Pull from develop

.github/workflows/main.yml

@@ -81,10 +81,10 @@ jobs:
             build_type: Debug
             build_python: ON
             build_qt_antimony: OFF
-        libroadrunner_deps_owner: [ "sys-bio" ]
-        libroadrunner_deps_repo: [ "libroadrunner-deps" ]
-        libroadrunner_deps_name: [ "libroadrunner-deps" ]
-        libroadrunner_deps_release_version: [ "v2.3.4" ]
+        antimony_deps_owner: [ "sys-bio" ]
+        antimony_deps_repo: [ "libroadrunner-deps" ]
+        antimony_deps_name: [ "antimony-deps" ]
+        antimony_deps_release_version: [ "v2.3.5" ]
         python_version: [ "3.13" ]
 
     runs-on: ${{ matrix.platform.os_name }}
@@ -180,7 +180,7 @@ jobs:
         if: matrix.platform.os_type != 'windows'
         uses: actions/cache@main
         with:
-          path: ${RUNNER_WORKSPACE}/.ccache
+          path: ${{ runner.workspace }}/.ccache
           key:
             ${{ runner.os }}-${{ steps.ccache_cache_timestamp.outputs.timestamp
             }}
@@ -224,28 +224,35 @@ jobs:
         shell: bash
         run: |
           cd ${RUNNER_WORKSPACE}
-          mkdir -p ${{ matrix.libroadrunner_deps_name }}-binaries
-          cd ${{ matrix.libroadrunner_deps_name }}-binaries
+          mkdir -p ${{ matrix.antimony_deps_name }}-binaries
+          cd ${{ matrix.antimony_deps_name }}-binaries
           if [ "${{ matrix.platform.os_type }}" == 'windows' ]; then
             compiler_version=$(ls "C:\Program Files\Microsoft Visual Studio")
-            binary_file_name=${{ matrix.libroadrunner_deps_name }}-${{ matrix.platform.os_type }}-msvc${compiler_version}-${host_architecture}-${{ matrix.platform.build_type }}
+            binary_file_name=${{ matrix.antimony_deps_name }}-${{ matrix.platform.os_type }}-msvc${compiler_version}-${host_architecture}-${{ matrix.platform.build_type }}
           elif [ "${{ matrix.platform.os_type }}" == 'macos' ]; then
             os_version=$(sw_vers -productVersion | cut -d '.' -f 1)
-            binary_file_name=${{ matrix.libroadrunner_deps_name }}-${{ matrix.platform.os_type }}-${os_version}-${host_architecture}-${{ matrix.platform.build_type }}
+            binary_file_name=${{ matrix.antimony_deps_name }}-${{ matrix.platform.os_type }}-${os_version}-${host_architecture}-${{ matrix.platform.build_type }}
           elif [ "${{ matrix.platform.os_type }}" == 'ubuntu' ]; then
             os_version=$(lsb_release -rs | cut -d '.' -f 1)
-            binary_file_name=${{ matrix.libroadrunner_deps_name }}-${{ matrix.platform.os_type }}-${os_version}-${host_architecture}-${{ matrix.platform.build_type }}
+            binary_file_name=${{ matrix.antimony_deps_name }}-${{ matrix.platform.os_type }}-${os_version}-${host_architecture}-${{ matrix.platform.build_type }}
           elif [ "${{ matrix.platform.os_type }}" == 'manylinux' ]; then
             os_name="${{ matrix.platform.name }}"
             os_name_without_build_type="${os_name%%-*}"
-            binary_file_name=${{ matrix.libroadrunner_deps_name }}-${os_name_without_build_type}-${host_architecture}-${{ matrix.platform.build_type }}
+            binary_file_name=${{ matrix.antimony_deps_name }}-${os_name_without_build_type}-${host_architecture}-${{ matrix.platform.build_type }}
           fi
-          curl -LO "https://github.com/${{ matrix.libroadrunner_deps_owner }}/${{ matrix.libroadrunner_deps_repo }}/releases/download/${{ matrix.libroadrunner_deps_release_version }}/$binary_file_name.zip"
+          curl -LO "https://github.com/${{ matrix.antimony_deps_owner }}/${{ matrix.antimony_deps_repo }}/releases/download/${{ matrix.antimony_deps_release_version }}/$binary_file_name.zip"
           unzip -q $binary_file_name.zip
           rm $binary_file_name.zip
-          echo ANT_DEPENDENCIES_INSTALL_PREFIX="-DANT_DEPENDENCIES_INSTALL_PREFIX=${RUNNER_WORKSPACE}/${{ matrix.libroadrunner_deps_name }}-binaries" >> "${GITHUB_ENV}"
+          if [ -d "$binary_file_name" ]; then
+            mv "$binary_file_name"/* .
+            rmdir "$binary_file_name"
+          fi
+
+          echo ANT_DEPENDENCIES_INSTALL_PREFIX="-DANT_DEPENDENCIES_INSTALL_PREFIX=${RUNNER_WORKSPACE}/${{ matrix.antimony_deps_name }}-binaries" >> "${GITHUB_ENV}"
+
+
           #if [ "${{ matrix.platform.os_type }}" == 'windows' ]; then
-          #  echo EXPAT_LIBRARY="-DEXPAT_LIBRARY=${RUNNER_WORKSPACE}/${{ matrix.libroadrunner_deps_name }}-binaries/lib/${{ matrix.platform.expat_lib_name }}" >> "${GITHUB_ENV}"
+          #  echo EXPAT_LIBRARY="-DEXPAT_LIBRARY=${RUNNER_WORKSPACE}/${{ matrix.antimony_deps_name }}-binaries/lib/${{ matrix.platform.expat_lib_name }}" >> "${GITHUB_ENV}"
           #fi
 
       - name: Install Qt
@@ -280,7 +287,6 @@ jobs:
           -DCMAKE_C_COMPILER_LAUNCHER=${COMPILER_LAUNCHER} \
           -DCMAKE_CXX_COMPILER_LAUNCHER=${COMPILER_LAUNCHER} \
           -DCMAKE_BUILD_TYPE=${{ matrix.platform.build_type }} \
-          -DUSE_UNIVERSAL_BINARIES=OFF \
           -DCMAKE_OSX_ARCHITECTURES=${{ matrix.platform.arch }} \
           -DCMAKE_INSTALL_PREFIX="${RUNNER_WORKSPACE}/install-antimony" \
           ${ANT_DEPENDENCIES_INSTALL_PREFIX} \
@@ -304,32 +310,17 @@ jobs:
 
       # Valgrind is Linux-only (no Windows support, weak/no Apple Silicon
       # support), so this only runs on one leg of the matrix rather than
-      # across every platform/config combination. See MEMORYCHECK_* in the
-      # root CMakeLists.txt and valgrind.supp for the suppressions file.
-      #
-      # This runs automatically on every push/PR, against the release build
-      # (which has -g added just for this leg -- see "Configure CMake for
-      # Antimony" above -- so it's still symbol-rich) so it's much faster
-      # than a full debug-build run and still gives usable stack traces, at
-      # the cost of somewhat less precise line numbers due to optimization
-      # (inlining etc.), and a small risk that -O3 could eliminate a
-      # provably-dead allocation an unoptimized debug build wouldn't.
+      # across every platform/config combination. 
       #
       # For a slower but fully accurate debug-build memcheck run (e.g. to
       # dig into something this one flagged), trigger
       # .github/workflows/valgrind-debug-memcheck.yml manually from the
-      # Actions tab -- see the comment at the top of that file for why it's
-      # a separate workflow rather than another leg here.
+      # Actions tab.
       #
       # `ctest -T memcheck` only prints a per-test defect *count* to the
       # console -- the actual valgrind report (stack traces, "definitely
       # lost" byte counts, etc.) goes to a per-test log file instead:
-      # Testing/Temporary/MemoryChecker.<test-id>.log, one per test. Rather
-      # than running every test as one opaque block and only finding out
-      # what broke at the very end, run them in numbered chunks (via
-      # `ctest -I <start>,<end>`) and print any defects from each chunk
-      # immediately after it finishes, so problems surface within minutes
-      # rather than at the end of the whole run.
+      # Testing/Temporary/MemoryChecker.<test-id>.log, one per test.
       - name: Run Antimony tests under valgrind (memcheck), in chunks
         if : matrix.platform.name == 'ubuntu-latest-release'
         shell: bash
@@ -396,14 +387,18 @@ jobs:
         run: |
           cd ${RUNNER_WORKSPACE}/install-antimony/bindings/python
           if [ "${{ matrix.platform.os_type }}" == 'windows' ]; then
-            ${{env.python_exe}} -m pip install setuptools wheel
-            ${{env.python_exe}} setup.py bdist_wheel
+            ${{env.python_exe}} -m pip install setuptools wheel build
+            ${{env.python_exe}} -m build --wheel --no-isolation --outdir dist
           elif [ "${{ matrix.platform.os_type }}" == 'manylinux' ]; then
-            python${{ matrix.python_version }} -m pip install --trusted-host pypi.org --trusted-host pypi.python.org --trusted-host files.pythonhosted.org setuptools wheel
-            python${{ matrix.python_version }} setup.py bdist_wheel
+            python${{ matrix.python_version }} -m pip install --root-user-action=ignore --trusted-host pypi.org --trusted-host pypi.python.org --trusted-host files.pythonhosted.org setuptools wheel build
+            python${{ matrix.python_version }} -m build --wheel --no-isolation --outdir dist
+          elif [ "${{ matrix.platform.os_type }}" == 'macos' ]; then
+            export MACOSX_DEPLOYMENT_TARGET="$(sw_vers -productVersion | cut -d '.' -f 1).0"
+            python${{ matrix.python_version }} -m pip install setuptools wheel build
+            python${{ matrix.python_version }} -m build --wheel --no-isolation --outdir dist
           else
-            python${{ matrix.python_version }} -m pip install setuptools wheel
-            python${{ matrix.python_version }} setup.py bdist_wheel
+            python${{ matrix.python_version }} -m pip install setuptools wheel build
+            python${{ matrix.python_version }} -m build --wheel --no-isolation --outdir dist
           fi
 
       - name: Rename Python wheel artifacts
@@ -436,3 +431,61 @@ jobs:
         with:
           name: ${{env.python_wheel_artifacts_name}}
           path: ${{env.python_wheel_artifacts_file}}
+
+      # The SBML Test Suite round-trip only runs on one leg of the matrix,
+      # same reasoning as valgrind above: it's slow, and doesn't need to run
+      # on every OS/config combination to be useful. macos-14-release is
+      # chosen since ubuntu-latest-release is already dedicated to valgrind.
+      - name: Build Antimony Python wheel for SBML Test Suite round-trip
+        if: matrix.platform.name == 'macos-14-release'
+        shell: bash
+        run: |
+          cd ${RUNNER_WORKSPACE}/install-antimony/bindings/python
+          python${{ matrix.python_version }} -m pip install setuptools wheel build
+          python${{ matrix.python_version }} -m build --wheel --no-isolation --outdir dist-sbml-test-suite
+          python${{ matrix.python_version }} -m pip install dist-sbml-test-suite/antimony*.whl
+          python${{ matrix.python_version }} -m pip install -r "${GITHUB_WORKSPACE}/src/bindings/python/sbml_test_suite/requirements.txt"
+
+      - name: Download SBML Test Suite semantic cases
+        if: matrix.platform.name == 'macos-14-release'
+        shell: bash
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          cd "${RUNNER_WORKSPACE}"
+          mkdir -p sbml-test-suite
+          asset_url=$(gh api repos/sbmlteam/sbml-test-suite/releases/latest \
+            --jq '.assets[] | select(.name | startswith("semantic_tests")) | .browser_download_url')
+          if [ -z "$asset_url" ]; then
+            echo "::error::Failed to find a semantic_tests asset in the latest sbml-test-suite release."
+            exit 1
+          fi
+          echo "Downloading ${asset_url}"
+          curl -fL "$asset_url" -o sbml-test-suite/semantic_tests.zip
+          unzip -q sbml-test-suite/semantic_tests.zip -d sbml-test-suite/extracted
+          # -quit makes find stop after the first match itself, rather than
+          # relying on a downstream `head -n 1` to cut it off -- piping into
+          # head closes the pipe early and GNU find treats that broken pipe
+          # as a fatal write error instead of exiting quietly.
+          settings_file=$(find "${RUNNER_WORKSPACE}/sbml-test-suite/extracted" -name '*-settings.txt' -print -quit)
+          if [ -z "$settings_file" ]; then
+            echo "::error::No *-settings.txt files found under sbml-test-suite/extracted -- unexpected archive layout."
+            exit 1
+          fi
+          cases_dir=$(dirname "$settings_file")
+          echo "SBML_TEST_SUITE_DIR=$(dirname "$cases_dir")" >> "${GITHUB_ENV}"
+
+      - name: Run SBML Test Suite round-trip tests
+        if: matrix.platform.name == 'macos-14-release'
+        shell: bash
+        run: |
+          cd "${GITHUB_WORKSPACE}/src/bindings/python/sbml_test_suite"
+          python${{ matrix.python_version }} -m pytest -ra --junitxml="${RUNNER_WORKSPACE}/sbml-test-suite-results.xml" \
+            --sbml-test-suite-dir="${SBML_TEST_SUITE_DIR}"
+
+      - name: Upload SBML Test Suite round-trip results
+        if: always() && matrix.platform.name == 'macos-14-release'
+        uses: actions/upload-artifact@main
+        with:
+          name: sbml-test-suite-results
+          path: ${{ runner.workspace }}/sbml-test-suite-results.xml

.github/workflows/valgrind-debug-memcheck.yml

@@ -99,7 +99,7 @@ jobs:
       - name: Cache ccache files
         uses: actions/cache@main
         with:
-          path: ${RUNNER_WORKSPACE}/.ccache
+          path: ${{ runner.workspace }}/.ccache
           key:
             ${{ runner.os }}-debug-memcheck-${{ steps.ccache_cache_timestamp.outputs.timestamp
             }}

CMakeLists.txt

@@ -11,8 +11,8 @@ project(libantimony)
 # Set up version information.
 #
 SET(LIBANTIMONY_VERSION_MAJOR 3)
-SET(LIBANTIMONY_VERSION_MINOR 1)
-SET(LIBANTIMONY_VERSION_PATCH ".3")
+SET(LIBANTIMONY_VERSION_MINOR 2)
+SET(LIBANTIMONY_VERSION_PATCH ".0")
 SET(LIBANTIMONY_VERSION_RELEASE "")
 
 
@@ -31,7 +31,12 @@ endif()
 # C++14 minimum: required by the vendored GoogleTest 1.16.x (see
 # src/test/googletest/README.md), which uses std::make_index_sequence
 # and friends internally.
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++14")
+# MSVC doesn't understand the GNU-style -std= flag (and already
+# defaults to a sufficiently modern standard), so only add it for
+# GCC/Clang to avoid a D9002 "unknown option" warning on every file.
+if(NOT MSVC)
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++14")
+endif()
 
 include (InstallRequiredSystemLibraries)
 include (CMakeTestCCompiler)
@@ -77,8 +82,11 @@ set(CMAKE_BUILD_TYPE "RelWithDebInfo" CACHE STRING "Choose the type of build, op
 
 # which language bindings should be build
 option(WITH_CELLML          "Generate CellML translations"    OFF )
+mark_as_advanced(WITH_CELLML)
+if(WITH_CELLML)
+  message(FATAL_ERROR "The ability to export Antimony to CellML is not currently functional.")
+endif()
 option(WITH_QTANTIMONY      "Generate QTAntimony"             ON )
-option(WITH_SWIG   "Regenerate SWIG-based language bindings." OFF )
 option(WITH_PYTHON       "Generate Python language bindings." OFF)
 if (WITH_PYTHON)
   option(PYTHON_SYSTEM_INSTALL  "Install the python bindings using setup.py and distutils.  May require admin privileges."    OFF )
@@ -290,36 +298,6 @@ set(LIBANTIMONY_LIBS ${LIBANTIMONY_LIBS} ${CMAKE_DL_LIBS} )
 
 message(STATUS "Antimony libs: ${LIBANTIMONY_LIBS}")
 
-###############################################################################
-#
-# If WITH_SWIG is selected, we need to find swig
-#
-if(WITH_SWIG)
-    find_program(SWIG_EXECUTABLE
-        NAMES swig
-        PATHS
-              "c:/Program Files (x86)/Swig"
-              c:/Program Files/Swig
-              c:/Program Files/swigwin-3.0.10
-              c:/Program Files/swigwin-4.0.2
-              /usr/local/bin
-              /opt/local/bin
-              /usr/bin
-        DOC "The file name of the swig executable."
-        )
-    find_package(SWIG)
-    set(SWIG_EXTRA_ARGS "" CACHE STRING "Extra arguments to SWIG" )
-endif(WITH_SWIG)
-
-if(WITH_SWIG)
-    message(STATUS "  Using SWIG                    = ${SWIG_EXECUTABLE}")
-
-    if (SWIG_FOUND AND SWIG_VERSION VERSION_LESS "2.0.4")
-        message(WARNING "   You are using swig version ${SWIG_VERSION} while we recommend at least version 2.0.4.")
-    endif()
-
-endif()
-
 if(WITH_PYTHON)
     message(STATUS "  Using Python                  = ${PYTHON_EXECUTABLE}")
 endif()

QTAntimony_src/QTAntimony.cpp

@@ -11,6 +11,8 @@
 #include <QDesktopServices>
 #include <QVariant>
 #include <QIcon>
+#include <QGuiApplication>
+#include <QScreen>
 
 #ifdef Q_OS_WIN
 #ifndef WIN32_LEAN_AND_MEAN
@@ -107,7 +109,7 @@ void QTAntimony::DisplayWindow(QMainWindow* t) {
     }
     QRect desk = desktop()->availableGeometry(focus);
     if (focus==NULL) {
-        desk = desktop()->availableGeometry(desktop()->primaryScreen());
+        desk = QGuiApplication::primaryScreen()->availableGeometry();
         QRect window;
         window.setTop(desk.height()/8);
         window.setBottom(desk.height()*7/8);