Problem with installing medaCy

[justachetan]

Description

Hi. I am trying to install medaCy on my system using the instructions given in the README, however, I am getting some error caused due to unavailability of some SpaCy models.

Steps/Code to Reproduce

Run:
pip install git+https://github.com/NLPatVCU/medaCy.git

Output

Collecting git+https://github.com/NLPatVCU/medaCy.git
       Cloning https://github.com/NLPatVCU/medaCy.git to /tmp/pip-k5kMwQ-build
Collecting en_core_web_sm@ https://github.com/explosion/spacy-models/releases/download/en_core_web_sm-2.0.0/en_core_web_sm-2.0.0.tar.gz#egg=en_core_web_sm-2.0.0 (from medacy==0.1.0)
        Could not find a version that satisfies the requirement en_core_web_sm@ https://github.com/explosion/spacy-models/releases/download/en_core_web_sm-2.0.0/en_core_web_sm-2.0.0.tar.gz#egg=en_core_web_sm-2.0.0 (from medacy==0.1.0) (from versions: )
No matching distribution found for en_core_web_sm@ https://github.com/explosion/spacy-models/releases/download/en_core_web_sm-2.0.0/en_core_web_sm-2.0.0.tar.gz#egg=en_core_web_sm-2.0.0 (from medacy==0.1.0)

Versions

• Linux-4.4.0-17134-Microsoft-x86_64-with-Ubuntu-18.04-bionic
• NumPy 1.16.3
• SciPy 1.3.0
• medaCy not installed, the issue is about that only

[jvargas2]

@justachetan Have you tried upgrading pip with pip install -U pip? If upgrading pip isn't an option then you should be able to download the en_core_web_sm model through spaCy. Other projects have had similar issues with automatically downloading spaCy models: allenai/allennlp#918

[justachetan]

Yes, I had to download the model separately. I must say I am kinda disappointed with the performance of the pre-trained models of medaCy.

[jyaoeplus]

encounter an error with code line "from medacy.pipelines import ClinicalPipeline"
Error message:
ModuleNotFoundError: No module named 'medacy.pipelines':

"pipelines" subdirectory not found under medacy, shown as:

ls /conda/envs/rapids/lib/python3.6/site-packages/medacy**

init.py pycache ner relation tools
main.py data pipeline_components tests

how to fix it?