@jbrowse/plugin-menus - npm Package Versions

3.6.0 (2025-07-10)

:rocket: Enhancement

• Other
  • #5102 Refactor CLI to use built-in nodejs parseArgs (@cmdcolin)
  • #5090 Optimize some MM tag parsing for performance and readability (@cmdcolin)
  • #5087 Better usage of dark mode on sequence track (@cmdcolin)
• core
  • #5095 Fix alpha rendering of SVG renderer box stroke/fill (@cmdcolin)
  • #5086 Add status message reporting for synteny view loading (@cmdcolin)

:bug: Bug Fix

• Other
  • #5100 Fix adding .pif file from dotplot and linear synteny import form (@cmdcolin)
  • #5098 Also migrate the linear-comparative-view rubberband tooltip to default MUI tooltip to avoid potential UI hangs (@cmdcolin)
  • #5097 Fix make pif on large files throwing ENOBUFS error in certain cases (@cmdcolin)
  • #5089 Additional type check to catch non-string MM tags from older Cell Ranger version BAM files (@haessar)
  • #5085 Fix rubberband getting stuck under certain conditions (@cmdcolin)
  • #5080 Fix crash on multi-wiggle importer on jbrowse-web (@cmdcolin)
• core
  • #5095 Fix alpha rendering of SVG renderer box stroke/fill (@cmdcolin)

:memo: Documentation

• #5099 Update readme with short description of what JBrowse 2 is, new links, and publications (@cmdcolin)

:house: Internal

• __mocks__, app-core, core
  • #5077 Bump generic-filehandle with mock for test environment (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Will Haese-Hill (@haessar) Done in 1.34s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.5.1

3.5.1 (2025-06-05)

:rocket: Enhancement

• Other
  • #5064 Optimize fetching many small sequences from IndexedFasta (e.g. MSA datasets) (@cmdcolin)
  • #5059 Canonicalize refNames in search results (@cmdcolin)
  • #5056 Use assembly displayName on synteny header and ruler (@garrettjstevens)
  • #5050 Use standard sessionId for linear synteny view to reduce data re-fetching (@cmdcolin)
• app-core, core, embedded-core
  • #5063 Improve usability of dropdown menus by making submenus not disappear immediately onMouseLeave (@cmdcolin)
• core
  • #5049 Add react compiler (@cmdcolin)
• app-core, core
  • #5044 Allow plugins to register entries onto the root configuration (@cmdcolin)

:bug: Bug Fix

• Other
  • #5062 Fix useSWR usage from plugins (@cmdcolin)
  • #5053 Fix @jbrowse/img using a no-op css import (@cmdcolin)
  • #5051 Fix race condition with text search using useEffect cleanup (@cmdcolin)
• core
  • #5058 Improve speed of navigation for fragmented assemblies (@cmdcolin)

:memo: Documentation

• #5047 Reduce the embedded website tutorial (@cmdcolin)

:house: Internal

• Other
  • #5057 Reduce S3 uploads per-branch (@cmdcolin)
  • #5054 Add ability to make commits to update docs only and avoid running CI (@cmdcolin)
• core
  • #5061 Modularize some integration tests for launching views (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens) Done in 1.94s.

yarn run v1.22.18 $ lerna-changelog --silent --silent --next-version 3.5.0

3.5.0 (2025-05-27)

:rocket: Enhancement

• #5042 Avoid inferring CDS subfeatures from non-coding gene pred features (@cmdcolin)
• #5035 Use trash icon for uninstall in plugin store, and add version number string (@cmdcolin)
• #4735 Remove jbrowse-web start screen (@cmdcolin)
• #5025 Allow hiding insertion and deletion in synteny view to help chain file visualization (@cmdcolin)

:bug: Bug Fix

• Other
  • #5037 Check that breakpoint split view is ready before fetching to avoid crash/large data fetching (@cmdcolin)
  • #5033 Bump @gmod/bbi to fix loading bigwig files from bigtools (@cmdcolin)
  • #5024 Fix lines crossing over view headers in breakpoint split view by only setting sticky view headers on top-level views (@cmdcolin)
• core
  • #5029 Fix data grid re-exports (@cmdcolin)

:house: Internal

• core
  • #5039 Add titleNode prop to @jbrowse/core/ui/Dialog (@cmdcolin)
• Other
  • #5036 Remove the async keyword from BaseLinearDisplayModel (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens) Done in 1.78s.

yarn run v1.22.18 $ lerna-changelog --silent --silent --next-version 3.4.0

3.4.0 (2025-05-13)

:rocket: Enhancement

• core
  • #5018 Avoid serializing large features to sessions to fix quota exceeded errors in localstorage (@cmdcolin)
  • #5010 Add mouseover metadata for fields in the base feature widget (@cmdcolin)
  • #4998 Add padding to the genomic window of search result hits (@cmdcolin)
  • #4995 Add uFuzzy to improve gene name search (@cmdcolin)
  • #4983 Update some data parser packages for ESM compat (@cmdcolin)
  • #4980 Synthesize displayId if none provided in display config (@cmdcolin)
  • #4972 Support cytoband bed files starting with "#" (@cmdcolin)
• Other
  • #5008 Allow parsing non-indexed BED files larger than 512MB (@cmdcolin)
  • #4997 Better message for "quota exceeded" message from localstorage (@cmdcolin)
  • #4974 Minor optimizations in multi-sample variant rendering (@cmdcolin)
  • #4973 Add basic cytoband for Drosophila (@cmdcolin)
  • #4970 Dynamically toggle wheel-scroll normalization to improve touchpad pinch-to-zoom usage (@cmdcolin)

:bug: Bug Fix

• core
  • #5013 Fix UCSC chain parsing which have header lines (@cmdcolin)
  • #4993 Fix re-export of @mui/material/styles, and re-export theme (@cmdcolin)
  • #4968 Fix theme augmentation for primary/secondary colors in v3.3.0 (@cmdcolin)
• Other
  • #5004 Fix modifications rendering broken in v3.2.0 (@cmdcolin)
  • #4992 Fix mouseover for some variable width bigwig features (@cmdcolin)
  • #4984 Avoid rendering 'yellow' for low scores in wiggle density renderings with 'log-scale' enabled (@cmdcolin)
  • #4969 Avoid aggregating bigbed features with geneName === 'none' (@cmdcolin)

:memo: Documentation

• #5005 Updated screenshots in gallery (@cmdcolin)
• #5001 Improve website docs with grammarly suggestions (@cmdcolin)
• #4982 Add example of disabling side-scroll/zoom in embedded lgv (@cmdcolin)
• #4977 Fix addToExtensionPoint example in docs (@garrettjstevens)

:house: Internal

• core, product-core
  • #5011 Remove some unused functions on the session model (@cmdcolin)
• core
  • #5003 Fix typescript on renderToAbstractCanvas (@cmdcolin)
  • #4994 Refactor some ReExport code (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens) Done in 1.68s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.3.0

3.3.0 (2025-04-18)

:rocket: Enhancement

• core
  • #4956 Add simplified display of REF/ALT to help with long strings produced by e.g. Cactus VCF (@cmdcolin)
  • #4954 Add genotype frequency table to variant feature details (@cmdcolin)
  • #4952 Add 'genotype' column to the Variant sample grid (@cmdcolin)
  • #4944 Show ALT allele description on multi-variant mouseover (@cmdcolin)
  • #4922 Add Multi-variant SV display (@cmdcolin)
• Other
  • #4950 Add ability to use jexl filters on multi-sample variant displays (@cmdcolin)
  • #4934 Add alpha-transparency to help show overlapping SVs in the Multi-sample variant display (@cmdcolin)
  • #4931 Show target zoom level in tooltip on slider (@cmdcolin)
  • #4930 Upload last release build to https://jbrowse.org/code/jb2/latest (@cmdcolin)
• app-core, core, embedded-core, product-core, sv-core, web-core
  • #4933 Upgrade to MUI v6 -> MUI v7 (@cmdcolin)

:bug: Bug Fix

• Other
  • #4929 Fix broken bigbed features when there is gene level aggregation (@cmdcolin)
• core
  • #4923 Fix dark stock theme showing bad colors (@cmdcolin)

:memo: Documentation

• core
  • #4949 Controlling navigation of embedded component - storybook examples (@cmdcolin)
  • #4924 Add config docs for pre-processors with simplified config snapshots (@cmdcolin)
• Other
  • #4925 Update docs with phased VCF tutorial (@cmdcolin)

:house: Internal

• core
  • #4926 Skip running hydration for server side rendering (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin) Done in 1.41s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.2.0

3.2.0 (2025-03-22)

:rocket: Enhancement

• core
  • #4919 Add in-app clustering method for multi-wiggle tracks (@cmdcolin)
  • #4909 Add ability to load refNameAliases from chromAliases.bb file (@cmdcolin)
  • #4906 Add in-app clustering method for genotype matrix (@cmdcolin)
• Other
  • #4914 Allow looking up header column by name for RefNameAliases (@cmdcolin)
  • #4910 Allow refNameColumn in RefNameAliasAdapter to override the default displayed refnames (@cmdcolin)
  • #4907 Simplified snapshot API for initial navigation of LGV (@cmdcolin)
• app-core, core, product-core, web-core
  • #4899 Add aborting to multi-variant rendering, multi-wiggle rendering (@cmdcolin)

:bug: Bug Fix

• #4920 Fix issue where multi-level linear synteny view would show a blank tracklist (@cmdcolin)
• #4913 Fix parent aggregation in BigBed files using larger request window (@cmdcolin)
• #4905 Fix bug where applying genotype clustering twice produces randomness (@cmdcolin)
• #4897 Fix clustering for certain sets of bigwig files (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin) Done in 1.00s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.1.0

3.1.0 (2025-03-14)

:rocket: Enhancement

• Other
  • #4876 Allow inferring default values of adapter urls to simplify config.json (@cmdcolin)
  • #4875 Add sample data from HGSVCv3 to 1000 genomes demo and config_demo (@cmdcolin)
  • #4880 Allow selecting track error messages with click and drag (@cmdcolin)
  • #4882 Allow clustering multi-wiggle tracks on the fly (@cmdcolin)
  • #4874 Use a '012' matrix to improve clustering of genotypes (@cmdcolin)
• core
  • #4871 Add deletion, insertion, skip, softclip, hardclip to theme (@cmdcolin)
• app-core, core, product-core
  • #4237 Add ability for views to pin elements, such as headers and tracks (@garrettjstevens)

:bug: Bug Fix

• core
  • #4867 Fix web worker usage of lollipop renderer (@cmdcolin)
• Other
  • #4883 Bump @gmod/bam for CSI index fix (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens) Done in 1.07s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.0.5