Code for producing AGAGE archival files
Clone this repository using the address in the green <> code dropdown at the top of the Github page using:
git clone <address>
It will be easiest to create a new conda environment, conda conda create --name agage_env then intall pip using conda install pip.
Alternatively, if avoiding conda, install a virtual environment using python -m venv agage_env and activate this using source agage_env/bin/activate.
Make sure that you have installed the required dependencies (see requirements.txt), which can be done using pip install -r requirements.txt.
Allow the package to be callable using pip install --no-build-isolation --no-deps -e.
If using conda, you can use conda develop, but note that this functionality is now depricated.
Before beginning, run the configuration setup script, which can be accessed as:
python agage_archive/config.py
Input a descriptive user name when prompted. This function will create a file agage_archive/config.yaml, which contains the default input and output data paths. Note that these paths will be relative to the data/network directory within this repository.
We use git and dvc to track code and data files for this project. Read the workflow document for usage details.
See the notes document for methodological details and citations.