search

kdpsingh / clinspacy

Clinical Natural Language Processing using spaCy, scispacy, and medspacy
Other
96 stars 19 forks source link

Update clinspacy.R #18

Open cjannuzzo opened 5 months ago

cjannuzzo commented 5 months ago

First - thank you so much for the development of this package. It truly is awesome. I was getting a few errors so I made tweaks and wanted to share. Would you be able to review and see if it works for you? Also, I couldn't test use_linker = TRUE because I don't have enough RAM

nlp$add_pipe now references “entity_linker”, “medspacy_context”, or “medspacy_sectionizer”

removed version specifications from all py_install or updated version

changed medspacy$context$ConTextComponent to medspacy$context$ConText

kdpsingh commented 5 months ago

Thank you thank you thank you. I will take a look at this in the next two days and will merge as long as it looks good on my end. Then we can release to CRAN. It's been a while since I've done that but I still have some vague memories.

kdpsingh commented 5 months ago

I had a chance to quickly look over the code (on my phone) and saw that you removed several of the version numbers from the Python packages.

Quick question: do you know if conda is smart enough to figure out which versions of spacy, scispacy, and medspacy are compatible with one another? I had an issue earlier on where a newer version of spacy was incompatible with medspacy, which is why I think I added version numbers in the first place.

In any case, I'll run this when I have some time on a computer. If the dependencies work, I'm okay with leaving things without version numbers for now at least to get the package back up and running.

cjannuzzo commented 5 months ago

I'm not sure about conda. The package worked without specifying versions, so at least right now everything is compatible. It installed medspacy 1.0.1, scispacy is 0.2.5 and spacy is 3.7.4 for adding them back into the package