shapeout 0.8.0

User interface for real-time deformability cytometry (RT-DC)

ShapeOut is 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.

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.

• Windows: Sketchy installation instructions are here and here.

• Debian: Run this script 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 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.

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. 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) is updated and that the version (develop) 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 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