Install pyvoro from pyvoro-rimoli, which bundles the current Voro++

pyvoro-mmalahe bundles Voro++ 0.4.6, whose radical (Laguerre)
tessellation can return a cell uncut: the cells then overlap, and
Triangle and TetGen can crash on the polygonal mesh. This is why the
tests fail on Linux and macOS in the continuous integration. The
pyvoro-rimoli fork provides the same pyvoro module with the current
Voro++, where this is fixed, and has wheels for Linux, macOS and
Windows.

The README and the installation guide tell users to uninstall
pyvoro-mmalahe before upgrading, since both packages install the same
files.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

Author: rimoli

CHANGELOG.rst

@@ -134,6 +134,15 @@ Fixed
 
 Changed
 '''''''
+- pyvoro is installed from the ``pyvoro-rimoli`` package instead of
+  ``pyvoro-mmalahe``. Both provide the same ``pyvoro`` module, but
+  pyvoro-mmalahe bundles Voro++ 0.4.6, whose radical (Laguerre)
+  tessellation can return a cell uncut: the cells then overlap, and
+  Triangle and TetGen can crash on the resulting polygonal mesh.
+  pyvoro-rimoli bundles the current Voro++, where this is fixed, and has
+  wheels for Linux, macOS and Windows. Uninstall pyvoro-mmalahe before
+  upgrading (``pip uninstall pyvoro-mmalahe``), since the two packages
+  install the same files.
 - The continuous integration installs the current pytest and no longer
   installs tox from the requirements: the pinned tox 3.14 forced an old
   pluggy that the current pytest-cov cannot load, so no test could run.

README.rst

@@ -44,6 +44,9 @@ To install MicroStructPy, download it from PyPI using::
 
 If there is an error with the install, try ``pip install pybind11`` first,
 then install MicroStructPy.
+When upgrading from an earlier version, run ``pip uninstall pyvoro-mmalahe``
+first: MicroStructPy now uses ``pyvoro-rimoli``, which installs the same
+``pyvoro`` module.
 
 
 MicroStructPy can also be installed from source::

docs/source/getting_started.rst

@@ -32,6 +32,15 @@ For Windows, it may be in a path similar to
     If the install fails and the last several error messages reference
     ``pybind11``, run ``pip install pybind11`` first then install MicroStructPy.
 
+.. note::
+    MicroStructPy computes the tessellations with the ``pyvoro`` module of the
+    ``pyvoro-rimoli`` package. Earlier versions used ``pyvoro-mmalahe``, which
+    installs the same module with an older Voro++. When upgrading, remove it
+    first::
+
+        pip uninstall pyvoro-mmalahe
+        pip install --upgrade microstructpy
+
 Running Demonstrations
 ----------------------
 

docs/source/package_guide.rst

@@ -293,7 +293,7 @@ phase-specific.
 .. _`MeshPy`: https://mathema.tician.de/software/meshpy/
 .. _`Power Diagram`: https://en.wikipedia.org/wiki/Power_diagram
 .. _`pygmsh`: https://pygmsh.readthedocs.io
-.. _`pyvoro`: https://github.com/mmalahe/pyvoro
+.. _`pyvoro`: https://github.com/rimoli/pyvoro
 .. _`TetGen`: http://wias-berlin.de/software/tetgen/
 .. _`Triangle`: https://www.cs.cmu.edu/~quake/triangle.html
 .. _`Voro++`: http://math.lbl.gov/voro++/

requirements.txt

@@ -5,7 +5,7 @@ pygmsh==7.1.17
 MeshPy==2022.1.3
 numpy>=1.24.4,<2.0
 pyquaternion==0.9.5
-pyvoro-mmalahe==1.3.4
+pyvoro-rimoli==1.4.0
 scipy>=1.10.1
 setuptools>=70.0.0 
 xmltodict==0.12.0

setup.py

@@ -85,7 +85,7 @@ def find_version(*fname):
         'numpy>=1.22.2',
         'pygmsh>=7.0.2',
         'pyquaternion',
-        'pyvoro-mmalahe>=1.3.4',  # install issue with pyvoro
+        'pyvoro-rimoli>=1.4.0',  # pyvoro with the current Voro++
         'scipy',
         'xmltodict'
     ],