Merge mixins branch back to master

README.md

@@ -1,159 +1,162 @@
-Introduction
-============
-
-The *Stoner* Python package is a set of utility classes for writing data
-analysis code. It was written within the Condensed Matter Physics group
-at the University of Leeds as a shared resource for quickly writing
-simple programs to do things like fitting functions to data, extract
-curve parameters and churn through large numbers of small text data
-files.
-
-For a general introduction, users are referred to the Users Guide, which
-is part of the [online documentation](http://pythonhosted.org/Stoner/)
-along with the API Reference guide. The [github
-repository](http://www.github.com/gb119/Stoner-PythonCode/) also
-contains some example scripts.
-
-Getting this Code
-=================
-
-The *Stoner* package requires numpy \>=1.8, scipy \>=0.14, matplotlib
-\>=1.4, h5py, numba lmfit, filemagic, and blist. Experimental code also
-makes use of the Enthought Tools Suite packages.
-
-Ananconda Python (and probably other scientific Python distributions)
-include nearly all of the dependencies, aprt from lmfit. However, this
-can by installed with the usual tools such as *easy\_install* or *pip*.
-
-``` {.sourceCode .sh}
-easy_install lmfit
-```
-
-The easiest way to install the Stoner package is via seuptools'
-easy\_install
-
-``` {.sourceCode .sh}
-easy_install Stoner
-```
-
-This will install the Stoner package and any missing dependencies into
-your current Python environment. Since the package is under fairly
-constant updates, you might want to follow the development with git. The
-source code, along with example scripts and some sample data files can
-be obtained from the github repository:
-<https://github.com/gb119/Stoner-PythonCode>
-
-The codebase is largely compatible with Python 3.4, with the expception
-of the 3D vector map plots which make use of Enthought's *mayavi*
-package which is still only Python 2 compatible due to the underlying
-Vtk toolkit. Other issues of broken 3.4 code are bugs to be squashed.
-
-Overview
-========
-
-The **Stoner** package provides two basic top-level classes that
-describe an individual file of experimental data and a list (such as a
-directory tree on disc) of many experimental files. For our research, a
-typical single experimental data file is essentially a single 2D table
-of floating point numbers with associated metadata, usually saved in
-some ASCII text format. This seems to cover most experiments in the
-physical sciences, but it you need a more complex format with more
-dimensions of data, we suggest you look elsewhere.
-
-DataFile and Friends
---------------------
-
-**Stoner.Core.DataFile** is the base class for representing individual
-experimental data sets. It provides basic methods to examine and
-manipulate data, manage metadata and load and save data files. It has a
-large number of sub classes - most of these are in Stoner.FileFormats
-and are used to handle the loading of specific file formats. Two,
-however, contain additional functionality for writing analysis programs.
-
--   **Stoner.Analysis.AnalyseFile** provides additional methods for curve-fitting, differentiating, smoothing and carrying out
-    :   basic calculations on data.
-
--   **Stoner.Plot.PlotFile** provides additional routines for plotting
-    data on 2D or 3D plots.
-
-As mentioned above, there are subclasses of **DataFile** in the
-**Stoner.FileFormats** module that support loading many of the common
-file formats used in our research.
-
-For rapid development of small scripts, we would recommend the
-**Stoner.Data** class which is a superclass of the above, and provides a
-'kitchen-sink' one stop shop for most of the package's functionality.
-
-DataFolder
-----------
-
-**Stoner.Folders.DataFolder** is a class for assisting with the work of
-processing lots of files in a common directory structure. It provides
-methods to list. filter and group data according to filename patterns or
-metadata and then to execute a function on each file or group of files.
-
-The **Stoner.HDF5** module provides some experimental classes to
-manipulate *DataFile* and *DataFolder* objects within HDF5 format files.
-These are not a way to handle arbitary HDF5 files - the format is much
-to complex and flexible to make that an easy task, rather it is a way to
-work with large numbers of experimental sets using just a single file
-which may be less brutal to your computer's OS than having directory
-trees with millions of individual files.
-
-Resources
-=========
-
-Included in the [github
-repository](http://www.github.com/gb119/Stoner-PythonCode/) are a
-(small) collection of sample scripts for carrying out various operations
-and some sample data files for testing the loading and processing of
-data. There is also a User\_Guide as part of this documentation, along
-with a complete API reference \<Stoner\>
-
-Contact and Licensing
-=====================
-
-The lead developer for this code is [Dr Gavin
-Burnell](http://www.stoner.leeds.ac.uk/people/gb)
-\<<g.burnell@leeds.ac.uk>\> . The User Guide gives the current list of
-other contributors to the project.
-
-This code and the sample data are all (C) The University of Leeds
-2008-2015 unless otherwise indficated in the source file. The contents
-of this package are licensed under the terms of the GNU Public License
-v3
-
-Recent Changes
-==============
-
-Development Version
--------------------
-
-Teh current development version is 0.7. Features of 0.7 include
-
-> -   DataFolder now defaults to using :pyStoner.Util.Data
-> -   DataFolder has an options to skip iterating over empty Data files
-> -   Further improvements to :pyStoner.Core.DataFile.setas handline.
-
-Online documentation for the development version can be found on the
-[githib repository pages](http://gb119.github.io/Stoner-PythonCode)
-
-[![image](https://zenodo.org/badge/17265/gb119/Stoner-PythonCode.svg)](https://zenodo.org/badge/latestdoi/17265/gb119/Stoner-PythonCode)
-
-Stable Version
---------------
-
-The current stable version is 0.6. This features some major changes in
-the architecture, switching from a numpy MaskedArray as the main data
-store to a custom sub-class that contains most of the logic for indexing
-data by column name and designation. The metadata storage has also been
-switched to using blist.sortteddict for a fast, alphabetically ordered
-dictionary storage. Other underlying changes are a switch to using
-properties rather than straight attribute access.
-
-0.6 now also makes use of filemagic to work out the mime type of files
-to be loaded to try and improve the resilience of the automatic file
-format detection on platforms where this is supported and adds some
-extra methods to AnalyseFile for extrapolation.
-
-0.6 should work on Python 2.7 and 3.5
+Introduction
+============
+
+The *Stoner* Python package is a set of utility classes for writing data
+analysis code. It was written within the Condensed Matter Physics group
+at the University of Leeds as a shared resource for quickly writing
+simple programs to do things like fitting functions to data, extract
+curve parameters and churn through large numbers of small text data
+files.
+
+For a general introduction, users are referred to the Users Guide, which
+is part of the [online documentation](http://pythonhosted.org/Stoner/)
+along with the API Reference guide. The [github
+repository](http://www.github.com/gb119/Stoner-PythonCode/) also
+contains some example scripts.
+
+Getting this Code
+=================
+
+The *Stoner* package requires numpy &gt;=1.8, scipy &gt;=0.14,
+matplotlib &gt;=1.5, h5py, numba lmfit, filemagic, and blist.
+Experimental code also makes use of the Enthought Tools Suite packages.
+
+Ananconda Python (and probably other scientific Python distributions)
+include nearly all of the dependencies, aprt from lmfit. However, this
+can by installed with the usual tools such as *easy\_install* or *pip*.
+
+``` {.sourceCode .sh}
+easy_install lmfit
+```
+
+The easiest way to install the Stoner package is via seuptools'
+easy\_install
+
+``` {.sourceCode .sh}
+easy_install Stoner
+```
+
+This will install the Stoner package and any missing dependencies into
+your current Python environment. Since the package is under fairly
+constant updates, you might want to follow the development with git. The
+source code, along with example scripts and some sample data files can
+be obtained from the github repository:
+<https://github.com/gb119/Stoner-PythonCode>
+
+The codebase is largely compatible with Python 3.4, with the expception
+of the 3D vector map plots which make use of Enthought's *mayavi*
+package which is still only Python 2 compatible due to the underlying
+Vtk toolkit. Other issues of broken 3.4 code are bugs to be squashed.
+
+Overview
+========
+
+The **Stoner** package provides two basic top-level classes that
+describe an individual file of experimental data and a list (such as a
+directory tree on disc) of many experimental files. For our research, a
+typical single experimental data file is essentially a single 2D table
+of floating point numbers with associated metadata, usually saved in
+some ASCII text format. This seems to cover most experiments in the
+physical sciences, but it you need a more complex format with more
+dimensions of data, we suggest you look elsewhere.
+
+DataFile and Friends
+--------------------
+
+**Stoner.Core.DataFile** is the base class for representing individual
+experimental data sets. It provides basic methods to examine and
+manipulate data, manage metadata and load and save data files. It has a
+large number of sub classes - most of these are in Stoner.FileFormats
+and are used to handle the loading of specific file formats. Two,
+however, contain additional functionality for writing analysis programs.
+
+-   
+
+    **Stoner.Analysis.AnalyseFile** provides additional methods for curve-fitting, differentiating, smoothing and carrying out
+
+    :   basic calculations on data.
+
+-   **Stoner.Plot.PlotFile** provides additional routines for plotting
+    data on 2D or 3D plots.
+
+As mentioned above, there are subclasses of **DataFile** in the
+**Stoner.FileFormats** module that support loading many of the common
+file formats used in our research.
+
+For rapid development of small scripts, we would recommend the
+**Stoner.Data** class which is a superclass of the above, and provides a
+'kitchen-sink' one stop shop for most of the package's functionality.
+
+DataFolder
+----------
+
+**Stoner.Folders.DataFolder** is a class for assisting with the work of
+processing lots of files in a common directory structure. It provides
+methods to list. filter and group data according to filename patterns or
+metadata and then to execute a function on each file or group of files.
+
+The **Stoner.HDF5** module provides some experimental classes to
+manipulate *DataFile* and *DataFolder* objects within HDF5 format files.
+These are not a way to handle arbitary HDF5 files - the format is much
+to complex and flexible to make that an easy task, rather it is a way to
+work with large numbers of experimental sets using just a single file
+which may be less brutal to your computer's OS than having directory
+trees with millions of individual files.
+
+Resources
+=========
+
+Included in the [github
+repository](http://www.github.com/gb119/Stoner-PythonCode/) are a
+(small) collection of sample scripts for carrying out various operations
+and some sample data files for testing the loading and processing of
+data. There is also a User\_Guide as part of this documentation, along
+with a complete API reference &lt;Stoner&gt;
+
+Contact and Licensing
+=====================
+
+The lead developer for this code is [Dr Gavin
+Burnell](http://www.stoner.leeds.ac.uk/people/gb)
+&lt;<g.burnell@leeds.ac.uk>&gt; . The User Guide gives the current list
+of other contributors to the project.
+
+This code and the sample data are all (C) The University of Leeds
+2008-2015 unless otherwise indficated in the source file. The contents
+of this package are licensed under the terms of the GNU Public License
+v3
+
+Recent Changes
+==============
+
+Development Version
+-------------------
+
+Teh current development version is 0.7. Features of 0.7 include
+
+> -   DataFolder now defaults to using :pyStoner.Util.Data
+> -   DataFolder has an options to skip iterating over empty Data files
+> -   Further improvements to :pyStoner.Core.DataFile.setas handline.
+
+Online documentation for the development version can be found on the
+[githib repository pages](http://gb119.github.io/Stoner-PythonCode)
+
+[![image](https://zenodo.org/badge/17265/gb119/Stoner-PythonCode.svg)](https://zenodo.org/badge/latestdoi/17265/gb119/Stoner-PythonCode)
+
+Stable Version
+--------------
+
+The current stable version is 0.6. This features some major changes in
+the architecture, switching from a numpy MaskedArray as the main data
+store to a custom sub-class that contains most of the logic for indexing
+data by column name and designation. The metadata storage has also been
+switched to using blist.sortteddict for a fast, alphabetically ordered
+dictionary storage. Other underlying changes are a switch to using
+properties rather than straight attribute access.
+
+0.6 now also makes use of filemagic to work out the mime type of files
+to be loaded to try and improve the resilience of the automatic file
+format detection on platforms where this is supported and adds some
+extra methods to AnalyseFile for extrapolation.
+
+0.6 should work on Python 2.7 and 3.5

Stoner/Analysis.py

@@ -17,7 +17,12 @@
 from inspect import getargspec,isclass
 from collections import Iterable
 try:  #Allow lmfit to be optional
-    from lmfit.model import Model, ModelFit
+    import lmfit
+    if LooseVersion(lmfit.__version__)<LooseVersion("0.9.0"):
+        from lmfit.model import Model, ModelFit
+    else:
+        from lmfit.model import Model
+        from lmfit.model import ModelResult as ModelFit
     from lmfit import Parameters
     _lmfit=True
 except ImportError:
@@ -709,8 +714,7 @@ def curve_fit(self, func, xcol=None, ycol=None, p0=None, sigma=None, **kargs):
         if output == "full":
             kargs["full_output"] = True
 
-        _=self._col_args(xcol=xcol,ycol=ycol,yerr=sigma,scalar=False)
-
+        _=self._col_args(scalar=False,xcol=xcol,ycol=ycol,yerr=sigma)
         xcol,ycol,sigma=_.xcol,_.ycol,_.yerr
 
         working = self.search(xcol, bounds)

Stoner/compat.py

@@ -85,3 +85,4 @@ def get_filedialog(what="file", **opts):
             return funcs[what](**opts)
 
 index_types = string_types + (int, _pattern_type)
+from distutils.version import LooseVersion

Stoner/stylelib/JTB.mplstyle

@@ -1,4 +1,4 @@
-axes.color_cycle:k,r,b,g,c,m,y
+axes.prop_cycle:cycler("color","krbgcmy")
 axes.formatter.limits:-3, 3
 axes.grid:False
 axes.labelsize:18

Stoner/stylelib/JTBinset.mplstyle

@@ -1,4 +1,4 @@
-axes.color_cycle:k,r,b,g,c,m,y
+axes.prop_cycle:cycler("color":"krbgcmy")
 axes.formatter.limits:-4, 4
 axes.grid:False
 axes.labelsize:16

Stoner/stylelib/default.mplstyle

@@ -1,4 +1,4 @@
-axes.color_cycle:K, r, g, b, c, m, y
+axes.prop_cycle:cycler('color',"Krgbcmy")
 axes.formatter.limits:-1, 1
 axes.grid:False
 axes.labelsize:12

Stoner/stylelib/sketch.mplstyle

@@ -1,4 +1,4 @@
-axes.color_cycle:b, r, g, c, m, y
+axes.prop_cycle:cycler("color":"brgcmy")
 font.family: Comic Sans MS
 xtick.direction:inout
 ytick.direction:inout

doc/UserGuide/credits.rst

@@ -6,13 +6,13 @@ A number of current and former members of the Condensed Matter Physics Group
 at the University of Leeds have contributed to this code in various forms.
 
 The original versions were developped by Dr Matthew Newman and Dr Chris Allen.
-Rowan Temple, Sophie Morely and Joe Batley have all contributed file formats,
-plot styles. They, and Dr May Wheeler, Philippa Shepley and Nathan Satchell have 
+Dr Rowan Temple, Dr Sophie Morely and Dr Joe Batley have all contributed file formats,
+plot styles. They, and Dr May Wheeler, Dr Philippa Shepley and Nathan Satchell have 
 found bugs and made helpful suggestions.
 
 The lead developer is Dr Gavin Burnell <g.burnell@leeds.ac.uk>. Most of the
 development of this code has been indirectly supported by the UK Engineering
 and Physical Sciences Research Council.
 
 The code, except where otherwise noted, is Copyrigt The University of Leeds 
-2008-2015 and is released under the GNU Public License v3.
+2008-2016 and is released under the GNU Public License v3.