Merge pull request #183 from FCS-analysis/develop

1.1.1

CHANGELOG

@@ -1,3 +1,6 @@
+1.1.1
+ - Fix plotting error with LaTeX (thanks @toubol) (#179)
+ - Update documentation
 1.1.0
  - BREAKING CHANGE: Move to Python3 (thanks @toubol) (#173)
  - GUI:

docs/sec_contribute.rst

@@ -33,46 +33,86 @@ the PyCorrFit issue page on GitHub such that we may coordinate a pull
 request.
 
 
+For documentation writers
+=========================
+To build this documentation, fork PyCorrFit, navigate
+to the `docs` (not `doc`) directory and run.
+
+- ``pip install -r requirements.txt`` followed by
+- ``sphinx-build . _build``.
+
+This will create the html documentation on your computer. Syntax warnings and errors
+will be displayed during the build (there should be none). After making your
+changes to your forked branch, create a pull request on GitHub.
+
+If you only found a typo or wish to make text-only changes, you can also
+use the GitHub interface to edit the files (without testing the build
+step on your computer).
+
+
 For developers
 ==============
-If you would like to know how a contribution to PyCorrFit should look
-like, please create an issue on GitHub and I will update this part
-of the documentation.
-
 
 Running from source
 -------------------
-The easiest way to run PyCorrFit from source is to use
-`Anaconda <http://continuum.io/downloads>`_. PyCorrFit requires wxPython which is not
-available at the Python package index. Make sure you install a unicode version of wxPython.
-Detailed installation instructions are `here <https://github.com/FCS-analysis/PyCorrFit/wiki/Running-from-source>`_.
-
-
-Contributing
-------------
-The main branch for developing PyCorrFit is *develop*. Small changes that do not
-break anything can be submitted to this branch.
-If you want to do big changes, please (fork ShapeOut and) create a separate branch,
-e.g. ``my_new_feature_dev``, and create a pull-request to *develop* once you are done making
-your changes.
-Please make sure to also update the 
-`changelog <https://github.com/FCS-analysis/PyCorrFit/blob/develop/CHANGELOG>`_. 
-
-Tests
------
+It is recommended to work with
+`virtual environments <https://docs.python.org/3/tutorial/venv.html>`_.
+
+Windows
+~~~~~~~
+The easiest way to run PyCorrFit from source on Windows is
+`Anaconda <http://continuum.io/downloads>`_.
+
+- ``conda install matplotlib numpy pip scipy wxpython``
+- ``pip install cython wheel simplejson sympy lmfit``
+- ``pip install -e .  # in the root directory of the repository`` 
+
+Ubuntu 17.10
+~~~~~~~~~~~~
+PyCorrFit requires wxPython >= 4.0.1 which is not available as a binary
+wheel on PyPI and thus must be built from the .tar.gz.
+Install all dependencies (https://github.com/wxWidgets/Phoenix/blob/master/README.rst):
+
+- ``pip install cython matplotlib lmfit numpy scipy sympy``
+- ``sudo apt-get install -qq libgtk2.0 libgtk2.0-dev libwebkitgtk-dev dpkg-dev build-essential python3.6-dev libjpeg-dev libtiff-dev libsdl1.2-dev libnotify-dev freeglut3 freeglut3-dev libsm-dev libgtk-3-dev libwebkit2gtk-4.0-dev libxtst-dev libgstreamer-plugins-base1.0-dev``
+- ``pip install wxPython  # this will take some time``
+- ``pip install -e .  # in the root directory of the repository`` 
+
+Testing
+-------
 PyCorrFit is tested using pytest. If you have the time, please write test
 methods for your code and put them in the ``tests`` directory. You may
-run the tests manually by issuing:
+run all tests by issuing:
 
 ::
 
     python setup.py test
 
 
+Pull request guidelines
+-----------------------
+Please fork PyCorrFit and create a pull request (PR) introducing your changes.
+
+- A new PR should always be made into the `develop` branch.
+- If a PR introduces a new functionality or fixes a bug, it should provide
+  a test case, i.e. a new file or function in the `tests` directory
+  (see `here <https://github.com/FCS-analysis/PyCorrFit/tree/develop/tests>`_
+  for examples).
+  Note that currently there is no recipe for testing the graphical user
+  interface code.
+- New code should follow the
+  `style guide for Python <https://www.python.org/dev/peps/pep-0008/>`_.
+  Please use `flake8 <http://flake8.pycqa.org/en/latest/index.html#quickstart>`_
+  to check the files you changed or created.
+- New code should be documented well.
+- Make sure to update the `changelog <https://github.com/FCS-analysis/PyCorrFit/blob/develop/CHANGELOG>`_. 
+
+
 Windows test binaries
 ---------------------
 After each commit to the PyCorrFit repository, a binary installer is created
 by `Appveyor <https://ci.appveyor.com/project/paulmueller/PyCorrFit>`_. Click
 on a build and navigate to ``ARTIFACTS`` (upper right corner right under
-the running time of the build). From there you can download the Windows installer of the commit.
+the running time of the build). From there you can download the Windows
+installer for the commit.
 

pycorrfit/gui/misc.py

@@ -108,6 +108,6 @@ def getMainIcon(pxlength=32):
     image = wx.Bitmap.ConvertToImage(iconBMP)
     image = image.Scale(pxlength, pxlength, wx.IMAGE_QUALITY_HIGH)
     iconBMP = wx.Bitmap(image)
-    iconICO = wx.Icon(iconBMP)  # wx.Bitmap.ConvertToImage(iconBMP)
+    iconICO = wx.Icon(iconBMP)
     return iconICO
 

pycorrfit/gui/plotting.py

@@ -7,6 +7,7 @@
 
 import matplotlib
 import numpy as np
+import re
 
 # We do catch warnings about performing this before matplotlib.backends stuff
 with warnings.catch_warnings():
@@ -70,6 +71,7 @@ def latexmath(string):
     unicodechars["³"] = r"^3"
     unicodechars["₁"] = r"_1"
     unicodechars["₂"] = r"_2"
+    unicodechars["₃"] = r"_3"
     unicodechars["₀"] = r"_0"
     #unicodechars["α"] = r"\alpha"
     # We need lambda in here, because unicode names it lamda sometimes.
@@ -107,6 +109,26 @@ def latexmath(string):
     return anew + r" \hspace{0.3em} \mathrm{"+b+r"}"
 
 
+def genLatexText(parm, labels):
+    """Generate the LaTeX text for the plot with handling multiple underscores
+    in the labels.
+    """
+    text = r''
+    for i in np.arange(len(parm)):
+        line = r' {} &= {:.3g} \\'.format(latexmath(labels[i]), parm[i])
+        match = re.search(r'\\text\{(.*?)\}', line)
+        if match:
+            if '_' in match.groups()[0]:
+                tmpstr = match.groups()[0].split('_')
+                if ''.join(tmpstr).isnumeric():
+                    line = line.replace(match.groups()[0], ''.join(tmpstr))
+                elif len(tmpstr) == 2:
+                    tmpstr = '$_'.join(tmpstr) + '$'
+                    line = line.replace(match.groups()[0], tmpstr)
+        text += line
+    return text
+
+
 def savePlotCorrelation(parent, dirname, Page, uselatex=False,
                         verbose=False, show_weights=True):
     """ Save plot from Page into file
@@ -215,11 +237,9 @@ def savePlotCorrelation(parent, dirname, Page, uselatex=False,
     # Add some nice text:
     if uselatex == True and len(parms) != 0:
         text = r""
-        text += r'\['            #every line is a separate raw string...
-        text += r'\begin{split}' # ...but they are all concatenated
-        #                          by the interpreter :-)
-        for i in np.arange(len(parms)):
-            text += r' {} &= {:.3g} \\'.format(latexmath(labels[i]), parms[i])
+        text += r'\['
+        text += r'\begin{split}'
+        text += genLatexText(parms, labels)
         ## According to issue #54, we remove fitting errors from plots
         #if errparms is not None:
         #    keys = errparms.keys()
@@ -422,4 +442,4 @@ def savePlotTrace(parent, dirname, Page, uselatex=False, verbose=False):
             pass
 
 # set dpi to 300
-matplotlib.rcParams['savefig.dpi'] = 300
+matplotlib.rcParams['savefig.dpi'] = 300