Release 0.12.0

[khoroshevskyi]

Changes:

• Added UMAP embedding of the file
• Added 2D UMAP visualization
• Added BED analyzer to bedbase

TODO:

• Version of pepdbagent updated in __version__.py file
• Changelog updated

[sanghoonio]

ui feedback and bugs

umap page:

• hover prevents tooltip focus
• summary figures on the right for given selection?
• deselect button from selection table
• show neighbors option for upload bed file

bed2bed search

• locate button should be on umap instead of search bar
• umap should have full width option

homepage:

• umap preview should either make main umap page easier to access (/umap redirect button?), or be replaced with a screenshot/graphic

[khoroshevskyi]

I was consulting with a few people who don’t know what Bedbase is, and these were their comments:

• Landing page

  • The text is too small and hard to read, and eyes are getting tired faster.
  • There are several fields (code), but no explanation of what they mean, so they didn’t know what to do with them. They prefer more text with visualization then compact fields
  • The UMAP on the front page was confusing — they didn’t know how to use it. They suggested having it as a link with a short description instead.
  • The top navbar text is too small. People preferred having icons so they don’t need to read as much.

• Bed page

  • Metadata appears in two places (left and right) and isn’t organized in columns, which is harder to navigate by eye.
  • The text is too small, and there’s too much white space
  • Since we can many items, they suggested using a table layout.
  • For lists of bedsets and similar files, a table layout is also better — it makes it easier to compare elements.(e.g. if all elements are chip-seq, or atac-seq). Looking at each file individually makes comparison harder.

• Search

  • Same as before: text is too small, metadata isn’t shown in a table way, and comparing items takes more time.
  • The UMAP in Bed-to-Bed search is nice, but people were confused why UMAP appears in two different places.

Because of this comments I will close this PR for now. I will leave main elements, that were added here, and move all code to new ui branch, for later discussion.