Sorted imports using isort.

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

src/fluctmatch/__init__.py

@@ -37,15 +37,17 @@
 
 import logging
 
-__version__: str = "3.4.1"
-
-_MODELS: dict = {}
-_DESCRIBE: dict = {}
+from .coordinates import COR
+from .intcor import IC
+from .libs.register import _DESCRIBE
+from .libs.register import _MODELS
+from .parameter import PRM
+from .topology import CORParser
+from .topology import PSFParser
+from .topology import RTF
+from .topology import STR
 
 logger: logging.Logger = logging.getLogger(__name__)
 logger.addHandler(logging.NullHandler())
 
-from .coordinates import COR
-from .intcor import IC
-from .parameter import PRM
-from .topology import CORParser, PSFParser, RTF, STR
+__version__: str = "3.4.1"

src/fluctmatch/__main__.py

@@ -24,13 +24,6 @@
 - https://docs.python.org/2/using/cmdline.html#cmdoption-m
 - https://docs.python.org/3/using/cmdline.html#cmdoption-m
 """
-from __future__ import (
-    absolute_import,
-    division,
-    print_function,
-    unicode_literals,
-)
-
 from fluctmatch.cli import main
 
 if __name__ == "__main__":

src/fluctmatch/analysis/entropy.py

@@ -14,12 +14,10 @@
 # Simulation. Meth Enzymology. 578 (2016), 327-342,
 # doi:10.1016/bs.mie.2016.05.024.
 #
-from __future__ import (
-    absolute_import,
-    division,
-    print_function,
-    unicode_literals,
-)
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
 
 import numpy as np
 import pandas as pd

src/fluctmatch/analysis/paramstats.py

@@ -14,12 +14,10 @@
 # Simulation. Meth Enzymology. 578 (2016), 327-342,
 # doi:10.1016/bs.mie.2016.05.024.
 #
-from __future__ import (
-    absolute_import,
-    division,
-    print_function,
-    unicode_literals,
-)
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
 
 import numpy as np
 import pandas as pd

src/fluctmatch/analysis/paramtable.py

@@ -14,15 +14,10 @@
 # Simulation. Meth Enzymology. 578 (2016), 327-342,
 # doi:10.1016/bs.mie.2016.05.024.
 #
-from __future__ import (
-    absolute_import,
-    division,
-    print_function,
-    unicode_literals,
-)
-from future.builtins import (
-    dict, )
-from future.utils import native_str
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
 
 import functools
 import glob
@@ -31,6 +26,8 @@
 
 import numpy as np
 import pandas as pd
+from future.builtins import dict
+from future.utils import native_str
 from MDAnalysis.coordinates.core import reader
 from MDAnalysis.lib.util import openany
 

src/fluctmatch/analysis/thermodynamics.py

@@ -14,14 +14,10 @@
 # Simulation. Meth Enzymology. 578 (2016), 327-342,
 # doi:10.1016/bs.mie.2016.05.024.
 #
-from __future__ import (
-    absolute_import,
-    division,
-    print_function,
-    unicode_literals,
-)
-from future.builtins import open
-from future.utils import native_str
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
 
 import functools
 import glob
@@ -30,6 +26,9 @@
 
 import numpy as np
 import pandas as pd
+from future.builtins import open
+from future.utils import native_str
+
 from fluctmatch.fluctmatch import charmmfluctmatch
 
 

src/fluctmatch/commands/cmd_convert.py

@@ -19,9 +19,11 @@
 from os import path
 
 import click
-from fluctmatch import _DESCRIBE, _MODELS
-from fluctmatch.models.core import modeller
+
+from fluctmatch import _DESCRIBE
+from fluctmatch import _MODELS
 from fluctmatch.fluctmatch.utils import write_charmm_files
+from fluctmatch.models.core import modeller
 
 
 @click.command("convert",

src/fluctmatch/commands/cmd_diff.py

@@ -19,6 +19,7 @@
 from os import path
 
 import click
+
 from fluctmatch.analysis import paramtable
 
 

src/fluctmatch/commands/cmd_entropy.py

@@ -19,6 +19,7 @@
 from os import path
 
 import click
+
 from fluctmatch.analysis import entropy
 
 

src/fluctmatch/commands/cmd_framediff.py

@@ -19,6 +19,7 @@
 from os import path
 
 import click
+
 from fluctmatch.analysis import paramtable
 
 

src/fluctmatch/commands/cmd_normdiff.py

@@ -20,6 +20,7 @@
 
 import click
 import numpy as np
+
 from fluctmatch.analysis import paramtable
 
 logger = logging.getLogger(__name__)

src/fluctmatch/commands/cmd_run_fm.py

@@ -20,6 +20,7 @@
 
 import click
 from MDAnalysis.lib.util import which
+
 from fluctmatch.fluctmatch import charmmfluctmatch
 
 

src/fluctmatch/commands/cmd_sca.py

@@ -27,6 +27,7 @@
 from sklearn.decomposition import PCA
 
 from fluctmatch.decomposition import ica
+
 from ..analysis import fluctsca
 from ..analysis.paramtable import ParamTable
 

src/fluctmatch/commands/cmd_splittraj.py

@@ -23,6 +23,7 @@
 
 import click
 from MDAnalysis.lib import util as mdutil
+
 from fluctmatch.fluctmatch import utils
 
 _CONVERT = dict(GMX=utils.split_gmx, CHARMM=utils.split_charmm)

src/fluctmatch/commands/cmd_stats.py

@@ -19,6 +19,7 @@
 from os import path
 
 import click
+
 from fluctmatch.analysis.paramstats import ParamStats
 from fluctmatch.analysis.paramtable import ParamTable
 

src/fluctmatch/commands/cmd_table.py

@@ -20,6 +20,7 @@
 
 import click
 from MDAnalysis.lib.util import filename
+
 from fluctmatch.analysis import paramtable
 
 

src/fluctmatch/commands/cmd_table_convert.py

@@ -18,8 +18,8 @@
 import os
 from os import path
 
-import MDAnalysis as mda
 import click
+import MDAnalysis as mda
 import pandas as pd
 
 

src/fluctmatch/commands/cmd_thermo.py

@@ -20,6 +20,7 @@
 
 import click
 from MDAnalysis.lib.util import which
+
 from fluctmatch.analysis import thermodynamics
 
 

src/fluctmatch/commands/cmd_write_charmm.py

@@ -13,10 +13,10 @@
 # Simulation. Meth Enzymology. 578 (2016), 327-342,
 # doi:10.1016/bs.mie.2016.05.024.
 #
-from __future__ import (
-    absolute_import, division, print_function,
-    unicode_literals,
-)
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
 
 import logging
 import logging.config
@@ -25,6 +25,7 @@
 
 import click
 import MDAnalysis as mda
+
 from fluctmatch.fluctmatch import utils as fmutils
 
 

src/fluctmatch/commands/cmd_write_rtf.py

@@ -18,8 +18,8 @@
 import os
 from os import path
 
-import MDAnalysis as mda
 import click
+import MDAnalysis as mda
 
 
 @click.command("write_rtf",

src/fluctmatch/decomposition/ica.py

@@ -25,9 +25,9 @@
 
 import numpy as np
 from scipy import linalg
+from sklearn.base import BaseEstimator
+from sklearn.base import TransformerMixin
 from sklearn.decomposition import FastICA
-from sklearn.base import BaseEstimator, TransformerMixin
-
 from sklearn.utils.validation import FLOAT_DTYPES
 from sklearn.utils.validation import as_float_array
 from sklearn.utils.validation import check_array

src/fluctmatch/decomposition/svd.py

@@ -20,13 +20,15 @@
 import numpy as np
 from scipy import linalg
 from scipy.sparse import issparse
-
-from sklearn.base import BaseEstimator, TransformerMixin
+from sklearn.base import BaseEstimator
+from sklearn.base import TransformerMixin
 from sklearn.decomposition.pca import _infer_dimension_
 from sklearn.decomposition.truncated_svd import TruncatedSVD
-from sklearn.utils import check_random_state
 from sklearn.utils import check_array
-from sklearn.utils.extmath import randomized_svd, stable_cumsum, svd_flip
+from sklearn.utils import check_random_state
+from sklearn.utils.extmath import randomized_svd
+from sklearn.utils.extmath import stable_cumsum
+from sklearn.utils.extmath import svd_flip
 
 logger = logging.getLogger(__name__)
 

src/fluctmatch/fluctmatch/__init__.py

@@ -14,23 +14,19 @@
 # Simulation. Meth Enzymology. 578 (2016), 327-342,
 # doi:10.1016/bs.mie.2016.05.024.
 #
-from __future__ import (
-    absolute_import,
-    division,
-    print_function,
-    unicode_literals,
-)
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
 
 import logging
 
 from fluctmatch.coordinates import COR
 from fluctmatch.intcor import IC
 from fluctmatch.parameter import PRM
-from fluctmatch.topology import (
-    PSFParser,
-    RTF,
-    STR,
-)
+from fluctmatch.topology import RTF
+from fluctmatch.topology import STR
+from fluctmatch.topology import PSFParser
 
 logger = logging.getLogger(__name__)
 logger.addHandler(logging.NullHandler())

src/fluctmatch/fluctmatch/data/__init__.py

@@ -14,12 +14,10 @@
 # Simulation. Meth Enzymology. 578 (2016), 327-342,
 # doi:10.1016/bs.mie.2016.05.024.
 #
-from __future__ import (
-    absolute_import,
-    division,
-    print_function,
-    unicode_literals,
-)
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
 
 import logging
 

src/fluctmatch/fluctmatch/data/charmm_nma.py

@@ -14,12 +14,10 @@
 # Simulation. Meth Enzymology. 578 (2016), 327-342,
 # doi:10.1016/bs.mie.2016.05.024.
 #
-from __future__ import (
-    absolute_import,
-    division,
-    print_function,
-    unicode_literals,
-)
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
 
 nma = ("""
     * Normal mode analysis of structure for parameter fitting. The original CHARMM

src/fluctmatch/fluctmatch/data/charmm_split.py

@@ -14,12 +14,10 @@
 # Simulation. Meth Enzymology. 578 (2016), 327-342,
 # doi:10.1016/bs.mie.2016.05.024.
 #
-from __future__ import (
-    absolute_import,
-    division,
-    print_function,
-    unicode_literals,
-)
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
 
 split_inp = ("""
     * Create a subtrajectory from a larger CHARMM trajectory.

src/fluctmatch/fluctmatch/data/charmm_thermo.py

@@ -14,12 +14,10 @@
 # Simulation. Meth Enzymology. 578 (2016), 327-342,
 # doi:10.1016/bs.mie.2016.05.024.
 #
-from __future__ import (
-    absolute_import,
-    division,
-    print_function,
-    unicode_literals,
-)
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
 
 thermodynamics = ("""
     * Calculate thermodynamic qunatities for an ENM structure.