fix the CI and conda build

.github/workflows/build-and-test.yml

@@ -26,7 +26,8 @@ jobs:
             # "macos-13", # x86_64
             "macos-latest", # arm64
           ]
-        python-version: ["3.9", "3.12"]
+        python-version: ["3.10", "3.12"]
+        # Python 3.13 excluded: VTK 9.3.1 has no 3.13 wheel on PyPI (tested via conda in integration.yml)
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/build-docs.yml

@@ -34,15 +34,14 @@ jobs:
           python-version: "3.12"
           cache: "pip"
 
+      - uses: pyvista/setup-headless-display-action@v3
+
       - name: Install libGLU
         run: sudo apt-get install libglu1-mesa
 
       - name: Install
         run: pip install .[docs]
 
-      - name: Install vtk
-        run: pip uninstall vtk -y && pip install vtk-osmesa --extra-index-url https://wheels.vtk.org
-
       - name: Build docs
         run: make -C docs html
 

.github/workflows/conda-packaging.yml

@@ -21,15 +21,18 @@ jobs:
           activate-environment: packaging
 
       - name: Conda build
-        shell: pwsh
+        shell: bash -l {0}
+        env:
+          PACKAGE_VERSION: ${{ github.ref_name }}
+          BRANCH_NAME: ${{ github.ref_name }}
         run: |
-          # export PACKAGE_VERSION="${BRANCH_NAME//-/_}"
-          $env:PACKAGE_VERSION = $env:BRANCH_NAME -replace "-", "_"
-          conda install python conda-build conda-verify anaconda-client
-          anaconda logout
-          anaconda login --username ${{ secrets.ANACONDA_USERNAME }} --password ${{ secrets.ANACONDA_PASSWORD }}
-          conda-build conda.recipe -c conda-forge --output-folder  .
-          anaconda upload noarch/*.tar.bz2 --force
-          anaconda logout
+          conda install -y conda-build anaconda-client
+          conda config --set anaconda_upload no
+          conda-build conda.recipe -c conda-forge --output-folder .
+
+      - name: Upload to Anaconda
+        shell: bash -l {0}
         env:
-          BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
+          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_API_TOKEN }}
+        run: |
+          anaconda upload noarch/*.conda --force --no-progress

.github/workflows/integration.yml

@@ -20,10 +20,11 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.9", "3.12"]
+        python-version: ["3.10", "3.12", "3.13"]
 
     steps:
       - uses: actions/checkout@v4
+      - uses: pyvista/setup-headless-display-action@v3
       - uses: mamba-org/setup-micromamba@v2
         with:
           generate-run-shell: true

.github/workflows/mmg-packaging.yml

@@ -20,15 +20,19 @@ jobs:
       - name: Conda build for Linux
         shell: bash -l {0}
         run: |
-          conda install python=3.9 conda-build anaconda-client
-          anaconda logout
-          anaconda login --username ${{ secrets.ANACONDA_USERNAME }} --password ${{ secrets.ANACONDA_PASSWORD }}
-          conda-build mmg.recipe -c conda-forge -c set3mah --output-folder  .
-          anaconda upload linux-64/*.tar.bz2 --force
+          conda install python=3.12 conda-build anaconda-client
+          conda config --set anaconda_upload no
+          conda-build mmg.recipe -c conda-forge -c set3mah --output-folder .
+      - name: Upload to Anaconda
+        shell: bash -l {0}
+        env:
+          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_API_TOKEN }}
+        run: |
+          anaconda upload linux-64/*.conda --force --no-progress
 
   macos:
     name: MacOS
-    runs-on: "macos-13"
+    runs-on: "macos-latest"
     steps:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3
@@ -38,11 +42,15 @@ jobs:
       - name: Conda build for MacOS
         shell: bash -l {0}
         run: |
-          conda install python=3.9 conda-build anaconda-client
-          anaconda logout
-          anaconda login --username ${{ secrets.ANACONDA_USERNAME }} --password ${{ secrets.ANACONDA_PASSWORD }}
-          conda-build mmg.recipe -c conda-forge -c set3mah --output-folder  .
-          anaconda upload osx-64/*.tar.bz2 --force
+          conda install python=3.12 conda-build anaconda-client
+          conda config --set anaconda_upload no
+          conda-build mmg.recipe -c conda-forge -c set3mah --output-folder .
+      - name: Upload to Anaconda
+        shell: bash -l {0}
+        env:
+          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_API_TOKEN }}
+        run: |
+          anaconda upload osx-arm64/*.conda --force --no-progress
 
   windows:
     name: Windows
@@ -54,10 +62,14 @@ jobs:
           miniconda-version: "latest"
           activate-environment: packaging
       - name: Conda build for Windows
-        shell: pwsh
+        shell: bash -l {0}
+        run: |
+          conda install python=3.12 conda-build anaconda-client
+          conda config --set anaconda_upload no
+          conda-build mmg.recipe -c conda-forge -c set3mah --output-folder .
+      - name: Upload to Anaconda
+        shell: bash -l {0}
+        env:
+          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_API_TOKEN }}
         run: |
-          conda install python=3.9 conda-build anaconda-client
-          anaconda logout
-          anaconda login --username ${{ secrets.ANACONDA_USERNAME }} --password ${{ secrets.ANACONDA_PASSWORD }}
-          conda-build mmg.recipe -c conda-forge -c set3mah --output-folder  .
-          anaconda upload win-64/*.tar.bz2 --force
+          anaconda upload win-64/*.conda --force --no-progress

.github/workflows/neper-packaging.yml

@@ -20,15 +20,19 @@ jobs:
       - name: Conda build for Linux
         shell: bash -l {0}
         run: |
-          conda install python=3.9 conda-build anaconda-client
-          anaconda logout
-          anaconda login --username ${{ secrets.ANACONDA_USERNAME }} --password ${{ secrets.ANACONDA_PASSWORD }}
-          conda-build neper.recipe -c conda-forge -c set3mah --output-folder  .
-          anaconda upload linux-64/*.tar.bz2 --force
+          conda install python=3.12 conda-build anaconda-client
+          conda config --set anaconda_upload no
+          conda-build neper.recipe -c conda-forge -c set3mah --output-folder .
+      - name: Upload to Anaconda
+        shell: bash -l {0}
+        env:
+          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_API_TOKEN }}
+        run: |
+          anaconda upload linux-64/*.conda --force --no-progress
 
   macos:
     name: MacOS
-    runs-on: "macos-13"
+    runs-on: "macos-latest"
     steps:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3
@@ -38,11 +42,15 @@ jobs:
       - name: Conda build for MacOS
         shell: bash -l {0}
         run: |
-          conda install python=3.9 conda-build anaconda-client
-          anaconda logout
-          anaconda login --username ${{ secrets.ANACONDA_USERNAME }} --password ${{ secrets.ANACONDA_PASSWORD }}
-          conda-build neper.recipe -c conda-forge -c set3mah --output-folder  .
-          anaconda upload osx-64/*.tar.bz2 --force
+          conda install python=3.12 conda-build anaconda-client
+          conda config --set anaconda_upload no
+          conda-build neper.recipe -c conda-forge -c set3mah --output-folder .
+      - name: Upload to Anaconda
+        shell: bash -l {0}
+        env:
+          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_API_TOKEN }}
+        run: |
+          anaconda upload osx-arm64/*.conda --force --no-progress
 
   windows:
     name: Windows
@@ -54,10 +62,14 @@ jobs:
           miniconda-version: "latest"
           activate-environment: packaging
       - name: Conda build for Windows
-        shell: pwsh
+        shell: bash -l {0}
+        run: |
+          conda install python=3.12 conda-build anaconda-client
+          conda config --set anaconda_upload no
+          conda-build neper.recipe -c conda-forge -c set3mah --output-folder .
+      - name: Upload to Anaconda
+        shell: bash -l {0}
+        env:
+          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_API_TOKEN }}
         run: |
-          conda install python=3.9 conda-build anaconda-client
-          anaconda logout
-          anaconda login --username ${{ secrets.ANACONDA_USERNAME }} --password ${{ secrets.ANACONDA_PASSWORD }}
-          conda-build neper.recipe -c conda-forge -c set3mah --output-folder  .
-          anaconda upload win-64/*.tar.bz2 --force
+          anaconda upload win-64/*.conda --force --no-progress

.github/workflows/test-conda-package.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: ["ubuntu-latest", "macos-13"]
+        os: ["ubuntu-latest", "macos-latest"]
     steps:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3

conda.recipe/meta.yaml

@@ -19,7 +19,7 @@ requirements:
     - python >=3.9,<3.13
     - numpy
     - vtk
-    - pyvista
+    - pyvista <0.47
     - python-gmsh
     - meshio
     - cadquery

environment.yml

@@ -4,8 +4,9 @@ channels:
   - set3mah
 
 dependencies:
-  - numpy <2
-  - pyvista
+  - numpy
+  - pyvista <0.47
+  - matplotlib
   - scipy
   - python-gmsh
   - meshio

microgen/box_mesh.py

@@ -14,7 +14,12 @@
 from .rve import Rve
 from .single_mesh import SingleMesh, check_if_only_linear_tetrahedral
 
-USE_MULTI_RAY = False
+try:
+    import trimesh
+
+    USE_MULTI_RAY = trimesh.ray.has_embree
+except ImportError:
+    USE_MULTI_RAY = False
 
 AXES = ("x", "y", "z")
 AXES_PAIRS = (("x", "y"), ("x", "z"), ("y", "z"))
@@ -573,6 +578,7 @@ def closest_cells_on_boundaries(
                 raytraceresult = surface_p.multi_ray_trace(
                     origins=face,
                     directions=directions,
+                    retry=True,
                 )
             else:
                 intersection_points = []

mmg.recipe/bld.bat

@@ -1,7 +1,8 @@
 cmake -S . -B build ^
       -G "Visual Studio 17 2022" ^
       -DCMAKE_BUILD_TYPE:STRING=Release ^
-      -DCMAKE_INSTALL_PREFIX:PATH=%PREFIX%
+      -DCMAKE_INSTALL_PREFIX:PATH=%PREFIX% ^
+      -DUSE_SCOTCH=OFF
 
 cmake --build build --target ALL_BUILD --config Release
 cmake --install build

mmg.recipe/meta.yaml

@@ -7,6 +7,7 @@ package:
 
 source:
   git_url: https://github.com/MmgTools/mmg.git
+  git_tag: v5.8.0
 
 build:
   number: 0
@@ -20,9 +21,9 @@ requirements:
     - make # [unix]
   host:
     - cmake
-    - scotch 6.0.*
+    - scotch  # [not win]
   run:
-    - scotch 6.0.*
+    - scotch  # [not win]
 
 about:
   home: https://github.com/MmgTools/mmg

neper.recipe/meta.yaml

@@ -23,13 +23,13 @@ requirements:
     - libblas
     - llvm-openmp  # [osx]
     - gsl
-    - scotch 6.0.*
+    - scotch
     - nlopt
     - openmp #[not osx]
     - occt 7.7.0
   run:
     - gsl
-    - scotch 6.*
+    - scotch
     - llvm-openmp  # [osx]
     - nlopt
     - openmp #[not osx]

pyproject.toml

@@ -4,7 +4,7 @@ version = "1.4.0.dev0"
 authors = [{ name = "3MAH", email = 'set3mah@gmail.com' }]
 description = "Microstructure generation and meshing"
 readme = "README.md"
-requires-python = ">=3.9,<3.13"
+requires-python = ">=3.10"
 keywords = ["microstructure", "lattice", "periodic", "TPMS", "mesh"]
 license = { text = "GPLv3" }
 classifiers = [
@@ -13,20 +13,12 @@ classifiers = [
     'Operating System :: Microsoft :: Windows',
     'Operating System :: POSIX',
     'Operating System :: MacOS',
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    # Python 3.13 not yet supported via pip (VTK 9.3.1 has no 3.13 wheel on PyPI)
 ]
-
-dependencies = [
-    "cadquery>=2.5.0,<2.6",
-    "gmsh>=4.13.1,<5",
-    "meshio>=5.3.5,<6",
-    "numpy>1.24.0,<3",
-    "pyvista>=0.44.2,<0.47",
-    "scipy>=1.13.1,<1.16",
-]
+dependencies = ["numpy", "pyvista", "gmsh", "meshio", "cadquery", "scipy", "nlopt"]
 
 [project.optional-dependencies]
 dev = [
@@ -46,6 +38,10 @@ docs = [
     "mock>=5.1.0",
     "myst-parser>=3.0.1",
 ]
+ray = [
+    "trimesh",
+    "embreex",
+]
 jupyter = [
     "jupyterlab>=3.6.8,<4.4",
     "jupyter-cadquery>=2.2.1",
@@ -54,7 +50,7 @@ jupyter = [
     "sidecar>=0.5.2",
     "jupyterview>=0.7.0",
 ]
-all = ["microgen[dev, docs, jupyter]"]
+all = ["microgen[dev, docs, jupyter, ray]"]
 
 [project.urls]
 Documentation = 'https://microgen.readthedocs.io/en/latest'
@@ -75,7 +71,7 @@ module = ["gmsh", "scipy.spatial"]
 ignore_missing_imports = true
 
 [tool.ruff]
-target-version = "py38"
+target-version = "py310"
 
 [tool.ruff.lint]
 exclude = [