Data analysis for real-time deformability cytometry (RTDC)
Project description
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.
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
Make sure that the changelog (develop) is updated and that the version (develop) is incremented.
Create a pull request from develop into master using the web interface or simply run
git checkout master git pull origin develop git push
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:
The rest should contain the change log. Make sure to check This is a pre-release box.
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.
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
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