Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Idhandling I #378

Merged
merged 75 commits into from
Nov 27, 2024
Merged

Idhandling I #378

merged 75 commits into from
Nov 27, 2024

Conversation

JuliaS92
Copy link
Collaborator

Major changes:

  • MaxQuant is now filtered for lines with overflowing ids
  • gene to protein id mapping is replaced by 3 new dictionaries (two are currenlty unused but will be in the next PRs)
  • Intensity plot is updated to handle lists of feature ids as facets

@JuliaS92 JuliaS92 mentioned this pull request Nov 20, 2024
Merged
@JuliaS92
Copy link
Collaborator Author

The failing tests are fixed in the next PR #379

@JuliaS92
Copy link
Collaborator Author

All resolved conversations were either addressed in the two child branches, or added as TODO in this commit: adb223e

JuliaS92 and others added 21 commits November 25, 2024 12:41
@JuliaS92
Implement quick wins or add TODOs according to PR comments #379
5dc8f2c
@JuliaS92
TODOs from PR conversation
d34cadc
@JuliaS92
Merge pull request #383 from MannLabs/annotation-retrieval
9b6131a 
Annotation retrieval and textualization
Squashing the whole id feature into one PR, step 1 of two.
@JuliaS92
Merge branch 'idhandling' into idhandling-ii
1e7634a
@JuliaS92
Merge pull request #379 from MannLabs/idhandling-ii
f96dc60 
Idhandling ii
Squashing the whole feature of renewed id handling into 1 PR step 2.
@JuliaS92
Fix test
df4281c
@JuliaS92
Iterator TODO
c4de9cb
@JuliaS92
Raise on invalid gene lookup, write tests for intensity plots from ge…
972a4e9 
…ne name
@JuliaS92
remove todo
5206286
@JuliaS92
Run LLM checkbox list on just one session state key.
e6ced77
@JuliaS92
pass session state elements to display function
4500b2f
@JuliaS92
2 minor changes
ac7e71b
@JuliaS92
Move uniprot retrieval from dict to list, and an empty one in case of…
0873ea0 
… errors or no data.
@JuliaS92
Add caution comments
f3ade6d
@JuliaS92
Split uniprot result selection into two functions
f1768ab
@JuliaS92
simplify pathway extraction
bb4e0e2
@JuliaS92
make intensity column calling a method of the base loader
eb8e43e
@JuliaS92
Document maxquant data handling better
0df1df3
@JuliaS92
Last minor changes
7e2ae7c
@JuliaS92
simplify formatting of uniprot content
dc3035d
@JuliaS92
fix test
af2f702
@JuliaS92
Copy link
Collaborator Author

I realize now this was not the best workflow to squash the reviews. You can get an overview of the changes made to address all your comments on the three squashed PRs here:
https://github.com/MannLabs/alphapeptstats/compare/f96dc60..af2f702

Quick fixes were included here and here

@JuliaS92 JuliaS92 requested a review from mschwoer November 26, 2024 13:52
mschwoer
mschwoer approved these changes Nov 27, 2024
View reviewed changes
Copy link
Contributor

@mschwoer mschwoer left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM!
(the code, not the review workflow :-p)

alphastats/gui/utils/llm_helper.py Outdated Show resolved Hide resolved
alphastats/gui/utils/llm_helper.py Outdated Show resolved Hide resolved
alphastats/gui/utils/llm_helper.py Outdated Show resolved Hide resolved
alphastats/gui/utils/llm_helper.py Outdated Show resolved Hide resolved
alphastats/gui/utils/llm_helper.py Outdated Show resolved Hide resolved
alphastats/gui/utils/ui_helper.py Outdated Show resolved Hide resolved
alphastats/llm/uniprot_utils.py Outdated Show resolved Hide resolved
alphastats/llm/uniprot_utils.py Show resolved Hide resolved
alphastats/gui/pages/05_Analysis.py Outdated Show resolved Hide resolved
alphastats/gui/pages/06_LLM.py Show resolved Hide resolved
@JuliaS92 JuliaS92 merged commit d5a8279 into development Nov 27, 2024
5 checks passed
@JuliaS92 JuliaS92 deleted the idhandling branch November 27, 2024 13:44
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@boopthesnoot boopthesnoot boopthesnoot approved these changes

@mschwoer mschwoer mschwoer approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@JuliaS92 @boopthesnoot @mschwoer