Add types for core.molecular_orbitals/operations/sites/spectrum/tensor/xcfunc (materialsproject#3829)

* fix `core.molecular_orbitals`

* fix `core.operations`

* add types for site, mypy errors to fix

* remove no_type_check decorator

* move dunder methods to the top

* fix mypy errors

* remove debug tag

* improve `spectrum`

* finish `core.tensors`

* finish `xcfunc`

* fix hash of `SymmOp`

* add a missing type

* Revert "fix hash of `SymmOp`"

This reverts commit bf2a953.

* fix some types in operations

* "TEST": remove one unused var, relocate another

* final tweak types

* avoid hard-code class name

* format tweaks

* type tweak

* fix unit test

* replace all `[0:x]` with `[:x]`

Author: DanielYang59

pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py

@@ -218,7 +218,7 @@ def points_wcs_csc(self, permutation=None):
         """
         if permutation is None:
             return self._points_wcs_csc
-        return np.concatenate((self._points_wcs_csc[0:1], self._points_wocs_csc.take(permutation, axis=0)))
+        return np.concatenate((self._points_wcs_csc[:1], self._points_wocs_csc.take(permutation, axis=0)))
 
     def points_wocs_csc(self, permutation=None):
         """
@@ -238,7 +238,7 @@ def points_wcs_ctwcc(self, permutation=None):
             return self._points_wcs_ctwcc
         return np.concatenate(
             (
-                self._points_wcs_ctwcc[0:1],
+                self._points_wcs_ctwcc[:1],
                 self._points_wocs_ctwcc.take(permutation, axis=0),
             )
         )
@@ -261,7 +261,7 @@ def points_wcs_ctwocc(self, permutation=None):
             return self._points_wcs_ctwocc
         return np.concatenate(
             (
-                self._points_wcs_ctwocc[0:1],
+                self._points_wcs_ctwocc[:1],
                 self._points_wocs_ctwocc.take(permutation, axis=0),
             )
         )

pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py

@@ -901,7 +901,7 @@ def project_and_to2dim(self, pps, plane_center):
         xypps = []
         for pp in proj:
             xyzpp = np.dot(pp, PP)
-            xypps.append(xyzpp[0:2])
+            xypps.append(xyzpp[:2])
         if str(plane_center) == "mean":
             mean = np.zeros(2, float)
             for pp in xypps:
@@ -910,7 +910,7 @@ def project_and_to2dim(self, pps, plane_center):
             xypps = [pp - mean for pp in xypps]
         elif plane_center is not None:
             projected_plane_center = self.projectionpoints([plane_center])[0]
-            xy_projected_plane_center = np.dot(projected_plane_center, PP)[0:2]
+            xy_projected_plane_center = np.dot(projected_plane_center, PP)[:2]
             xypps = [pp - xy_projected_plane_center for pp in xypps]
         return xypps
 
@@ -960,7 +960,7 @@ def coefficients(self):
     @property
     def abcd(self):
         """A tuple with the plane coefficients."""
-        return tuple(self._coefficients[0:4])
+        return tuple(self._coefficients[:4])
 
     @property
     def a(self):

pymatgen/analysis/ferroelectricity/polarization.py

@@ -130,7 +130,7 @@ def get_nearest_site(struct: Structure, coords: Sequence[float], site: PeriodicS
     # Sort by distance to coords
     ns.sort(key=lambda x: x[1])
     # Return PeriodicSite and distance of closest image
-    return ns[0][0:2]
+    return ns[0][:2]
 
 
 class Polarization:

pymatgen/analysis/magnetism/analyzer.py

@@ -1011,7 +1011,7 @@ def _add_structures(ordered_structures, ordered_structures_origins, structures_t
 
             # ...and decide which ones to keep
             if len(max_symmetries) > self.truncate_by_symmetry:
-                max_symmetries = max_symmetries[0:5]
+                max_symmetries = max_symmetries[:5]
             structs_to_keep = [(idx, num) for idx, num in enumerate(num_sym_ops) if num in max_symmetries]
 
             # sort so that highest symmetry structs are first

pymatgen/command_line/gulp_caller.py

@@ -585,7 +585,7 @@ def get_relaxed_structure(gout: str):
                 # read the site coordinates in the following lines
                 idx += 6
                 line = output_lines[idx]
-                while line[0:2] != "--":
+                while line[:2] != "--":
                     structure_lines.append(line)
                     idx += 1
                     line = output_lines[idx]

pymatgen/command_line/mcsqs_caller.py

@@ -261,7 +261,7 @@ def _parse_clusters(filename):
         for point in range(cluster_dict["num_points_in_cluster"]):
             line = cluster[3 + point].split(" ")
             point_dict = {}
-            point_dict["coordinates"] = [float(line) for line in line[0:3]]
+            point_dict["coordinates"] = [float(line) for line in line[:3]]
             point_dict["num_possible_species"] = int(line[3]) + 2  # see ATAT manual for why +2
             point_dict["cluster_function"] = float(line[4])  # see ATAT manual for what "function" is
             points.append(point_dict)