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[Snyk] Upgrade @jbrowse/react-linear-genome-view from 1.5.8 to 1.7.11 #1

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[Snyk] Upgrade @jbrowse/react-linear-genome-view from 1.5.8 to 1.7.11 #1

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Snyk has created this PR to upgrade @jbrowse/react-linear-genome-view from 1.5.8 to 1.7.11.

merge advice
ℹ️ Keep your dependencies up-to-date. This makes it easier to fix existing vulnerabilities and to more quickly identify and fix newly disclosed vulnerabilities when they affect your project.

  • The recommended version is 19 versions ahead of your current version.
  • The recommended version was released 2 months ago, on 2022-06-22.
Release notes
Package name: @jbrowse/react-linear-genome-view
  • 1.7.11 - 2022-06-22

    We are excited to announce v1.7.11!

    This release has some relatively small fixes to the UI, docs, and examples. For
    developers, they may notice that we have removed node-canvas due to it's need
    for having extra system dependencies, and becuase it only really was needed in
    niche circumstances. This will improve the ease of installing packages like
    @ jbrowse/react-linear-genome-view.

    🚀 Enhancement

    • core
      • #3044 Remove node-canvas from @ jbrowse/core dependencies (@ cmdcolin)
      • #3041 Fix ability to search and load data files using lower case refName aliases (@ cmdcolin)
    • Other

    🐛 Bug Fix

    • #3049 Fix ability to use callbacks for the linear arc renderer (@ cmdcolin)

    📝 Documentation

    🏠 Internal

    Committers: 1

  • 1.7.10 - 2022-06-13

    We are pleased to present the latest JBrowse 2 release!

    This has some great new features including

    Feature detail formatter

    Here is an example which adds a link to the "Name" panel in the feature
    details. It uses the jexl callback that returns an object with keys for each
    field to modify (e.g. the key name is used here). See

    {
  "type": "FeatureTrack",
  "trackId": "ncbi_gff_hg19_2",
  "name": "NCBI RefSeq",
  "formatDetails": {
    "feature": "jexl:{name:'<a href=https://google.com/?q='+feature.name+'>'+feature.name+'</a>'}"
  },
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "gffGzLocation": {
      "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/ncbi_refseq/GRCh37_latest_genomic.sort.gff.gz"
    },
    "index": {
      "location": {
        "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/ncbi_refseq/GRCh37_latest_genomic.sort.gff.gz.tbi"
      }
    }
  }
}

    Example screenshot

    See https://jbrowse.org/jb2/docs/config_guide/#customizing-feature-details-panels for more info

    Clearer configuration panel with explicit "Add item" button with "OK"/"Cancel" to confirm

    Large track menus no longer disappear off the screen

    Before

    After

    Automatically generate clickable links for data files in About track dialog

    See also the "Copy config" button to download the config

    🚀 Enhancement

    • Other
    • core
      • #2981 Add simplified URL format for loading spreadsheet and SV inspector (@ cmdcolin)
      • #2990 Use shortened megabases (M) display when zoomed out, and option to hide the "open track selector" button (@ carolinebridge-oicr)
      • #3003 Add ability to run field formatters on the feature details panel (@ cmdcolin)
      • #3017 Add button to copy track config in About track dialog (@ cmdcolin)
      • #2999 Generate clickable links to track data in about track dialog (@ cmdcolin)
    • __mocks__, core
      • #3005 Use cascading menu helper library for track menu to avoid menu going offscreen (@ cmdcolin)

    🐛 Bug Fix

    Committers: 3

  • 1.7.9 - 2022-06-02

    We are pleased to present v1.7.9!

    This release features several bugfixes and improvements submitted by community
    members, including a CLI fix when specifying --indexFile with CSI files, and a
    new feature to get FASTA metadata from an external file.

    Additionally, we have switched to canvas2svg for SVG exports, which can now
    handle more sophisticated operations like bezierCurves (used for sashimi-style
    arc in RNA-seq data), and circles (used by jbrowse-plugin-gwas)

    Before (note bad intron and lack of arcs rendered on bottom track)

    After (fixed intron rendering and arcs)

    🚀 Enhancement

    • core
      • #2991 Use canvas2svg for SVG export, fixes non-rasterized usage of bezier, arcs, and more (@ cmdcolin)
      • #2483 Add setting to color by query score per alignment for dotplot, support HTML in config slot descriptions (@ cmdcolin)
      • #2983 Set target=_blank by default in user HTML links (@ cmdcolin)
    • Other

    🐛 Bug Fix

    🏠 Internal

    Committers: 4

  • 1.7.8 - 2022-05-20
    Read more
  • 1.7.7 - 2022-05-04

    This is a small bugfix release, where in v1.7.0-1.7.6 the read vs ref and
    sequence panels in the feature details failed to load

    🐛 Bug Fix

    🏠 Internal

    • core
      • #2944 Avoid stalling on undefined assemblyName during ref name renaming (@ cmdcolin)

    Committers: 1

  • 1.7.6 - 2022-04-26

    This fixes a bug that affected v1.7.0-v1.7.5 in which CRAM, TwoBit, and other file types would not load on jbrowse-desktop. This was due to the upgrade to webpack 5/CRA5, but is fixed in this release!

  • 1.7.5 - 2022-04-26
    Read more
  • 1.7.4 - 2022-04-19

    This is a small patch release that fixes our UMD builds for embedded components fixes the @ babel/runtime dependency in some npm packages

    For the latest feature set see https://github.com/GMOD/jbrowse-components/releases/tag/v1.7.0

  • 1.7.3 - 2022-04-15

    This is a release that fixed issues for users of the embedded apps and follows from a botched release of v1.7.2 on npm

    See https://github.com/GMOD/jbrowse-components/releases/tag/v1.7.0 for the latest feature-set

  • 1.7.1 - 2022-04-15
  • 1.7.0 - 2022-04-14
  • 1.6.9 - 2022-03-25
  • 1.6.8 - 2022-03-25
  • 1.6.7 - 2022-03-16
  • 1.6.6 - 2022-03-15
  • 1.6.5 - 2022-02-18
  • 1.6.4 - 2022-01-29
  • 1.6.3 - 2022-01-29
  • 1.5.9 - 2022-01-13
  • 1.5.8 - 2022-01-13
from @jbrowse/react-linear-genome-view GitHub release notes
Commit messages
Package name: @jbrowse/react-linear-genome-view

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