Add Cell-like types interface

.github/workflows/ci-python.yaml

@@ -44,7 +44,7 @@ jobs:
         run: |
           set -e
           pip install moyopy --no-index --find-links dist
-          pip install -r moyopy/examples/requirements.txt
+          pip install moyopy[interface]
           python moyopy/examples/basic.py
           python moyopy/examples/pymatgen_structure.py
 

moyopy/README.md

@@ -6,6 +6,14 @@
 
 Python interface of Moyo
 
+## Installation
+
+```shell
+pip install moyopy
+# If you want to convert structures into Pymatgen or ASE objects
+pip install moyopy[interface]
+```
+
 ## Examples
 
 See [example directory](examples)

moyopy/examples/pymatgen_structure.py

@@ -1,28 +1,10 @@
 from __future__ import annotations
 
 import numpy as np
-from pymatgen.core import Element, Structure
+from pymatgen.core import Structure
 
 import moyopy
-
-
-class MoyoAdapter:
-    @staticmethod
-    def get_structure(cell: moyopy.Cell) -> Structure:
-        species = [Element.from_Z(number) for number in cell.numbers]
-        return Structure(lattice=cell.basis, species=species, coords=cell.positions)
-
-    @staticmethod
-    def get_moyo_cell(structure: Structure) -> moyopy.Cell:
-        basis = structure.lattice.matrix
-        positions = structure.frac_coords
-        numbers = [site.specie.Z for site in structure]
-
-        return moyopy.Cell(
-            basis=basis.tolist(),
-            positions=positions.tolist(),
-            numbers=numbers,
-        )
+from moyopy.interface import MoyoAdapter
 
 
 class MoyoSpacegroupAnalyzer:
@@ -33,7 +15,7 @@ def __init__(
         angle_tolerance: float | None = None,
         setting: moyopy.Setting | None = None,
     ):
-        self._cell = MoyoAdapter.get_moyo_cell(structure)
+        self._cell = MoyoAdapter.from_structure(structure)
         self._dataset = moyopy.MoyoDataset(
             cell=self._cell,
             symprec=symprec,

moyopy/pyproject.toml

@@ -30,10 +30,15 @@ classifiers = [
 ]
 
 [project.optional-dependencies]
+interface = [
+    "numpy<2",  # pymatgen seems to be still imcompatible with numpy>=2
+    "pymatgen",
+    "ase>=3.23",
+]
 dev = [
+    "moyopy[interface]",
     "pytest",
     "pre-commit",
-    "numpy",
 ]
 
 [tool.maturin]

moyopy/python/moyopy/interface.py

@@ -0,0 +1,50 @@
+from __future__ import annotations
+
+try:
+    import ase
+    from pymatgen.core import Element, Structure
+except ImportError:
+    raise ImportError("Try installing dependencies with `pip install moyopy[interface]`")
+
+import moyopy
+
+
+class MoyoAdapter:
+    @staticmethod
+    def get_structure(cell: moyopy.Cell) -> Structure:
+        species = [Element.from_Z(number) for number in cell.numbers]
+        return Structure(lattice=cell.basis, species=species, coords=cell.positions)
+
+    @staticmethod
+    def get_atoms(cell: moyopy.Cell) -> ase.Atoms:
+        atoms = ase.Atoms(
+            cell=cell.basis,
+            scaled_positions=cell.positions,
+            numbers=cell.numbers,
+            pbc=True,
+        )
+        return atoms
+
+    @staticmethod
+    def from_structure(structure: Structure) -> moyopy.Cell:
+        basis = structure.lattice.matrix
+        positions = structure.frac_coords
+        numbers = [site.specie.Z for site in structure]
+
+        return moyopy.Cell(
+            basis=basis.tolist(),
+            positions=positions.tolist(),
+            numbers=numbers,
+        )
+
+    @staticmethod
+    def from_atoms(atoms: ase.Atoms) -> moyopy.Cell:
+        basis = list(atoms.cell)
+        positions = atoms.get_scaled_positions()
+        numbers = atoms.get_atomic_numbers()
+
+        return moyopy.Cell(
+            basis=basis,
+            positions=positions,
+            numbers=numbers,
+        )

moyopy/python/tests/conftest.py

@@ -25,7 +25,7 @@ def wurtzite() -> moyopy.Cell:
         [1 / 3, 2 / 3, z2_2b],
         [2 / 3, 1 / 3, z2_2b + 0.5],
     ]
-    numbers = [0, 0, 1, 1]
+    numbers = [1, 1, 2, 2]
 
     cell = moyopy.Cell(basis, positions, numbers)
     return cell

moyopy/python/tests/test_interface.py

@@ -0,0 +1,22 @@
+from __future__ import annotations
+
+import numpy as np
+
+import moyopy
+from moyopy.interface import MoyoAdapter
+
+
+def test_pymatgen_moyopy(wurtzite: moyopy.Cell):
+    structure = MoyoAdapter.get_structure(wurtzite)
+    cell = MoyoAdapter.from_structure(structure)
+    assert np.allclose(cell.basis, wurtzite.basis)
+    assert np.allclose(cell.positions, wurtzite.positions)
+    assert cell.numbers == wurtzite.numbers
+
+
+def test_ase_moyopy(wurtzite: moyopy.Cell):
+    atoms = MoyoAdapter.get_atoms(wurtzite)
+    cell = MoyoAdapter.from_atoms(atoms)
+    assert np.allclose(cell.basis, wurtzite.basis)
+    assert np.allclose(cell.positions, wurtzite.positions)
+    assert cell.numbers == wurtzite.numbers