Impact assists scientists and engineers to interpret data describing microbial physiology. Impact parses raw data from common equipment such as chromatography (HPLC), and plate readers. Data is automatically interpreted and built into hierarchical objects which describe the experiments and extract features.
Download a Python 3 installation for your platform, or you can use Anaconda. If you are on windows, you will need a way to install numpy, scipy, matplotlib - packaged with Anaconda.
First, clone the repository. You will need your github username and password but if you are here presumably you are logged in.
git clone http://github.com/nvenayak/impact
cd impact
Install the dependencies for the project using requirements.txt:
pip install -r requirements.txt
You may also want to install the additional packages as needed, especially the plotting requirements
pip install -r requirements_plotting.txt
pip install -r requirements_modeling.txt
pip install -r requirements_docs.txt
Install the package
python setup.py install
Optionally, developers may wish to use the develop flag to install the package from the current location, rather than installing in the default Python installation
python setup.py develop
To update to the latest version, run the following in the root folder:
git pull
Impact comes with scripts that test the proper functioning of the package. These are available in the tests folder. Every build of impact is tested with these scripts before deployment on github.
The documentation is available in docs or a rendered version is available here
A starter ipynb which can be opened with Jupyter notebook has been provided in the Examples_and_Helpers folders. The file comes with comments which will assist users in analyzing their data. A helper file to create trial identifiers has also been provided in the Examples_and_Helpers folder.