Fix all type checks for current set of critical classes.

.circleci/config.yml

@@ -43,7 +43,7 @@ jobs:
             pycodestyle pymatgen
             echo "--- Done ---"
             echo "mypy checks..."
-            mypy pymatgen/core pymatgen/symmetry pymatgen/transformations pymatgen/command_line pymatgen/analysis
+            mypy pymatgen/core pymatgen/symmetry pymatgen/transformations pymatgen/command_line pymatgen/analysis pymatgen/entries
             echo "--- Done ---"
             # Command line tests
             pmg structure --convert --filenames test_files/Li2O.cif POSCAR.pmg

pymatgen/core/structure.py

@@ -740,7 +740,7 @@ def from_spacegroup(cls,
     @classmethod
     def from_magnetic_spacegroup(
             cls,
-            msg: Union[str, 'MagneticSpaceGroup'],
+            msg: Union[str, 'MagneticSpaceGroup'],  # type: ignore
             lattice: Union[List, np.ndarray, Lattice],
             species: Sequence[Union[str, Element, Specie, DummySpecie, Composition]],
             coords: Sequence[Sequence[float]],
@@ -826,8 +826,7 @@ def from_magnetic_spacegroup(
                 "different!" % (len(species), len(magmoms))
             )
 
-        frac_coords = coords if not coords_are_cartesian else \
-            lattice.get_fractional_coords(coords)
+        frac_coords = coords if not coords_are_cartesian else latt.get_fractional_coords(coords)
 
         all_sp = []  # type: List[Union[str, Element, Specie, DummySpecie, Composition]]
         all_coords = []  # type: List[List[float]]

pymatgen/entries/entry_tools.py

@@ -23,7 +23,7 @@
 import csv
 import re
 
-from typing import List, Union
+from typing import List, Union, Iterable, Set
 from pymatgen.core.periodic_table import Element
 from pymatgen.core.composition import Composition
 from pymatgen.analysis.phase_diagram import PDEntry
@@ -152,7 +152,7 @@ class EntrySet(collections.abc.MutableSet, MSONable):
     subsets, dumping into files, etc.
     """
 
-    def __init__(self, entries: List[Union[PDEntry, ComputedEntry, ComputedStructureEntry]]):
+    def __init__(self, entries: Iterable[Union[PDEntry, ComputedEntry, ComputedStructureEntry]]):
         """
         Args:
             entries: All the entries.
@@ -211,14 +211,14 @@ def get_subset_in_chemsys(self, chemsys: List[str]):
         Returns:
             EntrySet
         """
-        chemsys = set(chemsys)
-        if not chemsys.issubset(self.chemsys):
-            raise ValueError("%s is not a subset of %s" % (chemsys,
+        chem_sys = set(chemsys)
+        if not chem_sys.issubset(self.chemsys):
+            raise ValueError("%s is not a subset of %s" % (chem_sys,
                                                            self.chemsys))
         subset = set()
         for e in self.entries:
             elements = [sp.symbol for sp in e.composition.keys()]
-            if chemsys.issuperset(elements):
+            if chem_sys.issuperset(elements):
                 subset.add(e)
         return EntrySet(subset)
 
@@ -238,19 +238,19 @@ def to_csv(self, filename: str, latexify_names: bool = False):
                 e.g., Li_{2}O
         """
 
-        elements = set()
+        els = set()  # type: Set[Element]
         for entry in self.entries:
-            elements.update(entry.composition.elements)
-        elements = sorted(list(elements), key=lambda a: a.X)
+            els.update(entry.composition.elements)
+        elements = sorted(list(els), key=lambda a: a.X)
         writer = csv.writer(open(filename, "w"), delimiter=unicode2str(","),
                             quotechar=unicode2str("\""),
                             quoting=csv.QUOTE_MINIMAL)
-        writer.writerow(["Name"] + elements + ["Energy"])
+        writer.writerow(["Name"] + [el.symbol for el in elements] + ["Energy"])
         for entry in self.entries:
             row = [entry.name if not latexify_names
                    else re.sub(r"([0-9]+)", r"_{\1}", entry.name)]
             row.extend([entry.composition[el] for el in elements])
-            row.append(entry.energy)
+            row.append(str(entry.energy))
             writer.writerow(row)
 
     @classmethod
@@ -270,7 +270,7 @@ def from_csv(cls, filename: str):
                                 quoting=csv.QUOTE_MINIMAL)
             entries = list()
             header_read = False
-            elements = None
+            elements = []  # type: List[str]
             for row in reader:
                 if not header_read:
                     elements = row[1:(len(row) - 1)]

pymatgen/symmetry/maggroups.py

@@ -9,7 +9,7 @@
 
 import textwrap
 
-from pymatgen.core import Lattice
+from pymatgen.core.lattice import Lattice
 from pymatgen.electronic_structure.core import Magmom
 from pymatgen.symmetry.groups import SymmetryGroup, in_array_list
 from pymatgen.core.operations import MagSymmOp