Metadata-Version: 1.1
Name: shapeout
Version: 0.7.8.dev29
Summary: Data analysis for real-time deformability cytometry (RTDC)
Home-page: https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut
Author: Paul Müller
Author-email: paul.mueller@biotec.tu-dresden.de
License: GPL v2
Description: |ShapeOut|
        ==========
        
        |PyPI Version| |Build Status Win| |Coverage Status|
        
        
        This repository contains a graphical user interface for the analysis
        and visualization of RT-DC data sets. For more informaion please visit
        http://zellmechanik.com/.
        
        
        Manual and User Guide
        ---------------------
        The manual and user guide can be found at http://www.zellmechanik.com/download.
        
        
        Installation
        ------------
        Installers for ShapeOut are available at the `release page <https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut/releases>`__.
        
        
        Citing ShapeOut
        ---------------
        Please cite ShapeOut either in-line
        
        ::
        
          (...) using the analysis software ShapeOut version X.X.X (available at
          https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut).
        
        or in a bibliography
        
        ::
          
          Paul Müller and others (2015), ShapeOut version X.X.X: Analysis software
          for real-time deformability cytometry [Software]. Available at
          https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut.
        
        and replace ``X.X.X`` with the version of ShapeOut that you used.
        
        
        Information for developers
        --------------------------
        
        Running from source
        ~~~~~~~~~~~~~~~~~~~
        The easiest way to run ShapeOut from source is to use
        `Anaconda <http://continuum.io/downloads>`__. 
        
        - **Windows**: Sketchy installation instructions are 
          `here <https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut/tree/master/freeze_appveyor>`__ and 
          `here <https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut/blob/master/appveyor.yml>`__.
        
        - **Debian**: Run `this script <https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut/blob/master/develop/activate_linux.sh>`__
          which will create a Python virtual environment.
        
        - **MacOS**: ShapeOut should work with Anaconda (see Windows above).
          It is also possible to install all dependencies with MacPorts:
        
          ::
          
            sudo port install python27 py27-ipython py27-scipy py27-matplotlib
            sudo port install opencv +python27
            sudo port install py27-wxpython-3.0 py27-statsmodels py27-kiwisolver py27-chaco py27-pip py27-simplejson py27-sip py27-macholib
            sudo pip-2.7 install nptdms
            sudo pip-2.7 install pyper
        
        
          Then select python27 (macports) as standard python interpreter:
        
          ::
          
            sudo port select --set python python27
            sudo port select --set pip pip27
        
          Check-out `dclab <https://github.com/ZELLMECHANIK-DRESDEN/dclab>`__ and
          append the following command to ``~/.bash_profile``
          
          ::
          
            #!/bin/bash
            export PYTHONPATH="${PYTHONPATH}:/path/to/dclab"
        
          start ShapeOut with
        
          ::
          
            python shapeout/ShapeOut.py
        
          This can be put into a .command file placed on the Desktop.
        
        
        
        Contributing
        ~~~~~~~~~~~~
        The main branch for developing ShapeOut 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 edit the 
        `Changelog <https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut/blob/master/CHANGELOG>`__. 
        
        **Very important:** Please always try to use 
        
        ::
        
        	git pull --rebase
        
        instead of
        
        ::
        
        	git pull
        	
        to prevent confusions in the commit history.
        
        Tests
        ~~~~~
        ShapeOut 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:
        
        ::
        
            python setup.py test
        	
        
        Test binaries
        ~~~~~~~~~~~~~
        After each commit to the ShapeOut repository, a binary installer is created
        by `Appveyor <https://ci.appveyor.com/project/paulmueller/ShapeOut>`__. 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 executable
        Windows installer.
        
        
        Creating releases
        ~~~~~~~~~~~~~~~~~
        Please **do not** create releases when you want to test if something you
        did works in the final Windows binary. Use the method described above to
        do so. Releases should be created when improvements were made,
        bugs were resolved, or new features were introduced.
        
        Procedure
        _________
        1. Make sure that the `changelog (develop) <https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut/blob/develop/CHANGELOG>`__
           is updated and that the `version (develop) <https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut/blob/develop/shapeout/_version.py>`__
           is incremented.
        
        2. Create a pull request from develop into master using the web interface or simply run
        
           ::
        
               git checkout master  
               git pull origin develop  
               git push  
        	
        3. Create the release at https://github.com/ZELLMECHANIK-DRESDEN/ShapeOut/releases.  
           Make sure that the tag of the release follows the version format of ShapeOut
           (e.g. `0.5.3`) and also name the release correctly (e.g. `ShapeOut 0.5.3`).
           Also, copy and paste the change log of the new version into the comments of the release.
           The first line of the release comments should contain the download counts shield like so:
           
           ::
           
               ![](https://img.shields.io/github/downloads/ZELLMECHANIK-DRESDEN/ShapeOut/0.5.3/total.svg)
           
           The rest should contain the change log.  
           Make sure to check `This is a pre-release` box.
           
        4. Once the release is created, `Appveyor <https://ci.appveyor.com/project/paulmueller/ShapeOut>`__
           will perform the build process and upload the installation files directly to the release. 
           If the binary works, edit the release and uncheck the `This is a pre-release` box.
        
        5. Make sure that all the changes you might have performed on the `master` branch are brought back
           to ``develop``.
           
           ::
        
               git checkout develop  
               git pull origin master  
               git pull --tags origin master
               git push     
        
        
        .. |ShapeOut| image:: https://raw.github.com/ZELLMECHANIK-DRESDEN/ShapeOut/master/art/shapeout_logotype_h50.png
        .. |PyPI Version| image:: http://img.shields.io/pypi/v/ShapeOut.svg
           :target: https://pypi.python.org/pypi/dclab
        .. |Build Status Win| image:: https://img.shields.io/appveyor/ci/paulmueller/ShapeOut/master.svg?label=build_win
           :target: https://ci.appveyor.com/project/paulmueller/ShapeOut
        .. |Coverage Status| image:: https://img.shields.io/codecov/c/github/ZELLMECHANIK-DRESDEN/ShapeOut/master.svg
           :target: https://codecov.io/gh/ZELLMECHANIK-DRESDEN/ShapeOut
Keywords: RT-DC,cytometry
Platform: ALL
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2.7
Classifier: Intended Audience :: Science/Research
