apply 'black' coding style (stricter subset of PEP8)

- supply consistent flake8 settings in setup.cfg

examples/MCMC_examples/fully_coherent_search_using_MCMC.py

@@ -4,7 +4,7 @@ import numpy as np
 # Properties of the GW data
 sqrtSX = 1e-23
 tstart = 1000000000
-duration = 100*86400
+duration = 100 * 86400
 tend = tstart + duration
 
 # Properties of the signal
@@ -13,39 +13,46 @@ F1 = -1e-10
 F2 = 0
 Alpha = np.radians(83.6292)
 Delta = np.radians(22.0144)
-tref = .5*(tstart+tend)
+tref = 0.5 * (tstart + tend)
 
 depth = 10
 h0 = sqrtSX / depth
-label = 'fully_coherent_search_using_MCMC'
-outdir = 'data'
+label = "fully_coherent_search_using_MCMC"
+outdir = "data"
 
 data = pyfstat.Writer(
-    label=label, outdir=outdir, tref=tref,
-    tstart=tstart, F0=F0, F1=F1, F2=F2, duration=duration, Alpha=Alpha,
-    Delta=Delta, h0=h0, sqrtSX=sqrtSX)
+    label=label,
+    outdir=outdir,
+    tref=tref,
+    tstart=tstart,
+    F0=F0,
+    F1=F1,
+    F2=F2,
+    duration=duration,
+    Alpha=Alpha,
+    Delta=Delta,
+    h0=h0,
+    sqrtSX=sqrtSX,
+)
 data.make_data()
 
 # The predicted twoF, given by lalapps_predictFstat can be accessed by
 twoF = data.predict_fstat()
-print('Predicted twoF value: {}\n'.format(twoF))
+print("Predicted twoF value: {}\n".format(twoF))
 
 DeltaF0 = 1e-7
 DeltaF1 = 1e-13
-VF0 = (np.pi * duration * DeltaF0)**2 / 3.0
-VF1 = (np.pi * duration**2 * DeltaF1)**2 * 4/45.
-print('\nV={:1.2e}, VF0={:1.2e}, VF1={:1.2e}\n'.format(VF0*VF1, VF0, VF1))
+VF0 = (np.pi * duration * DeltaF0) ** 2 / 3.0
+VF1 = (np.pi * duration ** 2 * DeltaF1) ** 2 * 4 / 45.0
+print("\nV={:1.2e}, VF0={:1.2e}, VF1={:1.2e}\n".format(VF0 * VF1, VF0, VF1))
 
-theta_prior = {'F0': {'type': 'unif',
-                      'lower': F0-DeltaF0/2.,
-                      'upper': F0+DeltaF0/2.},
-               'F1': {'type': 'unif',
-                      'lower': F1-DeltaF1/2.,
-                      'upper': F1+DeltaF1/2.},
-               'F2': F2,
-               'Alpha': Alpha,
-               'Delta': Delta
-               }
+theta_prior = {
+    "F0": {"type": "unif", "lower": F0 - DeltaF0 / 2.0, "upper": F0 + DeltaF0 / 2.0},
+    "F1": {"type": "unif", "lower": F1 - DeltaF1 / 2.0, "upper": F1 + DeltaF1 / 2.0},
+    "F2": F2,
+    "Alpha": Alpha,
+    "Delta": Delta,
+}
 
 ntemps = 2
 log10beta_min = -0.5
@@ -53,13 +60,22 @@ nwalkers = 100
 nsteps = [300, 300]
 
 mcmc = pyfstat.MCMCSearch(
-    label=label, outdir=outdir,
-    sftfilepattern='{}/*{}*sft'.format(outdir, label), theta_prior=theta_prior,
-    tref=tref, minStartTime=tstart, maxStartTime=tend, nsteps=nsteps,
-    nwalkers=nwalkers, ntemps=ntemps, log10beta_min=log10beta_min)
+    label=label,
+    outdir=outdir,
+    sftfilepattern="{}/*{}*sft".format(outdir, label),
+    theta_prior=theta_prior,
+    tref=tref,
+    minStartTime=tstart,
+    maxStartTime=tend,
+    nsteps=nsteps,
+    nwalkers=nwalkers,
+    ntemps=ntemps,
+    log10beta_min=log10beta_min,
+)
 mcmc.transform_dictionary = dict(
-    F0=dict(subtractor=F0, symbol='$f-f^\mathrm{s}$'),
-    F1=dict(subtractor=F1, symbol='$\dot{f}-\dot{f}^\mathrm{s}$'))
+    F0=dict(subtractor=F0, symbol="$f-f^\mathrm{s}$"),
+    F1=dict(subtractor=F1, symbol="$\dot{f}-\dot{f}^\mathrm{s}$"),
+)
 mcmc.run()
 mcmc.plot_corner(add_prior=True)
 mcmc.print_summary()

examples/MCMC_examples/semi_coherent_search_using_MCMC.py

@@ -4,7 +4,7 @@ import numpy as np
 # Properties of the GW data
 sqrtSX = 1e-23
 tstart = 1000000000
-duration = 100*86400
+duration = 100 * 86400
 tend = tstart + duration
 
 # Properties of the signal
@@ -13,39 +13,46 @@ F1 = -1e-10
 F2 = 0
 Alpha = np.radians(83.6292)
 Delta = np.radians(22.0144)
-tref = .5*(tstart+tend)
+tref = 0.5 * (tstart + tend)
 
 depth = 10
 h0 = sqrtSX / depth
-label = 'semicoherent_search_using_MCMC'
-outdir = 'data'
+label = "semicoherent_search_using_MCMC"
+outdir = "data"
 
 data = pyfstat.Writer(
-    label=label, outdir=outdir, tref=tref,
-    tstart=tstart, F0=F0, F1=F1, F2=F2, duration=duration, Alpha=Alpha,
-    Delta=Delta, h0=h0, sqrtSX=sqrtSX)
+    label=label,
+    outdir=outdir,
+    tref=tref,
+    tstart=tstart,
+    F0=F0,
+    F1=F1,
+    F2=F2,
+    duration=duration,
+    Alpha=Alpha,
+    Delta=Delta,
+    h0=h0,
+    sqrtSX=sqrtSX,
+)
 data.make_data()
 
 # The predicted twoF, given by lalapps_predictFstat can be accessed by
 twoF = data.predict_fstat()
-print('Predicted twoF value: {}\n'.format(twoF))
+print("Predicted twoF value: {}\n".format(twoF))
 
 DeltaF0 = 1e-7
 DeltaF1 = 1e-13
-VF0 = (np.pi * duration * DeltaF0)**2 / 3.0
-VF1 = (np.pi * duration**2 * DeltaF1)**2 * 4/45.
-print('\nV={:1.2e}, VF0={:1.2e}, VF1={:1.2e}\n'.format(VF0*VF1, VF0, VF1))
+VF0 = (np.pi * duration * DeltaF0) ** 2 / 3.0
+VF1 = (np.pi * duration ** 2 * DeltaF1) ** 2 * 4 / 45.0
+print("\nV={:1.2e}, VF0={:1.2e}, VF1={:1.2e}\n".format(VF0 * VF1, VF0, VF1))
 
-theta_prior = {'F0': {'type': 'unif',
-                      'lower': F0-DeltaF0/2.,
-                      'upper': F0+DeltaF0/2.},
-               'F1': {'type': 'unif',
-                      'lower': F1-DeltaF1/2.,
-                      'upper': F1+DeltaF1/2.},
-               'F2': F2,
-               'Alpha': Alpha,
-               'Delta': Delta
-               }
+theta_prior = {
+    "F0": {"type": "unif", "lower": F0 - DeltaF0 / 2.0, "upper": F0 + DeltaF0 / 2.0},
+    "F1": {"type": "unif", "lower": F1 - DeltaF1 / 2.0, "upper": F1 + DeltaF1 / 2.0},
+    "F2": F2,
+    "Alpha": Alpha,
+    "Delta": Delta,
+}
 
 ntemps = 1
 log10beta_min = -1
@@ -53,14 +60,23 @@ nwalkers = 100
 nsteps = [300, 300]
 
 mcmc = pyfstat.MCMCSemiCoherentSearch(
-    label=label, outdir=outdir, nsegs=10,
-    sftfilepattern='{}/*{}*sft'.format(outdir, label),
-    theta_prior=theta_prior, tref=tref, minStartTime=tstart, maxStartTime=tend,
-    nsteps=nsteps, nwalkers=nwalkers, ntemps=ntemps,
-    log10beta_min=log10beta_min)
+    label=label,
+    outdir=outdir,
+    nsegs=10,
+    sftfilepattern="{}/*{}*sft".format(outdir, label),
+    theta_prior=theta_prior,
+    tref=tref,
+    minStartTime=tstart,
+    maxStartTime=tend,
+    nsteps=nsteps,
+    nwalkers=nwalkers,
+    ntemps=ntemps,
+    log10beta_min=log10beta_min,
+)
 mcmc.transform_dictionary = dict(
-    F0=dict(subtractor=F0, symbol='$f-f^\mathrm{s}$'),
-    F1=dict(subtractor=F1, symbol='$\dot{f}-\dot{f}^\mathrm{s}$'))
+    F0=dict(subtractor=F0, symbol="$f-f^\mathrm{s}$"),
+    F1=dict(subtractor=F1, symbol="$\dot{f}-\dot{f}^\mathrm{s}$"),
+)
 mcmc.run()
 mcmc.plot_corner(add_prior=True)
 mcmc.print_summary()

examples/followup_examples/semi_coherent_directed_follow_up.py

@@ -11,39 +11,47 @@ Delta = np.radians(22.0144)
 # Properties of the GW data
 sqrtSX = 1e-23
 tstart = 1000000000
-duration = 100*86400
-tend = tstart+duration
-tref = .5*(tstart+tend)
+duration = 100 * 86400
+tend = tstart + duration
+tref = 0.5 * (tstart + tend)
 
 depth = 40
-label = 'semicoherent_directed_follow_up'
-outdir = 'data'
+label = "semicoherent_directed_follow_up"
+outdir = "data"
 
 h0 = sqrtSX / depth
 
 data = pyfstat.Writer(
-    label=label, outdir=outdir, tref=tref, tstart=tstart, F0=F0, F1=F1,
-    F2=F2, duration=duration, Alpha=Alpha, Delta=Delta, h0=h0, sqrtSX=sqrtSX)
+    label=label,
+    outdir=outdir,
+    tref=tref,
+    tstart=tstart,
+    F0=F0,
+    F1=F1,
+    F2=F2,
+    duration=duration,
+    Alpha=Alpha,
+    Delta=Delta,
+    h0=h0,
+    sqrtSX=sqrtSX,
+)
 data.make_data()
 
 # The predicted twoF, given by lalapps_predictFstat can be accessed by
 twoF = data.predict_fstat()
-print('Predicted twoF value: {}\n'.format(twoF))
+print("Predicted twoF value: {}\n".format(twoF))
 
 # Search
 VF0 = VF1 = 1e5
-DeltaF0 = np.sqrt(VF0) * np.sqrt(3)/(np.pi*duration)
-DeltaF1 = np.sqrt(VF1) * np.sqrt(180)/(np.pi*duration**2)
-theta_prior = {'F0': {'type': 'unif',
-                      'lower': F0-DeltaF0/2.,
-                      'upper': F0+DeltaF0/2},
-               'F1': {'type': 'unif',
-                      'lower': F1-DeltaF1/2.,
-                      'upper': F1+DeltaF1/2},
-               'F2': F2,
-               'Alpha': Alpha,
-               'Delta': Delta
-               }
+DeltaF0 = np.sqrt(VF0) * np.sqrt(3) / (np.pi * duration)
+DeltaF1 = np.sqrt(VF1) * np.sqrt(180) / (np.pi * duration ** 2)
+theta_prior = {
+    "F0": {"type": "unif", "lower": F0 - DeltaF0 / 2.0, "upper": F0 + DeltaF0 / 2},
+    "F1": {"type": "unif", "lower": F1 - DeltaF1 / 2.0, "upper": F1 + DeltaF1 / 2},
+    "F2": F2,
+    "Alpha": Alpha,
+    "Delta": Delta,
+}
 
 ntemps = 3
 log10beta_min = -0.5
@@ -51,23 +59,35 @@ nwalkers = 100
 nsteps = [100, 100]
 
 mcmc = pyfstat.MCMCFollowUpSearch(
-    label=label, outdir=outdir,
-    sftfilepattern='{}/*{}*sft'.format(outdir, label),
-    theta_prior=theta_prior, tref=tref, minStartTime=tstart, maxStartTime=tend,
-    nwalkers=nwalkers, nsteps=nsteps, ntemps=ntemps,
-    log10beta_min=log10beta_min)
+    label=label,
+    outdir=outdir,
+    sftfilepattern="{}/*{}*sft".format(outdir, label),
+    theta_prior=theta_prior,
+    tref=tref,
+    minStartTime=tstart,
+    maxStartTime=tend,
+    nwalkers=nwalkers,
+    nsteps=nsteps,
+    ntemps=ntemps,
+    log10beta_min=log10beta_min,
+)
 
 NstarMax = 1000
 Nsegs0 = 100
 fig, axes = plt.subplots(nrows=2, figsize=(3.4, 3.5))
 fig, axes = mcmc.run(
-    NstarMax=NstarMax, Nsegs0=Nsegs0, labelpad=0.01,
-    plot_det_stat=False, return_fig=True, fig=fig,
-    axes=axes)
+    NstarMax=NstarMax,
+    Nsegs0=Nsegs0,
+    labelpad=0.01,
+    plot_det_stat=False,
+    return_fig=True,
+    fig=fig,
+    axes=axes,
+)
 for ax in axes:
     ax.grid()
     ax.set_xticks(np.arange(0, 600, 100))
     ax.set_xticklabels([str(s) for s in np.arange(0, 700, 100)])
-axes[-1].set_xlabel(r'$\textrm{Number of steps}$', labelpad=0.1)
+axes[-1].set_xlabel(r"$\textrm{Number of steps}$", labelpad=0.1)
 fig.tight_layout()
-fig.savefig('{}/{}_walkers.png'.format(mcmc.outdir, mcmc.label), dpi=400)
+fig.savefig("{}/{}_walkers.png".format(mcmc.outdir, mcmc.label), dpi=400)

examples/glitch_examples/make_simulated_data.py

 from pyfstat import Writer, GlitchWriter
 import numpy as np
 
-outdir = 'data'
+outdir = "data"
 # First, we generate data with a reasonably strong smooth signal
 
 # Define parameters of the Crab pulsar as an example
@@ -17,37 +17,75 @@ h0 = 5e-24
 # Properties of the GW data
 sqrtSX = 1e-22
 tstart = 1000000000
-duration = 50*86400
-tend = tstart+duration
-tref = tstart + 0.5*duration
+duration = 50 * 86400
+tend = tstart + duration
+tref = tstart + 0.5 * duration
 
 data = Writer(
-    label='0_glitch', outdir=outdir, tref=tref, tstart=tstart, F0=F0, F1=F1,
-    F2=F2, duration=duration, Alpha=Alpha, Delta=Delta, h0=h0, sqrtSX=sqrtSX)
+    label="0_glitch",
+    outdir=outdir,
+    tref=tref,
+    tstart=tstart,
+    F0=F0,
+    F1=F1,
+    F2=F2,
+    duration=duration,
+    Alpha=Alpha,
+    Delta=Delta,
+    h0=h0,
+    sqrtSX=sqrtSX,
+)
 data.make_data()
 
 # Next, taking the same signal parameters, we include a glitch half way through
-dtglitch = duration/2.0
+dtglitch = duration / 2.0
 delta_F0 = 5e-6
 delta_F1 = 0
 
 glitch_data = GlitchWriter(
-    label='1_glitch', outdir=outdir, tref=tref, tstart=tstart, F0=F0, F1=F1,
-    F2=F2, duration=duration, Alpha=Alpha, Delta=Delta, h0=h0, sqrtSX=sqrtSX,
-    dtglitch=dtglitch, delta_F0=delta_F0, delta_F1=delta_F1)
+    label="1_glitch",
+    outdir=outdir,
+    tref=tref,
+    tstart=tstart,
+    F0=F0,
+    F1=F1,
+    F2=F2,
+    duration=duration,
+    Alpha=Alpha,
+    Delta=Delta,
+    h0=h0,
+    sqrtSX=sqrtSX,
+    dtglitch=dtglitch,
+    delta_F0=delta_F0,
+    delta_F1=delta_F1,
+)
 glitch_data.make_data()
 
 # Making data with two glitches
 
-dtglitch_2 = [duration/4.0, 4*duration/5.0]
+dtglitch_2 = [duration / 4.0, 4 * duration / 5.0]
 delta_phi_2 = [0, 0]
 delta_F0_2 = [4e-6, 3e-7]
 delta_F1_2 = [0, 0]
 delta_F2_2 = [0, 0]
 
 two_glitch_data = GlitchWriter(
-    label='2_glitch', outdir=outdir, tref=tref, tstart=tstart, F0=F0, F1=F1,
-    F2=F2, duration=duration, Alpha=Alpha, Delta=Delta, h0=h0, sqrtSX=sqrtSX,
-    dtglitch=dtglitch_2, delta_phi=delta_phi_2, delta_F0=delta_F0_2,
-    delta_F1=delta_F1_2, delta_F2=delta_F2_2)
+    label="2_glitch",
+    outdir=outdir,
+    tref=tref,
+    tstart=tstart,
+    F0=F0,
+    F1=F1,
+    F2=F2,
+    duration=duration,
+    Alpha=Alpha,
+    Delta=Delta,
+    h0=h0,
+    sqrtSX=sqrtSX,
+    dtglitch=dtglitch_2,
+    delta_phi=delta_phi_2,
+    delta_F0=delta_F0_2,
+    delta_F1=delta_F1_2,
+    delta_F2=delta_F2_2,
+)
 two_glitch_data.make_data()

examples/glitch_examples/semicoherent_glitch_robust_directed_MCMC_search_on_1_glitch.py

@@ -3,34 +3,42 @@ import matplotlib.pyplot as plt
 import pyfstat
 import gridcorner
 import time
-from make_simulated_data import tstart, duration, tref, F0, F1, F2, Alpha, Delta, delta_F0, dtglitch, outdir
+from make_simulated_data import (
+    tstart,
+    duration,
+    tref,
+    F0,
+    F1,
+    F2,
+    Alpha,
+    Delta,
+    delta_F0,
+    dtglitch,
+    outdir,
+)
 
-plt.style.use('./paper.mplstyle')
+plt.style.use("./paper.mplstyle")
 
-label = 'semicoherent_glitch_robust_directed_MCMC_search_on_1_glitch'
+label = "semicoherent_glitch_robust_directed_MCMC_search_on_1_glitch"
 
 Nstar = 1000
-F0_width = np.sqrt(Nstar)*np.sqrt(12)/(np.pi*duration)
-F1_width = np.sqrt(Nstar)*np.sqrt(180)/(np.pi*duration**2)
+F0_width = np.sqrt(Nstar) * np.sqrt(12) / (np.pi * duration)
+F1_width = np.sqrt(Nstar) * np.sqrt(180) / (np.pi * duration ** 2)
 
 theta_prior = {
-    'F0': {'type': 'unif',
-           'lower': F0-F0_width/2.,
-           'upper': F0+F0_width/2.},
-    'F1': {'type': 'unif',
-           'lower': F1-F1_width/2.,
-           'upper': F1+F1_width/2.},
-    'F2': F2,
-    'delta_F0': {'type': 'unif',
-                 'lower': 0,
-                 'upper': 1e-5},
-    'delta_F1': 0,
-    'tglitch': {'type': 'unif',
-                'lower': tstart+0.1*duration,
-                'upper': tstart+0.9*duration},
-    'Alpha': Alpha,
-    'Delta': Delta,
-    }
+    "F0": {"type": "unif", "lower": F0 - F0_width / 2.0, "upper": F0 + F0_width / 2.0},
+    "F1": {"type": "unif", "lower": F1 - F1_width / 2.0, "upper": F1 + F1_width / 2.0},
+    "F2": F2,
+    "delta_F0": {"type": "unif", "lower": 0, "upper": 1e-5},
+    "delta_F1": 0,
+    "tglitch": {
+        "type": "unif",
+        "lower": tstart + 0.1 * duration,
+        "upper": tstart + 0.9 * duration,
+    },
+    "Alpha": Alpha,
+    "Delta": Delta,
+}
 
 ntemps = 3
 log10beta_min = -0.5
@@ -38,33 +46,49 @@ nwalkers = 100
 nsteps = [250, 250]
 
 mcmc = pyfstat.MCMCGlitchSearch(
-    label=label, sftfilepattern='data/*1_glitch*sft', theta_prior=theta_prior,
-    tref=tref, minStartTime=tstart, maxStartTime=tstart+duration,
-    nsteps=nsteps, nwalkers=nwalkers, ntemps=ntemps,
-    log10beta_min=log10beta_min, nglitch=1)
-mcmc.transform_dictionary['F0'] = dict(
-    subtractor=F0, multiplier=1e6, symbol='$f-f_\mathrm{s}$')
-mcmc.unit_dictionary['F0'] = '$\mu$Hz'
-mcmc.transform_dictionary['F1'] = dict(
-    subtractor=F1, multiplier=1e12, symbol='$\dot{f}-\dot{f}_\mathrm{s}$')
-mcmc.unit_dictionary['F1'] = '$p$Hz/s'
-mcmc.transform_dictionary['delta_F0'] = dict(
-    multiplier=1e6, subtractor=delta_F0,
-    symbol='$\delta f-\delta f_\mathrm{s}$')
-mcmc.unit_dictionary['delta_F0'] = '$\mu$Hz/s'
-mcmc.transform_dictionary['tglitch']['subtractor'] = tstart + dtglitch
-mcmc.transform_dictionary['tglitch']['label'] ='$t^\mathrm{g}-t^\mathrm{g}_\mathrm{s}$\n[d]'
+    label=label,
+    sftfilepattern="data/*1_glitch*sft",
+    theta_prior=theta_prior,
+    tref=tref,
+    minStartTime=tstart,
+    maxStartTime=tstart + duration,
+    nsteps=nsteps,
+    nwalkers=nwalkers,
+    ntemps=ntemps,
+    log10beta_min=log10beta_min,
+    nglitch=1,
+)
+mcmc.transform_dictionary["F0"] = dict(
+    subtractor=F0, multiplier=1e6, symbol="$f-f_\mathrm{s}$"
+)
+mcmc.unit_dictionary["F0"] = "$\mu$Hz"
+mcmc.transform_dictionary["F1"] = dict(
+    subtractor=F1, multiplier=1e12, symbol="$\dot{f}-\dot{f}_\mathrm{s}$"
+)
+mcmc.unit_dictionary["F1"] = "$p$Hz/s"
+mcmc.transform_dictionary["delta_F0"] = dict(
+    multiplier=1e6, subtractor=delta_F0, symbol="$\delta f-\delta f_\mathrm{s}$"
+)
+mcmc.unit_dictionary["delta_F0"] = "$\mu$Hz/s"
+mcmc.transform_dictionary["tglitch"]["subtractor"] = tstart + dtglitch
+mcmc.transform_dictionary["tglitch"][
+    "label"
+] = "$t^\mathrm{g}-t^\mathrm{g}_\mathrm{s}$\n[d]"
 
 t1 = time.time()
 mcmc.run()
 dT = time.time() - t1
 fig_and_axes = gridcorner._get_fig_and_axes(4, 2, 0.05)
-mcmc.plot_corner(label_offset=0.25, truths=[0, 0, 0, 0],
-                 fig_and_axes=fig_and_axes, quantiles=(0.16, 0.84),
-                 hist_kwargs=dict(lw=1.5, zorder=-1),
-                 truth_color='C3')
+mcmc.plot_corner(
+    label_offset=0.25,
+    truths=[0, 0, 0, 0],
+    fig_and_axes=fig_and_axes,
+    quantiles=(0.16, 0.84),
+    hist_kwargs=dict(lw=1.5, zorder=-1),
+    truth_color="C3",
+)
 
 mcmc.print_summary()
 
-print(('Prior widths =', F0_width, F1_width))
+print(("Prior widths =", F0_width, F1_width))
 print(("Actual run time = {}".format(dT)))

examples/glitch_examples/semicoherent_glitch_robust_directed_grid_search_on_1_glitch.py

 import pyfstat
 import numpy as np
 import matplotlib.pyplot as plt
-from make_simulated_data import tstart, duration, tref, F0, F1, F2, Alpha, Delta, delta_F0, outdir, dtglitch
+from make_simulated_data import (
+    tstart,
+    duration,
+    tref,
+    F0,
+    F1,