Release announcement draft v1.4.0

[teresam856]

Unreleased (2021-09-07)

🚀 Enhancement

• Other
  • #2287 Use react-popper to reduce tooltip lag on pages with many elements (@cmdcolin)
  • #2294 Don't rely on SVTYPE=BND for breakend split view options and thicker mouseover chords on circular views (@cmdcolin)
  • #2272 Auto adjust box RefNameAutocomplete width based on refName length (@cmdcolin)
  • #2243 Import bookmarks functionality for grid bookmark widget (@cmdcolin)
• core
  • #2247 New jbrowse-desktop start screen design (@cmdcolin)
  • #2254 Better error reporting from web worker and chrom sizes adapter errors (@cmdcolin)
  • #1881 Add new text searching functionality to core, with jbrowse text-index CLI command to generate trix index (@teresam856)

🐛 Bug Fix

• Other
  • #2283 Fix ability for the variant detail panel to create breakpoint split view for elements (@cmdcolin)
  • #2268 Fix autocomplete height on small displays (@cmdcolin)
• core
  • #2250 Prevent the ToggleButton for the FileSelector toggling to local file when only URL should be available (@cmdcolin)

📝 Documentation

• #2290 Updates user guide docs to show text searching example (@teresam856)
• #2253 Add note about legacy-peer-deps to readme (@cmdcolin)
• #2262 Add more MDX documentation pages to @jbrowse/react-linear-genome-view storybooks (@cmdcolin)

🏠 Internal

• #2263 Force publish all packages on release (@cmdcolin)

Committers: 3

• Colin Diesh (@cmdcolin)
• Teresa Martinez (@teresam856)
• @Akusem

[codecov]

Codecov Report

Merging #2300 (214937b) into main (82f1318) will decrease coverage by 0.00%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##             main    #2300      +/-   ##
==========================================
- Coverage   61.92%   61.92%   -0.01%     
==========================================
  Files         511      511              
  Lines       23296    23296              
  Branches     5333     5333              
==========================================
- Hits        14427    14426       -1     
- Misses       8601     8602       +1     
  Partials      268      268              

Impacted Files	Coverage Δ
packages/core/assemblyManager/assemblyManager.ts	67.10% <0.00%> (-1.32%)	⬇️
packages/core/util/index.ts	79.84% <0.00%> (ø)

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[garrettjstevens]

Maybe this should be v1.4.0?

Also, are we sure #2289 and #2296 will be backward compatible? If not, I think delaying a couple days until those are done would be worth it.

[cmdcolin]

They should be backwards compatible ....unless we decide we need typed arrays for #2289 (e.g. whole note field instead of just the keyword in the note field that matched)

I'd be ok to delay release to make sure that is ironed out

[teresam856]

Ok. @garrettjstevens @cmdcolin Yeah I think it's good idea to delay. We can release once #2296, #2301 ,and maybe #2303 go in. These three affect the the trix files. Will get to #2301 today.

• Allow text-index to index single files or use a embedded-style config.json #2303 index files when using the embedded mode
• trix index metadata's "dateCreated" isn't always easily parseable #2301 will modify the the dateCreated
• and Update trix to return the matched search term if it is not part of the label #2289 may change the fields in the ix files

[cmdcolin]

I believe we have stabalized the trix format, it resulted actually in no actual change to the format but now allows more than name and id to be serialized. it is actually literally the fields from --attributes that are serialized into the record e.g.

[locString,trackId,...attributes]

by putting all attributes, we can possibly match rich context such as a note attribute. the driver case is e.g. I type kinase on the volvox example, the search result can give me gene name and description

EDEN (protein kinase)

or if it's a long description, it is excerpted and ellipses'd)

EDEN (...something something kinase ....)

it is not currently implemented as a typed array. typed array could allow e.g. a thing like advanced google searches where the fieldname:searchterm is specified but i think we can ship without this for now and i believe we could extend our current format to allow this in the future also (a type id could be part of the record e.g. [locString,trackId,typeId,...typedarray]

[cmdcolin]

final review welcome. try config_demo and volvox demos...links below will be ready soon

large dataset with many dbsnp IDs

https://jbrowse.org/code/jb2/main/index.html?config=test_data/config_demo.json

supports description searching

https://jbrowse.org/code/jb2/main/index.html?config=test_data/volvox/config.json