Merge branch 'navis-org:master' into fix_numpy_doctest

Author: floesche

.github/workflows/test-package.yml

@@ -15,39 +15,47 @@ jobs:
         # igraph: ["igraph", "no-igraph"]
     steps:
       # This cancels any such job that is still runnning
-    - name: Cancel Previous Runs
-      uses: styfle/cancel-workflow-action@0.9.1
-      with:
-        access_token: ${{ github.token }}
-    - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install Linux libraries
-      run: |
-        sudo apt-get update -y -qq
-        sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0 libxcb-icccm4 \
-          libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 \
-          libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0 graphviz graphviz-dev \
-          mesa-vulkan-drivers
-    - name: Install dependencies
-      run: |
-        pip install --upgrade pip
-        pip install zstandard==0.16.0
-        pip install numpy
-        pip install flybrains --no-deps
-        pip install git+https://github.com/siavashk/pycpd@master
-        pip install pyarrow
-    - name: Install navis
-      run: pip install -e .[dev,all]
-    # - run: pip install python-igraph
-    #   if: ${{ matrix.igraph == 'igraph' }}
-    - name: Report dependency versions
-      run: pip freeze -r requirements.txt
-    - name: Test
-      uses: coactions/setup-xvfb@v1
-      with:
+      - name: Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@0.9.1
+        with:
+          access_token: ${{ github.token }}
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Set up Blender
         run: |
-          export NAVIS_HEADLESS=TRUE
-          pytest --verbose
+          pwd
+          wget -qO- https://mirrors.iu13.net/blender/release/Blender4.2/blender-4.2.4-linux-x64.tar.xz | tar xJ
+          mv blender-4.2.4-linux-x64 ../
+          echo "PATH=../blender-4.2.4-linux-x64/:$PATH" >> $GITHUB_ENV
+      - name: Install Linux libraries
+        run: |
+          sudo apt-get update -y -qq
+          sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0 libxcb-icccm4 \
+            libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 \
+            libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0 graphviz graphviz-dev \
+            mesa-vulkan-drivers
+      - name: Install dependencies
+        run: |
+          pip install --upgrade pip
+          pip install zstandard==0.16.0
+          pip install numpy
+          pip install flybrains --no-deps
+          pip install git+https://github.com/siavashk/pycpd@master
+          pip install pyarrow
+      - name: Install navis
+        run: pip install -e .[dev,all]
+      # - run: pip install python-igraph
+      #   if: ${{ matrix.igraph == 'igraph' }}
+      - name: Report dependency versions
+        run: |
+          which blender
+          pip freeze -r requirements.txt
+      - name: Test
+        uses: coactions/setup-xvfb@v1
+        with:
+          run: |
+            export NAVIS_HEADLESS=TRUE
+            pytest --verbose

navis/meshes/b3d.py

@@ -37,6 +37,16 @@ def simplify_mesh_blender(x, F, inplace=False):
     simp
                 Simplified mesh object.
 
+    Examples
+    --------
+    >>> import navis
+    >>> n = navis.example_neurons(1, kind="mesh")
+    >>> n_sm = simplify_mesh_blender(n,
+    ...         F=0.2,
+    ...         inplace=False)
+    >>> n.n_vertices > n_sm.n_vertices
+    True
+
     """
     if not tm.interfaces.blender.exists:
         raise ModuleNotFoundError('No Blender 3D unavailable (executable not found).')

navis/meshes/templates/blender_decimate.py.template

@@ -5,21 +5,29 @@ import os
 if __name__ == '__main__':
     # clear scene of default box
     bpy.ops.wm.read_homefile()
-    try:
-        bpy.ops.object.mode_set(mode='OBJECT')
-    except BaseException:
-        pass
-    bpy.ops.object.select_all(action='SELECT')
-    bpy.ops.object.delete(use_global=True)
+    if bpy.app.version > (3, 2, 0):
+        objs = [bpy.context.scene.objects['Camera'], bpy.context.scene.objects['Cube'], bpy.context.scene.objects['Light']]
+        with bpy.context.temp_override(selected_objects=objs):
+            bpy.ops.object.delete()
+    else:
+        try:
+            bpy.ops.object.mode_set(mode='OBJECT')
+        except BaseException:
+            pass
+        bpy.ops.object.select_all(action='SELECT')
+        bpy.ops.object.delete(use_global=True)
 
     # get temporary files from templated locations
     mesh_pre = $MESH_PRE
     mesh_post = os.path.abspath(r'$MESH_POST')
 
     for filename in mesh_pre:  # use data.objects instead of context.scene.objects
-        bpy.ops.import_mesh.stl(filepath=os.path.abspath(filename))
-
+        if bpy.app.version > (4, 0, 0):
+            bpy.ops.wm.stl_import(filepath=os.path.abspath(filename))
+        else:
+            bpy.ops.import_mesh.stl(filepath=os.path.abspath(filename))
     mesh = bpy.data.objects[0]
+
     # Make sure mesh is the active object
     try:
         # earlier than blender <2.8
@@ -29,13 +37,17 @@ if __name__ == '__main__':
         bpy.context.view_layer.objects.active = mesh
 
     # add decimate modifier
+
     mod = mesh.modifiers.new('decimate', 'DECIMATE')
     mod.decimate_type = 'COLLAPSE'
     mod.ratio = $RATIO
     mod.use_collapse_triangulate = True
 
     bpy.ops.object.modifier_apply(modifier=mod.name)
 
-    bpy.ops.export_mesh.stl(
-        filepath=mesh_post,
-        use_mesh_modifiers=True)
+    if bpy.app.version > (4, 0, 0):
+        bpy.ops.wm.stl_export(filepath=mesh_post, apply_modifiers=True)
+    else:
+        bpy.ops.export_mesh.stl(
+            filepath=mesh_post,
+            use_mesh_modifiers=True)