patch to allow pyzeo to work (#4315)

Author: daniel-sintef

.github/workflows/test.yml

@@ -1,4 +1,5 @@
 # Run the complete test suite incl. many external command line dependencies (like Openbabel)
+
 # as well as the pymatgen.ext package. Coverage used to be computed based on this workflow.
 name: Tests
 
@@ -76,6 +77,28 @@ jobs:
       - name: Install uv
         uses: astral-sh/setup-uv@v4
 
+      - name: Install ZEO++ (Linux and macOS)
+        if: matrix.config.os == 'ubuntu-latest' || matrix.config.os == 'macos-latest'
+        run: |
+          # Download and extract ZEO++
+          wget -q http://www.zeoplusplus.org/zeo++-0.3.tar.gz
+          tar -xzf zeo++-0.3.tar.gz
+
+          # Compile Voro++ library first
+          cd zeo++-0.3/voro++/src
+          make
+
+          # Add Voro++ to PATH
+          echo "$(pwd)" >> $GITHUB_PATH
+
+          # Compile ZEO++
+          cd ../../
+          make
+
+          # Add ZEO++ to PATH
+          echo "$(pwd)" >> $GITHUB_PATH
+
+
       - name: Install pymatgen and dependencies via uv
         run: |
           micromamba activate pmg
@@ -110,6 +133,12 @@ jobs:
           PMG_TEST_FILES_DIR: "${{ github.workspace }}/tests/files"
         run: |
           micromamba activate pmg
+          # Print environment info and if ZEO++ is available
+          if [ "${{ matrix.config.os }}" == "ubuntu-latest" ] || [ "${{ matrix.config.os }}" == "macos-latest" ]; then
+            which network || echo "ZEO++ not found in PATH"
+            python -c "try: import zeo; print('ZEO++ Python module found'); except ImportError: print('ZEO++ Python module not found')"
+          fi
+
           pytest --splits 10 --group ${{ matrix.split }} --durations-path tests/files/.pytest-split-durations tests
 
   trigger_atomate2_ci:

pyproject.toml

@@ -95,6 +95,7 @@ electronic_structure = ["fdint>=2.0.2"]
 mlp = ["chgnet>=0.3.8", "matgl>=1.1.3"]
 numba = ["numba>=0.55"]
 numpy-v1 = ["numpy>=1.25.0,<2"] # Test NP1 on Windows (quite buggy ATM)
+zeopp = ["pyzeo"]  # Note: requires voro++ and zeo++ to be installed as binaries
 optional = [
     "pymatgen[abinit,ase,mlp,tblite]",
     "beautifulsoup4",

src/pymatgen/io/zeopp.py

@@ -42,9 +42,19 @@
     from zeo.netstorage import AtomNetwork
 
     zeo_found = True
+    zeo_source = "zeo"
 except ImportError:
-    zeo_found = False
-    AtomNetwork = prune_voronoi_network_close_node = None
+    try:
+        from pyzeo import AtomNetwork
+        from pyzeo.extension import prune_voronoi_network_close_node
+
+        zeo_found = True
+        zeo_source = "pyzeo"
+    except ImportError:
+        zeo_found = False
+        zeo_source = None
+        AtomNetwork = prune_voronoi_network_close_node = None
+
 
 if TYPE_CHECKING:
     from pathlib import Path

tests/io/test_zeopp.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import importlib.util
 import unittest
 from unittest import TestCase
 
@@ -14,10 +15,16 @@
     get_free_sphere_params,
     get_high_accuracy_voronoi_nodes,
     get_voronoi_nodes,
+    zeo_found,
+    zeo_source,
 )
 from pymatgen.util.testing import TEST_FILES_DIR, VASP_IN_DIR
 
-pytest.importorskip("zeo", reason="zeo not installed")
+# Check if either zeo or pyzeo is available
+HAS_ZEO = importlib.util.find_spec("zeo") is not None or importlib.util.find_spec("pyzeo") is not None
+
+if not HAS_ZEO:
+    pytest.skip("neither zeo nor pyzeo is installed", allow_module_level=True)
 
 TEST_DIR = f"{TEST_FILES_DIR}/io/zeopp"
 
@@ -230,3 +237,15 @@ def test_get_voronoi_nodes(self):
         assert isinstance(vor_node_struct, Structure)
         assert isinstance(vor_edge_center_struct, Structure)
         assert isinstance(vor_face_center_struct, Structure)
+
+
+class TestZeoSource(TestCase):
+    """Test for zeo_source to verify which library was imported."""
+
+    def test_zeo_source_is_defined(self):
+        """Test that zeo_source is defined and is either 'zeo' or 'pyzeo'."""
+        assert zeo_source in ["zeo", "pyzeo"]
+
+    def test_zeo_found_is_true(self):
+        """Test that zeo_found is True when either library is imported."""
+        assert zeo_found is True