pulling default into ares-dev branch (i.e., syncing up branches)

README

@@ -130,3 +130,4 @@ Additional contributions / corrections / suggestions from:
 - Keith Tauscher (CU-Boulder)
 - Saurabh Singh (RRI)
 
+

ares/analysis/ModelSet.py

@@ -2692,12 +2692,12 @@ def AssembleParametersList(self, N=None, loc=None, include_bkw=False):
                     kwargs[parameter] = self.chain[i,j]
 
             all_kwargs.append(kwargs.copy())
-            
+
         if loc is not None:
             return all_kwargs[0]
         else:
             return all_kwargs
-            
+
     def CorrelationMatrix(self, pars, ivar=None, fig=1, ax=None):
         """
         Plot correlation matrix.

ares/physics/Cosmology.py

@@ -16,13 +16,7 @@
 from .Constants import c, G, km_per_mpc, m_H, m_He, sigma_SB, g_per_msun
 
 class Cosmology(object):
-    def __init__(self, **kwargs):
-        """Initialize a Cosmology object.
-        
-        :param: omega_m_0: Pretty self-explanatory.
-        
-        """
-
+    def __init__(self, **kwargs):        
         self.pf = ParameterFile(**kwargs)
 
         self.omega_m_0 = self.pf['omega_m_0']
@@ -105,7 +99,7 @@ def LookbackTime(self, z_i, z_f):
         """
 
         return self.t_of_z(z_i) - self.t_of_z(z_f)
-        
+
     def TCMB(self, z):
         return self.cmb_temp_0 * (1. + z)
 

ares/util/PrintInfo.py

@@ -667,19 +667,16 @@ def print_fit(fitter):
         return
 
     warnings = []
-
+        
     is_cov = False
 
     header = 'Parameter Estimation'
     print "\n" + "#"*width
     print "%s %s %s" % (pre, header.center(twidth), post)
     print "#"*width
 
-    if is_cov:
-        cols = ['position', 'error (diagonal of cov)']
-    else:
-        cols = ['position', 'error']   
-
+    cols = ['position', 'error']   
+
     if fit_TP:
 
         print line('-'*twidth)       

ares/util/SetDefaultParameterValues.py

@@ -616,7 +616,6 @@ def ControlParameters():
     "solver_rtol": 1e-8,
     "solver_atol": 1e-8,
     "interp_method": 'cubic',
-
     "interp_cc": 'linear',
 
     # Initialization

doc/troubleshooting.rst

@@ -29,7 +29,6 @@ This is known to occur in ``ares.physics.Hydrogen`` when using ``scipy.interpola
 ---------------------------------
 If the derivative of the signal is noisy (due to numerical artifacts, for example) then the extrema-finding can fail. If you can visually see three extrema in the global 21-cm signal but they are either absent or crazy in ``ares.simulations.Global21cm.turning_points``, then this might be going on. Try setting the ``smooth_derivative`` parameter to a value of 0.1 or 0.2.  This parameter will smooth the derivative with a boxcar of width :math:`\Delta z=` ``smooth_derivative`` before performing the extrema finding. Let me know if this happens (and under what circumstances), as it would be better to eliminate numerical artifacts than to smooth them out after the fact.
 
-
 ``AttributeError: No attribute blobs.``
 ---------------------------------------
 This is a bit of a red herring. If you're running an MCMC fit and saving 2-D blobs, which always require you to pass the name of the function, this error occurs if you supply a function that does not exist. Check for typos and/or that the function exists where it should.

input/litdata/eldridge2009.py

@@ -45,7 +45,7 @@ def _kwargs_to_fn(**kwargs):
     """
     Determine filename of appropriate BPASS lookup table based on kwargs.
     """
-    
+
     # All files share this prefix
     fn = 'sed.bpass'  
 

remote.py

@@ -39,19 +39,39 @@
 
 os.chdir('input')
 
-if 'minimal' in options:
-    to_download = ['inits', 'secondary_electrons']
+files = []
+if len(options) > 0:
+    if 'minimal' in options:
+        to_download = ['inits', 'secondary_electrons']
+        files = [None, None]
+    else:
+        to_download = []
+        for key in options:
+            if re.search(':', key):
+                pre, post = key.split(':')
+                to_download.append(pre)
+                files.append(int(post))
+            else:
+                to_download.append(key)
+                files.append(None)
 else:
     to_download = aux_data.keys()
+    files = [None] * len(to_download)
 
-for direc in to_download:
+for i, direc in enumerate(to_download):
     if not os.path.exists(direc):
         os.mkdir(direc)
 
     os.chdir(direc)
 
     web = aux_data[direc][0]
-    for fn in aux_data[direc][1:-1]:
+
+    if files[i] is None:
+        fns = aux_data[direc][1:-1]
+    else:
+        fns = [aux_data[direc][1:-1][files[i]]]
+
+    for fn in fns:
 
         if os.path.exists(fn):
             if 'fresh' or 'clean' in options:
@@ -63,9 +83,11 @@
         print "Downloading %s/%s..." % (web, fn)
         urllib.urlretrieve('%s/%s' % (web, fn), fn)
 
+        # If it's not a tarball, move on
         if not re.search('tar', fn):
             continue
 
+        # Otherwise, unpack it
         tar = tarfile.open(fn)
         tar.extractall()
         tar.close()

tests/test_physics_HI_cc.py

@@ -75,4 +75,4 @@ def test():
 if __name__ == '__main__':
     test()
 
-    
+