Merge branch 'develop-GA' of gitlab.aei.uni-hannover.de:GregAshton/PyFstat into develop-GA

README.md

@@ -46,7 +46,7 @@ $ git clone https://gitlab.aei.uni-hannover.de/GregAshton/PyFstat.git
 * [numpy](http://www.numpy.org/)
 * [matplotlib](http://matplotlib.org/) >= 1.4
 * [scipy](https://www.scipy.org/)
-* [emcee](http://dan.iel.fm/emcee/current/)
+* [ptemcee](https://github.com/willvousden/ptemcee)
 * [corner](https://pypi.python.org/pypi/corner/)
 * [dill](https://pypi.python.org/pypi/dill)
 * [peakutils](https://pypi.python.org/pypi/PeakUtils)

examples/semi_coherent_directed_follow_up.py

@@ -2,6 +2,8 @@ import pyfstat
 import numpy as np
 import matplotlib.pyplot as plt
 
+plt.style.use('./paper-style.mplstyle')
+
 F0 = 30.0
 F1 = -1e-10
 F2 = 0

examples/semi_coherent_search_using_MCMC.py

@@ -17,7 +17,7 @@ tref = .5*(tstart+tend)
 
 depth = 10
 h0 = sqrtSX / depth
-label = 'semi_coherent_search_using_MCMC'
+label = 'semicoherent_search_using_MCMC'
 outdir = 'data'
 
 data = pyfstat.Writer(
@@ -53,7 +53,7 @@ nwalkers = 100
 nsteps = [300, 300]
 
 mcmc = pyfstat.MCMCSemiCoherentSearch(
-    label=label, outdir=outdir, nsegs=3,
+    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,

requirements.txt

 numpy
 matplotlib>=1.4
 scipy
-emcee
+ptemcee
 corner
 dill
 tqdm

tests.py

@@ -326,7 +326,6 @@ class TestMCMCSearch(Test):
             sftfilepattern='{}/*{}*sft'.format(Writer.outdir, Writer.label),
             minStartTime=minStartTime, maxStartTime=maxStartTime,
             nsteps=[100, 100], nwalkers=100, ntemps=2, log10beta_min=-1)
-        search.setup_burnin_convergence_testing()
         search.run(create_plots=False)
         _, FS = search.get_max_twoF()