canonicalFileName() changes the process-wide working directory, which breaks relative paths on other threads

.github/workflows/buildThirdPartyLibrary.yml

@@ -63,27 +63,29 @@ jobs:
     steps:
       - name: Set the timezone to New Zealand
         if: ${{ runner.os != 'Linux' }}
-        uses: szenius/[email protected]
-        with:
-          timezoneWindows: 'New Zealand Standard Time'
-          timezoneMacos: 'Pacific/Auckland'
+        shell: bash
+        run: |
+          case "${RUNNER_OS}" in
+            Windows) MSYS_NO_PATHCONV=1 tzutil /s "New Zealand Standard Time" ;;
+            macOS) sudo systemsetup -settimezone Pacific/Auckland ;;
+          esac
       - name: Set up the manylinux container
         if: ${{ runner.os == 'Linux' }}
         shell: bash
         run: |
           echo "TZ=Pacific/Auckland" >> "$GITHUB_ENV"
           dnf install -y git make openssl-libs perl-core
       - name: Check out libOpenCOR
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
       - name: Install CMake and Ninja
         uses: lukka/get-cmake@latest
       - name: Install buildcache
-        uses: opencor/buildcache-action@v1
+        uses: opencor/buildcache-action@v3
         with:
           cache_key: ${{ inputs.third_party_library_name }}-${{ matrix.os }}-${{ matrix.arch }}-${{ matrix.build_type }}
       - name: Configure MSVC
         if: ${{ runner.os == 'Windows' }}
-        uses: ilammy/msvc-dev-cmd@v1
+        uses: TheMrMilchmann/setup-msvc-dev@v4.1.0
         with:
           arch: ${{ matrix.arch }}
       - name: Configure libOpenCOR (for LLVM)
@@ -98,7 +100,7 @@ jobs:
         run: cmake -G Ninja -S . -B build -DBUILD_TYPE=${{ matrix.build_type }} -DONLY_BUILD_THIRD_PARTY_LIBRARIES=ON -DPREBUILT_LIBCELLML=OFF -DPREBUILT_LIBCOMBINE=OFF -DPREBUILT_LIBCURL=OFF -DPREBUILT_LIBNUML=OFF -DPREBUILT_LIBSBML=OFF -DPREBUILT_LIBSEDML=OFF -DPREBUILT_LIBXML2=OFF -DPREBUILT_OPENSSL=OFF -DPREBUILT_SUNDIALS=OFF -DPREBUILT_ZIPPER=OFF -DPREBUILT_ZLIB=OFF
       - name: Upload library artifact
         if: ${{ !startsWith(github.ref, 'refs/tags/v') }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: ${{ matrix.name }}
           path: ./build/*.tar.gz
@@ -113,15 +115,13 @@ jobs:
       BUILDCACHE_LOG_FILE: ""
     steps:
       - name: Set the timezone to New Zealand
-        uses: szenius/[email protected]
-        with:
-          timezoneMacos: 'Pacific/Auckland'
+        run: sudo systemsetup -settimezone Pacific/Auckland
       - name: Check out libOpenCOR
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
       - name: Install CMake and Ninja
         uses: lukka/get-cmake@latest
       - name: Install buildcache
-        uses: opencor/buildcache-action@v1
+        uses: opencor/buildcache-action@v3
         with:
           cache_key: webassembly
       - name: Install Emscripten
@@ -136,7 +136,7 @@ jobs:
         run: cmake --build build
       - name: Upload WebAssembly artifact
         if: ${{ !startsWith(github.ref, 'refs/tags/v') }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: WebAssembly
           path: ./build/*.tar.gz

.github/workflows/cd.yml

@@ -86,22 +86,24 @@ jobs:
       BUILDCACHE_LOG_FILE: ""
     steps:
       - name: Set the timezone to New Zealand
-        uses: szenius/[email protected]
-        with:
-          timezoneWindows: 'New Zealand Standard Time'
-          timezoneLinux: 'Pacific/Auckland'
-          timezoneMacos: 'Pacific/Auckland'
+        shell: bash
+        run: |
+          case "${RUNNER_OS}" in
+            Windows) MSYS_NO_PATHCONV=1 tzutil /s "New Zealand Standard Time" ;;
+            Linux) sudo timedatectl set-timezone Pacific/Auckland ;;
+            macOS) sudo systemsetup -settimezone Pacific/Auckland ;;
+          esac
       - name: Check out libOpenCOR
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
       - name: Install CMake and Ninja
         uses: lukka/get-cmake@latest
       - name: Install buildcache
-        uses: opencor/buildcache-action@v1
+        uses: opencor/buildcache-action@v3
         with:
           cache_key: cd-${{ matrix.os }}-${{ matrix.build_type }}-${{ matrix.shared_libs }}
       - name: Configure MSVC
         if: ${{ runner.os == 'Windows' }}
-        uses: ilammy/msvc-dev-cmd@v1
+        uses: TheMrMilchmann/setup-msvc-dev@v4.1.0
         with:
           arch: ${{ matrix.arch }}
       - name: Install GCC 16
@@ -124,13 +126,13 @@ jobs:
           cpack
       - name: Upload libOpenCOR artifacts
         if: ${{ !startsWith(github.ref, 'refs/tags/v') }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: ${{ matrix.name }}
           path: ./build/libOpenCOR-*
       - name: Release libOpenCOR
         if: ${{ startsWith(github.ref, 'refs/tags/v') }}
-        uses: softprops/action-gh-release@v2
+        uses: softprops/action-gh-release@v3
         with:
           files: ./build/libOpenCOR-*
   python_wheels:
@@ -156,21 +158,23 @@ jobs:
             os: macos-15
     steps:
       - name: Set the timezone to New Zealand
-        uses: szenius/[email protected]
-        with:
-          timezoneWindows: 'New Zealand Standard Time'
-          timezoneLinux: 'Pacific/Auckland'
-          timezoneMacos: 'Pacific/Auckland'
+        shell: bash
+        run: |
+          case "${RUNNER_OS}" in
+            Windows) MSYS_NO_PATHCONV=1 tzutil /s "New Zealand Standard Time" ;;
+            Linux) sudo timedatectl set-timezone Pacific/Auckland ;;
+            macOS) sudo systemsetup -settimezone Pacific/Auckland ;;
+          esac
       - name: Check out libOpenCOR
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
       - name: Free disk space
         if: ${{ runner.os == 'Linux' }}
         run: |
           sudo rm -rf /opt/hostedtoolcache
           sudo docker image prune --all --force
       - name: Configure MSVC
         if: ${{ runner.os == 'Windows' }}
-        uses: ilammy/msvc-dev-cmd@v1
+        uses: TheMrMilchmann/setup-msvc-dev@v4.1.0
         with:
           arch: ${{ matrix.arch }}
       - name: Build Python wheels
@@ -191,13 +195,13 @@ jobs:
           #       must be kept in sync with the above images (and the version of cibuildwheel that we use).
           CIBW_SKIP: '*musllinux*'
       - name: Upload Python wheel artifacts
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: ${{ matrix.name }}
           path: ./wheelhouse/*.whl
       - name: Release Python wheels
         if: ${{ startsWith(github.ref, 'refs/tags/v') }}
-        uses: softprops/action-gh-release@v2
+        uses: softprops/action-gh-release@v3
         with:
           files: ./wheelhouse/*.whl
   python_pypi:
@@ -208,7 +212,7 @@ jobs:
     if: ${{ startsWith(github.ref, 'refs/tags/v') }}
     steps:
       - name: Download Python wheels
-        uses: actions/download-artifact@v5
+        uses: actions/download-artifact@v8
         with:
           pattern: "*Python wheels*"
           path: ./dist
@@ -226,13 +230,11 @@ jobs:
       NODE_AUTH_TOKEN: ${{ secrets.NPM_TOKEN }}
     steps:
       - name: Set the timezone to New Zealand
-        uses: szenius/[email protected]
-        with:
-          timezoneLinux: 'Pacific/Auckland'
+        run: sudo timedatectl set-timezone Pacific/Auckland
       - name: Check out libOpenCOR
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
       - name: Install Node.js
-        uses: actions/setup-node@v4
+        uses: actions/setup-node@v7
         with:
           node-version: 'lts/*'
           registry-url: 'https://registry.npmjs.org'
@@ -248,24 +250,24 @@ jobs:
       - name: Install CMake and Ninja
         uses: lukka/get-cmake@latest
       - name: Install buildcache
-        uses: opencor/buildcache-action@v1
+        uses: opencor/buildcache-action@v3
         with:
           cache_key: cd-webassembly
       - name: Install Emscripten
-        uses: mymindstorm/setup-emsdk@v14
+        uses: emscripten-core/setup-emsdk@v16
       - name: Configure libOpenCOR
         run: cmake -G Ninja -S . -B build -DBUILD_TYPE=Release -DCODE_ANALYSIS=OFF -DCODE_COVERAGE=OFF -DDOCUMENTATION=OFF -DJAVASCRIPT_BINDINGS=ON -DJAVASCRIPT_UNIT_TESTING=OFF -DMEMORY_CHECKS=OFF -DPYTHON_BINDINGS=OFF -DPYTHON_UNIT_TESTING=OFF -DSHARED_LIBS=OFF -DUNIT_TESTING=OFF
       - name: Build WebAssembly
         run: cmake --build build
       - name: Upload WebAssembly artifact
         if: ${{ !startsWith(github.ref, 'refs/tags/v') }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: WebAssembly
           path: ./build/libopencor-*.tgz
       - name: Release WebAssembly
         if: ${{ startsWith(github.ref, 'refs/tags/v') }}
-        uses: softprops/action-gh-release@v2
+        uses: softprops/action-gh-release@v3
         with:
           files: ./build/libopencor-*.tgz
       - name: Compress WebAssembly using Brotli

.github/workflows/ci.yml

@@ -334,27 +334,29 @@ jobs:
       BUILDCACHE_LOG_FILE: ""
     steps:
       - name: Set the timezone to New Zealand
-        uses: szenius/[email protected]
-        with:
-          timezoneWindows: 'New Zealand Standard Time'
-          timezoneLinux: 'Pacific/Auckland'
-          timezoneMacos: 'Pacific/Auckland'
+        shell: bash
+        run: |
+          case "${RUNNER_OS}" in
+            Windows) MSYS_NO_PATHCONV=1 tzutil /s "New Zealand Standard Time" ;;
+            Linux) sudo timedatectl set-timezone Pacific/Auckland ;;
+            macOS) sudo systemsetup -settimezone Pacific/Auckland ;;
+          esac
       - name: Check out libOpenCOR
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
       - name: Install Python
         if: ${{ matrix.documentation == 'ON' || matrix.python_support == 'ON' || matrix.target == 'python_check_code_formatting' }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v7
         with:
           python-version: '3.12'
       - name: Install CMake and Ninja
         uses: lukka/get-cmake@latest
       - name: Install buildcache
-        uses: opencor/buildcache-action@v1
+        uses: opencor/buildcache-action@v3
         with:
           cache_key: ci-${{ matrix.os }}-${{ matrix.build_type }}-${{ matrix.code_analysis }}-${{ matrix.code_coverage }}-${{ matrix.documentation }}-${{ matrix.javascript_support }}-${{ matrix.memory_checks }}-${{ matrix.python_support }}-${{ matrix.shared_libs }}-${{ matrix.unit_testing }}-${{ matrix.target }}
       - name: Configure MSVC
         if: ${{ runner.os == 'Windows' }}
-        uses: ilammy/msvc-dev-cmd@v1
+        uses: TheMrMilchmann/setup-msvc-dev@v4.1.0
         with:
           arch: ${{ matrix.arch }}
       - name: Install GCC 16
@@ -384,7 +386,7 @@ jobs:
           sudo mv clang-tidy /usr/local/bin
       - name: Install Emscripten
         if: ${{ matrix.javascript_support == 'ON' }}
-        uses: mymindstorm/setup-emsdk@v14
+        uses: emscripten-core/setup-emsdk@v16
       - name: Install Biome
         if: ${{ matrix.target == 'javascript_check_code_formatting' }}
         run: |
@@ -393,7 +395,7 @@ jobs:
           mv biome /usr/local/bin
       - name: Install uv
         if: ${{ matrix.documentation == 'ON' || matrix.python_support == 'ON' || matrix.target == 'python_check_code_formatting' }}
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v10.2.0
       - name: Install Ruff
         if: ${{ matrix.target == 'python_check_code_formatting' }}
         run: uv pip install --system ruff
@@ -508,11 +510,9 @@ jobs:
             os: ubuntu-24.04-arm
     steps:
       - name: Set the timezone to New Zealand
-        uses: szenius/[email protected]
-        with:
-          timezoneLinux: 'Pacific/Auckland'
+        run: sudo timedatectl set-timezone Pacific/Auckland
       - name: Check out libOpenCOR
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
       - name: Free disk space
         run: |
           sudo rm -rf /opt/hostedtoolcache
@@ -530,11 +530,9 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: Set the timezone to New Zealand
-        uses: szenius/[email protected]
-        with:
-          timezoneLinux: 'Pacific/Auckland'
+        run: sudo timedatectl set-timezone Pacific/Auckland
       - name: Check out libOpenCOR
-        uses: actions/checkout@v4
+        uses: actions/checkout@v7
       - name: Spell check
         uses: codespell-project/actions-codespell@v2
         with:

README.md

@@ -10,5 +10,4 @@ You might also be interested in our [users](https://groups.google.com/forum/#!fo
 
 Please [contact us](https://opencor.ws/libopencor/contactUs.html) if you have any questions about libOpenCOR.
 
-[![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/opencor/libopencor)
 ![Alt](https://repobeats.axiom.co/api/embed/e57859796c7c35c163c88238f9bfd3f2aad9649f.svg "Repobeats analytics image")

VERSION.txt

@@ -1 +1 @@
-1.20261009.3
+1.20261009.4

cmake/environmentchecks.cmake

@@ -168,12 +168,14 @@ if(Python_EXECUTABLE)
 endif()
 
 # Check some compiler flags.
+# Note: we use -fprofile-update=atomic since some of our tests are multithreaded and non-atomic profile counters would
+#       then get corrupted (e.g., a covered branch could be reported as not covered).
 
 include(CheckCXXCompilerFlag)
 
 set(ORIG_CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS})
 
-set(CODE_COVERAGE_COMPILER_FLAGS "-fprofile-instr-generate -fcoverage-mapping")
+set(CODE_COVERAGE_COMPILER_FLAGS "-fprofile-instr-generate -fcoverage-mapping -fprofile-update=atomic")
 set(CODE_COVERAGE_LINKER_FLAGS "-fprofile-instr-generate")
 set(CMAKE_REQUIRED_FLAGS ${CODE_COVERAGE_COMPILER_FLAGS})
 

src/bindings/python/file.cpp

@@ -35,7 +35,11 @@ void fileApi(nb::module_ &m)
         .value("CombineArchive", libOpenCOR::File::Type::COMBINE_ARCHIVE)
         .value("IrretrievableFile", libOpenCOR::File::Type::IRRETRIEVABLE_FILE);
 
-    file.def(nb::new_(&libOpenCOR::File::create), "Create a File object.", nb::arg("file_name_or_url"), nb::arg("retrieve_contents") = true)
+    // Note: we release the GIL when creating a file, as well as when retrieving managed files, since it may take a
+    //       while (e.g., when downloading a remote file) and since it allows other Python threads to create files
+    //       concurrently.
+
+    file.def(nb::new_(&libOpenCOR::File::create), "Create a File object.", nb::arg("file_name_or_url"), nb::arg("retrieve_contents") = true, nb::call_guard<nb::gil_scoped_release>())
         .def_prop_ro("type", &libOpenCOR::File::type, "Return the type.")
         .def_prop_ro("file_name", &libOpenCOR::File::fileName, "Return the file name.")
         .def_prop_ro("url", &libOpenCOR::File::url, "Return the URL.")
@@ -63,9 +67,9 @@ void fileApi(nb::module_ &m)
         .def("reset", &libOpenCOR::FileManager::reset, "Reset the file manager.")
         .def_prop_ro("has_files", &libOpenCOR::FileManager::hasFiles, "Return whether there are some managed files.")
         .def_prop_ro("file_count", &libOpenCOR::FileManager::fileCount, "Return the number of managed files.")
-        .def_prop_ro("files", &libOpenCOR::FileManager::files, "Return the managed files.")
-        .def("file", nb::overload_cast<size_t>(&libOpenCOR::FileManager::file, nb::const_), "Return the managed file at the given index.", nb::arg("index"))
-        .def("file", nb::overload_cast<const std::string &>(&libOpenCOR::FileManager::file, nb::const_), "Return the managed file with the given name or URL.", nb::arg("file_name_or_url"))
+        .def_prop_ro("files", &libOpenCOR::FileManager::files, "Return the managed files.", nb::call_guard<nb::gil_scoped_release>())
+        .def("file", nb::overload_cast<size_t>(&libOpenCOR::FileManager::file, nb::const_), "Return the managed file at the given index.", nb::arg("index"), nb::call_guard<nb::gil_scoped_release>())
+        .def("file", nb::overload_cast<const std::string &>(&libOpenCOR::FileManager::file, nb::const_), "Return the managed file with the given name or URL.", nb::arg("file_name_or_url"), nb::call_guard<nb::gil_scoped_release>())
         .def("__len__", &libOpenCOR::FileManager::fileCount)
         .def("__iter__", [](const libOpenCOR::FileManager &self) {
             return nb::iter(nb::cast(self.files()));