J. Sebastian Paez

other random thoughts... Questions: 1. Why is the 'id' key in the dict object if the key is also that same identifier? ('analytes': {'1': {id = '1', ...}}). Reading the...

@wfondrie any insights on this and opinion on adopting it for depth charge?

@RalfG what do you thinks ? (if we reach any consensus I would love to add a simple train/test split tutorial in proteomicsML)

@sh0rtcircuit Thanks for the nudge! I added the suggestions in [a51d43f](https://github.com/kynan/nbstripout/pull/195/commits/a51d43ffade1031bb405d73a5da600ee60ab72a9) Also took care of updating to the main branch. @kynan LMK If there is anything else you would like...

Updated the readme on f5b02d2c5abb9e8503f45b39484d8c5cccbd1c69

I had a question on commit 466838cc07095522cc7047a571ea71a82f597477 ... in my system `tests/system_tests/test_cli.py::test_cli_aggregate` (https://github.com/msaid-de/mokapot/blob/c021f0906121c11b457f42e35d9979a7aff53f5c/tests/system_tests/test_cli.py#L136) fails with `assert count_lines(Path(tmp_path, "blah.targets.psms")) == 10256` where the diff is `10298 == 10256`. could we specify...

Just noticed that a lot of the docstrings in your functions are numpy style, whilst the project mostly uses sphinx style ... @wfondrie should we migrate to numpy style? (and...

Hi @ezander ! I submitted a PR to the branch of this PR over here: https://github.com/msaid-de/mokapot/pull/42 ... its mostly chores but it handles lil things like the hard-coded number. LMK...

Post Megamerge wishlist (capture as checklists the future issues detected while discussing this PR): - [ ] Brew refactor https://github.com/wfondrie/mokapot/pull/119/files#r1646576640 - [ ] Break function up - [ ] Remove...

I think T20 can be disabled in everything under the docs dir ...