Issue with deidentification script

[slstaples]

Hi! Just reporting an issue I've encountered running the automatic deidentification script in CIABATTA. It's removing text from the body of the paper, which is not our intended/expected outcome.

[markfullmer]

@vnatara , I was chatting with @cbdilger earlier today and he mentioned that you were working on updating some of the regular expressions so that punctuation wouldn't be stripped out. I'm wondering if this is the same as the issue that @slstaples is reporting, above.

If it seems distinct, can you create a new issue in this repository to describe the punctuation stripping problem, and give an example (without any real identifying information)? We can then collaboratively use the example(s) to ensure that changes to the regular expression do what they should, and have the Github issue as a reference point for the future.

[vnatara]

Hmm, I think this is a different issue. My issue is with the interactive manual de-identification tool, not the automatic script like she mentioned. By the way, I've just finished writing up a fix to the punctuation issue and I was going to push it but I don't see the de-id improvements branch anymore. How should I go about pushing some new code?