From e6d6bc2b2e08744664d284849c5f971b24cd78fe Mon Sep 17 00:00:00 2001
From: Miguel Zumalacarregui <zumalacarregui@thphys.uni-heidelberg.de>
Date: Tue, 22 Mar 2016 13:31:30 -0700
Subject: [PATCH 01/35] fixed typo in analyze.py

---
 montepython/analyze.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/montepython/analyze.py b/montepython/analyze.py
index c302bbdc..abe5806c 100644
--- a/montepython/analyze.py
+++ b/montepython/analyze.py
@@ -683,7 +683,7 @@ def compute_posterior(information_instances):
                     # store the coordinates of the points for further
                     # plotting.
                     store_contour_coordinates(
-                        conf, standard_name, second_standard_name, cotours)
+                        conf, standard_name, second_standard_name, contours)
 
                     for info in information_instances:
                         if not info.ignore_param and info.has_second_param:

From 7d72cfc8ccb48436df8930883bf7681e9e1b75dd Mon Sep 17 00:00:00 2001
From: Miguel Zumalacarregui <miguelzuma@berkeley.edu>
Date: Wed, 12 Oct 2016 21:38:35 -0700
Subject: [PATCH 02/35] writes error_log for failed models

---
 montepython/data.py    |  5 +++++
 montepython/io_mp.py   | 40 ++++++++++++++++++++++++++++++++++++++++
 montepython/mcmc.py    |  2 +-
 montepython/sampler.py |  6 +++++-
 4 files changed, 51 insertions(+), 2 deletions(-)

diff --git a/montepython/data.py b/montepython/data.py
index 05382341..714e62c7 100644
--- a/montepython/data.py
+++ b/montepython/data.py
@@ -189,6 +189,11 @@ def __init__(self, command_line, path):
         self.out = None
         self.out_name = ''
 
+        # Create the variable err, and err_name to keep the errors
+        # will be initialised later by the :mod:`io_mp` module
+        self.err = None
+        self.err_name = ''
+
         # If the parameter file is not a log.param, the path will be read
         # before reading the parameter file.
         if self.param.find('log.param') == -1:
diff --git a/montepython/io_mp.py b/montepython/io_mp.py
index 7eecba6c..82bce9fa 100644
--- a/montepython/io_mp.py
+++ b/montepython/io_mp.py
@@ -211,6 +211,36 @@ def print_vector(out, N, loglkl, data):
         out[j].write('\n')
 
 
+def print_error(error_msg, data):
+    """
+    Register parameters leading to class_error to :code:`out`
+
+    Parameters
+    ----------
+    out : list
+        Array containing both standard output and the output file.
+
+        This way, if you run in interactive mode, you will be able to monitor
+        the progress of the chain.
+    error_msg : string
+        Error message: the idea is not to keep the whole error message, 
+        but to read part of it and asign it an error tag
+        0 => error not identified
+        n>0 => different error codes
+
+    .. note::
+
+        It is the `current` point that is printed, which produced the error
+        No derived parameters are written (maybe not produced)
+    """
+    out = data.err
+    for elem in data.get_mcmc_parameters(['varying']):
+      out.write('%.6e\t' %
+		data.mcmc_parameters[elem]['current'])
+    out.write(error_msg)
+    out.write('\n')
+        
+
 def refresh_file(data):
     """
     Closes and reopen the output file to write any buffered quantities
@@ -218,6 +248,9 @@ def refresh_file(data):
     """
     data.out.close()
     data.out = open(data.out_name, 'a')
+    
+    data.err.close()
+    data.err = open(data.err_name, 'a')
 
 
 def create_output_files(command_line, data):
@@ -273,6 +306,13 @@ def create_output_files(command_line, data):
     if command_line.restart is not None:
         for line in open(command_line.restart, 'r'):
             data.out.write(line)
+            
+    #open/create error file        
+    data.err_name = os.path.join(command_line.folder,"error_log.txt")
+    data.err = open(data.err_name,'a')
+    print 'Creating error file %s\n' % data.err_name
+            
+        
 
 
 def get_tex_name(name, number=1):
diff --git a/montepython/mcmc.py b/montepython/mcmc.py
index b1ef1af7..84227d72 100644
--- a/montepython/mcmc.py
+++ b/montepython/mcmc.py
@@ -452,7 +452,7 @@ def chain(cosmo, data, command_line):
             # just computed ('current' flag), but really the previous one.)
             # with its proper multiplicity (number of times the system stayed
             # there).
-            io_mp.print_vector(outputs, N, loglike, data)
+            io_mp.print_vector(outputs, N, loglike, data)                    
 
             # Report the 'current' point to the 'last_accepted'
             sampler.accept_step(data)
diff --git a/montepython/sampler.py b/montepython/sampler.py
index e29c8aba..9318c117 100644
--- a/montepython/sampler.py
+++ b/montepython/sampler.py
@@ -489,10 +489,14 @@ def compute_lkl(cosmo, data):
         # point, but with minimum likelihood, so will be rejected, resulting in
         # the choice of a new point.
         try:
-            cosmo.compute(["lensing"])
+            cosmo.compute(["lensing"])            
         except CosmoComputationError as failure_message:
             sys.stderr.write(str(failure_message)+'\n')
             sys.stderr.flush()
+            
+            #write the error file            
+            io_mp.print_error(str(failure_message), data)
+            
             return data.boundary_loglike
         except CosmoSevereError as critical_message:
             raise io_mp.CosmologicalModuleError(

From 7ed9391b5c2ca8908a38296ab45a0ff78964e6a4 Mon Sep 17 00:00:00 2001
From: Miguel Zumalacarregui <miguelzuma@berkeley.edu>
Date: Thu, 13 Oct 2016 18:13:52 -0700
Subject: [PATCH 03/35] added error codes to record error_log

---
 montepython/io_mp.py | 30 +++++++++++++++++++++++++++++-
 1 file changed, 29 insertions(+), 1 deletion(-)

diff --git a/montepython/io_mp.py b/montepython/io_mp.py
index 82bce9fa..65705b42 100644
--- a/montepython/io_mp.py
+++ b/montepython/io_mp.py
@@ -229,15 +229,43 @@ def print_error(error_msg, data):
         n>0 => different error codes
 
     .. note::
+    
+	We use error codes instead of recording the full error messages
+	unless the error is not identified
 
         It is the `current` point that is printed, which produced the error
         No derived parameters are written (maybe not produced)
+    
     """
+    
+    # -1 is for unmarked error
+    err_code = -1
+    # rewrite with different possibilities 
+    # errors in background are 1-10, perturbations 10-99...
+    if 'Shooting failed' in error_msg:
+      err_code = 0
+    if 'Gradient instability' and 'scalar' in error_msg:
+      err_code = 1
+    if 'Gradient instability' and 'tensor' in error_msg:
+      err_code = 2
+    if 'Ghost instability' and 'scalar' in error_msg:
+      err_code = 3
+    if 'Ghost instability' and 'tensor' in error_msg:
+      err_code = 4
+      
+    if "Isnan v_X" in error_msg:
+      err_code = 10
+    
+    
     out = data.err
     for elem in data.get_mcmc_parameters(['varying']):
       out.write('%.6e\t' %
 		data.mcmc_parameters[elem]['current'])
-    out.write(error_msg)
+    # if error unidentified write full message      
+    if err_code == -1:
+      out.write(str(err_code) + "\t" + error_msg)
+    else:
+      out.write(str(err_code))
     out.write('\n')
         
 

From 5c493d780a514530ae3dceee053905c98683e934 Mon Sep 17 00:00:00 2001
From: ardok-m <ardok@openmailbox.org>
Date: Tue, 6 Dec 2016 12:35:08 +0100
Subject: [PATCH 04/35] fixed conditionals for err_code selection

---
 montepython/io_mp.py | 38 +++++++++++++++++++-------------------
 1 file changed, 19 insertions(+), 19 deletions(-)

diff --git a/montepython/io_mp.py b/montepython/io_mp.py
index 65705b42..a2fd7692 100644
--- a/montepython/io_mp.py
+++ b/montepython/io_mp.py
@@ -223,51 +223,51 @@ def print_error(error_msg, data):
         This way, if you run in interactive mode, you will be able to monitor
         the progress of the chain.
     error_msg : string
-        Error message: the idea is not to keep the whole error message, 
+        Error message: the idea is not to keep the whole error message,
         but to read part of it and asign it an error tag
         0 => error not identified
         n>0 => different error codes
 
     .. note::
-    
+
 	We use error codes instead of recording the full error messages
 	unless the error is not identified
 
         It is the `current` point that is printed, which produced the error
         No derived parameters are written (maybe not produced)
-    
+
     """
-    
+
     # -1 is for unmarked error
     err_code = -1
-    # rewrite with different possibilities 
+    # rewrite with different possibilities
     # errors in background are 1-10, perturbations 10-99...
     if 'Shooting failed' in error_msg:
       err_code = 0
-    if 'Gradient instability' and 'scalar' in error_msg:
+    if all(x in error_msg for x in ['Gradient instability', 'scalar']):
       err_code = 1
-    if 'Gradient instability' and 'tensor' in error_msg:
+    if all(x in error_msg for x in ['Gradient instability', 'tensor']):
       err_code = 2
-    if 'Ghost instability' and 'scalar' in error_msg:
+    if all(x in error_msg for x in ['Ghost instability', 'scalar']):
       err_code = 3
-    if 'Ghost instability' and 'tensor' in error_msg:
+    if all(x in error_msg for x in ['Ghost instability', 'tensor']):
       err_code = 4
-      
+
     if "Isnan v_X" in error_msg:
       err_code = 10
-    
-    
+
+
     out = data.err
     for elem in data.get_mcmc_parameters(['varying']):
       out.write('%.6e\t' %
 		data.mcmc_parameters[elem]['current'])
-    # if error unidentified write full message      
+    # if error unidentified write full message
     if err_code == -1:
       out.write(str(err_code) + "\t" + error_msg)
     else:
       out.write(str(err_code))
     out.write('\n')
-        
+
 
 def refresh_file(data):
     """
@@ -276,7 +276,7 @@ def refresh_file(data):
     """
     data.out.close()
     data.out = open(data.out_name, 'a')
-    
+
     data.err.close()
     data.err = open(data.err_name, 'a')
 
@@ -334,13 +334,13 @@ def create_output_files(command_line, data):
     if command_line.restart is not None:
         for line in open(command_line.restart, 'r'):
             data.out.write(line)
-            
-    #open/create error file        
+
+    #open/create error file
     data.err_name = os.path.join(command_line.folder,"error_log.txt")
     data.err = open(data.err_name,'a')
     print 'Creating error file %s\n' % data.err_name
-            
-        
+
+
 
 
 def get_tex_name(name, number=1):

From 7211aa3ceab66871b550605e603d76e1bc1cfb96 Mon Sep 17 00:00:00 2001
From: ardok-m <ardok@openmailbox.org>
Date: Tue, 6 Dec 2016 12:35:36 +0100
Subject: [PATCH 05/35] fixed missing __init__.py file

---
 montepython/likelihoods/__init__.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 montepython/likelihoods/__init__.py

diff --git a/montepython/likelihoods/__init__.py b/montepython/likelihoods/__init__.py
new file mode 100644
index 00000000..e69de29b

From 30286564521c40362371a1d1f38244a68d9229c8 Mon Sep 17 00:00:00 2001
From: Miguel Zumalacarregui <miguelzuma@berkeley.edu>
Date: Tue, 6 Dec 2016 10:11:12 -0800
Subject: [PATCH 06/35] changes in print_error

---
 montepython/io_mp.py | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/montepython/io_mp.py b/montepython/io_mp.py
index 65705b42..fab600f4 100644
--- a/montepython/io_mp.py
+++ b/montepython/io_mp.py
@@ -244,17 +244,19 @@ def print_error(error_msg, data):
     # errors in background are 1-10, perturbations 10-99...
     if 'Shooting failed' in error_msg:
       err_code = 0
-    if 'Gradient instability' and 'scalar' in error_msg:
+    if 'Gradient' and 'scalar' in error_msg:
       err_code = 1
-    if 'Gradient instability' and 'tensor' in error_msg:
+    if 'Gradient' and 'tensor' in error_msg:
       err_code = 2
-    if 'Ghost instability' and 'scalar' in error_msg:
+    if 'Ghost' and 'scalar' in error_msg:
       err_code = 3
-    if 'Ghost instability' and 'tensor' in error_msg:
+    if 'Ghost' and 'tensor' in error_msg:
       err_code = 4
       
-    if "Isnan v_X" in error_msg:
+    if 'Isnan v_X' in error_msg:
       err_code = 10
+    if 'early_smg' and 'adiabatic' in error_msg:
+      err_code = 11
     
     
     out = data.err
@@ -265,6 +267,7 @@ def print_error(error_msg, data):
     if err_code == -1:
       out.write(str(err_code) + "\t" + error_msg)
     else:
+      #print "error",err_code
       out.write(str(err_code))
     out.write('\n')
         

From e5498ec9eb7200348fe1eab48f803428eadeb22f Mon Sep 17 00:00:00 2001
From: Miguel Zumalacarregui <miguelzuma@berkeley.edu>
Date: Tue, 6 Dec 2016 13:07:09 -0800
Subject: [PATCH 07/35] commented out CMASS data (use bao_boss_aniso instead)

---
 data/bao_2014.txt | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/data/bao_2014.txt b/data/bao_2014.txt
index bd879e5a..5a2072e2 100644
--- a/data/bao_2014.txt
+++ b/data/bao_2014.txt
@@ -19,13 +19,14 @@ LOWZ    0.32    8.47    0.17    3
 #
 # BOSS CMASS DR10&11 (D_V in Mpc divided by r_s^fid in Mpc) Anderson et al. 1312.4877
 # found in Section 8.2 (directly using the exact sound horizon)
-CMASS   0.57    13.77   0.13    3
+#CMASS   0.57    13.77   0.13    3
+#NOTE: commented out because of using anisotropic BOSS-CMASS
 #
 # BOSS LyaQSO (DA/rs) Font-Ribera et al. 1311.1767
-# LyaQSO  2.36   10.8     0.4     5
+ LyaQSO  2.36   10.8     0.4     5
 #
 # BOSS LyaQSO c/(H rs) Font-Ribera et al. 1311.1767
-# LyaQSO	2.36    9.0     0.3     6
+ LyaQSO	2.36    9.0     0.3     6
 #
 # SDSS DR7 MGS, Ross et al. 1409.3242v1
 MGS     0.15   4.47     0.16    3

From 15652943a9e6c7ba3054bf2731624a7cad7c46fa Mon Sep 17 00:00:00 2001
From: Miguel Zumalacarregui <miguelzuma@berkeley.edu>
Date: Tue, 6 Dec 2016 18:07:49 -0800
Subject: [PATCH 08/35] uncommented data: exclusion was made automatic

---
 data/bao_2014.txt | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/data/bao_2014.txt b/data/bao_2014.txt
index 5a2072e2..0dec83bc 100644
--- a/data/bao_2014.txt
+++ b/data/bao_2014.txt
@@ -19,8 +19,7 @@ LOWZ    0.32    8.47    0.17    3
 #
 # BOSS CMASS DR10&11 (D_V in Mpc divided by r_s^fid in Mpc) Anderson et al. 1312.4877
 # found in Section 8.2 (directly using the exact sound horizon)
-#CMASS   0.57    13.77   0.13    3
-#NOTE: commented out because of using anisotropic BOSS-CMASS
+CMASS   0.57    13.77   0.13    3
 #
 # BOSS LyaQSO (DA/rs) Font-Ribera et al. 1311.1767
  LyaQSO  2.36   10.8     0.4     5

From 17cf1ec710180f2079f73bd61c4d5a0386b86e45 Mon Sep 17 00:00:00 2001
From: ardok-m <ardok@openmailbox.org>
Date: Wed, 14 Dec 2016 18:52:05 +0100
Subject: [PATCH 09/35] improved input param handling: error with param scale 0

---
 montepython/data.py  | 7 ++++++-
 montepython/io_mp.py | 5 +++++
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/montepython/data.py b/montepython/data.py
index 714e62c7..158ae434 100644
--- a/montepython/data.py
+++ b/montepython/data.py
@@ -1000,7 +1000,12 @@ def __init__(self, array, key):
         dict.__init__(self)
 
         self['initial'] = array[0:4]
-        self['scale'] = array[4]
+        if array[4]:
+            self['scale'] = array[4]
+        else:
+            raise io_mp.ParameterError("You chose scale 0 to param {}. Correct\
+                                       it.".format(key))
+
         self['role'] = array[-1]
         self['tex_name'] = io_mp.get_tex_name(key)
         if array[3] == 0:
diff --git a/montepython/io_mp.py b/montepython/io_mp.py
index a2fd7692..998a5ef5 100644
--- a/montepython/io_mp.py
+++ b/montepython/io_mp.py
@@ -622,3 +622,8 @@ class FiducialModelWritten(MyError):
 class AnalyzeError(MyError):
     """Used when encountering a fatal mistake in analyzing chains"""
     pass
+
+
+class ParameterError(MyError):
+    """Used when some MontePython parameter is not correctly set"""
+    pass

From a69f5bc94cdb237c57ef4789b76b6f375368e40f Mon Sep 17 00:00:00 2001
From: ardok-m <ardok@openmailbox.org>
Date: Mon, 17 Apr 2017 17:12:44 +0200
Subject: [PATCH 10/35] fixed TypeError np.max for numpy 1.12

---
 montepython/analyze.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/montepython/analyze.py b/montepython/analyze.py
index a7c6df0a..2402875c 100644
--- a/montepython/analyze.py
+++ b/montepython/analyze.py
@@ -788,8 +788,8 @@ def minimum_credible_intervals(info):
     bounds = np.zeros((len(levels), 2))
     j = 0
     delta = bincenters[1]-bincenters[0]
-    left_edge = np.max(histogram[0] - 0.5*(histogram[1]-histogram[0]), 0.)
-    right_edge = np.max(histogram[-1] + 0.5*(histogram[-1]-histogram[-2]), 0.)
+    left_edge = np.max(histogram[0] - 0.5*(histogram[1]-histogram[0]), 0)
+    right_edge = np.max(histogram[-1] + 0.5*(histogram[-1]-histogram[-2]), 0)
     failed = False
     for level in levels:
         norm = float(

From 9674a286acade1cd936d6b2b70b6e2f2cbafff85 Mon Sep 17 00:00:00 2001
From: ardok-m <ardok@openmailbox.org>
Date: Tue, 18 Apr 2017 10:57:04 +0200
Subject: [PATCH 11/35] fixed contours level error handling.

Matplotlib must have promoted it from a Warning to a Value Error
---
 montepython/analyze.py | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/montepython/analyze.py b/montepython/analyze.py
index 2402875c..26ce89f0 100644
--- a/montepython/analyze.py
+++ b/montepython/analyze.py
@@ -672,6 +672,23 @@ def compute_posterior(information_instances):
                                 "'%s-%s' 2d-plot" % (
                                     info.plotted_parameters[info.native_index],
                                     info.plotted_parameters[info.native_second_index]))
+                        except ValueError as e:
+                            if str(e) == "Contour levels must be increasing":
+                                warnings.warn(
+                                    "The routine could not find the contour of the " +
+                                    "'%s-%s' 2d-plot. \n " % (
+                                        info.plotted_parameters[info.native_index],
+                                        info.plotted_parameters[info.native_second_index]) +
+                                    'The error is: "Contour levels must be increasing"' +
+                                    " but " + str(ctr_level(info.n, info.levels[:2])) +
+                                    " were found. This may happen when most" +
+                                    " points fall in the same bin.")
+                            else:
+                                warnings.warn(
+                                    "The routine could not find the contour of the " +
+                                    "'%s-%s' 2d-plot" % (
+                                        info.plotted_parameters[info.native_index],
+                                        info.plotted_parameters[info.native_second_index]))
 
                         ax2dsub.set_xticks(info.ticks[info.native_second_index])
                         if index == len(plotted_parameters)-1:

From aa0498499cad2e5653d09a09845690970d7089e6 Mon Sep 17 00:00:00 2001
From: ardok-m <ardok@openmailbox.org>
Date: Mon, 22 May 2017 11:24:10 +0200
Subject: [PATCH 12/35] added Planck_compressed likelihood arXiv:1502.01590

---
 .../Planck_compressed/Planck_compressed.data  | 24 +++++++++++++
 .../likelihoods/Planck_compressed/__init__.py | 34 +++++++++++++++++++
 2 files changed, 58 insertions(+)
 create mode 100644 montepython/likelihoods/Planck_compressed/Planck_compressed.data
 create mode 100644 montepython/likelihoods/Planck_compressed/__init__.py

diff --git a/montepython/likelihoods/Planck_compressed/Planck_compressed.data b/montepython/likelihoods/Planck_compressed/Planck_compressed.data
new file mode 100644
index 00000000..4229176d
--- /dev/null
+++ b/montepython/likelihoods/Planck_compressed/Planck_compressed.data
@@ -0,0 +1,24 @@
+# Covriance matrix of the compressed likelihood for Planck TT + lowP
+# (arXiv:1502.01590v2, Table 4)
+                                       # R, l_A, omega_b, n_s
+#Planck_compressed.correlation_matrix = [[1., 0.54, -0.63, -0.86],\ # R
+#                                        [0.54, 1., -0.43, -0.48],\ # l_A  
+#                                        [-0.63, -0.43, 1., 0.58],\ # omega_b
+#                                        [-0.86, -0.48, 0.58, 1.]] # n_s 
+
+# Covariance matrix_ij = sigma_i sigma_j Correlation_matrix_ij
+
+#Planck_compressed.inverse_correlation_matrix = np.linalg.inv([[1., 0.54, -0.63, -0.86], [0.54, 1., -0.43, -0.48],  [-0.63, -0.43, 1., 0.58], [-0.86, -0.48, 0.58, 1.]]) 
+
+Planck_compressed.inverse_correlation_matrix = [[ 4.51266537, -0.59697118, 0.75581806,  3.15597158], [-0.59697118,  1.43957767,  0.21084593,  0.05531143], [ 0.75581806,  0.21084593,  1.70453221, -0.2374191 ], [ 3.15597158, 0.05531143, -0.2374191 ,  3.87838813]]
+
+                      # mean, std. dev. (sigma)
+#Planck_compressed.R = [1.7488, 0.0074]
+#Planck_compressed.l_a = [301.76, 0.14]
+#Planck_compressed.omega_b = [0.02228, 0.00023]
+#Planck_compressed.n_s = [0.9660, 0.0061]
+
+#Planck_compressed.planck_values = np.array([[1.7488, 0.0074], [301.76, 0.14], [0.02228, 0.00023], [0.9660, 0.0061]])
+Planck_compressed.planck_values = [[1.7488, 0.0074], [301.76, 0.14], [0.02228, 0.00023], [0.9660, 0.0061]]
+
+               
diff --git a/montepython/likelihoods/Planck_compressed/__init__.py b/montepython/likelihoods/Planck_compressed/__init__.py
new file mode 100644
index 00000000..7b0bf127
--- /dev/null
+++ b/montepython/likelihoods/Planck_compressed/__init__.py
@@ -0,0 +1,34 @@
+from montepython.likelihood_class import Likelihood_prior
+import numpy as np
+
+
+class Planck_compressed(Likelihood_prior):
+
+    # initialisation of the class is done within the parent Likelihood_prior. For
+    # this case, it does not differ, actually, from the __init__ method in
+    # Likelihood class.
+
+    def loglkl(self, cosmo, data):
+
+        z_star = cosmo.z_optical_depth_unity()  # z at which the optical depth is unity
+        D_A_star = cosmo.angular_distance(z_star)
+        rs_star = cosmo.rs_at_z(z_star)
+
+        R = np.sqrt(cosmo.Omega_m()) * cosmo.Hubble(0) * D_A_star
+        l_a = np.pi * D_A_star / rs_star
+        omega_b = cosmo.omega_b()
+        n_s = cosmo.n_s()
+
+        values = np.array([R, l_a, omega_b, n_s])
+        planck_values = zip(*self.planck_values)
+
+        # loglkl = -1/2 * (x_i - x_mean_i) * 1/sigma_i * corr_mat_ij^-1 *
+        #                 1/sigma_j * (x_j - x_mean_j)
+
+        differences_over_sigma = ((values[:][0] - planck_values[0]) /
+                                  planck_values[1])
+
+        loglkl = -0.5 * np.dot(differences_over_sigma,
+                               np.dot(self.inverse_correlation_matrix,
+                                      differences_over_sigma))
+        return loglkl

From a6cb5935ab6871e391f4873a310596653176d84b Mon Sep 17 00:00:00 2001
From: ardok-m <ardok@openmailbox.org>
Date: Mon, 22 May 2017 13:15:31 +0200
Subject: [PATCH 13/35] fix angular diamter distance. Needed comoving

---
 montepython/likelihoods/Planck_compressed/__init__.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/montepython/likelihoods/Planck_compressed/__init__.py b/montepython/likelihoods/Planck_compressed/__init__.py
index 7b0bf127..b3f0c4de 100644
--- a/montepython/likelihoods/Planck_compressed/__init__.py
+++ b/montepython/likelihoods/Planck_compressed/__init__.py
@@ -11,7 +11,8 @@ class Planck_compressed(Likelihood_prior):
     def loglkl(self, cosmo, data):
 
         z_star = cosmo.z_optical_depth_unity()  # z at which the optical depth is unity
-        D_A_star = cosmo.angular_distance(z_star)
+        # comoving angular diameter distance
+        D_A_star = cosmo.angular_distance(z_star) * (z_star + 1)
         rs_star = cosmo.rs_at_z(z_star)
 
         R = np.sqrt(cosmo.Omega_m()) * cosmo.Hubble(0) * D_A_star

From a1ce2739afe61c1296b214b99bba85fe0e5f3b71 Mon Sep 17 00:00:00 2001
From: ardok-m <ardok@openmailbox.org>
Date: Tue, 23 May 2017 10:04:43 +0200
Subject: [PATCH 14/35] separed mean and sigma values

---
 .../likelihoods/Planck_compressed/Planck_compressed.data   | 7 +++----
 montepython/likelihoods/Planck_compressed/__init__.py      | 5 ++---
 2 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/montepython/likelihoods/Planck_compressed/Planck_compressed.data b/montepython/likelihoods/Planck_compressed/Planck_compressed.data
index 4229176d..9d6bb8b2 100644
--- a/montepython/likelihoods/Planck_compressed/Planck_compressed.data
+++ b/montepython/likelihoods/Planck_compressed/Planck_compressed.data
@@ -8,8 +8,6 @@
 
 # Covariance matrix_ij = sigma_i sigma_j Correlation_matrix_ij
 
-#Planck_compressed.inverse_correlation_matrix = np.linalg.inv([[1., 0.54, -0.63, -0.86], [0.54, 1., -0.43, -0.48],  [-0.63, -0.43, 1., 0.58], [-0.86, -0.48, 0.58, 1.]]) 
-
 Planck_compressed.inverse_correlation_matrix = [[ 4.51266537, -0.59697118, 0.75581806,  3.15597158], [-0.59697118,  1.43957767,  0.21084593,  0.05531143], [ 0.75581806,  0.21084593,  1.70453221, -0.2374191 ], [ 3.15597158, 0.05531143, -0.2374191 ,  3.87838813]]
 
                       # mean, std. dev. (sigma)
@@ -18,7 +16,8 @@ Planck_compressed.inverse_correlation_matrix = [[ 4.51266537, -0.59697118, 0.755
 #Planck_compressed.omega_b = [0.02228, 0.00023]
 #Planck_compressed.n_s = [0.9660, 0.0061]
 
-#Planck_compressed.planck_values = np.array([[1.7488, 0.0074], [301.76, 0.14], [0.02228, 0.00023], [0.9660, 0.0061]])
-Planck_compressed.planck_values = [[1.7488, 0.0074], [301.76, 0.14], [0.02228, 0.00023], [0.9660, 0.0061]]
+#Planck_compressed.planck_values = [[1.7488, 0.0074], [301.76, 0.14], [0.02228, 0.00023], [0.9660, 0.0061]]
 
+Planck_compressed.planck_values_mean = [1.7488, 301.76, 0.02228, 0.9660]
+Planck_compressed.planck_values_sigma = [0.0074, 0.14, 0.00023, 0.0061]
                
diff --git a/montepython/likelihoods/Planck_compressed/__init__.py b/montepython/likelihoods/Planck_compressed/__init__.py
index b3f0c4de..37b2e09c 100644
--- a/montepython/likelihoods/Planck_compressed/__init__.py
+++ b/montepython/likelihoods/Planck_compressed/__init__.py
@@ -21,15 +21,14 @@ def loglkl(self, cosmo, data):
         n_s = cosmo.n_s()
 
         values = np.array([R, l_a, omega_b, n_s])
-        planck_values = zip(*self.planck_values)
 
         # loglkl = -1/2 * (x_i - x_mean_i) * 1/sigma_i * corr_mat_ij^-1 *
         #                 1/sigma_j * (x_j - x_mean_j)
 
-        differences_over_sigma = ((values[:][0] - planck_values[0]) /
-                                  planck_values[1])
+        differences_over_sigma = (values - np.array(self.planck_values_mean)) / self.planck_values_sigma
 
         loglkl = -0.5 * np.dot(differences_over_sigma,
                                np.dot(self.inverse_correlation_matrix,
                                       differences_over_sigma))
+
         return loglkl

From a5c6cf2d23b677caacbd8d057c1b24372477cf94 Mon Sep 17 00:00:00 2001
From: ardok-m <ardok@openmailbox.org>
Date: Tue, 23 May 2017 13:59:23 +0200
Subject: [PATCH 15/35] added triangular prior and fixed some bugs

---
 montepython/data.py  |  2 +-
 montepython/prior.py | 23 ++++++++++++++++++++---
 2 files changed, 21 insertions(+), 4 deletions(-)

diff --git a/montepython/data.py b/montepython/data.py
index 158ae434..9c6975c8 100644
--- a/montepython/data.py
+++ b/montepython/data.py
@@ -1006,7 +1006,7 @@ def __init__(self, array, key):
             raise io_mp.ParameterError("You chose scale 0 to param {}. Correct\
                                        it.".format(key))
 
-        self['role'] = array[-1]
+        self['role'] = array[5]
         self['tex_name'] = io_mp.get_tex_name(key)
         if array[3] == 0:
             self['status'] = 'fixed'
diff --git a/montepython/prior.py b/montepython/prior.py
index f86db5a6..12e15a19 100644
--- a/montepython/prior.py
+++ b/montepython/prior.py
@@ -50,11 +50,25 @@ def __init__(self, array):
                         "You asked for a gaussian prior, but provided no " +
                         "mean nor sigma. Please add them in the parameter " +
                         "file.")
+            # in case of a triangular prior, one expects one more entry, the
+            # position of the mode
+            elif self.prior_type == 'triangular':
+                try:
+                    self.mode = array[7]
+                    # TODO: Consider unifying prior variable names.
+                except IndexError:
+                    raise io_mp.ConfigurationError(
+                        "You asked for a triangular prior, but provided no " +
+                        "position for the mode. Please add it in the parameter " +
+                        "file.")
 
         # Store boundaries for convenient access later
         # Put all fields that are -1 to None to avoid confusion later on.
         self.prior_range = [a if not((a is -1) or (a is None)) else None
                             for a in deepcopy(array[1:3])]
+        # TODO: As implemented above, you wouldn't be able to set -1 as
+        # boundary for one of the parameters. Consider leaving the None part
+        # only
 
     def draw_from_prior(self):
         """
@@ -76,10 +90,13 @@ def draw_from_prior(self):
             while not within_bounds:
                 value = rd.gauss(self.mu, self.sigma)
                 # Check for boundaries problem
-                within_bounds = calue_within_prior_range(value)
+                within_bounds = self.value_within_prior_range(value)
 
             return value
-                
+
+        elif self.prior_type == 'triangular':
+            return rd.triangular(self.prior_range[0], self.prior_range[1], self.mode)
+
     def value_within_prior_range(self, value):
         """
         Check for a value being in or outside the prior range
@@ -112,5 +129,5 @@ def map_from_unit_interval(self, value):
         which should have been previously checked with :func:`is_bound`
 
         """
-        return (self.prior_range[0] + 
+        return (self.prior_range[0] +
                 value * (self.prior_range[1] - self.prior_range[0]))

From 3954be28584f00060643ad66d79fb9f36eda3cf0 Mon Sep 17 00:00:00 2001
From: ardok-m <ardok@openmailbox.org>
Date: Thu, 25 May 2017 10:27:42 +0200
Subject: [PATCH 16/35] changed name of parent likelihood, behavior is the same

---
 montepython/likelihoods/Planck_compressed/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/montepython/likelihoods/Planck_compressed/__init__.py b/montepython/likelihoods/Planck_compressed/__init__.py
index 37b2e09c..ca9be4ae 100644
--- a/montepython/likelihoods/Planck_compressed/__init__.py
+++ b/montepython/likelihoods/Planck_compressed/__init__.py
@@ -1,8 +1,8 @@
-from montepython.likelihood_class import Likelihood_prior
+from montepython.likelihood_class import Likelihood
 import numpy as np
 
 
-class Planck_compressed(Likelihood_prior):
+class Planck_compressed(Likelihood):
 
     # initialisation of the class is done within the parent Likelihood_prior. For
     # this case, it does not differ, actually, from the __init__ method in

From 20cba93886c9933f5e298861bb321fbf66740019 Mon Sep 17 00:00:00 2001
From: ardok-m <ardok@openmailbox.org>
Date: Wed, 31 May 2017 10:46:23 +0200
Subject: [PATCH 17/35] store values as object to be accesible by wic
 data_mp_likelihoods.py

---
 montepython/likelihoods/Planck_compressed/__init__.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/montepython/likelihoods/Planck_compressed/__init__.py b/montepython/likelihoods/Planck_compressed/__init__.py
index ca9be4ae..f378df47 100644
--- a/montepython/likelihoods/Planck_compressed/__init__.py
+++ b/montepython/likelihoods/Planck_compressed/__init__.py
@@ -20,12 +20,16 @@ def loglkl(self, cosmo, data):
         omega_b = cosmo.omega_b()
         n_s = cosmo.n_s()
 
-        values = np.array([R, l_a, omega_b, n_s])
+        # Using self in order to be accesible by data_mp_likelihoods.py
+        # work-in-class module.
+        # https://github.com/miguelzuma/work-in-class &&
+        # https://github.com/ardok-m/work-in-class &&
+        self.values = np.array([R, l_a, omega_b, n_s])
 
         # loglkl = -1/2 * (x_i - x_mean_i) * 1/sigma_i * corr_mat_ij^-1 *
         #                 1/sigma_j * (x_j - x_mean_j)
 
-        differences_over_sigma = (values - np.array(self.planck_values_mean)) / self.planck_values_sigma
+        differences_over_sigma = (self.values - np.array(self.planck_values_mean)) / self.planck_values_sigma
 
         loglkl = -0.5 * np.dot(differences_over_sigma,
                                np.dot(self.inverse_correlation_matrix,

From 814138565ef564ef9682182dd46aa09eabc7144f Mon Sep 17 00:00:00 2001
From: ardok-m <ardok@openmailbox.org>
Date: Thu, 27 Jul 2017 13:35:59 +0200
Subject: [PATCH 18/35] added only_error optiont to create error file when
 using NS

---
 montepython/initialise.py |  1 +
 montepython/io_mp.py      | 18 +++++++++++-------
 2 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/montepython/initialise.py b/montepython/initialise.py
index ca09f782..009fe172 100644
--- a/montepython/initialise.py
+++ b/montepython/initialise.py
@@ -84,6 +84,7 @@ def initialise(custom_command=''):
             io_mp.create_output_files(command_line, data)
         # NS: Creating the NS subfolder and the MultiNest arguments
         elif command_line.method == 'NS':
+            io_mp.create_output_files(command_line, data, only_error=True)
             from nested_sampling import initialise as initialise_ns
             initialise_ns(cosmo, data, command_line)
 
diff --git a/montepython/io_mp.py b/montepython/io_mp.py
index cd85713f..fca41ab5 100644
--- a/montepython/io_mp.py
+++ b/montepython/io_mp.py
@@ -255,12 +255,12 @@ def print_error(error_msg, data):
 
     if "Isnan v_X" in error_msg:
       err_code = 10
-      
+
     if 'Isnan v_X' in error_msg:
       err_code = 10
     if 'early_smg' and 'adiabatic' in error_msg:
       err_code = 11
-    
+
     out = data.err
     for elem in data.get_mcmc_parameters(['varying']):
       out.write('%.6e\t' %
@@ -286,7 +286,7 @@ def refresh_file(data):
     data.err = open(data.err_name, 'a')
 
 
-def create_output_files(command_line, data):
+def create_output_files(command_line, data, only_error=False):
     """
     Automatically create a new name for the chain.
 
@@ -302,6 +302,14 @@ def create_output_files(command_line, data):
         changing things here.
 
     """
+
+    if only_error:
+        #open/create error file
+        data.err_name = os.path.join(command_line.folder,"error_log.txt")
+        data.err = open(data.err_name,'a')
+        print 'Creating error file %s\n' % data.err_name
+        return
+
     if command_line.restart is None:
         number = command_line.N
     else:
@@ -340,10 +348,6 @@ def create_output_files(command_line, data):
         for line in open(command_line.restart, 'r'):
             data.out.write(line)
 
-    #open/create error file
-    data.err_name = os.path.join(command_line.folder,"error_log.txt")
-    data.err = open(data.err_name,'a')
-    print 'Creating error file %s\n' % data.err_name
 
 
 

From fa8d9746990231375944d196f8a3aaa34610430d Mon Sep 17 00:00:00 2001
From: ardok-m <ardok@openmailbox.org>
Date: Thu, 27 Jul 2017 15:49:40 +0200
Subject: [PATCH 19/35] error_log file per chain

---
 montepython/io_mp.py | 99 ++++++++++++++++++++++++--------------------
 1 file changed, 55 insertions(+), 44 deletions(-)

diff --git a/montepython/io_mp.py b/montepython/io_mp.py
index fca41ab5..a88e201c 100644
--- a/montepython/io_mp.py
+++ b/montepython/io_mp.py
@@ -303,53 +303,64 @@ def create_output_files(command_line, data, only_error=False):
 
     """
 
-    if only_error:
-        #open/create error file
-        data.err_name = os.path.join(command_line.folder,"error_log.txt")
-        data.err = open(data.err_name,'a')
-        print 'Creating error file %s\n' % data.err_name
-        return
+    for f in ('out', 'err'):
+        if (f == 'out') and only_error:
+            continue
 
-    if command_line.restart is None:
-        number = command_line.N
-    else:
-        number = int(
-            command_line.restart.split(os.path.sep)[-1].split('__')[0].
-            split('_')[1]) + command_line.N
-
-    # output file
-    outname_base = '{0}_{1}__'.format(date.today(), number)
-    suffix = 0
-    trying = True
-    if command_line.chain_number is None:
-        for files in os.listdir(command_line.folder):
-            if files.find(outname_base) != -1:
-                if int(files.split('__')[-1].split('.')[0]) > suffix:
-                    suffix = int(files.split('__')[-1].split('.')[0])
-        suffix += 1
-        while trying:
-            data.out = open(os.path.join(
-                command_line.folder, outname_base)+str(suffix)+'.txt', 'w')
-            try:
-                lock(data.out, fcntl.LOCK_EX | fcntl.LOCK_NB)
-                trying = False
-            except LockError:
+        if command_line.restart is None:
+            number = command_line.N
+        else:
+            number = int(
+                command_line.restart.split(os.path.sep)[-1].split('__')[0].
+                split('_')[1]) + command_line.N
+
+        # output file
+        outname_base = '{0}_{1}__'.format(date.today(), number)
+        suffix = 0
+        suffix_err = ""
+        if f == 'err':
+            suffix_err = "-error_log"
+
+        trying = True
+        if command_line.chain_number is None:
+            for files in os.listdir(command_line.folder):
+                if files.find(outname_base) != -1:
+                    matched_number = re.search('\d*', files.split('__')[-1])
+                    number = int(matched_number.group(0))
+                    if number > suffix:
+                        suffix = number
+
+            if (f == 'out') or only_error:
                 suffix += 1
-        data.out_name = os.path.join(
-            command_line.folder, outname_base)+str(suffix)+'.txt'
-        print 'Creating %s\n' % data.out_name
-    else:
-        data.out_name = os.path.join(
-            command_line.folder, outname_base)+command_line.chain_number+'.txt'
-        data.out = open(data.out_name, 'w')
-        print 'Creating %s\n' % data.out_name
-    # in case of a restart, copying the whole thing in the new file
-    if command_line.restart is not None:
-        for line in open(command_line.restart, 'r'):
-            data.out.write(line)
-
-
 
+            while trying:
+                open_file = open(os.path.join(
+                    command_line.folder, outname_base)+str(suffix)+suffix_err+'.txt', 'w')
+
+                try:
+                    lock(open_file, fcntl.LOCK_EX | fcntl.LOCK_NB)
+                    trying = False
+                except LockError:
+                    suffix += 1
+            name = os.path.join(
+                command_line.folder, outname_base)+str(suffix)+ suffix_err+'.txt'
+            print 'Creating %s\n' % name
+        else:
+            name = os.path.join(
+                command_line.folder, outname_base)+command_line.chain_number+suffix_err+'.txt'
+            open_file = open(name, 'w')
+            print 'Creating %s\n' % name
+        # in case of a restart, copying the whole thing in the new file
+        if command_line.restart is not None:
+            for line in open(command_line.restart[:-4]+suffix_err+txt, 'r'):
+                open_file.write(line)
+
+        if f == 'out':
+            data.out = open_file
+            data.out_name = name
+        else:
+            data.err = open_file
+            data.err_name = name
 
 
 def get_tex_name(name, number=1):

From 343b5b0f060815e7bef40e909cee0c8390d2bdcc Mon Sep 17 00:00:00 2001
From: ardok-m <ardok@openmailbox.org>
Date: Tue, 8 Aug 2017 15:07:59 +0200
Subject: [PATCH 20/35] exclude from analysis error_log files

---
 montepython/analyze.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/montepython/analyze.py b/montepython/analyze.py
index 26ce89f0..5c8e7ce3 100644
--- a/montepython/analyze.py
+++ b/montepython/analyze.py
@@ -1144,6 +1144,10 @@ def recover_folder_and_files(files):
     # The following list defines the substring that a chain should contain for
     # the code to recognise it as a proper chain.
     substrings = ['.txt', '__']
+    # The following variable defines the substring that identify error_log
+    # files and therefore there must not be taken into account in the analysis.
+    substring_err = 'error_log'
+
     limit = 10
     # If the first element is a folder, grab all chain files inside
     if os.path.isdir(files[0]):
@@ -1151,6 +1155,7 @@ def recover_folder_and_files(files):
         files = [os.path.join(folder, elem) for elem in os.listdir(folder)
                  if not os.path.isdir(os.path.join(folder, elem))
                  and not os.path.getsize(os.path.join(folder, elem)) < limit
+                 and (substring_err not in elem)
                  and all([x in elem for x in substrings])]
     # Otherwise, extract the folder from the chain file-name.
     else:
@@ -1164,6 +1169,7 @@ def recover_folder_and_files(files):
                  if os.path.join(folder, elem) in np.copy(files)
                  and not os.path.isdir(os.path.join(folder, elem))
                  and not os.path.getsize(os.path.join(folder, elem)) < limit
+                 and (substring_err not in elem)
                  and all([x in elem for x in substrings])]
     basename = os.path.basename(folder)
     return folder, files, basename

From b86ddd62599c9d285840e9349758af3032a56486 Mon Sep 17 00:00:00 2001
From: ardok-m <carlosgarcia@iff.csic.es>
Date: Thu, 14 Sep 2017 15:36:02 +0200
Subject: [PATCH 21/35] fixed missing ''

---
 montepython/io_mp.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 mode change 100644 => 100755 montepython/io_mp.py

diff --git a/montepython/io_mp.py b/montepython/io_mp.py
old mode 100644
new mode 100755
index a88e201c..26babacb
--- a/montepython/io_mp.py
+++ b/montepython/io_mp.py
@@ -352,7 +352,7 @@ def create_output_files(command_line, data, only_error=False):
             print 'Creating %s\n' % name
         # in case of a restart, copying the whole thing in the new file
         if command_line.restart is not None:
-            for line in open(command_line.restart[:-4]+suffix_err+txt, 'r'):
+            for line in open(command_line.restart[:-4]+suffix_err+'txt', 'r'):
                 open_file.write(line)
 
         if f == 'out':

From b81e79126ff6684f2670591dca3031c4a2187177 Mon Sep 17 00:00:00 2001
From: ardok-m <carlosgarcia@iff.csic.es>
Date: Thu, 14 Sep 2017 15:38:02 +0200
Subject: [PATCH 22/35] fixed missing . in suffix

---
 montepython/io_mp.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/montepython/io_mp.py b/montepython/io_mp.py
index 26babacb..f7f3f8c7 100755
--- a/montepython/io_mp.py
+++ b/montepython/io_mp.py
@@ -352,7 +352,7 @@ def create_output_files(command_line, data, only_error=False):
             print 'Creating %s\n' % name
         # in case of a restart, copying the whole thing in the new file
         if command_line.restart is not None:
-            for line in open(command_line.restart[:-4]+suffix_err+'txt', 'r'):
+            for line in open(command_line.restart[:-4]+suffix_err+'.txt', 'r'):
                 open_file.write(line)
 
         if f == 'out':

From f9c326915116e86ee7e670d6ebdad200dbe89bd3 Mon Sep 17 00:00:00 2001
From: ardok-m <carlosgarcia@iff.csic.es>
Date: Wed, 11 Oct 2017 10:42:22 +0200
Subject: [PATCH 23/35] modified bao_boss to interact with work_in_class

---
 montepython/likelihoods/bao_boss/__init__.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/montepython/likelihoods/bao_boss/__init__.py b/montepython/likelihoods/bao_boss/__init__.py
index faf5dd81..76028d79 100644
--- a/montepython/likelihoods/bao_boss/__init__.py
+++ b/montepython/likelihoods/bao_boss/__init__.py
@@ -60,6 +60,9 @@ def loglkl(self, cosmo, data):
 
         chi2 = 0.
 
+        # This object is meant to be used with data_mp_likelihoods.py
+        self.theo = []
+
         # for each point, compute angular distance da, radial distance dr,
         # volume distance dv, sound horizon at baryon drag rs_d,
         # theoretical prediction and chi2 contribution
@@ -92,6 +95,8 @@ def loglkl(self, cosmo, data):
 
             chi2 += ((theo - self.data[i]) / self.error[i]) ** 2
 
+            self.theo.append(theo)
+
         # return ln(L)
         lkl = - 0.5 * chi2
 

From a55a5517c0026da07e90327bc57d1d904af92cab Mon Sep 17 00:00:00 2001
From: ardok-m <carlosgarcia@iff.csic.es>
Date: Mon, 23 Oct 2017 12:39:43 +0200
Subject: [PATCH 24/35] updated to match stable CosmoHammer version

---
 montepython/cosmo_hammer.py | 10 ++++++----
 montepython/run.py          |  2 ++
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/montepython/cosmo_hammer.py b/montepython/cosmo_hammer.py
index efec34d4..50339f76 100644
--- a/montepython/cosmo_hammer.py
+++ b/montepython/cosmo_hammer.py
@@ -22,9 +22,11 @@
 
 import io_mp
 import sampler
-from cosmoHammer.likelihood.chain.LikelihoodComputationChain import (
-    LikelihoodComputationChain)
-from cosmoHammer.sampler.CosmoHammerSampler import CosmoHammerSampler
+from cosmoHammer import MpiCosmoHammerSampler
+from cosmoHammer import LikelihoodComputationChain
+#from cosmoHammer.likelihood.chain.LikelihoodComputationChain import (
+#    LikelihoodComputationChain)
+#from cosmoHammer.sampler.CosmoHammerSampler import CosmoHammerSampler
 from cosmoHammer.util.SampleFileUtil import SampleFileUtil
 
 # Cosmo Hammer subfolder and name separator
@@ -127,7 +129,7 @@ def run(cosmo, data, command_line):
         num_threads = 1
 
     # Create the Sampler object
-    sampler_hammer = CosmoHammerSampler(
+    sampler_hammer = MpiCosmoHammerSampler(
         params=params,
         likelihoodComputationChain=chain,
         filePrefix=file_prefix,
diff --git a/montepython/run.py b/montepython/run.py
index c74a8068..3787f9de 100644
--- a/montepython/run.py
+++ b/montepython/run.py
@@ -115,6 +115,8 @@ def mpi_run(custom_command=""):
                 status = suffix
             elif command_line.method == "NS":
                 status = 1
+            elif command_line.method == "CH":
+                status = 1
             else:
                 warnings.warn(
                     "The method '%s' is not supported"%(command_line.method) +

From afeb21d06f16e8fa4c97977f1343f288bcfc3135 Mon Sep 17 00:00:00 2001
From: ardok-m <carlosgarcia@iff.csic.es>
Date: Tue, 24 Oct 2017 10:14:52 +0200
Subject: [PATCH 25/35] fixed option input cosmo_hammer

---
 montepython/cosmo_hammer.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/montepython/cosmo_hammer.py b/montepython/cosmo_hammer.py
index 50339f76..b0f8e311 100644
--- a/montepython/cosmo_hammer.py
+++ b/montepython/cosmo_hammer.py
@@ -103,7 +103,9 @@ def run(cosmo, data, command_line):
     file_prefix = os.path.join(command_line.folder, CH_subfolder, chain_name)
 
     # Recover the User options
-    data.CH_arguments = {}
+    data.CH_arguments = {'walkersRatio': 50,
+                         'burninIterations': 10,
+                         'sampleIterations': 30}
     for arg in CH_user_arguments:
         value = getattr(command_line, CH_prefix+arg)
         if value != -1:
@@ -133,9 +135,6 @@ def run(cosmo, data, command_line):
         params=params,
         likelihoodComputationChain=chain,
         filePrefix=file_prefix,
-        walkersRatio=50,
-        burninIterations=10,
-        sampleIterations=30,
         storageUtil=derived_util,
         threadCount=num_threads,
         **data.CH_arguments)

From a738c0c5374650d3add8fbdab6c8d3d0caded67e Mon Sep 17 00:00:00 2001
From: ardok-m <carlosgarcia@iff.csic.es>
Date: Wed, 25 Oct 2017 13:19:30 +0200
Subject: [PATCH 26/35] fixed derived CH when not computed

---
 montepython/cosmo_hammer.py | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/montepython/cosmo_hammer.py b/montepython/cosmo_hammer.py
index b0f8e311..16f45a1f 100644
--- a/montepython/cosmo_hammer.py
+++ b/montepython/cosmo_hammer.py
@@ -50,6 +50,10 @@
     {'help': 'Number of sample iterations',
      'type': int}}
 
+# List of strings that will contain the derived parameters names.
+# Filled in run using the MontePython class data
+# Used in DerivedUtil.persistValues
+CH_derived_names = []
 
 def run(cosmo, data, command_line):
     """
@@ -59,6 +63,9 @@ def run(cosmo, data, command_line):
     # Store the parameters inside the format expected by CosmoHammer
     # TODO: about the derived params?
     parameter_names = data.get_mcmc_parameters(["varying"])
+    # Fill now CH_derived_names to be used in DerivedUtil.persistValues
+    global CH_derived_names
+    CH_derived_names= data.get_mcmc_parameters(["derived"])
 
     # Ensure that their prior is bound and flat
     is_flat, is_bound = sampler.check_flat_bound_priors(
@@ -196,8 +203,11 @@ def persistValues(self, posFile, probFile, pos, prob, data):
         """
         # extend the pos array to also contain the value of the derived
         # parameters
+
+        derived_not_computed = [np.NaN] * len(CH_derived_names)
+
         derived = np.array(
-            [[a for a in elem.itervalues()] for elem in data])
+            [[a for a in elem.itervalues()] if elem else derived_not_computed for elem in data])
         final = np.concatenate((pos, derived), axis=1)
 
         posFile.write("\n".join(

From b70913f0dad68c10502332f0d3898637dc0b78ed Mon Sep 17 00:00:00 2001
From: ardok-m <carlosgarcia@iff.csic.es>
Date: Wed, 25 Oct 2017 15:04:49 +0200
Subject: [PATCH 27/35] save errors in different file

---
 montepython/cosmo_hammer.py | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/montepython/cosmo_hammer.py b/montepython/cosmo_hammer.py
index 16f45a1f..de05bab8 100644
--- a/montepython/cosmo_hammer.py
+++ b/montepython/cosmo_hammer.py
@@ -35,6 +35,7 @@
 # Cosmo Hammer file names ending, after the defined 'base_name'
 name_arguments = '.arguments'
 name_chain = 'chain_CH__sampling.txt'
+name_error_chain =  'chain_CH__sampling-error_log.txt'
 
 # Cosmo Hammer option prefix
 CH_prefix = 'CH_'
@@ -166,6 +167,8 @@ def from_CH_output_to_chains(folder):
 
     This function will be called by the module :mod:`analyze`.
     """
+    chainsClean, lklClean = [], []  # Arrays to store the valid steps.
+    error = []  # Array to store the step did not could not be computed.
 
     chain_name = [a for a in folder.split(os.path.sep) if a][-2]
     base_name = os.path.join(folder, chain_name)
@@ -186,11 +189,20 @@ def from_CH_output_to_chains(folder):
     ## Create the array of ones
     ones = np.array([[1] for _ in range(len(lkl))])
 
+    for x, p in [chains, lkl]:
+        if p is not -np.inf:
+            chainsClean.append(x)
+            lklClean.append(p)
+        else:
+            error.append(x)
+
     ## Concatenate everything and save to file
-    final = np.concatenate((ones, lkl, chains), axis=1)
+    final = np.concatenate((ones, lkl, chainsClean), axis=1)
     output_folder = os.path.join(folder, '..')
     output_chain_path = os.path.join(output_folder, name_chain)
+    output_error_chain_path = os.path.join(output_folder, name_error_chain)
     np.savetxt(output_chain_path, final)
+    np.savetxt(output_error_chain_path, error)
 
 
 class DerivedUtil(SampleFileUtil):

From 50ad1506630032faae6c7352afe1a65d98e3f05a Mon Sep 17 00:00:00 2001
From: ardok-m <carlosgarcia@iff.csic.es>
Date: Wed, 25 Oct 2017 15:54:53 +0200
Subject: [PATCH 28/35] fixed problems saving errors diff files

---
 montepython/cosmo_hammer.py | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/montepython/cosmo_hammer.py b/montepython/cosmo_hammer.py
index de05bab8..67f12a1c 100644
--- a/montepython/cosmo_hammer.py
+++ b/montepython/cosmo_hammer.py
@@ -183,21 +183,22 @@ def from_CH_output_to_chains(folder):
     # multiplicity. This does not mean that the acceptance rate is one, but
     # points where the code stayed are duplicated in the file.
 
+    for x, p in zip(chains, lkl):
+        if p != -np.inf:
+            chainsClean.append(x)
+            lklClean.append([p])
+        else:
+            error.append(x)
+
     ## First, reshape the lkl array
-    lkl = np.array([[elem] for elem in lkl])
+    #lkl = np.array([[elem] for elem in lkl])
 
     ## Create the array of ones
-    ones = np.array([[1] for _ in range(len(lkl))])
+    ones = np.array([[1] for _ in range(len(lklClean))])
 
-    for x, p in [chains, lkl]:
-        if p is not -np.inf:
-            chainsClean.append(x)
-            lklClean.append(p)
-        else:
-            error.append(x)
 
     ## Concatenate everything and save to file
-    final = np.concatenate((ones, lkl, chainsClean), axis=1)
+    final = np.concatenate((ones, lklClean, chainsClean), axis=1)
     output_folder = os.path.join(folder, '..')
     output_chain_path = os.path.join(output_folder, name_chain)
     output_error_chain_path = os.path.join(output_folder, name_error_chain)

From 13f0ab793d044adddb800260ab77f161778481b8 Mon Sep 17 00:00:00 2001
From: ardok-m <carlosgarcia@iff.csic.es>
Date: Fri, 27 Oct 2017 11:59:35 +0200
Subject: [PATCH 29/35] added function to store derived paramters from cosmo

---
 montepython/cosmo_hammer.py | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/montepython/cosmo_hammer.py b/montepython/cosmo_hammer.py
index 67f12a1c..9595b612 100644
--- a/montepython/cosmo_hammer.py
+++ b/montepython/cosmo_hammer.py
@@ -101,6 +101,7 @@ def run(cosmo, data, command_line):
     # here, since data must be called before cosmo.
     chain.addCoreModule(data)
     chain.addCoreModule(cosmo)
+    chain.addCoreModule(store_cosmo_derived)
 
     # Add each likelihood class as a LikelihoodModule
     for likelihood in data.lkl.itervalues():
@@ -231,3 +232,30 @@ def persistValues(self, posFile, probFile, pos, prob, data):
         probFile.write("\n".join([str(p) for p in prob]))
         probFile.write("\n")
         probFile.flush()
+
+
+def store_cosmo_derived(ctx):
+    """
+    Store derived parameters. Copied from sampler.compute_lkl
+    """
+    from classy import CosmoSevereError
+
+    cosmo = ctx.get("cosmo")
+    data = ctx.get("data")
+
+    if data.get_mcmc_parameters(['derived']) != []:
+        try:
+            derived = cosmo.get_current_derived_parameters(
+                data.get_mcmc_parameters(['derived']))
+            for name, value in derived.iteritems():
+                data.mcmc_parameters[name]['current'] = value
+        except AttributeError:
+            # This happens if the classy wrapper is still using the old
+            # convention, expecting data as the input parameter
+            cosmo.get_current_derived_parameters(data)
+        except CosmoSevereError:
+            raise io_mp.CosmologicalModuleError(
+                "Could not write the current derived parameters")
+    for elem in data.get_mcmc_parameters(['derived']):
+        data.mcmc_parameters[elem]['current'] /= \
+            data.mcmc_parameters[elem]['scale']

From 47b2fa44c467479c074b47bbedd5ab301c9a0adf Mon Sep 17 00:00:00 2001
From: ardok-m <carlosgarcia@iff.csic.es>
Date: Fri, 27 Oct 2017 13:55:54 +0200
Subject: [PATCH 30/35] remove nan's from error-log file

---
 montepython/cosmo_hammer.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/montepython/cosmo_hammer.py b/montepython/cosmo_hammer.py
index 9595b612..0d5bb184 100644
--- a/montepython/cosmo_hammer.py
+++ b/montepython/cosmo_hammer.py
@@ -184,15 +184,13 @@ def from_CH_output_to_chains(folder):
     # multiplicity. This does not mean that the acceptance rate is one, but
     # points where the code stayed are duplicated in the file.
 
+    # First, separe errors from accepted points:
     for x, p in zip(chains, lkl):
         if p != -np.inf:
             chainsClean.append(x)
             lklClean.append([p])
         else:
-            error.append(x)
-
-    ## First, reshape the lkl array
-    #lkl = np.array([[elem] for elem in lkl])
+            error.append([val for val in x if not np.isnan(val)])  # Remove nan's
 
     ## Create the array of ones
     ones = np.array([[1] for _ in range(len(lklClean))])

From 16085a36b8f51a4ec5a93ed4a511936f8d7f474d Mon Sep 17 00:00:00 2001
From: ardok-m <carlosgarcia@iff.csic.es>
Date: Tue, 14 Nov 2017 14:52:36 +0100
Subject: [PATCH 31/35] convert to -loglkl the CH loglkl when analyzing

---
 montepython/cosmo_hammer.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/montepython/cosmo_hammer.py b/montepython/cosmo_hammer.py
index 0d5bb184..f73de175 100644
--- a/montepython/cosmo_hammer.py
+++ b/montepython/cosmo_hammer.py
@@ -188,7 +188,7 @@ def from_CH_output_to_chains(folder):
     for x, p in zip(chains, lkl):
         if p != -np.inf:
             chainsClean.append(x)
-            lklClean.append([p])
+            lklClean.append([-p])  # MP stores -loglkl in its files.
         else:
             error.append([val for val in x if not np.isnan(val)])  # Remove nan's
 

From f8b41424040b691acb22975a3939737b56b1a3eb Mon Sep 17 00:00:00 2001
From: ardok-m <carlosgarcia@iff.csic.es>
Date: Mon, 14 May 2018 13:07:36 +0200
Subject: [PATCH 32/35] sort by name the derived parameters (placed at the end
 of the param list)

---
 montepython/cosmo_hammer.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/montepython/cosmo_hammer.py b/montepython/cosmo_hammer.py
index f73de175..28be6c8f 100644
--- a/montepython/cosmo_hammer.py
+++ b/montepython/cosmo_hammer.py
@@ -219,7 +219,8 @@ def persistValues(self, posFile, probFile, pos, prob, data):
         derived_not_computed = [np.NaN] * len(CH_derived_names)
 
         derived = np.array(
-            [[a for a in elem.itervalues()] if elem else derived_not_computed for elem in data])
+            #[[a for a in elem.itervalues()] if elem else derived_not_computed for elem in data])
+            [[elem[key] for key in sorted(elem.iterkeys())] if elem else derived_not_computed for elem in data])
         final = np.concatenate((pos, derived), axis=1)
 
         posFile.write("\n".join(

From 62315b912c18bbd83787de99d6a392a2398bca1b Mon Sep 17 00:00:00 2001
From: ardok-m <carlosgarcia@iff.csic.es>
Date: Mon, 28 May 2018 10:49:07 +0200
Subject: [PATCH 33/35] fixed Planck_compressed. Use default CLASS vars

---
 montepython/likelihoods/Planck_compressed/__init__.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/montepython/likelihoods/Planck_compressed/__init__.py b/montepython/likelihoods/Planck_compressed/__init__.py
index f378df47..0390461b 100644
--- a/montepython/likelihoods/Planck_compressed/__init__.py
+++ b/montepython/likelihoods/Planck_compressed/__init__.py
@@ -10,10 +10,14 @@ class Planck_compressed(Likelihood):
 
     def loglkl(self, cosmo, data):
 
-        z_star = cosmo.z_optical_depth_unity()  # z at which the optical depth is unity
+        derived_params = cosmo.get_current_derived_parameters(['z_rec', 'rs_rec'])
+
+        #z_star = cosmo.z_optical_depth_unity()  # z at which the optical depth is unity
+        z_star = derived_params['z_rec']  # z at which the optical depth is unity
         # comoving angular diameter distance
         D_A_star = cosmo.angular_distance(z_star) * (z_star + 1)
-        rs_star = cosmo.rs_at_z(z_star)
+        #rs_star = cosmo.rs_at_z(z_star)
+        rs_star = derived_params['rs_rec']
 
         R = np.sqrt(cosmo.Omega_m()) * cosmo.Hubble(0) * D_A_star
         l_a = np.pi * D_A_star / rs_star

From 81788c56e89749f7bff0831c5b2dffe5c8d7da75 Mon Sep 17 00:00:00 2001
From: ardok-m <carlosgarcia@iff.csic.es>
Date: Wed, 20 Jun 2018 10:42:10 +0200
Subject: [PATCH 34/35] fixed error storing derived parameters

---
 montepython/cosmo_hammer.py | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/montepython/cosmo_hammer.py b/montepython/cosmo_hammer.py
index 28be6c8f..93d3a108 100644
--- a/montepython/cosmo_hammer.py
+++ b/montepython/cosmo_hammer.py
@@ -235,7 +235,7 @@ def persistValues(self, posFile, probFile, pos, prob, data):
 
 def store_cosmo_derived(ctx):
     """
-    Store derived parameters. Copied from sampler.compute_lkl
+    Store derived parameters. Based on sampler.compute_lkl
     """
     from classy import CosmoSevereError
 
@@ -246,8 +246,6 @@ def store_cosmo_derived(ctx):
         try:
             derived = cosmo.get_current_derived_parameters(
                 data.get_mcmc_parameters(['derived']))
-            for name, value in derived.iteritems():
-                data.mcmc_parameters[name]['current'] = value
         except AttributeError:
             # This happens if the classy wrapper is still using the old
             # convention, expecting data as the input parameter
@@ -255,6 +253,9 @@ def store_cosmo_derived(ctx):
         except CosmoSevereError:
             raise io_mp.CosmologicalModuleError(
                 "Could not write the current derived parameters")
-    for elem in data.get_mcmc_parameters(['derived']):
-        data.mcmc_parameters[elem]['current'] /= \
-            data.mcmc_parameters[elem]['scale']
+
+    # If we want the derived parameters stored rescaled
+    # derived_scaled = {elem: value/data.mcmc_parameters[elem]['scale'] for elem, value in derived.iteritems()}
+    # ctx.add('key_data', derived_scaled)
+
+    ctx.add('key_data', derived)

From bbcedf87904ecfc7033e4fbbf866ac55109dbdd6 Mon Sep 17 00:00:00 2001
From: ardok-m <carlosgarcia@iff.csic.es>
Date: Wed, 20 Jun 2018 11:25:50 +0200
Subject: [PATCH 35/35] fixed identation in store_cosmo_derived

---
 montepython/cosmo_hammer.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/montepython/cosmo_hammer.py b/montepython/cosmo_hammer.py
index 93d3a108..a384f71e 100644
--- a/montepython/cosmo_hammer.py
+++ b/montepython/cosmo_hammer.py
@@ -254,8 +254,8 @@ def store_cosmo_derived(ctx):
             raise io_mp.CosmologicalModuleError(
                 "Could not write the current derived parameters")
 
-    # If we want the derived parameters stored rescaled
-    # derived_scaled = {elem: value/data.mcmc_parameters[elem]['scale'] for elem, value in derived.iteritems()}
-    # ctx.add('key_data', derived_scaled)
+        ctx.add('key_data', derived)
 
-    ctx.add('key_data', derived)
+        # If we want the derived parameters stored rescaled
+        # derived_scaled = {elem: value/data.mcmc_parameters[elem]['scale'] for elem, value in derived.iteritems()}
+        # ctx.add('key_data', derived_scaled)