Merge pull request #2285 from janosh/str-fixes

Fix oddly split strings and a few typos

dev_scripts/update_pt_data.py

@@ -6,12 +6,11 @@
 """
 
 import json
+import re
 from itertools import product
 
 import ruamel.yaml as yaml
-import re
-
-from monty.serialization import loadfn, dumpfn
+from monty.serialization import dumpfn, loadfn
 
 from pymatgen.core import Element
 from pymatgen.core.periodic_table import get_el_sp
@@ -88,7 +87,7 @@ def parse_ionic_radii():
 
         ionic_radii = {}
         for j in range(3, len(toks)):
-            m = re.match("^\s*([0-9\.]+)", toks[j])
+            m = re.match(r"^\s*([0-9\.]+)", toks[j])
             if m:
                 ionic_radii[int(header[j])] = float(m.group(1))
 
@@ -109,7 +108,7 @@ def parse_radii():
     radiidata = f.read()
     f.close()
     radiidata = radiidata.split("\r")
-    header = radiidata[0].split(",")
+
     for i in range(1, len(radiidata)):
         line = radiidata[i]
         toks = line.strip().split(",")
@@ -164,9 +163,10 @@ def update_ionic_radii():
 def parse_shannon_radii():
     with open("periodic_table.yaml", "r") as f:
         data = yaml.load(f)
-    from openpyxl import load_workbook
     import collections
 
+    from openpyxl import load_workbook
+
     wb = load_workbook("Shannon Radii.xlsx")
     print(wb.get_sheet_names())
     sheet = wb["Sheet1"]
@@ -259,8 +259,8 @@ def add_electron_affinities():
     """
     Update the periodic table data file with electron affinities.
     """
-    from bs4 import BeautifulSoup
     import requests
+    from bs4 import BeautifulSoup
 
     req = requests.get("https://en.wikipedia.org/wiki/Electron_affinity_(data_page)")
     soup = BeautifulSoup(req.text, "html.parser")
@@ -287,9 +287,10 @@ def add_ionization_energies():
     """
     Update the periodic table data file with ground level and ionization energies from NIST.
     """
-    from bs4 import BeautifulSoup
     import collections
 
+    from bs4 import BeautifulSoup
+
     with open("NIST Atomic Ionization Energies Output.html") as f:
         soup = BeautifulSoup(f.read(), "html.parser")
     for t in soup.find_all("table"):

docs_rst/conf-docset.py

@@ -11,8 +11,8 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys
 import os
+import sys
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -22,7 +22,7 @@
 sys.path.insert(0, os.path.dirname("../pymatgen"))
 sys.path.insert(0, os.path.dirname("../.."))
 
-from pymatgen.core import __version__, __author__
+from pymatgen.core import __author__, __version__
 
 # -- General configuration -----------------------------------------------------
 

docs_rst/conf-normal.py

@@ -11,8 +11,8 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys
 import os
+import sys
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -22,7 +22,7 @@
 sys.path.insert(0, os.path.dirname("../pymatgen"))
 sys.path.insert(0, os.path.dirname("../.."))
 
-from pymatgen.core import __version__, __author__, __file__
+from pymatgen.core import __author__, __file__, __version__
 
 # -- General configuration -----------------------------------------------------
 

pre-commit

@@ -1,7 +1,7 @@
 #!/bin/bash
 #
 # An example hook script to verify what is about to be committed.
-# Called by "git commit" with no arguments.  The hook should
+# Called by "git commit" with no arguments. The hook should
 # exit with non-zero status after issuing an appropriate message if
 # it wants to stop the commit.
 #

pymatgen/alchemy/materials.py

@@ -63,7 +63,7 @@ def undo_last_change(self):
         if len(self.history) == 0:
             raise IndexError("Can't undo. Already at oldest change.")
         if "input_structure" not in self.history[-1]:
-            raise IndexError("Can't undo. Latest history has no " "input_structure")
+            raise IndexError("Can't undo. Latest history has no input_structure")
         h = self.history.pop()
         self._undone.append((h, self.final_structure))
         s = h["input_structure"]
@@ -301,7 +301,7 @@ def from_poscar_string(poscar_string, transformations=None):
         p = Poscar.from_string(poscar_string)
         if not p.true_names:
             raise ValueError(
-                "Transformation can be craeted only from POSCAR " "strings with proper VASP5 element symbols."
+                "Transformation can be created only from POSCAR strings with proper VASP5 element symbols."
             )
         raw_string = re.sub(r"'", '"', poscar_string)
         s = p.structure
@@ -341,7 +341,7 @@ def to_snl(self, authors, **kwargs):
         :return: StructureNL
         """
         if self.other_parameters:
-            warn("Data in TransformedStructure.other_parameters discarded " "during type conversion to SNL")
+            warn("Data in TransformedStructure.other_parameters discarded during type conversion to SNL")
         hist = []
         for h in self.history:
             snl_metadata = h.pop("_snl", {})

pymatgen/alchemy/tests/test_materials.py

@@ -111,7 +111,7 @@ def test_snl(self):
             self.assertEqual(
                 len(w),
                 1,
-                "Warning not raised on type conversion " "with other_parameters",
+                "Warning not raised on type conversion with other_parameters",
             )
         ts = TransformedStructure.from_snl(snl)
         self.assertEqual(ts.history[-1]["@class"], "SubstitutionTransformation")

pymatgen/analysis/bond_valence.py

@@ -514,4 +514,4 @@ def add_oxidation_state_by_site_fraction(structure, oxidation_states):
             structure[i] = new_sp
         return structure
     except IndexError:
-        raise ValueError("Oxidation state of all sites must be " "specified in the list.")
+        raise ValueError("Oxidation state of all sites must be specified in the list.")

pymatgen/analysis/chemenv/connectivity/connected_components.py

@@ -838,7 +838,7 @@ def _edgekey_to_edgedictkey(key):
         if isinstance(key, str):
             try:
                 int(key)
-                raise RuntimeError("Cannot pass an edge key which is a str " "representation of an int.")
+                raise RuntimeError("Cannot pass an edge key which is a str representation of an int.")
             except ValueError:
                 return key
         raise ValueError("Edge key should be either a str or an int.")
@@ -853,9 +853,7 @@ def _edgedictkey_to_edgekey(key):
             except ValueError:
                 return key
         else:
-            raise ValueError(
-                "Edge key in a dict of dicts representation of a graph" "should be either a str or an int."
-            )
+            raise ValueError("Edge key in a dict of dicts representation of a graph should be either a str or an int.")
 
     @staticmethod
     def _retuplify_edgedata(edata):

pymatgen/analysis/chemenv/connectivity/connectivity_finder.py

@@ -54,7 +54,7 @@ def get_structure_connectivity(self, light_structure_environments):
             if len(site_neighbors_sets) > 1:
                 if self.multiple_environments_choice is None:
                     raise ValueError(
-                        "Local environment of site {:d} is a mix and " "nothing is asked about it".format(isite)
+                        "Local environment of site {:d} is a mix and nothing is asked about it".format(isite)
                     )
                 if self.multiple_environments_choice == "TAKE_HIGHEST_FRACTION":
                     imax = np.argmax(

pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py

@@ -725,7 +725,7 @@ def compute_structure_environments(
         for isite, site in enumerate(self.structure):
             if isite not in sites_indices:
                 logging.debug(
-                    " ... in site #{:d}/{:d} ({}) : " "skipped".format(isite, len(self.structure), site.species_string)
+                    " ... in site #{:d}/{:d} ({}) : skipped".format(isite, len(self.structure), site.species_string)
                 )
                 continue
             if breakit:

pymatgen/analysis/chemenv/coordination_environments/structure_environments.py

@@ -1514,7 +1514,7 @@ def __ne__(self, other):
         def __str__(self):
             out = "Neighbors Set for site #{:d} :\n".format(self.isite)
             out += " - Coordination number : {:d}\n".format(len(self))
-            out += " - Neighbors sites indices : {}" "\n".format(
+            out += " - Neighbors sites indices : {}\n".format(
                 ", ".join(["{:d}".format(nb_list_index) for nb_list_index in self.all_nbs_sites_indices])
             )
             return out
@@ -1647,7 +1647,7 @@ def from_structure_environments(cls, strategy, structure_environments, valences=
                         rounddiff = np.round(diff)
                         if not np.allclose(diff, rounddiff):
                             raise ValueError(
-                                "Weird, differences between one site in a periodic image cell is not " "integer ..."
+                                "Weird, differences between one site in a periodic image cell is not integer ..."
                             )
                         nb_image_cell = np.array(rounddiff, np.int_)
                         nb_allnbs_sites_index = len(_all_nbs_sites)
@@ -2135,9 +2135,7 @@ def from_dict(cls, d):
                 diff = site.frac_coords - structure[nb_site["index"]].frac_coords
                 rounddiff = np.round(diff)
                 if not np.allclose(diff, rounddiff):
-                    raise ValueError(
-                        "Weird, differences between one site in a periodic image cell is not " "integer ..."
-                    )
+                    raise ValueError("Weird, differences between one site in a periodic image cell is not integer ...")
                 image_cell = np.array(rounddiff, np.int_)
             all_nbs_sites.append({"site": site, "index": nb_site["index"], "image_cell": image_cell})
         neighbors_sets = [
@@ -2177,7 +2175,7 @@ def __init__(self, coord_geoms=None):
             self.coord_geoms = {}
         else:
             raise NotImplementedError(
-                "Constructor for ChemicalEnvironments with the coord_geoms argument is not" "yet implemented"
+                "Constructor for ChemicalEnvironments with the coord_geoms argument is not yet implemented"
             )
 
     def __getitem__(self, mp_symbol):

pymatgen/analysis/chemenv/coordination_environments/tests/test_coordination_geometries.py

@@ -56,7 +56,7 @@ def test_algorithms(self):
 
         self.assertEqual(
             sepplane_algos_oct[0].__str__(),
-            "Separation plane algorithm with the following reference separation :\n" "[[4]] | [[0, 2, 1, 3]] | [[5]]",
+            "Separation plane algorithm with the following reference separation :\n[[4]] | [[0, 2, 1, 3]] | [[5]]",
         )
 
     def test_hints(self):

pymatgen/analysis/chemenv/coordination_environments/tests/test_read_write.py

@@ -180,7 +180,7 @@ def test_structure_environments_neighbors_sets(self):
 
         self.assertEqual(
             nb_set.__str__(),
-            "Neighbors Set for site #6 :\n" " - Coordination number : 4\n" " - Voronoi indices : 1, 4, 5, 6\n",
+            "Neighbors Set for site #6 :\n - Coordination number : 4\n - Voronoi indices : 1, 4, 5, 6\n",
         )
 
         self.assertFalse(nb_set.__ne__(nb_set))

pymatgen/analysis/chemenv/coordination_environments/voronoi.py

@@ -167,7 +167,7 @@ def setup_voronoi_list(self, indices, voronoi_cutoff):
                     ridge_vertices_indices = voro.ridge_vertices[iridge]
                     if -1 in ridge_vertices_indices:
                         raise RuntimeError(
-                            "This structure is pathological," " infinite vertex in the voronoi " "construction"
+                            "This structure is pathological, infinite vertex in the voronoi construction"
                         )
 
                     ridge_point2 = max(ridge_points)

pymatgen/analysis/chemenv/utils/chemenv_errors.py

@@ -77,7 +77,7 @@ def __init__(self, cosinus):
         self.cosinus = cosinus
 
     def __str__(self):
-        return "Value of cosinus ({}) from which an angle should be retrieved" "is not between -1.0 and 1.0".format(
+        return "Value of cosinus ({}) from which an angle should be retrieved is not between -1.0 and 1.0".format(
             self.cosinus
         )
 

pymatgen/analysis/chemenv/utils/graph_utils.py

@@ -24,7 +24,7 @@ def get_delta(node1, node2, edge_data):
         return np.array(edge_data["delta"], dtype=np.int_)
     if node2.isite == edge_data["start"] and node1.isite == edge_data["end"]:
         return -np.array(edge_data["delta"], dtype=np.int_)
-    raise ValueError("Trying to find a delta between two nodes with an edge " "that seems not to link these nodes.")
+    raise ValueError("Trying to find a delta between two nodes with an edge that seems not to link these nodes.")
 
 
 def get_all_simple_paths_edges(graph, source, target, cutoff=None, data=True):
@@ -229,7 +229,7 @@ def order(self, raise_on_fail=True):
         node_classes = set(n.__class__ for n in self.nodes)
         if len(node_classes) > 1:
             if raise_on_fail:
-                raise ValueError("Could not order simple graph cycle as the nodes " "are of different classes.")
+                raise ValueError("Could not order simple graph cycle as the nodes are of different classes.")
             self.ordered = False
             return
 
@@ -420,7 +420,7 @@ def order(self, raise_on_fail=True):
         node_classes = set(n.__class__ for n in self.nodes)
         if len(node_classes) > 1:
             if raise_on_fail:
-                raise ValueError("Could not order simple graph cycle as the nodes " "are of different classes.")
+                raise ValueError("Could not order simple graph cycle as the nodes are of different classes.")
             self.ordered = False
             return