Merge pull request #257 from lbluque/main

Remove CanonicalEnsemble and SemigrandEnsemble + some minor fixes

smol/cofe/extern/ewald.py

@@ -93,7 +93,7 @@ def get_ewald_structure(structure):
                 inds[i] = len(ewald_sites)
                 ewald_sites.append(PeriodicSite(spec, site.frac_coords, site.lattice))
             ewald_inds.append(inds)
-        ewald_inds = np.array(ewald_inds, dtype=np.int)
+        ewald_inds = np.array(ewald_inds, dtype=int)
         ewald_structure = Structure.from_sites(ewald_sites)
 
         return ewald_structure, ewald_inds
@@ -124,7 +124,7 @@ def get_ewald_occu(occu, num_ewald_sites, ewald_inds):
         #   i_inds = i_inds[i_inds != -1]
         # just make b_inds one longer than it needs to be and don't return
         # the last value
-        b_inds = np.zeros(num_ewald_sites + 1, dtype=np.bool)
+        b_inds = np.zeros(num_ewald_sites + 1, dtype=bool)
         b_inds[i_inds] = True
         return b_inds[:-1]
 

smol/cofe/space/clusterspace.py

@@ -713,7 +713,7 @@ def occupancy_from_structure(
         if site_mapping is None:
             site_mapping = self.structure_site_mapping(supercell, structure)
 
-        occu = []  # np.zeros(len(self.supercell_structure), dtype=np.int)
+        occu = []  # np.zeros(len(self.supercell_structure), dtype=int)
 
         for i, allowed_species in enumerate(get_allowed_species(supercell)):
             # rather than starting with all vacancies and looping

smol/cofe/space/orbit.py

@@ -142,7 +142,7 @@ def bit_combos(self):
             all_combos = []
             for bit_combo in product(*self.bits):
                 if not any(np.array_equal(bit_combo, bc) for bc in chain(*all_combos)):
-                    bit_combo = np.array(bit_combo, dtype=np.int_)
+                    bit_combo = np.array(bit_combo, dtype=int)
                     new_bits = np.unique(bit_combo[self.cluster_permutations], axis=0)
                     all_combos.append(new_bits)
             self._bit_combos = tuple(all_combos)

smol/cofe/wrangling/wrangler.py

@@ -618,7 +618,7 @@ def remove_properties(self, *property_keys):
                 for entry in self._entries:
                     del entry.data["properties"][key]
             except KeyError:
-                warnings.warn(f"Propertiy {key} does not exist.", RuntimeWarning)
+                warnings.warn(f"Property {key} does not exist.", RuntimeWarning)
 
     def remove_entry(self, entry):
         """Remove a given structure and associated data."""
@@ -877,7 +877,7 @@ def as_dict(self):
             "@class": self.__class__.__name__,
             "_subspace": self._subspace.as_dict(),
             "_entries": [entry.as_dict() for entry in self._entries],
-            "_ind_sets": jsanitize(self._ind_sets),  # jic for np.int's
+            "_ind_sets": jsanitize(self._ind_sets),  # jic for int's
             "metadata": self.metadata,
         }
         return wrangler_dict

smol/moca/__init__.py

@@ -5,23 +5,18 @@
 Monte Carlo simulations using Cluster Expansion Hamiltonians.
 """
 
+from smol.moca.ensemble import Ensemble
+from smol.moca.processor.composite import CompositeProcessor
+from smol.moca.processor.ewald import EwaldProcessor
+from smol.moca.processor.expansion import ClusterExpansionProcessor
 from smol.moca.sampler.container import SampleContainer
-
-from .ensemble.canonical import CanonicalEnsemble
-from .ensemble.ensemble import Ensemble
-from .ensemble.semigrand import SemiGrandEnsemble
-from .processor.composite import CompositeProcessor
-from .processor.ewald import EwaldProcessor
-from .processor.expansion import ClusterExpansionProcessor
-from .sampler.sampler import Sampler
+from smol.moca.sampler.sampler import Sampler
 
 __all__ = [
     "ClusterExpansionProcessor",
     "EwaldProcessor",
     "CompositeProcessor",
     "Ensemble",
-    "CanonicalEnsemble",
-    "SemiGrandEnsemble",
     "Sampler",
     "SampleContainer",
 ]