Alex Dewar

> PS -- the tests are failing on this branch because my PAT has expired. I'll generate a new one. Done. The new one will expire in 30 days.

> LGTM and merging since it passes and the handover meeting has passed, assuming no further changes to remaining PRs outside of mine and Antoine's ownership. We'll finish up anything...

Sure. I'll do that now. This PR might break some of the regression tests for private data. I guess maybe it would be worth merging #265 first so that we...

Done. Amusingly, now "Auto-CORPus" itself appears in the list of abbreviations, when it didn't before (there are no other changes, except that "CRIS-CODE" is now included again). Auto-CORPus is 11...

For anyone who's interested, I reran AC over the private test data to see how the results changed for the abbreviations file. Here's the result: ```patch diff --git c/html/PMC/PMC10627243_abbreviations.json w/html/PMC/PMC10627243_abbreviations.json...

I'm also having this problem. Links to local files in markdown files in the reference style seem to be ignored even when they're broken 😞

I have a branch with this on, but as some of the items on the checklist refer to things we haven't implemented yet (e.g. `pytest`, `pre-commit`) I'll hold off on...

@Thomas-Rowlands This is the library we're already using: https://pypi.org/project/filetype/ Might be worth seeing if it does what you need. If you end up using a different library instead, it probably...

I've written some notes based on a quick audit of the code I've done and a conversation with @AdrianDAlessandro. I figured it would be easiest if I put these in...

Click's neat. It also supports setting console colours, so we could use this to colourise the log output. It also has its own progress bar implementation, so we could replace...