Some cleanup of entries package. Make pydocstyle the last thing to run.

If documentation is an issue for failure, pymatgen maintainers will make
a determination.

.circleci/config.yml

@@ -42,19 +42,19 @@ jobs:
             # Add executables and path.
             for EXEPATH in `pwd`/cmd_line/*/Linux_64bit; do export PATH=$PATH:$EXEPATH; done
             pip install --quiet -e .
-            echo "Checks will be performed in the order of pycodestyle -> pydocstyle -> mypy"
+            echo "Checks will be performed in the order of pycodestyle -> mypy -> pytest -> pydocstyle "
             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."
             echo "pycodestyle checks..."
             pycodestyle pymatgen
             echo "--- Done ---"
-            export MODIFIED_FILES=`git diff --diff-filter=d --name-only HEAD v2019.9.12 | grep -E '\.(py)' | tr '\n' ' '`
-            echo "pydocstyle checks for $MODIFIED_FILES..."
-            pydocstyle --count pymatgen/core $MODIFIED_FILES
-            echo "--- Done ---"
             echo "mypy checks..."
             mypy pymatgen
             echo "--- Done ---"
             pytest --ignore=pymatgen/analysis/tests/test_pourbaix_diagram.py --cov=pymatgen --cov-report html:coverage_reports pymatgen
+            export MODIFIED_FILES=`git diff --diff-filter=d --name-only HEAD v2019.9.12 | grep -E '\.(py)' | tr '\n' ' '`
+            echo "pydocstyle checks for $MODIFIED_FILES..."
+            pydocstyle --count pymatgen/core $MODIFIED_FILES
+            echo "--- Done ---"
             # Command line tests
             pmg structure --convert --filenames test_files/Li2O.cif POSCAR.pmg
             pmg structure --convert --filenames POSCAR.pmg pmg.cif

.travis.yml

@@ -34,10 +34,12 @@ before_script:
 script:
   - export PATH="$HOME/miniconda/bin:$PATH"
   - source activate test-environment
-  - export MODIFIED_FILES=`git diff --diff-filter=d --name-only HEAD v2019.9.12 | grep -E '\.(py)' | tr '\n' ' '`
-  - echo "pycodestyle->pydocstyle->mypy->pytest... Note that this fails on the first command with error."
+  - echo "pycodestyle->mypy->pytest->pydocstyle... Note that this fails on the first command with error."
   - 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 && pydocstyle --count pymatgen/core $MODIFIED_FILES && mypy pymatgen && pytest $EXCLUDE_TESTS pymatgen
+  - travis_wait 28800 pycodestyle pymatgen && mypy pymatgen && pytest $EXCLUDE_TESTS pymatgen
+  - export MODIFIED_FILES=`git diff --diff-filter=d --name-only HEAD v2019.9.12 | grep -E '\.(py)' | tr '\n' ' '`
+  - pydocstyle --count pymatgen/core $MODIFIED_FILES
+
 notifications:
   email:
     recipients:

pymatgen/entries/computed_entries.py

@@ -2,6 +2,13 @@
 # Copyright (c) Pymatgen Development Team.
 # Distributed under the terms of the MIT License.
 
+"""
+This module implements equivalents of the basic ComputedEntry objects, which
+is the basic entity that can be used to perform many analyses. ComputedEntries
+contain calculated information, typically from VASP or other electronic
+structure codes. For example, ComputedEntries can be used as inputs for phase
+diagram analysis.
+"""
 
 import json
 
@@ -11,13 +18,6 @@
 from pymatgen.core.structure import Structure
 from monty.json import MSONable
 
-"""
-This module implements equivalents of the basic ComputedEntry objects, which
-is the basic entity that can be used to perform many analyses. ComputedEntries
-contain calculated information, typically from VASP or other electronic
-structure codes. For example, ComputedEntries can be used as inputs for phase
-diagram analysis.
-"""
 
 __author__ = "Shyue Ping Ong, Anubhav Jain"
 __copyright__ = "Copyright 2011, The Materials Project"
@@ -93,17 +93,23 @@ def normalize(self, mode: str = "formula_unit") -> None:
 
     @property
     def is_element(self) -> bool:
+        """
+        :return: Whether composition of entry is an element.
+        """
         return self.composition.is_element
 
     @property
     def energy(self) -> float:
         """
-        Returns the *corrected* energy of the entry.
+        :return: the *corrected* energy of the entry.
         """
         return self.uncorrected_energy + self.correction
 
     @property
     def energy_per_atom(self) -> float:
+        """
+        :return: the *corrected* energy per atom of the entry.
+        """
         return self.energy / self.composition.num_atoms
 
     def __repr__(self):
@@ -123,7 +129,11 @@ def __str__(self):
         return self.__repr__()
 
     @classmethod
-    def from_dict(cls, d):
+    def from_dict(cls, d) -> 'ComputedEntry':
+        """
+        :param d: Dict representation.
+        :return: ComputedEntry
+        """
         dec = MontyDecoder()
         return cls(d["composition"], d["energy"], d["correction"],
                    parameters={k: dec.process_decoded(v)
@@ -133,6 +143,9 @@ def from_dict(cls, d):
                    entry_id=d.get("entry_id", None))
 
     def as_dict(self) -> dict:
+        """
+        :return: MSONable dict.
+        """
         return {"@module": self.__class__.__module__,
                 "@class": self.__class__.__name__,
                 "energy": self.uncorrected_energy,
@@ -194,14 +207,21 @@ def __str__(self):
         return self.__repr__()
 
     def as_dict(self) -> dict:
+        """
+        :return: MSONAble dict.
+        """
         d = super().as_dict()
         d["@module"] = self.__class__.__module__
         d["@class"] = self.__class__.__name__
         d["structure"] = self.structure.as_dict()
         return d
 
     @classmethod
-    def from_dict(cls, d):
+    def from_dict(cls, d) -> 'ComputedStructureEntry':
+        """
+        :param d: Dict representation.
+        :return: ComputedStructureEntry
+        """
         dec = MontyDecoder()
         return cls(dec.process_decoded(d["structure"]),
                    d["energy"], d["correction"],