prep for version 3.7.1

gplepage · May 30, 2014 · 8f80cc5 · 8f80cc5
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diff --git a/CHANGES b/CHANGES
@@ -11,13 +11,33 @@
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
 
-Version 3.7+ - ????
-====================
+Version 3.7.1 - 2014-05-30
+===========================
+Small updates.
 
 - Allow tol=(reltol,abstol) in CorrFitter so relative and absolute 
   fit tolerances can be set separately. In the past tol was a single
   number which was used for both reltol and abstol. This is still 
   supported but one can instead use a tuple to specify them separately.
+  The default tolerance (1e-10) is probably smaller than it should be;
+  1e-4 is probably good enough for many applications.
+
+- New function corrfitter.read_dataset(files) reads Monte Carlo data
+  for correlators into a gvar.dataset.Dataset. Instead of writing
+
+    dset = gvar.dataset.Dataset(files)
+
+  one can now write
+
+    dset = corrfitter.read_dataset(files)
+
+  Either method works, but the second method supports a new file format
+  for correlator data. A lot of simulation code dumps each correlator 
+  into a separate file, with each line having a t and G(t). This format
+  can be read by read_data directly, without having to convert to the 
+  traditional gvar.dataset.Dataset format. To use this format, argument
+  files has to be a dictionary. Each key k is the name (datatag) of a correlator,
+  and files[k] is the name of the file containing that correlator's data.
 
 Version 3.7 - 2014-05-12
 =========================

diff --git a/INSTALLATION b/INSTALLATION
@@ -31,7 +31,8 @@ To install:
    successful if the output ends with "OK". (To test an installation
    for a different version of Python, say python3, use 'make PYTHON=python3 
 	tests'.) If 'make' is unavailable (non-unix systems), 
-	'python -m unittest discover' can be used to run the tests.
+	'python -m unittest discover' can be used to run the tests from 
+	inside the tests/ directory.
 
 4. (Optional) Look at the examples of corrfitter use in the examples/
    directory; run them all using 'make run-examples'.

diff --git a/corrfitter.py b/corrfitter.py
@@ -56,9 +56,10 @@
 import numpy
 import math
 import collections
+import fileinput
 import copy
 import time
-__version__ = '3.7'
+__version__ = '3.7.1'
 
 if not hasattr(collections,'OrderedDict'):
     # for older versions of python
@@ -1612,4 +1613,77 @@ def __init__(
         self.Q = numpy.array([self.Q, lsqfit.wavg.Q])
 
 
+def read_dataset(inputfiles, tcol=0, Gcol=1):
+    """ Read correlator Monte Carlo data from files into a :class:`gvar.dataset.Dataset`.
+
+    Two files formats are supported by :func:`read_dataset`, depending upon the 
+    data type of ``inputfiles``. 
+
+    The first file format is that normally used by :class:`gvar.dataset.Dataset`:
+    each line consists of a  tag or key identifying a correlator
+    followed by data corresponding to  a single Monte Carlo measurement of the
+    correlator. This format is assumed if ``inputfiles`` is a filename or a
+    list of filenames. It allows a single file to contain an arbitrary number
+    of measurements for an arbitrary number of different correlators. The data
+    can also be spread over multiple files. A typical file might look like ::
+
+        # this is a comment; it is ignored
+        aa 1.237 0.912 0.471            
+        bb 3.214 0.535 0.125 
+        aa 1.035 0.851 0.426            
+        bb 2.951 0.625 0.091
+        ...
+
+    which describes two correlators, ``aa`` and ``bb``, each having 
+    three different ``t`` values.
+
+    The second file format is assumed when ``inputfiles`` is a dictionary. The
+    dictionary's keys and values identify the (one-dimensional) correlators
+    and the files containing their Monte Carlo data, respectively. So the
+    data for correlators ``aa`` and ``bb`` above are in separate files::
+
+        fileinputs = dict(aa='aafile', bb='bbfile')
+
+    Each line in these data files consists of an index ``t`` value followed by
+    the corresponding value for correlator ``G(t)``.  The ``t``\s increase
+    from line to line up to their maximum value,  at which point they repeat.
+    The ``aafile`` file for correlator ``aa`` above  would look like::
+
+        # this is a comment; it is ignored
+        1 1.237                
+        2 0.912
+        3 0.471
+        1 1.035                 
+        2 0.851
+        3 0.426
+        ...
+
+    The columns in these files containing ``t`` and ``G(t)`` are 
+    assumed to be columns 0 and 1, respectively. These can be changed 
+    by setting arguments ``tcol`` and ``Gcol``, respectively.
+    """
+    if not hasattr(inputfiles, 'keys'):
+        # inputfiles is a filename or list of filenames (or files)
+        return _gvar.dataset.Dataset(inputfiles)
+    # inputfiles is a dictionary 
+    # files are in t-G format
+    dset = _gvar.dataset.Dataset()
+    for k in inputfiles:
+        tlast = - float('inf')
+        G = []
+        for line in fileinput.input([inputfiles[k]]):
+            f = line.split()
+            if f[0][0] == '#':
+                # comment
+                continue
+            t = eval(f[tcol])
+            if t <= tlast:
+                dset.append(k, numpy.array(G))
+                G = [eval(f[Gcol])]
+            else:
+                G.append(eval(f[Gcol]))
+            tlast = t
+        dset.append(k, numpy.array(G))
+    return dset
+
 
diff --git a/doc/html/.buildinfo b/doc/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: c14d310d52f00576391659d848229956
+config: f129d7bbd794bbe8b972258072992f86
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/doc/html/.doctrees/corrfitter.doctree b/doc/html/.doctrees/corrfitter.doctree
diff --git a/doc/html/.doctrees/environment.pickle b/doc/html/.doctrees/environment.pickle
diff --git a/doc/html/corrfitter.html b/doc/html/corrfitter.html
@@ -6,15 +6,15 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 
-    <title>corrfitter - Least-Squares Fit to Correlators &mdash; corrfitter 3.7 documentation</title>
+    <title>corrfitter - Least-Squares Fit to Correlators &mdash; corrfitter 3.7.1 documentation</title>
 
     <link rel="stylesheet" href="_static/pyramid.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
 
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    './',
-        VERSION:     '3.7',
+        VERSION:     '3.7.1',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -23,7 +23,7 @@
     <script type="text/javascript" src="_static/jquery.js"></script>
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
-    <link rel="top" title="corrfitter 3.7 documentation" href="index.html" />
+    <link rel="top" title="corrfitter 3.7.1 documentation" href="index.html" />
     <link rel="prev" title="corrfitter Documentation" href="index.html" />
 <link rel="stylesheet" href="http://fonts.googleapis.com/css?family=Neuton&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
 <link rel="stylesheet" href="http://fonts.googleapis.com/css?family=Nobile:regular,italic,bold,bolditalic&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
@@ -43,7 +43,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="index.html" title="corrfitter Documentation"
              accesskey="P">previous</a> |</li>
-        <li><a href="index.html">corrfitter 3.7 documentation</a> &raquo;</li> 
+        <li><a href="index.html">corrfitter 3.7.1 documentation</a> &raquo;</li> 
       </ul>
     </div>  
 
@@ -2802,7 +2802,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="index.html" title="corrfitter Documentation"
              >previous</a> |</li>
-        <li><a href="index.html">corrfitter 3.7 documentation</a> &raquo;</li> 
+        <li><a href="index.html">corrfitter 3.7.1 documentation</a> &raquo;</li> 
       </ul>
     </div>
     <div class="footer">

diff --git a/doc/html/genindex.html b/doc/html/genindex.html
@@ -7,15 +7,15 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 
-    <title>Index &mdash; corrfitter 3.7 documentation</title>
+    <title>Index &mdash; corrfitter 3.7.1 documentation</title>
 
     <link rel="stylesheet" href="_static/pyramid.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
 
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    './',
-        VERSION:     '3.7',
+        VERSION:     '3.7.1',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -24,7 +24,7 @@
     <script type="text/javascript" src="_static/jquery.js"></script>
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
-    <link rel="top" title="corrfitter 3.7 documentation" href="index.html" />
+    <link rel="top" title="corrfitter 3.7.1 documentation" href="index.html" />
 <link rel="stylesheet" href="http://fonts.googleapis.com/css?family=Neuton&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
 <link rel="stylesheet" href="http://fonts.googleapis.com/css?family=Nobile:regular,italic,bold,bolditalic&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
 <!--[if lte IE 6]>
@@ -40,7 +40,7 @@ <h3>Navigation</h3>
         <li class="right" style="margin-right: 10px">
           <a href="#" title="General Index"
              accesskey="I">index</a></li>
-        <li><a href="index.html">corrfitter 3.7 documentation</a> &raquo;</li> 
+        <li><a href="index.html">corrfitter 3.7.1 documentation</a> &raquo;</li> 
       </ul>
     </div>  
 
@@ -312,7 +312,7 @@ <h3>Navigation</h3>
         <li class="right" style="margin-right: 10px">
           <a href="#" title="General Index"
              >index</a></li>
-        <li><a href="index.html">corrfitter 3.7 documentation</a> &raquo;</li> 
+        <li><a href="index.html">corrfitter 3.7.1 documentation</a> &raquo;</li> 
       </ul>
     </div>
     <div class="footer">

diff --git a/doc/html/index.html b/doc/html/index.html
@@ -6,15 +6,15 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 
-    <title>corrfitter Documentation &mdash; corrfitter 3.7 documentation</title>
+    <title>corrfitter Documentation &mdash; corrfitter 3.7.1 documentation</title>
 
     <link rel="stylesheet" href="_static/pyramid.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
 
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    './',
-        VERSION:     '3.7',
+        VERSION:     '3.7.1',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -23,7 +23,7 @@
     <script type="text/javascript" src="_static/jquery.js"></script>
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
-    <link rel="top" title="corrfitter 3.7 documentation" href="#" />
+    <link rel="top" title="corrfitter 3.7.1 documentation" href="#" />
     <link rel="next" title="corrfitter - Least-Squares Fit to Correlators" href="corrfitter.html" />
 <link rel="stylesheet" href="http://fonts.googleapis.com/css?family=Neuton&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
 <link rel="stylesheet" href="http://fonts.googleapis.com/css?family=Nobile:regular,italic,bold,bolditalic&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
@@ -43,7 +43,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="corrfitter.html" title="corrfitter - Least-Squares Fit to Correlators"
              accesskey="N">next</a> |</li>
-        <li><a href="#">corrfitter 3.7 documentation</a> &raquo;</li> 
+        <li><a href="#">corrfitter 3.7.1 documentation</a> &raquo;</li> 
       </ul>
     </div>  
 
@@ -129,7 +129,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="corrfitter.html" title="corrfitter - Least-Squares Fit to Correlators"
              >next</a> |</li>
-        <li><a href="#">corrfitter 3.7 documentation</a> &raquo;</li> 
+        <li><a href="#">corrfitter 3.7.1 documentation</a> &raquo;</li> 
       </ul>
     </div>
     <div class="footer">

diff --git a/doc/html/objects.inv b/doc/html/objects.inv
diff --git a/doc/html/search.html b/doc/html/search.html
@@ -6,15 +6,15 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 
-    <title>Search &mdash; corrfitter 3.7 documentation</title>
+    <title>Search &mdash; corrfitter 3.7.1 documentation</title>
 
     <link rel="stylesheet" href="_static/pyramid.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
 
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    './',
-        VERSION:     '3.7',
+        VERSION:     '3.7.1',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -24,7 +24,7 @@
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
     <script type="text/javascript" src="_static/searchtools.js"></script>
-    <link rel="top" title="corrfitter 3.7 documentation" href="index.html" />
+    <link rel="top" title="corrfitter 3.7.1 documentation" href="index.html" />
   <script type="text/javascript">
     jQuery(function() { Search.loadIndex("searchindex.js"); });
   </script>
@@ -47,7 +47,7 @@ <h3>Navigation</h3>
         <li class="right" style="margin-right: 10px">
           <a href="genindex.html" title="General Index"
              accesskey="I">index</a></li>
-        <li><a href="index.html">corrfitter 3.7 documentation</a> &raquo;</li> 
+        <li><a href="index.html">corrfitter 3.7.1 documentation</a> &raquo;</li> 
       </ul>
     </div>  
 
@@ -95,7 +95,7 @@ <h3>Navigation</h3>
         <li class="right" style="margin-right: 10px">
           <a href="genindex.html" title="General Index"
              >index</a></li>
-        <li><a href="index.html">corrfitter 3.7 documentation</a> &raquo;</li> 
+        <li><a href="index.html">corrfitter 3.7.1 documentation</a> &raquo;</li> 
       </ul>
     </div>
     <div class="footer">