Bumpped Describe, Removed pyrho (#132)

* deps

* deps

* python vers

* teset

* tests

* cleaner strict

* cleaner strict

* wf

.github/workflows/testing.yml

@@ -24,6 +24,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install -e .[strict]
+          pip install -e .[dev]
           pre-commit install
 
       - name: Lint
@@ -34,7 +35,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     env:
       PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
@@ -51,6 +52,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install -e .[strict]
+          pip install -e .[tests]
 
       - name: Test
         run: pytest --cov=pymatgen --cov-report=xml

pymatgen/analysis/defects/core.py

@@ -13,10 +13,11 @@
 from pymatgen.core import Element, PeriodicSite, Species, Structure
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.symmetry.structure import SymmetrizedStructure
-from pyrho.utils import get_plane_spacing
 
 from pymatgen.analysis.defects.supercells import get_sc_fromstruct
 
+from .utils import get_plane_spacing
+
 # TODO Possible redesign idea: ``DefectSite`` class defined with a defect object.
 # This makes some of the accounting logic a bit harder since we will probably
 # just have one concrete ``Defect`` class so you can write custom multiplicity functions
@@ -414,7 +415,7 @@ def _guess_oxi_state(self) -> float:
                 f"No common oxidation states found for {self.site.specie}."
                 "Please specify the oxidation state manually."
             )
-        sub_oxi = sub_states[0]
+        sub_oxi = min(sub_states, key=lambda x: abs(x - rm_oxi))
         return sub_oxi - rm_oxi
 
     def __repr__(self) -> str:

pymatgen/analysis/defects/finder.py

@@ -228,7 +228,7 @@ def get_soap_vec(struct: Structure) -> NDArray:
     dummy_structure = struct.copy()
     for el in species_:
         dummy_structure.replace_species({str(el): DUMMY_SPECIES})
-    soap_desc = SOAP(species=[DUMMY_SPECIES], rcut=5, nmax=8, lmax=6, periodic=True)
+    soap_desc = SOAP(species=[DUMMY_SPECIES], r_cut=5, n_max=8, l_max=6, periodic=True)
     vecs = soap_desc.create(adaptor.get_atoms(dummy_structure))
     return vecs
 

pymatgen/analysis/defects/utils.py

@@ -1043,3 +1043,41 @@ def group_docs(
             else:
                 for itr, group in enumerate(sgroups):
                     yield f"{h}:{itr}", group
+
+
+def get_plane_spacing(lattice: npt.NDArray) -> list[float]:
+    """Get the cartesian spacing between periodic planes of a unit cell.
+    Copied from materialsproject/pyrho
+
+    >>> get_plane_spacing([[1,0,0], [1,1,0], [0,0,2]])
+    [0.7653..., 1.042..., 2.0]
+
+    Args:
+    lattice:
+        List of lattice vectors in cartesian coordinates
+
+    Returns:
+    List[float]:
+        List where the k-th element is is the spacing of planes generated by all
+        lattice vectors EXCEPT the k-th one
+
+    """
+    # get all pairwise projections i must be smaller than j
+    ndim = len(lattice)
+    idx_pairs = [*itertools.combinations(range(ndim), 2)]
+    latt_len = [np.linalg.norm(lattice[i]) for i in range(ndim)]
+    pproj = {
+        (i, j): np.dot(lattice[i], lattice[j]) / latt_len[i] / latt_len[j]
+        for i, j in idx_pairs
+    }
+    # get the spacing in each direction:
+    spacing = []
+    for idir in range(ndim):
+        idir_proj = [
+            np.array(lattice[j]) * pproj[tuple(sorted([idir, j]))]  # type: ignore
+            for j in range(ndim)
+            if j != idir
+        ]
+        v_perp_subspace = lattice[idir] - sum(idir_proj)
+        spacing.append(np.linalg.norm(v_perp_subspace))
+    return spacing

pyproject.toml

@@ -15,7 +15,11 @@ classifiers = [
   "Topic :: Other/Nonlisted Topic",
   "Topic :: Scientific/Engineering",
 ]
-dependencies = ["pymatgen>=2023.5.8", "scikit-image>=0.19.3", "mp-pyrho>=0.3.0", "numpy<=1.23.5"]
+dependencies = [
+  "pymatgen>=2023.5.8",
+  "scikit-image>=0.19.3",
+  "numpy"
+]
 description = "Pymatgen extension for defects analysis"
 dynamic = ["version"]
 keywords = ["high-throughput", "automated", "dft", "defects"]
@@ -25,22 +29,18 @@ readme = "README.rst"
 requires-python = '>=3.8'
 
 [project.optional-dependencies]
-finder = ["dscribe>=1.2.1"]
+finder = ["dscribe>=2.0.0"]
 dev = ["pre-commit>=2.12.1"]
 docs = [
   "jupyter-book>=0.13.1",
 ]
 pydefect = ["pydefect>=0.6.2"]
 
 strict = [
-  "pymatgen>=2023.5.8",
-  "dscribe==1.2.2",
-  "scikit-image==0.20.0",
-  "pytest==7.2.2",
-  "pytest-cov==4.0.0",
-  "pre-commit==3.3.3",
-  "mp-pyrho==0.3.0",
-  "numpy==1.23.5"
+  "pymatgen==2023.7.20",
+  "dscribe==2.0.0",
+  "scikit-image==0.21.0",
+  "numpy==1.24.4",
 ]
 
 tests = ["pytest==7.2.2", "pytest-cov==4.0.0"]

tests/test_utils.py

@@ -12,6 +12,7 @@
     get_avg_chg,
     get_local_extrema,
     get_localized_states,
+    get_plane_spacing,
     group_docs,
 )
 
@@ -158,3 +159,8 @@ def get_interstitial(fpos):
         res.append(defect_names)
     assert "|".join(sorted(res)) == "N_i|N_i,N_i|v_Ga,v_Ga|v_N,v_N"
     assert "|".join(sorted(g_names)) == "N_i:0|N_i:1|v_Ga|v_N"
+
+
+def test_plane_spacing(gan_struct):
+    lattice = gan_struct.lattice.matrix
+    assert np.allclose(get_plane_spacing(lattice), [2.785, 2.785, 5.239], atol=0.001)