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.
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.
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
Run the unit tests with:
python -m unittest discover -v
Or if you have Make:
make test
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.
Please follow the next steps:
- Fork the project on github.com.
- Create a new branch.
- Commit changes to the new branch.
- 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
SETLyze is free software. See LICENSE.txt for details.