JOSS Review Overview - Githubissues

j-andrews7 commented 6 months ago

I am going to keep a list/links to individual issues here for the JOSS review to help keep things organized for myself as I go through. This is well put together - much of this will be stuff that I'd like to see as a user and a few things that stand out from the developer side.

I'll ping you here when I am done with my initial review.

Should be done:

[x] Minor text edits & cite networkx - #3
[x] Fix duplicate inputs bug - #8
[x] Custom GAF index use unclear - #12
[x] Document custom index should be made from gzipped GAF - #11

Would prefer to see done:

[x] Host web server - #4
[x] Utilize bottle via imports rather than inclusion in source - #5
[x] High resolution image download from GUI - #6
[x] Download annotations table directly from GUI - #10
[x] Leaf node coloring when filtering applied - #13

Worth considering:

[x] Support other gene identifiers - #7

Nitpicks/oddities:

[x] Input box resizing - #9

j-andrews7 commented 6 months ago

Alright @ialbert, I think I'm done with a first pass. All of my points have individual issues, so I'm happy to discuss any of them individually. Many are quick fixes, a few are questions - just let me know if anything is unclear.

ialbert commented 6 months ago

@j-andrews7 all issues addressed,

thanks for the suggestion for using Shiny - it worked out really well and I learned a new skill, that of developing Shiny apps with Python.

j-andrews7 commented 6 months ago

Okay, I'm pretty happy with the changes. Will mark my review complete over on the JOSS issue as well. Nice job on the quick fixes.

ialbert / genescape-central

JOSS Review Overview #2