Installation¶
Stable release¶
To install ehrapy, run this command in your terminal:
pip install ehrapy
This is the preferred method to install ehrapy, as it will always install the most recent stable release.
If you don’t have pip installed, this Python installation guide can guide you through the process.
If you run into “RuntimeError: CMake must be installed to build qdldl” ensure that you have CMake installed to build lightgbm.
Run conda install -c anaconda cmake
and conda install -c conda-forge lightgbm
to do so.
If you intend to run MedCAT you have to install a language model like:
python -m spacy download en_core_web_sm
From sources¶
The sources for ehrapy can be downloaded from the Github repo.
You can either clone the public repository:
git clone git://github.com/theislab/ehrapy
Or download the tarball:
curl -OJL https://github.com/theislab/ehrapy/tarball/master
MedCAT/Spacy language models¶
If you want to run and use medcat with ehrapy, you first have to install the medcat extra:
pip install ehrapy[medcat]
Available language models are
en_core_web_md (python -m spacy download en_core_web_md)
en-core-sci-sm (pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_sm-0.4.0.tar.gz)
en-core-sci-md (pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_md-0.4.0.tar.gz)
en-core-sci-lg (pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_lg-0.4.0.tar.gz)