Made flake8 compliant

Signed-off-by: Timothy Click <tclick@alumni.ou.edu>

.flake8

@@ -1,5 +1,5 @@
 [flake8]
 ignore = E203, E266, E501, W503, F403, F401
-max-line-length = 88
+max-line-length = 82
 max-complexity = 18
 select = B,C,E,F,W,T4,B9

.travis.yml

@@ -3,6 +3,7 @@ language: python
 python:
     - "3.6"
     - "3.7"
+    - "3.8"
 sudo: false
 cache: pip
 env:
@@ -17,6 +18,7 @@ branches:
     only:
         - master
         - develop
+        - start_4.0.0
 before_install:
     - python --version
     - uname -a

setup.py

@@ -1,18 +1,42 @@
-#!/usr/bin/env python
+# ------------------------------------------------------------------------------
+#   python-fluctmatch
+#   Copyright (c) 2013-2020 Timothy H. Click, Ph.D.
 #
-# fluctmatch --- https://github.com/tclick/python-fluctmatch
-# Copyright (c) 2013-2017 The fluctmatch Development Team and contributors
-# (see the file AUTHORS for the full list of names)
+#   All rights reserved.
 #
-# Released under the New BSD license.
+#   Redistribution and use in source and binary forms, with or without
+#   modification, are permitted provided that the following conditions are met:
 #
-# Please cite your use of fluctmatch in published work:
+#   Redistributions of source code must retain the above copyright notice, this
+#   list of conditions and the following disclaimer.
 #
-# Timothy H. Click, Nixon Raj, and Jhih-Wei Chu.
-# Calculation of Enzyme Fluctuograms from All-Atom Molecular Dynamics
-# Simulation. Meth Enzymology. 578 (2016), 327-342,
-# doi:10.1016/bs.mie.2016.05.024.
+#   Redistributions in binary form must reproduce the above copyright notice,
+#   this list of conditions and the following disclaimer in the documentation
+#   and/or other materials provided with the distribution.
 #
+#   Neither the name of the author nor the names of its contributors may be used
+#   to endorse or promote products derived from this software without specific
+#   prior written permission.
+#
+#    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS”
+#    AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+#    IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+#    ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR
+#    ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+#    DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+#    SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+#    CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+#    LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+#    OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+#    DAMAGE.
+#
+#   Timothy H. Click, Nixon Raj, and Jhih-Wei Chu.
+#   Simulation. Meth Enzymology. 578 (2016), 327-342,
+#   Calculation of Enzyme Fluctuograms from All-Atom Molecular Dynamics
+#   doi:10.1016/bs.mie.2016.05.024.
+#
+# ------------------------------------------------------------------------------
+
 import re
 import sys
 from glob import glob
@@ -24,8 +48,8 @@
 from setuptools import setup
 
 # NOTE: keep in sync with DNApersist.__version__ in version.py
-RELEASE = "4.0.0-dev"
-is_release = "dev" not in RELEASE
+RELEASE: str = "4.0.0-dev"
+is_release: str = "dev" not in RELEASE
 
 # Make sure I have the right Python version.
 major, minor = sys.version_info[:2]
@@ -48,7 +72,7 @@ def read(*names, **kwargs):
 if __name__ == "__main__":
     setup(
         name="fluctmatch",
-        version="3.4.1",
+        version="4.0.0",
         license="BSD license",
         description="Elastic network model using fluctuation matching.",
         long_description="%s\n%s"
@@ -61,7 +85,7 @@ def read(*names, **kwargs):
                                     read("CHANGELOG.rst")),
                          ),
         author="Timothy Click",
-        author_email="tclick@nctu.edu.tw",
+        author_email="tclick@tabor.edu",
         url="https://www.github.com/tclick/python-fluctmatch",
         packages=find_packages("src"),
         package_dir={"": "src"},
@@ -85,6 +109,7 @@ def read(*names, **kwargs):
         install_requires=[
             "click",
             "MDAnalysis",
+            "matplotlib",
             "numpy",
             "pandas",
             "scipy",

src/fluctmatch/analysis/entropy.py

@@ -37,10 +37,11 @@
 #
 # ------------------------------------------------------------------------------
 
+from typing import List
+
 import numpy as np
 import pandas as pd
 from scipy import stats
-from typing import List
 
 from fluctmatch.analysis.paramtable import ParamTable
 
@@ -125,8 +126,8 @@ def windiff_entropy(self, bins: int = 100) -> pd.DataFrame:
         determined by the highest probability of nonzero force constants within
         the overall time series.
 
-        The required table must be a time series of an internal coordinates table
-        containing bond force constants.
+        The required table must be a time series of an internal coordinates
+        table containing bond force constants.
 
         Parameters
         ----------

src/fluctmatch/analysis/fluctsca.py

@@ -238,7 +238,7 @@ def figUnits(v1, v2, v3, units, filename, fig_path=Path.cwd(), marker='o',
        in the background.
 
     :Example:
-      >>> figUnits(v1, v2, units, marker='o', gradcol=0, dotsize=9, notinunits=1)
+     >>> figUnits(v1, v2, units, marker='o', gradcol=0, dotsize=9, notinunits=1)
 
      '''
     import colorsys

src/fluctmatch/analysis/thermodynamics.py

@@ -43,8 +43,8 @@
 import multiprocessing as mp
 from os import path
 from pathlib import Path
-from typing import Union
 from typing import Tuple
+from typing import Union
 
 import numpy as np
 import pandas as pd

src/fluctmatch/commands/cmd_convert.py

@@ -179,36 +179,36 @@ def cli(topology, trajectory, logfile, outdir, prefix, rmin, rmax, model,
         charmm_version, com, extended, resid, cmap, cheq, nonbonded, mass,
         write_traj, model_list):
     logging.config.dictConfig(
-        {
-            "version": 1,
-            "disable_existing_loggers": False,  # this fixes the problem
-            "formatters": {
-                "standard": {
-                    "class": "logging.Formatter",
-                    "format": "%(name)-12s %(levelname)-8s %(message)s",
-                },
-                "detailed": {
-                    "class": "logging.Formatter",
-                    "format": "%(asctime)s %(name)-15s %(levelname)-8s %(message)s",
-                    "datefmt": "%m-%d-%y %H:%M",
-                },
-            },
-            "handlers": {
-                "console": {
-                    "class": "logging.StreamHandler",
-                    "level": "INFO",
-                    "formatter": "standard",
-                },
-                "file": {
-                    "class": "logging.FileHandler",
-                    "filename": logfile,
-                    "level": "INFO",
-                    "mode": "w",
-                    "formatter": "detailed",
-                },
-            },
-            "root": {"level": "INFO", "handlers": ["console", "file"]},
-        }
+        dict(version=1,
+             disable_existing_loggers=False,  # this fixes the problem
+             formatters=dict(
+                 standard={
+                     "class": "logging.Formatter",
+                     "format": "%(name)-12s %(levelname)-8s %(message)s",
+                 },
+                 detailed={
+                     "class": "logging.Formatter",
+                     "format": ("%(asctime)s %(name)-15s %(levelname)-8s "
+                                "%(message)s"),
+                     "datefmt": "%m-%d-%y %H:%M",
+                 },
+             ),
+             handlers=dict(
+                 console={
+                     "class": "logging.StreamHandler",
+                     "level": "INFO",
+                     "formatter": "standard",
+                 },
+                 file={
+                     "class": "logging.FileHandler",
+                     "filename": logfile,
+                     "level": "INFO",
+                     "mode": "w",
+                     "formatter": "detailed",
+                 },
+             ),
+             root=dict(level="INFO", handlers=["console", "file"]),
+             )
     )
     logger: logging.Logger = logging.getLogger(__name__)
 

src/fluctmatch/commands/cmd_diff.py

@@ -82,36 +82,36 @@
 )
 def cli(logfile, outdir, ressep, table1, table2):
     logging.config.dictConfig(
-        {
-            "version": 1,
-            "disable_existing_loggers": False,  # this fixes the problem
-            "formatters": {
-                "standard": {
-                    "class": "logging.Formatter",
-                    "format": "%(name)-12s %(levelname)-8s %(message)s",
-                },
-                "detailed": {
-                    "class": "logging.Formatter",
-                    "format": "%(asctime)s %(name)-15s %(levelname)-8s %(message)s",
-                    "datefmt": "%m-%d-%y %H:%M",
-                },
-            },
-            "handlers": {
-                "console": {
-                    "class": "logging.StreamHandler",
-                    "level": "INFO",
-                    "formatter": "standard",
-                },
-                "file": {
-                    "class": "logging.FileHandler",
-                    "filename": logfile,
-                    "level": "INFO",
-                    "mode": "w",
-                    "formatter": "detailed",
-                },
-            },
-            "root": {"level": "INFO", "handlers": ["console", "file"]},
-        }
+        dict(version=1,
+             disable_existing_loggers=False,  # this fixes the problem
+             formatters=dict(
+                 standard={
+                     "class": "logging.Formatter",
+                     "format": "%(name)-12s %(levelname)-8s %(message)s",
+                 },
+                 detailed={
+                     "class": "logging.Formatter",
+                     "format": ("%(asctime)s %(name)-15s %(levelname)-8s "
+                                "%(message)s"),
+                     "datefmt": "%m-%d-%y %H:%M",
+                 },
+             ),
+             handlers=dict(
+                 console={
+                     "class": "logging.StreamHandler",
+                     "level": "INFO",
+                     "formatter": "standard",
+                 },
+                 file={
+                     "class": "logging.FileHandler",
+                     "filename": logfile,
+                     "level": "INFO",
+                     "mode": "w",
+                     "formatter": "detailed",
+                 },
+             ),
+             root=dict(level="INFO", handlers=["console", "file"]),
+             )
     )
     logger: logging.Logger = logging.getLogger(__name__)
 

src/fluctmatch/commands/cmd_entropy.py

@@ -83,36 +83,36 @@
 def cli(logfile, outdir, ressep, table):
     # Setup logger
     logging.config.dictConfig(
-        {
-            "version": 1,
-            "disable_existing_loggers": False,  # this fixes the problem
-            "formatters": {
-                "standard": {
-                    "class": "logging.Formatter",
-                    "format": "%(name)-12s %(levelname)-8s %(message)s",
-                },
-                "detailed": {
-                    "class": "logging.Formatter",
-                    "format": "%(asctime)s %(name)-15s %(levelname)-8s %(message)s",
-                    "datefmt": "%m-%d-%y %H:%M",
-                },
-            },
-            "handlers": {
-                "console": {
-                    "class": "logging.StreamHandler",
-                    "level": "INFO",
-                    "formatter": "standard",
-                },
-                "file": {
-                    "class": "logging.FileHandler",
-                    "filename": logfile,
-                    "level": "INFO",
-                    "mode": "w",
-                    "formatter": "detailed",
-                },
-            },
-            "root": {"level": "INFO", "handlers": ["console", "file"]},
-        }
+        dict(version=1,
+             disable_existing_loggers=False,  # this fixes the problem
+             formatters=dict(
+                 standard={
+                     "class": "logging.Formatter",
+                     "format": "%(name)-12s %(levelname)-8s %(message)s",
+                 },
+                 detailed={
+                     "class": "logging.Formatter",
+                     "format": ("%(asctime)s %(name)-15s %(levelname)-8s "
+                                "%(message)s"),
+                     "datefmt": "%m-%d-%y %H:%M",
+                 },
+             ),
+             handlers=dict(
+                 console={
+                     "class": "logging.StreamHandler",
+                     "level": "INFO",
+                     "formatter": "standard",
+                 },
+                 file={
+                     "class": "logging.FileHandler",
+                     "filename": logfile,
+                     "level": "INFO",
+                     "mode": "w",
+                     "formatter": "detailed",
+                 },
+             ),
+             root=dict(level="INFO", handlers=["console", "file"]),
+             )
     )
     logger: logging.Logger = logging.getLogger(__name__)