isort

Author: Max Imakaev

docs/conf.py

@@ -6,10 +6,10 @@
 
 # -- Path setup --------------------------------------------------------------
 
-import sys
 import os
 import re
 import shlex
+import sys
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the

docs/olddocs/conf.py

@@ -11,8 +11,8 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys
 import os
+import sys
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the

examples/customIntegrators/activeBD.py

@@ -9,16 +9,19 @@
 
 """
 
+import os
+import sys
 import time
+from pathlib import Path
+
 import numpy as np
-import os, sys
+import openmm
+from simtk import unit
+
 import polychrom
-from polychrom import simulation, starting_conformations, forces, forcekits
+from polychrom import forcekits, forces, simulation, starting_conformations
 from polychrom.contrib.integrators import ActiveBrownianIntegrator
-import openmm
 from polychrom.hdf5_format import HDF5Reporter
-from simtk import unit
-from pathlib import Path
 
 N = 1000  # 1000 monomers
 ids = np.ones(N)  # aray of 1s and 0s assigning type A and type B comonomers

examples/customIntegrators/corr_noise.py

@@ -12,16 +12,19 @@
 >>> python corr_noise.py [gpuid]
 
 """
+import os
+import sys
 import time
+from pathlib import Path
+
 import numpy as np
-import os, sys
+import openmm
+from simtk import unit
+
 import polychrom
-from polychrom import simulation, starting_conformations, forces, forcekits
+from polychrom import forcekits, forces, simulation, starting_conformations
 from polychrom.contrib.integrators import CorrelatedNoiseIntegrator
-import openmm
 from polychrom.hdf5_format import HDF5Reporter
-from simtk import unit
-from pathlib import Path
 
 N = 100  # 100 monomers
 

examples/example/example.py

@@ -6,11 +6,13 @@
 """
 
 
-import os, sys
-import polychrom
-from polychrom import simulation, starting_conformations, forces, forcekits
-import openmm
 import os
+import sys
+
+import openmm
+
+import polychrom
+from polychrom import forcekits, forces, simulation, starting_conformations
 from polychrom.hdf5_format import HDF5Reporter
 
 N = 10000

examples/loopExtrusion/LEF_Dynamics.pyx

@@ -4,9 +4,12 @@
 #cython: initializedcheck=True
 
 import numpy as np
-cimport numpy as np 
+
+cimport numpy as np
+
 import cython
-cimport cython 
+
+cimport cython
 
 
 cdef extern from "<stdlib.h>":

examples/loopExtrusion/directionalModel/flagshipNormLifetime.py

@@ -3,26 +3,25 @@
 
 matplotlib.use("Agg")
 
+import ctypes
+import multiprocessing as mp
 import os
-import numpy as np
+
 import matplotlib.pyplot as plt
+import numpy as np
 import pandas as pd
-import ctypes
-from mirnylib.plotting import nicePlot
-import multiprocessing as mp
 import pyximport
-
+from mirnylib.plotting import nicePlot
 from openmmlib import polymerutils
-
 from openmmlib.polymerutils import scanBlocks
 
 pyximport.install()
+import sys
+from contextlib import closing
+
 from mirnylib.h5dict import h5dict
+from mirnylib.numutils import coarsegrain, completeIC, zoomArray
 from mirnylib.systemutils import fmap, setExceptionHook
-from mirnylib.numutils import coarsegrain, completeIC
-from mirnylib.numutils import zoomArray
-from contextlib import closing
-import sys
 from smcTranslocator import smcTranslocatorDirectional
 
 filename = "/net/levsha/share/nezar/ctcf_sites/GM12878.ctcf_narrowPeak.loj.encodeMotif.rad21.txt"
@@ -245,9 +244,10 @@ def calculateAverageLoop():
 
 
 def doPolymerSimulation(steps, dens, stiff, folder):
+    import time
+
     from openmmlib.openmmlib import Simulation
     from openmmlib.polymerutils import grow_rw
-    import time
 
     SMCTran = initModel()
 

examples/loopExtrusion/directionalModel/showContactmap.py

@@ -1,23 +1,21 @@
-import matplotlib
-
-# matplotlib.use("Agg")
-
-from mirnylib.plotting import nicePlot
 import os
 import pickle
-from openmmlib import contactmaps
-from mirnylib.numutils import zoomArray
-from openmmlib import polymerutils
 
+import matplotlib
 import matplotlib.pyplot as plt
 import numpy as np
-from mirnylib.h5dict import h5dict
+import pandas as pd
 from mirnylib.genome import Genome
-from mirnylib.numutils import completeIC, coarsegrain
+from mirnylib.h5dict import h5dict
+from mirnylib.numutils import coarsegrain, completeIC, zoomArray
+from mirnylib.plotting import nicePlot
 from mirnylib.systemutils import setExceptionHook
+from openmmlib import contactmaps, polymerutils
 from openmmlib.contactmapManager import averageContacts
-import pandas as pd
-from mirnylib.numutils import coarsegrain
+
+# matplotlib.use("Agg")
+
+
 
 setExceptionHook()
 
@@ -33,8 +31,8 @@ def __init__(self, i, forw, rev, blocks, steps):
         import pyximport
 
         pyximport.install()
-        from smcTranslocatorDirectional import smcTranslocator
         import numpy as np
+        from smcTranslocatorDirectional import smcTranslocator
 
         N = len(forw)
         birthArray = np.zeros(N, dtype=np.double) + 0.1

examples/loopExtrusion/newSimulatorCode.py

@@ -1,18 +1,16 @@
-import pickle
 import os
+import pickle
 import time
+
 import numpy as np
+import pyximport
 from openmmlib import polymerutils
-from openmmlib.polymerutils import scanBlocks
 from openmmlib.openmmlib import Simulation
-from openmmlib.polymerutils import grow_rw
-
-import pyximport
+from openmmlib.polymerutils import grow_rw, scanBlocks
 
 pyximport.install()
 from smcTranslocator import smcTranslocatorDirectional
 
-
 # -------defining parameters----------
 #  -- basic loop extrusion parameters
 SEPARATION = 200

polychrom/_polymer_math.pyx

@@ -1,9 +1,10 @@
 # distutils: language=c++ 
 
-cimport cython 
+cimport cython
 
 import numpy as np
 
+
 cdef extern from "__polymer_math.h":
     long int _getLinkingNumberCpp(int M, double *olddata, int N)
     void _mutualSimplifyCpp ( 

polychrom/cli/dif

@@ -23,12 +23,15 @@ you likely have mixed enough to reach some kind of equilibrium (and if you haven
 reached equilibrium). 
 """
 from __future__ import absolute_import, division, print_function
+
+import os
 import sys
-import numpy as np 
+
+import numpy as np
 import scipy.optimize
-from polychrom.polymerutils import load, fetch_block
+
 from polychrom.polymer_analyses import kabsch_msd
-import os 
+from polychrom.polymerutils import fetch_block, load
 
 filename = sys.argv[1]
 try:

polychrom/cli/show

@@ -1,9 +1,12 @@
 #!/usr/bin/env python
 from __future__ import absolute_import, division, print_function
-import os, tempfile, sys
-import numpy as np
-import joblib
 
+import os
+import sys
+import tempfile
+
+import joblib
+import numpy as np
 
 usage = """
 Usage: show filename [start end step]
@@ -132,8 +135,7 @@ def showData(data):
         )
 
 
-from polychrom.polymerutils import load, fetch_block
-
+from polychrom.polymerutils import fetch_block, load
 
 filename = sys.argv[1]
 

polychrom/cli/traj_convert.py

@@ -80,15 +80,17 @@
 
 """
 
+import glob
 import os
-import sys
-import shutil
-import click
 import pickle
-import glob
 import re
-import pandas as pd
+import shutil
+import sys
+
+import click
 import numpy as np
+import pandas as pd
+
 from polychrom.hdf5_format import HDF5Reporter, list_URIs, load_URI
 from polychrom.polymerutils import load
 

polychrom/cli/xyz

@@ -1,10 +1,14 @@
 #!/usr/bin/env python
 from __future__ import absolute_import, division, print_function
-import os, tempfile, sys
-import numpy as np
-import joblib
+
+import os
+import sys
+import tempfile
 import textwrap
 
+import joblib
+import numpy as np
+
 usage = """
 Usage: xyz filename [start end step]
 
@@ -126,8 +130,7 @@ def showData(data):
     exit()
 
 
-from polychrom.polymerutils import load, fetch_block
-
+from polychrom.polymerutils import fetch_block, load
 
 filename = sys.argv[1]
 

polychrom/contactmaps.py

@@ -48,14 +48,15 @@
 
 """
 
-import numpy as np
-import random
 import ctypes
 import multiprocessing as mp
-from contextlib import closing
-from . import polymerutils
+import random
 import warnings
-from . import polymer_analyses
+from contextlib import closing
+
+import numpy as np
+
+from . import polymer_analyses, polymerutils
 
 
 def indexing(smaller, larger, M):

polychrom/contrib/integrators.py

@@ -31,10 +31,10 @@
 
 """
 import numpy as np
-from simtk import unit
 import openmm as mm
 from openmmtools import utils
 from openmmtools.integrators import PrettyPrintableIntegrator
+from simtk import unit
 
 
 class ActiveBrownianIntegrator(utils.RestorableOpenMMObject, PrettyPrintableIntegrator, mm.CustomIntegrator):

polychrom/forcekits.py

@@ -18,6 +18,7 @@
 """
 
 import numpy as np
+
 from . import forces
 
 

polychrom/forces.py

@@ -54,9 +54,9 @@
 
 """
 
+import itertools
 import re
 import warnings
-import itertools
 from collections.abc import Iterable
 
 import numpy as np
@@ -65,6 +65,7 @@
     import openmm
 except Exception:
     import simtk.openmm as openmm
+
 import simtk.unit