figure002 / setlyze

An application for analyzing the settlement of marine species on SETL plates.

SETLyze

The purpose of SETLyze is to provide the people involved with the SETL project an easy and fast way of getting useful information from the data stored in the SETL database. The SETL database at GiMaRIS contains data about the settlement of species in Dutch waters. SETLyze helps provide more insight in a set of biological questions by performing a set of analyses on this data.

Requirements

SETLyze has the following dependencies:

• GTK+ (>=2.24.0,!=2.24.8,!=2.24.10)
• R
• Python (>=2.6 & <2.8)
  • appdirs
  • PyGTK, PyCairo, and PyGObject
  • pandas
  • RPy2
  • xlrd (>=0.8)

On Debian (based) systems, the dependencies can be installed from the software repository:

sudo apt-get install python-appdirs python-gtk2 python-pandas python-rpy2 \
python-xlrd r-base-core

More recent versions of some Python packages can be obtained via the Python Package Index:

pip install -r requirements.txt

Windows users can install the PyGTK all-in-one Windows installer. Then use pip as described above to install the remaining dependencies. Note that this step is not needed if you have the Windows installer for SETLyze, which comes bundeled with the requirements.

Installation

From the GitHub repository:

git clone https://github.com/figure002/setlyze.git
pip install setlyze/

Or if you have a source archive file:

pip install setlyze-x.x.tar.gz

Tests

Run the unit tests with:

python -m unittest discover -v

Or if you have Make:

make test

Documentation

The documentation can be found here:

http://setlyze.readthedocs.org/

Alternatively, the same documentation can be built using Sphinx:

$ python setup.py build_sphinx

Then launch build/sphinx/html/index.html in your browser.

Contributing

Please follow the next steps:

1. Fork the project on github.com.
2. Create a new branch.
3. Commit changes to the new branch.
4. Send a pull request.

First make sure that all dependencies are installed as described above. Then follow the next steps to run and develop SETLyze within a virtualenv isolated Python environment:

$ git clone https://github.com/YOUR-USERNAME/setlyze.git
$ cd setlyze/
$ virtualenv --system-site-packages env
$ source env/bin/activate
(env)$ pip install -r requirements.txt
(env)$ python setup.py develop
(env)$ setlyze

License

SETLyze is free software. See LICENSE.txt for details.