Update CI dependencies (PedestrianDynamics#1437)

* Update GH ACtions

Now provide python 3.13 packages.
Clang-format 19 is now target version for formatting c++ and c code.

* Update python dependencies

.github/workflows/cibuildwheel.yml

@@ -26,13 +26,20 @@ jobs:
     - name: Checkout
       uses: actions/checkout@v4
 
-    - name: Set up Python 3.12
+    - name: Set up Python 3.13
       uses: actions/setup-python@v5
       with:
-        python-version: "3.12"
+        python-version: "3.13"
     - name: Install dependencies
       run: pip install ruff
 
+    - name: Install clang-format-19
+      run: |
+        sudo add-apt-repository 'deb http://apt.llvm.org/jammy/ llvm-toolchain-jammy-19 main'
+        wget -qO- https://apt.llvm.org/llvm-snapshot.gpg.key | sudo tee /etc/apt/trusted.gpg.d/apt.llvm.org.asc
+        sudo apt update
+        sudo apt install clang-format-19
+
     - name: Run checks
       run: ./scripts/ci/check_format.sh
 
@@ -48,10 +55,10 @@ jobs:
     - name: Checkout
       uses: actions/checkout@v4
 
-    - name: Set up Python 3.12
+    - name: Set up Python 3.13
       uses: actions/setup-python@v5
       with:
-        python-version: "3.12"
+        python-version: "3.13"
     - name: Install dependencies
       run: pip install -r requirements.txt
 
@@ -68,6 +75,7 @@ jobs:
     - name: Checkout
       uses: actions/checkout@v4
 
+    # Still need to use 3.12 because hdf5 is not yet available for python 3.13 and we are using this in our notbooks
     - name: Set up Python 3.12
       uses: actions/setup-python@v5
       with:
@@ -165,7 +173,7 @@ jobs:
       - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: 3.12
+          python-version: 3.13
 
       - name: Install dependencies
         run: python -m pip install wheel build setuptools
@@ -187,7 +195,7 @@ jobs:
     env:
       CIBW_MANYLINUX_X86_64_IMAGE: manylinux_2_28
       CIBW_SKIP: "*musllinux*"
-      MACOSX_DEPLOYMENT_TARGET: 10.16
+      MACOSX_DEPLOYMENT_TARGET: 12.05
     strategy:
       matrix:
         include:
@@ -200,6 +208,9 @@ jobs:
           - os: ubuntu-latest
             cibw_archs: "x86_64"
             cibw_build: "cp312-*"
+          - os: ubuntu-latest
+            cibw_archs: "x86_64"
+            cibw_build: "cp313-*"
           - os: windows-latest
             cibw_archs: "auto64"
             cibw_build: "cp310-*"
@@ -209,29 +220,38 @@ jobs:
           - os: windows-latest
             cibw_archs: "auto64"
             cibw_build: "cp312-*"
-          - os: macos-12
+          - os: windows-latest
+            cibw_archs: "auto64"
+            cibw_build: "cp313-*"
+          - os: macos-13
             cibw_archs: "x86_64"
             cibw_build: "cp310-*"
-          - os: macos-12
+          - os: macos-13
             cibw_archs: "x86_64"
             cibw_build: "cp311-*"
-          - os: macos-12
+          - os: macos-13
             cibw_archs: "x86_64"
             cibw_build: "cp312-*"
-          - os: macos-12
+          - os: macos-13
+            cibw_archs: "x86_64"
+            cibw_build: "cp313-*"
+          - os: macos-13
             cibw_archs: "arm64"
             cibw_build: "cp310-*"
-          - os: macos-12
+          - os: macos-13
             cibw_archs: "arm64"
             cibw_build: "cp311-*"
-          - os: macos-12
+          - os: macos-13
             cibw_archs: "arm64"
             cibw_build: "cp312-*"
+          - os: macos-13
+            cibw_archs: "arm64"
+            cibw_build: "cp313-*"
 
     steps:
       - uses: actions/checkout@v4
       - name: Build wheels for CPython ${{ matrix.cibw_build }} on ${{ matrix.cibw_archs }}
-        uses: pypa/cibuildwheel@v2.16.5
+        uses: pypa/cibuildwheel@v2.22.0
         env:
           CIBW_BUILD: ${{ matrix.cibw_build }}
           CIBW_ARCHS: ${{ matrix.cibw_archs }}
@@ -261,8 +281,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-12, macos-14]
-        python-version: ["3.10", "3.11", "3.12"]
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14, macos-15]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}
@@ -292,10 +312,10 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - name: Set up Python 3.12
+      - name: Set up Python 3.13
         uses: actions/setup-python@v5
         with:
-          python-version: 3.12
+          python-version: 3.13
 
       - name: Download packages
         uses: actions/Download-artifact@v4

CMakeLists.txt

@@ -224,7 +224,7 @@ add_subdirectory(python_bindings_jupedsim)
 # Code formatting
 ################################################################################
 if(UNIX AND WITH_FORMAT)
-    set(clang-format-version 15)
+    set(clang-format-version 19)
     find_program(CLANG_FORMAT
         NAMES
             clang-format-${clang-format-version}

libsimulator/src/Journey.hpp

@@ -96,7 +96,7 @@ class FixedTransition : public Transition
     BaseStage* next;
 
 public:
-    FixedTransition(BaseStage* next_) : next(next_){};
+    FixedTransition(BaseStage* next_) : next(next_) {};
 
     BaseStage* NextStage() override { return next; }
 };

libsimulator/src/Mesh.cpp

@@ -416,9 +416,7 @@ std::vector<glm::vec2> Mesh::FVertices() const
         std::begin(vertices),
         std::end(vertices),
         std::back_inserter(f_vertices),
-        [](const auto& v) {
-            return glm::vec2{v.x, v.y};
-        });
+        [](const auto& v) { return glm::vec2{v.x, v.y}; });
     return f_vertices;
 }
 

libsimulator/src/NeighborhoodSearch.hpp

@@ -73,7 +73,7 @@ class NeighborhoodSearch
     }
 
 public:
-    explicit NeighborhoodSearch(double cellSize) : _cellSize(cellSize){};
+    explicit NeighborhoodSearch(double cellSize) : _cellSize(cellSize) {};
 
     void AddAgent(const Value& item)
     {

libsimulator/src/Point.hpp

@@ -15,7 +15,7 @@ class Point
     double y{};
 
 public:
-    Point(double x = 0, double y = 0) : x(x), y(y){};
+    Point(double x = 0, double y = 0) : x(x), y(y) {};
 
     /// Norm
     double Norm() const;

libsimulator/src/SocialForceModel.cpp

@@ -17,7 +17,7 @@
 #include <stdexcept>
 
 SocialForceModel::SocialForceModel(double bodyForce_, double friction_)
-    : bodyForce(bodyForce_), friction(friction_){};
+    : bodyForce(bodyForce_), friction(friction_) {};
 
 OperationalModelType SocialForceModel::Type() const
 {

notebooks/direct_steering.ipynb

@@ -132,7 +132,7 @@
     "    for idx, waypoint in enumerate(waypoints):\n",
     "        axes.plot(waypoint[0], waypoint[1], \"ro\")\n",
     "        axes.annotate(\n",
-    "            f\"WP {idx+1}\",\n",
+    "            f\"WP {idx + 1}\",\n",
     "            (waypoint[0], waypoint[1]),\n",
     "            textcoords=\"offset points\",\n",
     "            xytext=(10, -15),\n",

notebooks/journey.ipynb

@@ -138,7 +138,7 @@
     "for idx, waypoint in enumerate(waypoints):\n",
     "    ax.plot(waypoint[0], waypoint[1], \"ro\")\n",
     "    ax.annotate(\n",
-    "        f\"WP {idx+1}\",\n",
+    "        f\"WP {idx + 1}\",\n",
     "        (waypoint[0], waypoint[1]),\n",
     "        textcoords=\"offset points\",\n",
     "        xytext=(10, -15),\n",

notebooks/lane-formation.ipynb

@@ -90,7 +90,7 @@
     "    plt.text(\n",
     "        centroid.x,\n",
     "        centroid.y,\n",
-    "        f\"Start {id+1}\",\n",
+    "        f\"Start {id + 1}\",\n",
     "        ha=\"center\",\n",
     "        va=\"center\",\n",
     "        fontsize=10,\n",
@@ -277,7 +277,7 @@
     "        every_nth_frame=5,\n",
     "        width=1200,\n",
     "        height=400,\n",
-    "        title_note=f\"Ratio: {min(number)/sum(number):0.2f}\",\n",
+    "        title_note=f\"Ratio: {min(number) / sum(number):0.2f}\",\n",
     "    ).show()"
    ]
   },
@@ -307,7 +307,7 @@
     "            traj_width=0.3,\n",
     "            traj_start_marker=\".\",\n",
     "        )\n",
-    "        ax.set_title(f\"Ratio: {min(number)/sum(number):.2f}\")\n",
+    "        ax.set_title(f\"Ratio: {min(number) / sum(number):.2f}\")\n",
     "plt.tight_layout()\n",
     "fig.set_size_inches((10, 12))\n",
     "plt.show()"
@@ -385,7 +385,7 @@
     "    pedpy.plot_density(\n",
     "        density=density_voronoi[number], axes=ax0, color=colors[i]\n",
     "    )\n",
-    "    labels.append(f\"Ratio: {min(number)/sum(number):.3f}\")\n",
+    "    labels.append(f\"Ratio: {min(number) / sum(number):.3f}\")\n",
     "\n",
     "ax0.legend(labels)\n",
     "plt.show()"
@@ -474,14 +474,14 @@
     "        pedpy.plot_speed(\n",
     "            speed=mean_speed_r[number],\n",
     "            axes=ax,\n",
-    "            title=f\"Mean speed. Ratio: {min(number)/sum(number):.3f}\",\n",
+    "            title=f\"Mean speed. Ratio: {min(number) / sum(number):.3f}\",\n",
     "            color=pedpy.PEDPY_BLUE,\n",
     "        )\n",
     "\n",
     "    if number in mean_speed_l:\n",
     "        pedpy.plot_speed(\n",
     "            speed=mean_speed_l[number],\n",
-    "            title=f\"Mean speed. Ratio: {min(number)/sum(number):.3f}\",\n",
+    "            title=f\"Mean speed. Ratio: {min(number) / sum(number):.3f}\",\n",
     "            axes=ax,\n",
     "            color=pedpy.PEDPY_RED,\n",
     "        )\n",

notebooks/routing.ipynb

@@ -93,7 +93,7 @@
     "for idx, (waypoint, distance) in enumerate(waypoints):\n",
     "    ax.plot(waypoint[0], waypoint[1], \"ro\")\n",
     "    ax.annotate(\n",
-    "        f\"WP {idx+1}\",\n",
+    "        f\"WP {idx + 1}\",\n",
     "        (waypoint[0], waypoint[1]),\n",
     "        textcoords=\"offset points\",\n",
     "        xytext=(10, -15),\n",

python_modules/jupedsim/jupedsim/internal/notebook_utils.py

@@ -46,7 +46,7 @@ def _speed_to_color(speed, min_speed, max_speed):
     """Map a speed value to a color using a colormap."""
     normalized_speed = (speed - min_speed) / (max_speed - min_speed)
     r, g, b = plt.cm.jet_r(normalized_speed)[:3]
-    return f"rgba({r*255:.0f}, {g*255:.0f}, {b*255:.0f}, 0.5)"
+    return f"rgba({r * 255:.0f}, {g * 255:.0f}, {b * 255:.0f}, 0.5)"
 
 
 def _get_line_color(disk_color):

requirements.txt

@@ -1,16 +1,16 @@
-numpy~=1.25
+numpy~=2.2
 shapely~=2.0
-pyside6~=6.5
-vtk~=9.3
+pyside6~=6.8
+vtk~=9.4
 
 # build deps
 wheel
 build
 setuptools
 
 # test deps
-pytest~=7.2
-pandas~=2.1
+pytest~=8.3
+pandas~=2.2
 
 # ci deps
 jinja2

setup.py

@@ -252,7 +252,7 @@ def build_extension(self, ext: CMakeExtension) -> None:
     ext_modules=[CMakeExtension("python_bindings_jupedsim")],
     cmdclass={"build_ext": CMakeBuild},
     zip_safe=False,
-    python_requires=">=3.10,<3.13",
+    python_requires=">=3.10,<3.14",
     packages=[
         "jupedsim",
         "jupedsim.models",
@@ -268,10 +268,10 @@ def build_extension(self, ext: CMakeExtension) -> None:
         "jupedsim_visualizer": "python_modules/jupedsim_visualizer/jupedsim_visualizer",
     },
     install_requires=[
-        "numpy~=1.25",
+        "numpy~=2.2",
         "shapely~=2.0",
-        "pyside6~=6.5",
-        "vtk~=9.3",
+        "pyside6~=6.8",
+        "vtk~=9.4",
     ],
     scripts=["python_modules/jupedsim_visualizer/bin/jupedsim-visualizer"],
     url="https://www.jupedsim.org",
@@ -294,6 +294,7 @@ def build_extension(self, ext: CMakeExtension) -> None:
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
         "Programming Language :: Python :: 3.12",
+        "Programming Language :: Python :: 3.13",
         "Intended Audience :: Developers",
         "Intended Audience :: Science/Research",
     ],