Apply linting to all of pymatgen unless excluded in setup.cfg.

.circleci/config.yml

@@ -48,8 +48,7 @@ jobs:
             pycodestyle pymatgen
             echo "--- Done ---"
             echo "flake8 checks..."
-            flake8 --count --select=E9,F63,F7,F82 --show-source --statistics pymatgen
-            flake8 --count --show-source --statistics pymatgen/core pymatgen/electronic_structure pymatgen/ext pymatgen/io pymatgen/transformations pymatgen/analysis
+            flake8 --count --show-source --statistics pymatgen
             # exit-zero treats all errors as warnings.
             flake8 --count --exit-zero --max-complexity=10 --statistics pymatgen
             echo "--- Done ---"

.github/workflows/pmg-lint.yml

@@ -31,7 +31,6 @@ jobs:
       run: |
         pip install flake8
         # stop the build if there are Python syntax errors or undefined names
-        flake8 --count --select=E9,F63,F7,F82 --show-source --statistics pymatgen
-        flake8 --count --show-source --statistics pymatgen/core pymatgen/electronic_structure pymatgen/ext pymatgen/io pymatgen/transformations pymatgen/analysis
+        flake8 --count --show-source --statistics pymatgen
         # exit-zero treats all errors as warnings.
         flake8 --count --exit-zero --max-complexity=10 --statistics pymatgen

.travis.yml

@@ -38,8 +38,7 @@ script:
   - echo "It is highly recommended that you use the pre-commit hook provided in pymatgen (simply copy pre-commit to .git/hooks) to check before pushing your code."
   - travis_wait 28800 pycodestyle pymatgen && mypy pymatgen && pytest $EXCLUDE_TESTS pymatgen
   # Docstyle checks are enforced for files that have been modified since the v2019.9.12 tagged release.
-  - flake8 --count --select=E9,F63,F7,F82 --show-source --statistics pymatgen
-  - flake8 --count --show-source --statistics pymatgen/core pymatgen/electronic_structure pymatgen/ext pymatgen/io pymatgen/transformations pymatgen/analysis
+  - flake8 --count --show-source --statistics pymatgen
   - flake8 --count --exit-zero --max-complexity=10 --statistics pymatgen
   - export MODIFIED_FILES=`git diff --diff-filter=ACMRTUXB --name-only HEAD v2019.9.12 | grep -E 'pymatgen.*\.(py)$' | sed '/test_/d' | sed 'post_processors_abc/d' | tr '\n' ' '`
   - pydocstyle --count pymatgen/core $MODIFIED_FILES

pymatgen/phonon/bandstructure.py

@@ -2,6 +2,9 @@
 # Copyright (c) Pymatgen Development Team.
 # Distributed under the terms of the MIT License.
 
+"""
+This module provides classes to define a phonon band structure.
+"""
 
 import collections
 import numpy as np
@@ -11,10 +14,6 @@
 from pymatgen.electronic_structure.bandstructure import Kpoint
 from monty.json import MSONable
 
-"""
-This module provides classes to define a phonon band structure.
-"""
-
 
 def get_reasonable_repetitions(natoms):
     """
@@ -239,6 +238,9 @@ def asr_breaking(self, tol_eigendisplacements=1e-5):
         return None
 
     def as_dict(self):
+        """
+        :return: MSONable dict
+        """
         d = {"@module": self.__class__.__module__,
              "@class": self.__class__.__name__,
              "lattice_rec": self.lattice_rec.as_dict(),
@@ -265,6 +267,10 @@ def as_dict(self):
 
     @classmethod
     def from_dict(cls, d):
+        """
+        :param d: Dict representation
+        :return: PhononBandStructure
+        """
         lattice_rec = Lattice(d['lattice_rec']['matrix'])
         eigendisplacements = np.array(d['eigendisplacements']['real']) + np.array(d['eigendisplacements']['imag']) * 1j
         nac_eigendisplacements = [(direction, np.array(e['real']) + np.array(e['imag']) * 1j)
@@ -276,7 +282,7 @@ def from_dict(cls, d):
 
 
 class PhononBandStructureSymmLine(PhononBandStructure):
-    """
+    r"""
     This object stores phonon band structures along selected (symmetry) lines in the
     Brillouin zone. We call the different symmetry lines (ex: \\Gamma to Z)
     "branches".
@@ -399,7 +405,7 @@ def get_equivalent_qpoints(self, index):
         return list_index_qpoints
 
     def get_branch(self, index):
-        """
+        r"""
         Returns in what branch(es) is the qpoint. There can be several
         branches.
 
@@ -429,7 +435,7 @@ def write_phononwebsite(self, filename):
         """
         import json
         with open(filename, 'w') as f:
-            phononwebsite_json = json.dump(self.as_phononwebsite(), f)
+            json.dump(self.as_phononwebsite(), f)
 
     def as_phononwebsite(self):
         """
@@ -541,6 +547,9 @@ def band_reorder(self):
             eig[:, nq] = eigq[order[nq]]
 
     def as_dict(self):
+        """
+        :return: MSONable dict
+        """
         d = super().as_dict()
         # remove nac_frequencies and nac_eigendisplacements as they are reconstructed
         # in the __init__ when the dict is deserialized
@@ -551,6 +560,10 @@ def as_dict(self):
 
     @classmethod
     def from_dict(cls, d):
+        """
+        :param d: Dict representation
+        :return: PhononBandStructureSummLine
+        """
         lattice_rec = Lattice(d['lattice_rec']['matrix'])
         eigendisplacements = np.array(d['eigendisplacements']['real']) + np.array(d['eigendisplacements']['imag']) * 1j
         structure = Structure.from_dict(d['structure']) if 'structure' in d else None