MERGE: upstream/black_pyproject_toml

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+max-line-length=120
+ignore: E302, W503, W504, E402, E731, F401, E203

.github/pull_request_template.md

@@ -0,0 +1,10 @@
+## Description
+
+_Describe what this PR is for_
+
+
+## PR Checklist
+
+- [] apply "black" to the whole codebase (`black .`) 
+- [] apply isort to the codebase (`isort .`)
+- [] fun `flake8` and try to resolve all the issues (work in progress!)

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

@@ -2,23 +2,30 @@
 Polymer simulations with ActiveBrownianIntegrator
 -------------------------------------------------
 
-This is a sample python script to run a polychrom simulation with the `ActiveBrownianIntegrator' custom integrator in polychrom.contrib.integrators. This integrator is used to simulate a polymer where each mononmer has a different effective temperature and thus a different diffusion coefficient :math:`D_i = k_B T_i / \xi`. Here, we consider an example where there are just two types of monomers, active (A) and inactive (B), where :math:`D_A > D_B` and the user chooses the ratio :math:`D_A / D_B`.
+This is a sample python script to run a polychrom simulation with the `ActiveBrownianIntegrator' custom integrator in
+polychrom.contrib.integrators. This integrator is used to simulate a polymer where each mononmer has a different
+effective temperature and thus a different diffusion coefficient :math:`D_i = k_B T_i / \xi`. Here, we consider an
+example where there are just two types of monomers, active (A) and inactive (B), where :math:`D_A > D_B` and the user
+chooses the ratio :math:`D_A / D_B`.
 
 Run this script using
 >>> python activeBD.py [gpuid] [activity_ratio]
 
 """
 
+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
@@ -27,9 +34,7 @@
 ids[int(N / 2) :] = 0
 
 
-def run_monomer_diffusion(
-    gpuid, N, ids, activity_ratio, timestep=170, nblocks=10, blocksize=100
-):
+def run_monomer_diffusion(gpuid, N, ids, activity_ratio, timestep=170, nblocks=10, blocksize=100):
     """Run a single simulation on a GPU of a hetero-polymer with A monomers and B monomers. A monomers
     have a larger diffusion coefficient than B monomers, with an activity ratio of D_A / D_B.
 
@@ -53,12 +58,8 @@ def run_monomer_diffusion(
 
     """
     if len(ids) != N:
-        raise ValueError(
-            "The array of monomer identities must have length equal to the total number of monomers."
-        )
-    D = np.ones(
-        (N, 3)
-    )  # Dx, Dy, Dz --> we assume the diffusion coefficient in each spatial dimension is the same
+        raise ValueError("The array of monomer identities must have length equal to the total number of monomers.")
+    D = np.ones((N, 3))  # Dx, Dy, Dz --> we assume the diffusion coefficient in each spatial dimension is the same
     # by default set the average diffusion coefficient to be 1 kT/friction
     # let D_A = 1 + Ddiff and D_B = 1 - Ddiff such that D_A / D_B is the given activity_ratio
     Ddiff = (activity_ratio - 1) / (activity_ratio + 1)
@@ -79,9 +80,7 @@ def run_monomer_diffusion(
     particleD = unit.Quantity(D, kT / friction)
     integrator = ActiveBrownianIntegrator(timestep, collision_rate, particleD)
     gpuid = f"{gpuid}"
-    reporter = HDF5Reporter(
-        folder="active_inactive", max_data_length=100, overwrite=True
-    )
+    reporter = HDF5Reporter(folder="active_inactive", max_data_length=100, overwrite=True)
     sim = simulation.Simulation(
         platform="CUDA",
         # for custom integrators, feed a tuple with the integrator class reference and a string specifying type,
@@ -99,9 +98,7 @@ def run_monomer_diffusion(
 
     polymer = starting_conformations.grow_cubic(N, int(np.ceil(r)))
     sim.set_data(polymer, center=True)  # loads a polymer, puts a center of mass at zero
-    sim.set_velocities(
-        v=np.zeros((N, 3))
-    )  # initializes velocities of all monomers to zero (no inertia)
+    sim.set_velocities(v=np.zeros((N, 3)))  # initializes velocities of all monomers to zero (no inertia)
     sim.add_force(forces.spherical_confinement(sim, density=density, k=5.0))
     sim.add_force(
         forcekits.polymer_chains(
@@ -117,7 +114,7 @@ def run_monomer_diffusion(
             nonbonded_force_func=forces.polynomial_repulsive,
             nonbonded_force_kwargs={
                 "trunc": 3.0,  # this will let chains cross sometimes
-                #'trunc':10.0, # this will resolve chain crossings and will not let chain cross anymore
+                # 'trunc':10.0, # this will resolve chain crossings and will not let chain cross anymore
             },
             except_bonds=True,
         )

examples/customIntegrators/corr_noise.py

@@ -2,26 +2,39 @@
 Polymer simulations with CorrelatedNoiseIntegrator
 --------------------------------------------------
 
-This is a sample python script to run a polychrom simulation with the `CorrelatedNoiseIntegrator' custom integrator in polychrom.contrib.integrators. This integrator is used to simulate a polymer where the Brownian forces acting on distinct monomers could be correlated in direction. In addition, as in `ActiveBrownianIntegrator`, each monomer can have a different diffusion coefficient :math:`D_i = k_B T_i / \xi`. 
-
-To define the correlations, we define a set of k attributes that specify the monomer's identity, such as charge, methylation status, etc. For each attribute, all monomers are assigned type 1, type -1, or type 0. The integrator defines a procedure by which type 1 monomers are correlated with one another with correlation coefficient :math:`\rho`, type -1 monomers are correlated with one another with coefficient :math:`\rho`, but type 1 and type -1 monomers are anticorrelated with coefficient :math:`-\rho`. Type 0 monomers do not experience correlated fluctuations.
-
-Here, we consider a simple example with just 1 feature (say, "charge"), and set all monomer diffusion coefficients to be the same. Thus, all same-charge monomers will be correlated with correlation coefficient 0.5 and opposing charge monomers are anticorrelated with coefficient -0.5. To visualize the Pearson correlation matrix of the N-dimensional Gaussian noise that drives the polymer, use the `compute_Pearson_correlation_matrix()` function.
+This is a sample python script to run a polychrom simulation with the `CorrelatedNoiseIntegrator' custom integrator
+in polychrom.contrib.integrators. This integrator is used to simulate a polymer where the Brownian forces acting on
+distinct monomers could be correlated in direction. In addition, as in `ActiveBrownianIntegrator`, each monomer can
+have a different diffusion coefficient :math:`D_i = k_B T_i / \xi`.
+
+To define the correlations, we define a set of k attributes that specify the monomer's identity, such as charge,
+methylation status, etc. For each attribute, all monomers are assigned type 1, type -1, or type 0. The integrator
+defines a procedure by which type 1 monomers are correlated with one another with correlation coefficient
+:math:`\rho`, type -1 monomers are correlated with one another with coefficient :math:`\rho`, but type 1 and type -1
+monomers are anticorrelated with coefficient :math:`-\rho`. Type 0 monomers do not experience correlated fluctuations.
+
+Here, we consider a simple example with just 1 feature (say, "charge"), and set all monomer diffusion coefficients to
+be the same. Thus, all same-charge monomers will be correlated with correlation coefficient 0.5 and opposing charge
+monomers are anticorrelated with coefficient -0.5. To visualize the Pearson correlation matrix of the N-dimensional
+Gaussian noise that drives the polymer, use the `compute_Pearson_correlation_matrix()` function.
 
 Run this script using
 >>> 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
 
@@ -88,16 +101,12 @@ def run_correlated_diffusion(gpuid, N, rhos, timestep=170, nblocks=10, blocksize
 
     """
     if rhos.shape[1] != N:
-        raise ValueError(
-            "The array of monomer identities must have length equal to the total number of monomers."
-        )
+        raise ValueError("The array of monomer identities must have length equal to the total number of monomers.")
     # monomer density in confinement in units of monomers/volume
     density = 0.224
     r = (3 * N / (4 * 3.141592 * density)) ** (1 / 3)
     print(f"Radius of confinement: {r}")
-    D = np.ones(
-        (N, 3)
-    )  # Diffusion coefficients of N monomers in x,y,z spatial dimensions
+    D = np.ones((N, 3))  # Diffusion coefficients of N monomers in x,y,z spatial dimensions
     timestep = timestep
     # the monomer diffusion coefficient should be in units of kT / friction, where friction = mass*collision_rate
     collision_rate = 2.0
@@ -143,7 +152,7 @@ def run_correlated_diffusion(gpuid, N, rhos, timestep=170, nblocks=10, blocksize
             nonbonded_force_func=forces.polynomial_repulsive,
             nonbonded_force_kwargs={
                 "trunc": 3.0,  # this will let chains cross sometimes
-                #'trunc':10.0, # this will resolve chain crossings and will not let chain cross anymore
+                # 'trunc':10.0, # this will resolve chain crossings and will not let chain cross anymore
             },
             except_bonds=True,
         )

examples/example/example.py

@@ -1,16 +1,18 @@
 """
-This is a sample simulation that does not represent any particular biological system. It is just a showcase 
-of how create a Simulation object, add forces, and initialize the reporter. 
+This is a sample simulation that does not represent any particular biological system. It is just a showcase
+of how create a Simulation object, add forces, and initialize the reporter.
 
-In this simulation, a simple polymer chain of 10,000 monomers is 
+In this simulation, a simple polymer chain of 10,000 monomers is simulated.
 """
 
 
-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
@@ -40,7 +42,7 @@
         chains=[(0, None, False)],
         # By default the library assumes you have one polymer chain
         # If you want to make it a ring, or more than one chain, use self.setChains
-        # self.setChains([(0,50,True),(50,None,False)]) will set a 50-monomer ring and a chain from monomer 50 to the end
+        # self.setChains([(0,50,True),(50,None,False)]) will set a 50-monomer ring and a chain from 50 to the end
         bond_force_func=forces.harmonic_bonds,
         bond_force_kwargs={
             "bondLength": 1.0,
@@ -55,7 +57,7 @@
         nonbonded_force_func=forces.polynomial_repulsive,
         nonbonded_force_kwargs={
             "trunc": 3.0,  # this will let chains cross sometimes
-            #'trunc':10.0, # this will resolve chain crossings and will not let chain cross anymore
+            # 'trunc':10.0, # this will resolve chain crossings and will not let chain cross anymore
         },
         except_bonds=True,
     )

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>":