Set the @c std::string for the name of the state variable type that is
      * used in a differential model.
      *
-     * @param stateTypeString The @c std::string to use for the name of the
+     * @param stateVariableTypeString The @c std::string to use for the name of the
      * state variable type.
      */
     void setStateVariableTypeString(const std::string &stateVariableTypeString);

From b6d52b0900c11c9b11ed3c70c38377f6deb581b0 Mon Sep 17 00:00:00 2001
From: Alan Garny <agarny@hellix.com>
Date: Wed, 16 Oct 2024 15:34:08 +1300
Subject: [PATCH 04/12] CI: added some "basic" GitHub Actions.

---
 .github/workflows/ci.yml | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 067e470736..49f3d1d342 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -164,3 +164,29 @@ jobs:
         run: |
           cd build
           ninja docs
+  coverage:
+    name: Code coverage
+    runs-on: macos-latest
+    strategy:
+      fail-fast: false
+    steps:
+      - name: Check out libCellML
+        uses: actions/checkout@v4
+      - name: Install CMake and Ninja
+        uses: lukka/get-cmake@latest
+      - name: Install buildcache
+        uses: mikehardy/buildcache-action@v2
+      - name: Install LLVM
+        run: |
+          brew install --overwrite llvm
+          brew info llvm
+      - name: Configure libCellML
+        run: |
+          mkdir build
+          cd build
+          cmake -G Ninja -DBINDINGS_PYTHON=OFF ..
+      - name: Code coverage
+        run: |
+          cd build
+          ninja llvm_coverage
+          if [ `ninja llvm_coverage | grep TOTAL | sed 's/ /\n/g' | grep "100.00%" | wc -l | sed 's/ //g'` -eq 4 ]; then exit 0; else exit 1; fi

From 1add1b6cabd8e4249d6f50dbc5e06430c53813c6 Mon Sep 17 00:00:00 2001
From: Alan Garny <agarny@hellix.com>
Date: Wed, 16 Oct 2024 15:53:43 +1300
Subject: [PATCH 05/12] CI: added some "basic" GitHub Actions.

---
 .github/workflows/ci.yml | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 49f3d1d342..679cfeba9a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -190,3 +190,28 @@ jobs:
           cd build
           ninja llvm_coverage
           if [ `ninja llvm_coverage | grep TOTAL | sed 's/ /\n/g' | grep "100.00%" | wc -l | sed 's/ //g'` -eq 4 ]; then exit 0; else exit 1; fi
+  memory_leaks:
+    name: Memory leaks
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    steps:
+      - name: Check out libCellML
+        uses: actions/checkout@v4
+      - name: Install CMake and Ninja
+        uses: lukka/get-cmake@latest
+      - name: Install buildcache
+        uses: mikehardy/buildcache-action@v2
+      - name: Install Valgrind
+        run: |
+          sudo apt update
+          sudo apt install valgrind
+      - name: Configure libCellML
+        run: |
+          mkdir build
+          cd build
+          cmake -G Ninja -DBINDINGS_PYTHON=OFF ..
+      - name: Memory leaks
+        run: |
+          cd build
+          ninja memcheck

From 1dce2018b41cb759be0e6f29afb1025d666ec44a Mon Sep 17 00:00:00 2001
From: Alan Garny <agarny@hellix.com>
Date: Wed, 16 Oct 2024 16:58:15 +1300
Subject: [PATCH 06/12] CI: added some "basic" GitHub Actions.

---
 .github/workflows/ci.yml | 50 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 679cfeba9a..6b4eb835a2 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -215,3 +215,53 @@ jobs:
         run: |
           cd build
           ninja memcheck
+  javascript:
+    name: JavaScript (BT)
+    runs-on: macos-latest
+    strategy:
+      fail-fast: false
+    env:
+      LIBCELLML_WASM_DIR: wasm
+      LIBXML2_VERSION: 2.9.10
+      ZLIB_VERSION: 1.2.3
+    steps:
+      - name: Check out libCellML
+        uses: actions/checkout@v4
+      - name: Install CMake and Ninja
+        uses: lukka/get-cmake@latest
+      - name: Install buildcache
+        uses: mikehardy/buildcache-action@v2
+      - name: Install Emscripten
+        run: |
+          brew install --overwrite emscripten
+      - name: Set up the build directory
+        run: |
+          mkdir build
+      - name: Build zlib
+        run: |
+          cd build
+          ZLIB_BUILD_DIR=zlib-wasm
+          git clone https://github.com/OpenCMISS-Dependencies/zlib.git -b v${ZLIB_VERSION}
+          mkdir ${ZLIB_BUILD_DIR}
+          emcmake cmake -G Ninja -S zlib -B ${ZLIB_BUILD_DIR} -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=~/${LIBCELLML_WASM_DIR} -DBUILD_SHARED_LIBS=OFF
+          cmake --build ${ZLIB_BUILD_DIR}
+          cmake --install ${ZLIB_BUILD_DIR}
+      - name: Build libxml2
+        run: |
+          cd build
+          LIBXML2_BUILD_DIR=libxml2-wasm
+          git clone https://github.com/OpenCMISS-Dependencies/libxml2.git -b v${LIBXML2_VERSION}
+          mkdir ${LIBXML2_BUILD_DIR}
+          emcmake cmake -G Ninja -S libxml2 -B ${LIBXML2_BUILD_DIR} -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=~/${LIBCELLML_WASM_DIR} -DZLIB_DIR=~/${LIBCELLML_WASM_DIR}/lib/cmake/ZLIB-${ZLIB_VERSION} -DBUILD_SHARED_LIBS=OFF -DLIBXML2_WITH_ICONV=OFF -DLIBXML2_WITH_LZMA=OFF -DLIBXML2_WITH_PYTHON=OFF -DLIBXML2_WITH_TESTS=OFF -DLIBXML2_WITH_PROGRAMS=OFF
+          cmake --build ${LIBXML2_BUILD_DIR}
+          cmake --install ${LIBXML2_BUILD_DIR}
+      - name: Build libCellML
+        run: |
+          cd build
+          mkdir ${LIBCELLML_WASM_DIR}
+          emcmake cmake -G Ninja -S .. -B ${LIBCELLML_WASM_DIR} -DLibXml2_DIR=~/${LIBCELLML_WASM_DIR}/lib/cmake/libxml2-${LIBXML2_VERSION} -DBUILD_TYPE=Release
+          cmake --build ${LIBCELLML_WASM_DIR}
+      - name: Unit testing
+        run: |
+          cd build
+          cmake --build ${LIBCELLML_WASM_DIR} --target jest_test

From aefa695f16ecacd271e9cdaf3de208167b8e1fa3 Mon Sep 17 00:00:00 2001
From: Alan Garny <agarny@hellix.com>
Date: Wed, 16 Oct 2024 17:42:03 +1300
Subject: [PATCH 07/12] CI: added some "basic" GitHub Actions.

---
 .github/workflows/ci.yml | 142 +++++++++++++++++++--------------------
 1 file changed, 71 insertions(+), 71 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6b4eb835a2..86d33ff01f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -19,46 +19,46 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - name: 'Windows static (BPT)'
+          - name: 'Windows static - C++/Python'
             os: windows-latest
             bindings_python: ON
             build_shared: OFF
             unit_tests: ON
             set_path: $env:Path="C:\libxml2\bin;C:\zlib\bin;"+$env:Path
             additional_cmake_options: -DLIBXML2_INCLUDE_DIR="C:\libxml2\include\libxml2" -DLIBXML2_LIBRARY="C:\libxml2\lib\libxml2.lib" -DZLIB_INCLUDE_DIR="C:\zlib\include" -DZLIB_LIBRARY="C:\zlib\lib\z_dll.lib"
-          - name: 'Windows shared (BPT)'
+          - name: 'Windows shared - C++/Python'
             os: windows-latest
             bindings_python: ON
             build_shared: ON
             unit_tests: ON
             set_path: $env:Path="C:\libxml2\bin;C:\zlib\bin;"+$env:Path
             additional_cmake_options: -DLIBXML2_INCLUDE_DIR="C:\libxml2\include\libxml2" -DLIBXML2_LIBRARY="C:\libxml2\lib\libxml2.lib" -DZLIB_INCLUDE_DIR="C:\zlib\include" -DZLIB_LIBRARY="C:\zlib\lib\z_dll.lib"
-          - name: 'Linux static (B)'
+          - name: 'Linux static - C++ (build only)'
             os: ubuntu-latest
             bindings_python: OFF
             build_shared: OFF
             unit_tests: OFF
-          - name: 'Linux shared (BPT)'
+          - name: 'Linux shared - C++/Python'
             os: ubuntu-latest
             bindings_python: ON
             build_shared: ON
             unit_tests: ON
-          - name: 'macOS static (Intel) (BT)'
+          - name: 'macOS static - C++ (Intel)'
             os: macos-13
             bindings_python: OFF
             build_shared: OFF
             unit_tests: ON
-          - name: 'macOS shared (Intel) (BPT)'
+          - name: 'macOS shared - C++/Python (Intel)'
             os: macos-13
             bindings_python: ON
             build_shared: ON
             unit_tests: ON
-          - name: 'macOS static (ARM) (BT)'
+          - name: 'macOS static - C++ (ARM)'
             os: macos-latest
             bindings_python: OFF
             build_shared: OFF
             unit_tests: ON
-          - name: 'macOS shared (ARM) (BPT)'
+          - name: 'macOS shared - C++/Python (ARM)'
             os: macos-latest
             bindings_python: ON
             build_shared: ON
@@ -109,61 +109,79 @@ jobs:
         run: |
           cd build
           ninja test
-  code_formatting:
-    name: Code formatting
-    runs-on: ubuntu-latest
+  javascript:
+    name: JavaScript
+    runs-on: macos-latest
     strategy:
       fail-fast: false
+    env:
+      LIBCELLML_WASM_DIR: wasm
+      LIBXML2_VERSION: 2.9.10
+      ZLIB_VERSION: 1.2.3
     steps:
       - name: Check out libCellML
         uses: actions/checkout@v4
-      - name: Install ClangFormat
-        run: |
-          sudo apt update
-          sudo apt install clang-format
       - name: Install CMake and Ninja
         uses: lukka/get-cmake@latest
-      - name: Configure libCellML
+      - name: Install buildcache
+        uses: mikehardy/buildcache-action@v2
+      - name: Install Emscripten
+        run: |
+          brew install --overwrite emscripten
+      - name: Set up the build directory
         run: |
           mkdir build
+      - name: Build zlib
+        run: |
           cd build
-          cmake -G Ninja ..
-      - name: Code formatting
+          ZLIB_BUILD_DIR=zlib-wasm
+          git clone https://github.com/OpenCMISS-Dependencies/zlib.git -b v${ZLIB_VERSION}
+          mkdir ${ZLIB_BUILD_DIR}
+          emcmake cmake -G Ninja -S zlib -B ${ZLIB_BUILD_DIR} -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=~/${LIBCELLML_WASM_DIR} -DBUILD_SHARED_LIBS=OFF
+          cmake --build ${ZLIB_BUILD_DIR}
+          cmake --install ${ZLIB_BUILD_DIR}
+      - name: Build libxml2
         run: |
           cd build
-          ninja test_clang_format
-  documentation:
-    name: Documentation
+          LIBXML2_BUILD_DIR=libxml2-wasm
+          git clone https://github.com/OpenCMISS-Dependencies/libxml2.git -b v${LIBXML2_VERSION}
+          mkdir ${LIBXML2_BUILD_DIR}
+          emcmake cmake -G Ninja -S libxml2 -B ${LIBXML2_BUILD_DIR} -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=~/${LIBCELLML_WASM_DIR} -DZLIB_DIR=~/${LIBCELLML_WASM_DIR}/lib/cmake/ZLIB-${ZLIB_VERSION} -DBUILD_SHARED_LIBS=OFF -DLIBXML2_WITH_ICONV=OFF -DLIBXML2_WITH_LZMA=OFF -DLIBXML2_WITH_PYTHON=OFF -DLIBXML2_WITH_TESTS=OFF -DLIBXML2_WITH_PROGRAMS=OFF
+          cmake --build ${LIBXML2_BUILD_DIR}
+          cmake --install ${LIBXML2_BUILD_DIR}
+      - name: Build libCellML
+        run: |
+          cd build
+          mkdir ${LIBCELLML_WASM_DIR}
+          emcmake cmake -G Ninja -S .. -B ${LIBCELLML_WASM_DIR} -DLibXml2_DIR=~/${LIBCELLML_WASM_DIR}/lib/cmake/libxml2-${LIBXML2_VERSION} -DBUILD_TYPE=Release
+          cmake --build ${LIBCELLML_WASM_DIR}
+      - name: Unit testing
+        run: |
+          cd build
+          cmake --build ${LIBCELLML_WASM_DIR} --target jest_test
+  code_formatting:
+    name: Code formatting
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
     steps:
       - name: Check out libCellML
         uses: actions/checkout@v4
-      - name: Install CMake and Ninja
-        uses: lukka/get-cmake@latest
-      - name: Install buildcache
-        uses: mikehardy/buildcache-action@v2
-      - name: Install dot
-        run: |
-          sudo apt update
-          sudo apt install graphviz
-      - name: Install Doxygen
+      - name: Install ClangFormat
         run: |
           sudo apt update
-          sudo apt install doxygen
-      - name: Install Sphinx
-        run: |
-          pip3 install sphinx
+          sudo apt install clang-format
+      - name: Install CMake and Ninja
+        uses: lukka/get-cmake@latest
       - name: Configure libCellML
         run: |
           mkdir build
           cd build
-          cmake -G Ninja -DBINDINGS_PYTHON=OFF ..
-      - name: Documentation
+          cmake -G Ninja ..
+      - name: Code formatting
         run: |
           cd build
-          ninja docs
+          ninja test_clang_format
   coverage:
     name: Code coverage
     runs-on: macos-latest
@@ -215,15 +233,11 @@ jobs:
         run: |
           cd build
           ninja memcheck
-  javascript:
-    name: JavaScript (BT)
-    runs-on: macos-latest
+  documentation:
+    name: Documentation
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
-    env:
-      LIBCELLML_WASM_DIR: wasm
-      LIBXML2_VERSION: 2.9.10
-      ZLIB_VERSION: 1.2.3
     steps:
       - name: Check out libCellML
         uses: actions/checkout@v4
@@ -231,37 +245,23 @@ jobs:
         uses: lukka/get-cmake@latest
       - name: Install buildcache
         uses: mikehardy/buildcache-action@v2
-      - name: Install Emscripten
-        run: |
-          brew install --overwrite emscripten
-      - name: Set up the build directory
+      - name: Install dot
         run: |
-          mkdir build
-      - name: Build zlib
+          sudo apt update
+          sudo apt install graphviz
+      - name: Install Doxygen
         run: |
-          cd build
-          ZLIB_BUILD_DIR=zlib-wasm
-          git clone https://github.com/OpenCMISS-Dependencies/zlib.git -b v${ZLIB_VERSION}
-          mkdir ${ZLIB_BUILD_DIR}
-          emcmake cmake -G Ninja -S zlib -B ${ZLIB_BUILD_DIR} -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=~/${LIBCELLML_WASM_DIR} -DBUILD_SHARED_LIBS=OFF
-          cmake --build ${ZLIB_BUILD_DIR}
-          cmake --install ${ZLIB_BUILD_DIR}
-      - name: Build libxml2
+          sudo apt update
+          sudo apt install doxygen
+      - name: Install Sphinx
         run: |
-          cd build
-          LIBXML2_BUILD_DIR=libxml2-wasm
-          git clone https://github.com/OpenCMISS-Dependencies/libxml2.git -b v${LIBXML2_VERSION}
-          mkdir ${LIBXML2_BUILD_DIR}
-          emcmake cmake -G Ninja -S libxml2 -B ${LIBXML2_BUILD_DIR} -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=~/${LIBCELLML_WASM_DIR} -DZLIB_DIR=~/${LIBCELLML_WASM_DIR}/lib/cmake/ZLIB-${ZLIB_VERSION} -DBUILD_SHARED_LIBS=OFF -DLIBXML2_WITH_ICONV=OFF -DLIBXML2_WITH_LZMA=OFF -DLIBXML2_WITH_PYTHON=OFF -DLIBXML2_WITH_TESTS=OFF -DLIBXML2_WITH_PROGRAMS=OFF
-          cmake --build ${LIBXML2_BUILD_DIR}
-          cmake --install ${LIBXML2_BUILD_DIR}
-      - name: Build libCellML
+          pip3 install sphinx
+      - name: Configure libCellML
         run: |
+          mkdir build
           cd build
-          mkdir ${LIBCELLML_WASM_DIR}
-          emcmake cmake -G Ninja -S .. -B ${LIBCELLML_WASM_DIR} -DLibXml2_DIR=~/${LIBCELLML_WASM_DIR}/lib/cmake/libxml2-${LIBXML2_VERSION} -DBUILD_TYPE=Release
-          cmake --build ${LIBCELLML_WASM_DIR}
-      - name: Unit testing
+          cmake -G Ninja -DBINDINGS_PYTHON=OFF ..
+      - name: Documentation
         run: |
           cd build
-          cmake --build ${LIBCELLML_WASM_DIR} --target jest_test
+          ninja docs

From c055c696f3d45fe5ae55460fa944c40b684715b5 Mon Sep 17 00:00:00 2001
From: Alan Garny <agarny@hellix.com>
Date: Tue, 22 Oct 2024 12:19:40 +1300
Subject: [PATCH 08/12] Make sure that we can find the version of llvm-cov that
 we installed.

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 86d33ff01f..13c2affa03 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -197,7 +197,7 @@ jobs:
       - name: Install LLVM
         run: |
           brew install --overwrite llvm
-          brew info llvm
+          echo 'export PATH="/opt/homebrew/opt/llvm/bin:$PATH"' >> ~/.bash_profile
       - name: Configure libCellML
         run: |
           mkdir build

From 6c63b5c6c4a983e9bd0d5dbdb9bab2c8fa18671f Mon Sep 17 00:00:00 2001
From: Alan Garny <agarny@hellix.com>
Date: Tue, 22 Oct 2024 12:41:01 +1300
Subject: [PATCH 09/12] CMake: use the PATH as a hint to find llvm-cov and
 llvm-profdata.

Indeed, someone might have a version of llvm-cov and llvm-profdata that they use and which is not located in /Library/Developer/CommandLineTools/usr/bin.
---
 cmake/environmentchecks.cmake | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cmake/environmentchecks.cmake b/cmake/environmentchecks.cmake
index 59c61a3baf..4a66b37fab 100644
--- a/cmake/environmentchecks.cmake
+++ b/cmake/environmentchecks.cmake
@@ -48,8 +48,8 @@ else ()
   find_program(DOT_EXE NAMES ${PREFERRED_FIND_NAMES} dot)
   find_program(FIND_EXE NAMES ${PREFERRED_FIND_NAMES} find)
   find_program(GCOV_EXE NAMES ${PREFERRED_GCOV_NAMES} gcov)
-  find_program(LLVM_COV_EXE NAMES ${PREFERRED_LLVM_COV_NAMES} llvm-cov HINTS ${LLVM_BIN_DIR} /Library/Developer/CommandLineTools/usr/bin/)
-  find_program(LLVM_PROFDATA_EXE NAMES ${PREFERRED_LLVM_PROFDATA_NAMES} llvm-profdata HINTS ${LLVM_BIN_DIR} /Library/Developer/CommandLineTools/usr/bin/)
+  find_program(LLVM_COV_EXE NAMES ${PREFERRED_LLVM_COV_NAMES} llvm-cov HINTS ${LLVM_BIN_DIR} ENV PATH /Library/Developer/CommandLineTools/usr/bin/)
+  find_program(LLVM_PROFDATA_EXE NAMES ${PREFERRED_LLVM_PROFDATA_NAMES} llvm-profdata HINTS ${LLVM_BIN_DIR} ENV PATH /Library/Developer/CommandLineTools/usr/bin/)
   find_program(VALGRIND_EXE NAMES ${PREFERRED_VALGRIND_NAMES} valgrind)
   find_program(INSTALL_NAME_TOOL_EXE NAMES ${PREFERRED_INSTALL_NAME_TOOL_NAMES} install_name_tool)
 

From 62a53310665f0cc88c635d6d8e3457c24f811465 Mon Sep 17 00:00:00 2001
From: Alan Garny <agarny@hellix.com>
Date: Tue, 22 Oct 2024 12:41:15 +1300
Subject: [PATCH 10/12] CMake: let the user know where the coverage report can
 be found.

---
 tests/CMakeLists.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index cf64a66c27..1dbf26da87 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -191,6 +191,7 @@ if(LIBCELLML_LLVM_COVERAGE)
 
   add_custom_target(llvm_coverage_report
     COMMAND ${LLVM_COV_EXE} show $<TARGET_FILE:cellml> -instr-profile=${DATA_PROFILE_FILENAME} -format=html -Xdemangler c++filt -Xdemangler -n -o coverage_report --show-expansions --show-branches=count
+    COMMAND echo "The coverage report can be found at ${CMAKE_CURRENT_BINARY_DIR}/${COVERAGE_REPORT_DIR}coverage_report/index.html."
     DEPENDS prepare_llvm_coverage
     WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
     COMMENT "Running LLVM coverage missing lines command")

From 81f7f8c29a3e9c27f3e0ae0cb750cec8d277c383 Mon Sep 17 00:00:00 2001
From: Alan Garny <agarny@hellix.com>
Date: Tue, 5 Nov 2024 15:00:50 +1300
Subject: [PATCH 11/12] Documentation: removed the need for dot.

---
 .github/workflows/ci.yml      | 4 ----
 cmake/environmentchecks.cmake | 2 --
 docs/CMakeLists.txt           | 2 +-
 3 files changed, 1 insertion(+), 7 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 13c2affa03..b7abf4e9f6 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -245,10 +245,6 @@ jobs:
         uses: lukka/get-cmake@latest
       - name: Install buildcache
         uses: mikehardy/buildcache-action@v2
-      - name: Install dot
-        run: |
-          sudo apt update
-          sudo apt install graphviz
       - name: Install Doxygen
         run: |
           sudo apt update
diff --git a/cmake/environmentchecks.cmake b/cmake/environmentchecks.cmake
index 9da1d7810f..260b5c0ae4 100644
--- a/cmake/environmentchecks.cmake
+++ b/cmake/environmentchecks.cmake
@@ -46,7 +46,6 @@ else ()
   endif()
   find_program(CLANG_FORMAT_EXE NAMES ${PREFERRED_CLANG_FORMAT_NAMES} clang-format)
   find_program(CLANG_TIDY_EXE NAMES ${PREFERRED_CLANG_TIDY_NAMES} clang-tidy)
-  find_program(DOT_EXE NAMES ${PREFERRED_FIND_NAMES} dot)
   find_program(FIND_EXE NAMES ${PREFERRED_FIND_NAMES} find)
   find_program(GCOV_EXE NAMES ${PREFERRED_GCOV_NAMES} gcov)
   find_program(LLVM_COV_EXE NAMES ${PREFERRED_LLVM_COV_NAMES} llvm-cov HINTS ${LLVM_BIN_DIR} ENV PATH /Library/Developer/CommandLineTools/usr/bin/)
@@ -95,7 +94,6 @@ else ()
     BUILDCACHE_EXE
     CLANG_TIDY_EXE
     CLANG_FORMAT_EXE
-    DOT_EXE
     FIND_EXE
     GCC_COVERAGE_COMPILER_FLAGS_OK
     GCOV_EXE
diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
index 8498fc7b4a..4c05459a24 100644
--- a/docs/CMakeLists.txt
+++ b/docs/CMakeLists.txt
@@ -49,7 +49,7 @@ if(SPHINX_FOUND)
     COMMENT "Building HTML documentation with Sphinx")
 endif()
 
-if(DOXYGEN_FOUND AND DOT_EXE)
+if(DOXYGEN_FOUND)
   set(DOXYGEN_DOCS_TARGET api_docs)
   configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in.config ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
   add_custom_target(${DOXYGEN_DOCS_TARGET}

From b19bdade7509a8fb941b4ed9dd944dbbfd73f631 Mon Sep 17 00:00:00 2001
From: Alan Garny <agarny@hellix.com>
Date: Tue, 5 Nov 2024 22:33:33 +1300
Subject: [PATCH 12/12] CMake: reverted the logic for the `docs` target.

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

diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
index 4c05459a24..bab96399b3 100644
--- a/docs/CMakeLists.txt
+++ b/docs/CMakeLists.txt
@@ -76,7 +76,7 @@ if(LIBCELLML_COVERAGE)
     COMMENT "Running coverage tests with html output")
 endif()
 
-if(SPHINX_FOUND AND DOXYGEN_FOUND AND LIBCELLML_COVERAGE)
+if(SPHINX_FOUND OR DOXYGEN_FOUND OR LIBCELLML_COVERAGE)
   add_custom_target(docs
     DEPENDS ${SPHINX_DOCS_TARGET} ${DOXYGEN_DOCS_TARGET} ${COVERAGE_DOCS_TARGET} ${DOXYGEN_API_XML_DOCS_TARGET}
     COMMENT "Generating documentation")