Fix error of linters (#38)

* Fix import orders

* Add pyling ignore list

* Update the rcfile for pylint in tox.ini

* Update the .gitignore

.gitignore

@@ -1,6 +1,163 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
 
-# Ignore (in-place) build results
-*.pyc
+# C extensions
+*.so
 
-# Ignore PyCharm
-.idea
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+doc/_build/
+doc/html/
+doc/latex/
+doc/man/
+doc/xml/
+doc/source
+doc/modules
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# Editor junk
+tags
+[._]*.s[a-v][a-z]
+[._]*.sw[a-p]
+[._]s[a-v][a-z]
+[._]sw[a-p]
+*~
+\#*\#
+.\#*
+.ropeproject
+.idea/
+.spyderproject
+.spyproject
+.vscode/
+# Mac .DS_Store
+.DS_Store
+
+# jupyter notebook checkpoints
+.ipynb_checkpoints
+
+# codecov files
+*.gcno
+*.gcda
+*.gcov
+
+*/*/_build
+*/_build

bfit/__init__.py

@@ -22,9 +22,9 @@
 # ---
 r"""Package for fitting densities to a linear combination of Gaussians."""
 
+from bfit.density import *
 from bfit.fit import *
+from bfit.greedy import *
 from bfit.grid import *
-from bfit.model import *
-from bfit.density import *
 from bfit.measure import *
-from bfit.greedy import *
+from bfit.model import *

bfit/_slater.py

@@ -26,7 +26,6 @@
 
 import numpy as np
 
-
 __all__ = ["load_slater_wfn"]
 
 
@@ -127,7 +126,7 @@ def _get_number_of_electrons_per_orbital(configuration):
         for x in orbitals:
             if x in electron_config_list:
                 index = electron_config_list.index(x)
-                orbital = (electron_config_list[index: index + 2])
+                orbital = electron_config_list[index : index + 2]
 
                 if orbital[1] == "D" or orbital[1] == "F":
                     num_electrons = re.search(orbital + r"\((.*?)\)", electron_config_list).group(1)

bfit/density.py

@@ -22,10 +22,10 @@
 # ---
 r"""Slater Atomic Density Module."""
 
-from bfit._slater import load_slater_wfn
 import numpy as np
 from scipy.special import factorial
 
+from bfit._slater import load_slater_wfn
 
 __all__ = ["SlaterAtoms"]
 

bfit/fit.py

@@ -22,13 +22,13 @@
 # ---
 r"""Fitting Algorithms."""
 
-from timeit import default_timer as timer
 import warnings
+from timeit import default_timer as timer
 
-from bfit.measure import KLDivergence, Measure, SquaredDifference
 import numpy as np
-from scipy.optimize import minimize, NonlinearConstraint
+from scipy.optimize import NonlinearConstraint, minimize
 
+from bfit.measure import KLDivergence, Measure, SquaredDifference
 
 __all__ = ["KLDivergenceFPI", "ScipyFit"]
 

bfit/greedy.py

@@ -24,12 +24,13 @@
 
 from abc import ABCMeta, abstractmethod
 
-from bfit.fit import _BaseFit, KLDivergenceFPI, ScipyFit
-from bfit.measure import SquaredDifference
-from bfit.model import AtomicGaussianDensity
 import numpy as np
 from scipy.optimize import nnls
 
+from bfit.fit import KLDivergenceFPI, ScipyFit, _BaseFit
+from bfit.measure import SquaredDifference
+from bfit.model import AtomicGaussianDensity
+
 __all__ = ["GreedyLeastSquares", "GreedyKLFPI"]
 
 
@@ -801,6 +802,7 @@ def optimize_using_nnls(true_dens, cofactor_matrix):
         row_nnls_coefficients = nnls(cofactor_matrix, b_vector)
         return row_nnls_coefficients[0]
 
+    # pylint: disable=arguments-differ
     def get_optimization_routine(self, params, local=False):
         r"""Optimize least-squares using nnls and scipy.optimize from ScipyFit."""
         # First solves the optimal coefficients (while exponents are fixed) using NNLS.
@@ -946,6 +948,7 @@ def get_best_one_function_solution(self):
         exps = 3. * self.integral_dens / (2. * 4. * np.pi * denom)
         return np.array([self.integral_dens, exps])
 
+    # pylint: disable=arguments-differ
     def get_optimization_routine(self, params, local=False):
         r"""Optimize KL using KL-FPI method."""
         coeffs, exps = params[:len(params)//2], params[len(params)//2:]

bfit/measure.py

@@ -26,7 +26,6 @@
 
 import numpy as np
 
-
 __all__ = ["SquaredDifference", "KLDivergence", "TsallisDivergence"]
 
 

bfit/test/test_density.py

@@ -22,11 +22,12 @@
 # ---
 r"""Test bfit.density module."""
 
-from bfit.density import SlaterAtoms
-from bfit.grid import ClenshawRadialGrid
 import numpy as np
-from numpy.testing import assert_almost_equal, assert_equal, assert_raises
 import scipy
+from numpy.testing import assert_almost_equal, assert_equal, assert_raises
+
+from bfit.density import SlaterAtoms
+from bfit.grid import ClenshawRadialGrid
 
 
 def slater(e, n, r, derivative=False):

bfit/test/test_fit.py

@@ -22,12 +22,13 @@
 # ---
 r"""Test bfit.fit module."""
 
+import numpy as np
+from numpy.testing import assert_almost_equal, assert_equal, assert_raises
+
 from bfit.fit import KLDivergenceFPI, ScipyFit
 from bfit.grid import CubicGrid, UniformRadialGrid
 from bfit.measure import KLDivergence, SquaredDifference
 from bfit.model import AtomicGaussianDensity, MolecularGaussianDensity
-import numpy as np
-from numpy.testing import assert_almost_equal, assert_equal, assert_raises
 
 
 def test_lagrange_multiplier():

bfit/test/test_greedy.py

@@ -22,13 +22,18 @@
 # ---
 r"""Test file for 'bfit.greedy'."""
 
+import numpy as np
+import numpy.testing as npt
+
 from bfit.greedy import (
-    get_next_choices, get_two_next_choices, GreedyKLFPI,
-    GreedyLeastSquares, pick_two_lose_one, remove_redundancies
+    GreedyKLFPI,
+    GreedyLeastSquares,
+    get_next_choices,
+    get_two_next_choices,
+    pick_two_lose_one,
+    remove_redundancies,
 )
 from bfit.grid import UniformRadialGrid
-import numpy as np
-import numpy.testing as npt
 
 
 def test_check_redundancies():

bfit/test/test_grid.py

@@ -22,10 +22,11 @@
 # ---
 r"""Test bfit.grid module."""
 
-from bfit.grid import _BaseRadialGrid, ClenshawRadialGrid, CubicGrid, UniformRadialGrid
 import numpy as np
 from numpy.testing import assert_almost_equal, assert_raises
 
+from bfit.grid import ClenshawRadialGrid, CubicGrid, UniformRadialGrid, _BaseRadialGrid
+
 
 def test_raises_base():
     r"""Test _BaseRadialGrid raises errors."""

bfit/test/test_measure.py

@@ -22,10 +22,11 @@
 # ---
 r"""Test bfit.measure module."""
 
-from bfit.measure import KLDivergence, SquaredDifference, TsallisDivergence
 import numpy as np
 from numpy.testing import assert_almost_equal, assert_raises
 
+from bfit.measure import KLDivergence, SquaredDifference, TsallisDivergence
+
 
 def test_raises_kl():
     r"""Test raise error when using Kullback-Leibler."""
@@ -193,8 +194,8 @@ def test_evaluating_tsallis_derivative_against_finite_difference():
     _, actual_deriv = measure.evaluate(dens, model, deriv=True)
     measure_pt_plus_1 = measure.evaluate(dens, model + eps, deriv=False)
     measure_pt_plus_2 = measure.evaluate(dens, model + 2.0 * eps, deriv=False)
-    desired = (measure_pt_minus_2 / 12.0 - (2.0 / 3.0) * measure_pt_minus_1)
-    desired += ((2.0 / 3.0) * measure_pt_plus_1 - measure_pt_plus_2 / 12.0)
+    desired = measure_pt_minus_2 / 12.0 - (2.0 / 3.0) * measure_pt_minus_1
+    desired += (2.0 / 3.0) * measure_pt_plus_1 - measure_pt_plus_2 / 12.0
     assert_almost_equal(actual_deriv, desired / eps, decimal=1)
 
 

bfit/test/test_model.py

@@ -22,11 +22,12 @@
 # ---
 r"""Test bfit.model module."""
 
-from bfit.grid import CubicGrid, UniformRadialGrid
-from bfit.model import AtomicGaussianDensity, MolecularGaussianDensity
 import numpy as np
 from numpy.testing import assert_almost_equal, assert_equal, assert_raises
 
+from bfit.grid import CubicGrid, UniformRadialGrid
+from bfit.model import AtomicGaussianDensity, MolecularGaussianDensity
+
 
 def test_raises_gaussian_model():
     r"""Test raises error of all Gaussian model classes."""

bfit/test/test_slater.py

@@ -22,9 +22,10 @@
 # ---
 r"""Test bfit._slater module."""
 
-from bfit._slater import load_slater_wfn
 import numpy as np
 
+from bfit._slater import load_slater_wfn
+
 
 def test_parsing_slater_density_be():
     r"""Test correct parsing of beryllium Slater file."""

docs/conf.py

@@ -12,6 +12,7 @@
 #
 import os
 import sys
+
 sys.path.insert(0, os.path.abspath('../'))