black with 120 character limit; pyproject.toml

examples/customIntegrators/activeBD.py

@@ -27,9 +27,7 @@
 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 +51,8 @@ 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 +73,7 @@ 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 +91,7 @@ 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(

examples/customIntegrators/corr_noise.py

@@ -88,16 +88,12 @@ 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

examples/loopExtrusion/directionalModel/flagshipNormLifetime.py

@@ -70,9 +70,7 @@ def averageContacts(contactFunction, inValues, N, **kwargs):
 
     filenameChunks = [filenames[i::nproc] for i in range(nproc)]
 
-    with closing(
-        mp.Pool(processes=nproc, initializer=init, initargs=sharedARrays_)
-    ) as p:
+    with closing(mp.Pool(processes=nproc, initializer=init, initargs=sharedARrays_)) as p:
         p.map(worker, filenameChunks)
 
 
@@ -201,9 +199,7 @@ def doSim(i):
     hicdata = np.clip(hicdata, 0, np.percentile(hicdata, 99.99))
     hicdata /= np.mean(np.sum(hicdata, axis=1))
 
-    fmap(
-        doSim, range(30), n=20
-    )  # number of threads to use.  On a 20-core machine I use 20.
+    fmap(doSim, range(30), n=20)  # number of threads to use.  On a 20-core machine I use 20.
 
     arr = coarsegrain(arr, 20)
     arr = np.clip(arr, 0, np.percentile(arr, 99.9))
@@ -322,7 +318,5 @@ def doPolymerSimulation(steps, dens, stiff, folder):
     steps=5000,
     stiff=2,
     dens=0.2,
-    folder="flagshipLifetime{1}Mu{2}_try={0}".format(
-        sys.argv[1], sys.argv[2], sys.argv[3]
-    ),
+    folder="flagshipLifetime{1}Mu{2}_try={0}".format(sys.argv[1], sys.argv[2], sys.argv[3]),
 )

examples/loopExtrusion/directionalModel/showContactmap.py

@@ -365,16 +365,8 @@ def showCmapNew():
                 if end > 75000:
                     continue
                 plt.xlim([st, end])
-                plt.savefig(
-                    os.path.join(
-                        "heatmaps", "{0}_st={1}_end={2}_r=2.png".format(fname, st, end)
-                    )
-                )
-                plt.savefig(
-                    os.path.join(
-                        "heatmaps", "{0}_st={1}_end={2}_r=2.pdf".format(fname, st, end)
-                    )
-                )
+                plt.savefig(os.path.join("heatmaps", "{0}_st={1}_end={2}_r=2.png".format(fname, st, end)))
+                plt.savefig(os.path.join("heatmaps", "{0}_st={1}_end={2}_r=2.pdf".format(fname, st, end)))
         plt.clf()
 
     plt.show()

examples/loopExtrusion/newSimulatorCode.py

@@ -31,9 +31,7 @@
 
 # new parameters because some things changed
 saveEveryBlocks = 10  # save every 10 blocks (saving every block is now too much almost)
-skipSavedBlocksBeginning = (
-    20  # how many blocks (saved) to skip after you restart LEF positions
-)
+skipSavedBlocksBeginning = 20  # how many blocks (saved) to skip after you restart LEF positions
 totalSavedBlocks = 40  # how many blocks to save (number of blocks done is totalSavedBlocks * saveEveryBlocks)
 restartMilkerEveryBlocks = 100
 
@@ -49,16 +47,8 @@
 
 savesPerMilker = restartMilkerEveryBlocks // saveEveryBlocks
 milkerInitsSkip = saveEveryBlocks * skipSavedBlocksBeginning // restartMilkerEveryBlocks
-milkerInitsTotal = (
-    (totalSavedBlocks + skipSavedBlocksBeginning)
-    * saveEveryBlocks
-    // restartMilkerEveryBlocks
-)
-print(
-    "Milker will be initialized {0} times, first {1} will be skipped".format(
-        milkerInitsTotal, milkerInitsSkip
-    )
-)
+milkerInitsTotal = (totalSavedBlocks + skipSavedBlocksBeginning) * saveEveryBlocks // restartMilkerEveryBlocks
+print("Milker will be initialized {0} times, first {1} will be skipped".format(milkerInitsTotal, milkerInitsSkip))
 
 
 class smcTranslocatorMilker(object):
@@ -93,9 +83,7 @@ def setup(self, bondForce, blocks=100, smcStepsPerBlock=1):
         """
 
         if len(self.allBonds) != 0:
-            raise ValueError(
-                "Not all bonds were used; {0} sets left".format(len(self.allBonds))
-            )
+            raise ValueError("Not all bonds were used; {0} sets left".format(len(self.allBonds)))
 
         self.bondForce = bondForce
 
@@ -115,11 +103,7 @@ def setup(self, bondForce, blocks=100, smcStepsPerBlock=1):
         self.curBonds = allBonds.pop(0)
 
         for bond in self.uniqueBonds:
-            paramset = (
-                self.activeParamDict
-                if (bond in self.curBonds)
-                else self.inactiveParamDict
-            )
+            paramset = self.activeParamDict if (bond in self.curBonds) else self.inactiveParamDict
             ind = bondForce.addBond(bond[0], bond[1], **paramset)
             self.bondInds.append(ind)
         self.bondToInd = {i: j for i, j in zip(self.uniqueBonds, self.bondInds)}
@@ -133,9 +117,7 @@ def step(self, context, verbose=False):
         :return: (current bonds, previous step bonds); just for reference
         """
         if len(self.allBonds) == 0:
-            raise ValueError(
-                "No bonds left to run; you should restart simulation and run setup  again"
-            )
+            raise ValueError("No bonds left to run; you should restart simulation and run setup  again")
 
         pastBonds = self.curBonds
         self.curBonds = self.allBonds.pop(0)  # getting current bonds
@@ -153,12 +135,8 @@ def step(self, context, verbose=False):
         for bond, isAdd in zip(bondsToChange, bondsIsAdd):
             ind = self.bondToInd[bond]
             paramset = self.activeParamDict if isAdd else self.inactiveParamDict
-            self.bondForce.setBondParameters(
-                ind, bond[0], bond[1], **paramset
-            )  # actually updating bonds
-        self.bondForce.updateParametersInContext(
-            context
-        )  # now run this to update things in the context
+            self.bondForce.setBondParameters(ind, bond[0], bond[1], **paramset)  # actually updating bonds
+        self.bondForce.updateParametersInContext(context)  # now run this to update things in the context
         return self.curBonds, pastBonds
 
 
@@ -195,9 +173,7 @@ def initModel():
 # now polymer simulation code starts
 
 # ------------feed smcTran to the milker---
-SMCTran.steps(
-    1000000
-)  # first steps to "equilibrate" SMC dynamics. If desired of course.
+SMCTran.steps(1000000)  # first steps to "equilibrate" SMC dynamics. If desired of course.
 milker = smcTranslocatorMilker(SMCTran)  # now feed this thing to milker (do it once!)
 # --------- end new code ------------
 
@@ -206,9 +182,7 @@ def initModel():
 
     # simulation parameters are defined below
     a = Simulation(timestep=80, thermostat=0.01)
-    a.setup(
-        platform="CUDA", PBC=True, PBCbox=[box, box, box], GPU=0, precision="mixed"
-    )  # set up GPU here
+    a.setup(platform="CUDA", PBC=True, PBCbox=[box, box, box], GPU=0, precision="mixed")  # set up GPU here
     a.saveFolder(folder)
     a.load(data)
     a.addHarmonicPolymerBonds(wiggleDist=0.1)
@@ -234,13 +208,9 @@ def initModel():
     )  # now only one step of SMC per step
     print("Restarting milker")
 
-    a.doBlock(
-        steps=steps, increment=False
-    )  # do block for the first time with first set of bonds in
+    a.doBlock(steps=steps, increment=False)  # do block for the first time with first set of bonds in
     for i in range(restartMilkerEveryBlocks - 1):
-        curBonds, pastBonds = milker.step(
-            a.context
-        )  # this updates bonds. You can do something with bonds here
+        curBonds, pastBonds = milker.step(a.context)  # this updates bonds. You can do something with bonds here
         if i % saveEveryBlocks == (saveEveryBlocks - 2):
             a.doBlock(steps=steps, increment=doSave)
             if doSave:
@@ -250,9 +220,7 @@ def initModel():
                     open(os.path.join(a.folder, "SMC{0}.dat".format(a.step)), "wb"),
                 )
         else:
-            a.integrator.step(
-                steps
-            )  # do steps without getting the positions from the GPU (faster)
+            a.integrator.step(steps)  # do steps without getting the positions from the GPU (faster)
 
     data = a.getData()  # save data and step, and delete the simulation
     block = a.step

polychrom/cli/traj_convert.py

@@ -103,9 +103,7 @@ def _find_matches(pat, filenames):
         a = re.search(pat, filename)
         if a is not None:
             if len(a.groups()) != 1:
-                raise ValueError(
-                    "You should have one group in regex denoting the number of the file"
-                )
+                raise ValueError("You should have one group in regex denoting the number of the file")
             assert len(a.groups()) == 1
             gr = int(a.groups()[0])
             result[filename] = gr
@@ -176,12 +174,8 @@ def _find_matches(pat, filenames):
     help="allow blocks to be non-consecutive (1,2,3...)",
 )
 @click.option("--verbose", is_flag=True)
-@click.option(
-    "--round-to", default=2, show_default=True, help="round to this number of digits"
-)
-@click.option(
-    "--skip-files", default=1, show_default=True, help="save only every Nth file"
-)
+@click.option("--round-to", default=2, show_default=True, help="round to this number of digits")
+@click.option("--skip-files", default=1, show_default=True, help="save only every Nth file")
 @click.option(
     "--HDF5-blocks-per-file",
     default=100,
@@ -251,10 +245,7 @@ def trajcopy(
     if kwargs["input_style"] == "old":
         blocks = _find_matches(block_pattern, all_files)
     elif kwargs["input_style"] == "new":
-        blocks = {
-            i: j
-            for j, i in list_URIs(in_dir, empty_error=True, return_dict=True).items()
-        }
+        blocks = {i: j for j, i in list_URIs(in_dir, empty_error=True, return_dict=True).items()}
     else:
         raise ValueError("input-style should be 'old' or 'new'")
 
@@ -300,15 +291,11 @@ def trajcopy(
         assert len(extra_loader) == len(extra_require)
 
         # matching patterns for extra files, populating the dataframe
-        for val_pat, val_name, require in zip(
-            extra_pattern, extra_pattern_name, extra_require
-        ):
+        for val_pat, val_name, require in zip(extra_pattern, extra_pattern_name, extra_require):
             datas = _find_matches(val_pat, all_files)
             if require:
                 if len(datas) != len(blocks):
-                    raise ValueError(
-                        f"files missing for {val_name}: need {len(blocks)} found {len(datas)}"
-                    )
+                    raise ValueError(f"files missing for {val_name}: need {len(blocks)} found {len(datas)}")
             if len(datas) > 0:
                 datas = pd.Series(data=list(datas.keys()), index=list(datas.values()))
                 datas.name = val_name
@@ -327,9 +314,7 @@ def trajcopy(
         print(other[:: len(other) // 20 + 1])
         print("Verify that none of these should be converted using extra_pattern")
         print("If not, increase max_unmatched_files")
-        raise ValueError(
-            "Limit exceeded: {0} files did not match anything".format(len(other))
-        )
+        raise ValueError("Limit exceeded: {0} files did not match anything".format(len(other)))
 
     # creating the reporter
     if (len(blocks) > 0) and (not kwargs["dry_run"]):
@@ -361,9 +346,7 @@ def trajcopy(
                 cur["block"] = i
             elif kwargs["input_style"] == "new":
                 cur = load_URI(data)
-                cur["pos"] = np.round(
-                    np.asarray(cur["pos"], dtype=np.float32), kwargs["round_to"]
-                )
+                cur["pos"] = np.round(np.asarray(cur["pos"], dtype=np.float32), kwargs["round_to"])
 
             # adding "extra" data in the dict to save
             for name, ldr in zip(extra_pattern_name, extra_loader):