aisdb

DSiP: AI for Sleep Disordered Breathing

Setup

I recommend using virtualenv for Python development. It is optional, but very helpful and a best practice when working on a team or with different projects. I assume Python 3.7 or newer as well. Personally, I also manage my Python installs using pyenv but that isn't necessary.

Virtual Env setup

You can change the venv directory, but it is handy to just store it inside the project at .venv.

python3 -m venv ./.venv --prompt aisdb
source ./.venv/bin/activate

Install dependencies

Install pip requirements. For some reason pyEDFlib requires separate installation of numpy first. Numpy is included in the requirements.txt.

# Must install numpy first for pyEDFlib
pip install numpy
pip install -r requirements.txt

Start Jupyter lab

jupyter lab

Download data

I am putting the EDF files into a folder called local-data which will not be in git. We do not want EDF files in git because they are far too large. Anything you put into the local-data directory will be ignored by git.

Installing new dependencies

If you need to add new dependencies to the project, be sure to update the requirements.txt so that we can all share the same libraries and run the code. This can be done by updating this file using pip freeze and then committing it to git. Then each of us can use it to make sure our environments match. First, use pip install to install the new libraries, then:

pip freeze > requirements.txt