Replaced old examples and documentation.

Updated prep tools, and added makesdist script.
Updated licenses.
More sensible default values for command-line tool.
Improved interface for creating and interrogating model covariance.
Improved automated qmax detection with forced oversampling, and a new exception.
Qmax now defaults to using the reported value, but using automatic value added as keyword.
Deleted Lorentzian from repository, since it was never fully implemented.
Deleted various obsolete test code.

All other changes are minor or superficial.

Author: Ainamacar

.gitignore

@@ -42,6 +42,3 @@ nosetests.xml
 # version information
 setup.cfg
 /diffpy/srmise/version.cfg
-
-# Any auxiliary files in documentation
-/diffpy/srmise/documentation

INSTALL.txt

@@ -5,8 +5,9 @@ program by citing the following paper in your publication:
     L. Granlund, S.J.B. Billinge, P.M. Duxbury, Algorithm for
     systematic peak extraction from atomic pair distribution
     functions, Acta Crystallographica A 71(4), ???-??? (2015).
+    doi:10.1107/S2053273315005276
 
-Copyright 2015, Board of Trustees of Michigan State University
+Copyright 2014-2015, Board of Trustees of Michigan State University
 
 For more information please visit the diffpy web-page at
     http://www.diffpy.org

LICENSE.txt

@@ -1,4 +1,4 @@
-SrMise incorporates source code from the PDFgui program in the file
+SrMise incorporates source code from diffpy.pdfgui in the file
 pdfdataset.py. The PDFgui license is reproduced in full below.
 ===================================================================
 

LICENSE_PDFgui.txt

@@ -0,0 +1,130 @@
+diffpy.srmise
+========================================================================
+
+Tool for unbiased peak extraction from atomic pair distribution functions.
+
+The diffpy.srmise package is an implementation of the `ParSCAPE algorithm  
+<https://dx.doi.org/10.1107/S2053273315005276>`_ for peak extraction from 
+atomic pair distribution functions (PDFs).  It is designed to function even 
+when *a priori* knowledge of the physical sample is limited, utilizing the 
+Akaike Information Criterion (AIC) to estimate whether peaks are 
+statistically justified relative to alternate models.  Three basic use cases 
+are anticipated for diffpy.srmise.  The first is peak fitting a user-supplied 
+collections of peaks.  The second is peak extraction from a PDF with no (or 
+only partial) user-supplied peaks.  The third is an AIC-driven multimodeling 
+analysis where the output of multiple diffpy.srmise trials are ranked. 
+
+The framework for peak extraction defines peak-like clusters within the data, 
+extracts a single peak within each cluster, and iteratively combines nearby 
+clusters while performing a recursive search on the residual to identify 
+occluded peaks.  Eventually this results in a single global cluster 
+containing many peaks fit over all the data.  Over- and underfitting are 
+discouraged by use of the AIC when adding or removing (during a pruning step) 
+peaks.  Termination effects, which can lead to physically spurious peaks in 
+the PDF, are incorporated in the mathematical peak model and the pruning step 
+attempts to remove peaks which are fit better as termination ripples due to 
+another peak. 
+
+Where possible, diffpy.srmise provides physically reasonable default values 
+for extraction parameters.  However, the PDF baseline should be estimated by 
+the user before extraction, or by performing provisional peak extraction with 
+varying baseline parameters.  The package defines a linear (crystalline) 
+baseline, arbitrary polynomial baseline, a spherical nanoparticle baseline, 
+and an arbitrary baseline interpolated from a list of user-supplied values.  
+In addition, PDFs with accurate experimentally-determined uncertainties are 
+necessary to provide the most reliable results, but historically such PDFs 
+are rare.  In the absence of accurate uncertainties an ad hoc uncertainty 
+must be specified. 
+
+For more information about the diffpy.srmise library, see the users manual at
+http://diffpy.github.io/diffpy.srmise.
+
+REQUIREMENTS
+------------------------------------------------------------------------
+
+The diffpy.srfit package requires Python 2.6 or 2.7 and the following software:
+
+* ``setuptools`` - software distribution tools for Python
+* ``NumPy`` - numerical mathematics and fast array operations for Python
+* ``SciPy`` - scientific libraries for Python
+* ``matplotlib`` - python plotting library
+
+On Ubuntu Linux, the required software can easily be installed using
+the system package manager::
+
+   sudo apt-get install \
+      python-setuptools python-numpy python-scipy python-matplotlib
+
+For Mac OS X systems with the MacPorts package manager, the required
+software can be installed with ::
+
+   sudo port install \
+      python27 py27-setuptools py27-numpy py27-scipy py27-matplotlib
+
+When installing for MacPorts, make sure the MacPorts bin directory is the first
+in the system PATH and that python27 is selected as the default Python version
+in MacPorts::
+
+   sudo port select --set python python27
+
+For Windows systems, it is recommended to install all dependencies using 
+prebuilt binaries.  Visit http://www.scipy.org and http://www.matplotlib.org 
+for instructions.  Alternately, install a full Python distribution such as 
+Python(x,y) or Enthought Canopy which already include the required 
+components. 
+
+INSTALLATION
+------------------------------------------------------------------------
+
+The simplest way to obtain diffpy.srmise on Unix, Linux, and Mac systems is 
+using ``easy_install`` to download and install the latest release from 
+`Python Package Index <https://pypi.python.org>`_ :: 
+
+   sudo easy_install diffpy.srmise
+
+If you prefer to install from sources, make sure all required software packages
+are in place and then run ::
+
+   sudo python setup.py install
+
+This installs diffpy.srmise for all users in the default system location. If 
+administrator (root) access is not available, see the usage info from 
+``python setup.py install --help`` for options to install to user-writable 
+directories.
+
+To install on Windows run either of the commands above omitting ``sudo``.  
+While diffpy.srmise will run on Windows, note that Windows is not currently 
+supported in the official DiffPy-CMI release containing all diffpy 
+subpackages. 
+
+
+DEVELOPMENT
+------------------------------------------------------------------------
+
+diffpy.srmise is open-source software developed with support of the Center of 
+Research Excellence in Complex Materials at Michigan State University, in 
+cooperation with the DiffPy-CMI complex modeling initiative at the Brookhaven 
+National Laboratory.  The diffpy.srmise sources are hosted at 
+https://github.com/diffpy/diffpy.srmise. 
+
+Feel free to fork the project and contribute.  To install diffpy.srmise in a 
+development mode, with its sources being directly used by Python rather than 
+copied to a package directory, use :: 
+
+   python setup.py develop --user
+
+
+ACKNOWLEDGEMENT
+------------------------------------------------------------------------
+
+The source code of *pdfdataset.py* was derived from diffpy.pdfgui.
+
+
+CONTACTS
+------------------------------------------------------------------------
+
+For more information on diffpy.srmise please visit the project web-page
+
+http://www.diffpy.org
+
+or email Prof. Simon Billinge at [email protected].

README.rst

@@ -0,0 +1,43 @@
+#!/usr/bin/env python
+
+'''Create source distribution tar.gz archive, where each file belongs
+to a root user and modification time is set to the git commit time.
+'''
+
+import sys
+import os
+import subprocess
+import time
+import glob
+import tarfile
+
+BASEDIR = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
+sys.path.insert(0, BASEDIR)
+
+from setup import versiondata
+timestamp = versiondata.getint('DEFAULT', 'timestamp')
+
+print 'Run "setup.py sdist --formats=tar"',
+cmd_sdist = [sys.executable] + 'setup.py sdist --formats=tar'.split()
+ec = subprocess.call(cmd_sdist, cwd=BASEDIR, stdout=open(os.devnull, 'w'))
+if ec:  sys.exit(ec)
+print "[done]"
+
+tarname = max(glob.glob(BASEDIR + '/dist/*.tar'), key=os.path.getmtime)
+
+tfin = tarfile.open(tarname)
+tfout = tarfile.open(tarname + '.gz', 'w:gz')
+
+def fixtarinfo(tinfo):
+    tinfo.uid = tinfo.gid = 0
+    tinfo.uname = tinfo.gname = 'root'
+    tinfo.mtime = timestamp
+    tinfo.mode &= ~0o022
+    return tinfo
+
+
+print 'Filter %s --> %s.gz' % (2 * (os.path.basename(tarname),)),
+for ti in tfin:
+    tfout.addfile(fixtarinfo(ti), tfin.extractfile(ti))
+os.remove(tarname)
+print "[done]"

devutils/makesdist

@@ -58,21 +58,25 @@ def scrubeol(directory, filerestr):
 
 if __name__ == "__main__":
 
+    # Temporarily add examples to path
+    lib_path = os.path.abspath(os.path.join('..','doc','examples'))
+    sys.path.append(lib_path)
+
     ### Testing examples
     examples = Test()
-    from diffpy.srmise.applications.examples import C60, caffeine, SrTiO3_qmax26, C60multiextract, C60multimodel
-    examples.test(C60.run, plot=False)
-    examples.test(caffeine.run, plot=False)
-    examples.test(SrTiO3_qmax26.run, plot=False)
-    examples.test(C60multiextract.run, plot=False)
-    examples.test(C60multimodel.main, ['--report', '--savepwa'])
-    
+    import Ag_singlepeak, Ag_multiplepeaks, TiO2_parameterdetail, TiO2_initialpeaks, C60_multimodelextraction, C60_multimodelanalysis
+    examples.test(Ag_singlepeak.run, plot=False)
+    examples.test(Ag_multiplepeaks.run, plot=False)
+    examples.test(TiO2_parameterdetail.run, plot=False)
+    examples.test(TiO2_initialpeaks.run, plot=False)
+    examples.test(C60_multimodelextraction.run, plot=False)
+    examples.test(C60_multimodelanalysis.run, plot=False)
     examples.report()
 
     ### Convert output of example files to Unix-style endlines for sdist.
     if os.linesep != '\n':
         print "==== Scrubbing Endlines ===="
         # All *.srmise and *.pwa files in examples directory.
-        scrubeol("diffpy/srmise/applications/examples", r".*(\.srmise|\.pwa)")
+        scrubeol("../doc/examples/output", r".*(\.srmise|\.pwa)")
 
 

prep.py devutils/prep.py

@@ -21,7 +21,7 @@
 
 from basefunction import BaseFunction
 from dataclusters import DataClusters
-from modelcluster import ModelCluster
+from modelcluster import ModelCluster, ModelCovariance
 from modelparts import ModelPart, ModelParts
 from pdfdataset import PDFDataSet
 from pdfpeakextraction import PDFPeakExtraction