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@jbrowse/plugin-authentication - npm Package Versions

1234

2.3.3

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Changelog

Source

2.3.3 (2023-01-11)

<details><summary>Packages in this release</summary> <p>

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/text-indexing | | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | https://www.npmjs.com/package/@jbrowse/plugin-authentication | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gccontent | https://www.npmjs.com/package/@jbrowse/plugin-gccontent | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-text-indexing | | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

</p> </details>
:rocket: Enhancement
  • core
    • #3440 "Show all regions" for dotplot and synteny views and refactor synteny rendering RPC to optimize scrolling (@cmdcolin)
:bug: Bug Fix
  • Other
    • #3451 Fix auto-updates on desktop not working since v2.2.2 (@cmdcolin)
  • core
    • #3428 Add missing dependencies to embedded component package.json's (@cmdcolin)
:memo: Documentation
:house: Internal
Committers: 1
cmdcolin
published 2.3.2 •

Changelog

Source

2.3.2 (2022-12-20)

<details><summary>Packages in this release</summary> <p>

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gccontent | https://www.npmjs.com/package/@jbrowse/plugin-gccontent | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

</p> </details>
:rocket: Enhancement
  • core
    • #3422 Auto-adjust height of reference sequence track to current settings (@cmdcolin)
  • Other
    • #3421 Add ability to revcomp sequence in the "Get sequence" dialog (@cmdcolin)
    • #3413 Add a "base" set of tracks and assemblies for the embedded demos (@cmdcolin)
:bug: Bug Fix
  • #3419 Fix rendering base-level alignments on synteny visualizations, especially in inverted regions (@cmdcolin)
  • #3416 Fix rendering alignment arcs on files that need refname renaming and add jitter setting (@cmdcolin)
  • #3415 Fix circular view being rendered as a blank area if tab is opened in the background (@cmdcolin)
Committers: 1
<details><summary>Packages in this release</summary> <p>

| Package | Download | | ----------------------------------- | ----------------------------------------------------------------- | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |

</p> </details>
cmdcolin
published 2.3.1 •

cmdcolin
published 2.3.0 •

Changelog

Source

2.3.0 (2022-12-15)

<details><summary>Packages in this release</summary> <p>

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/text-indexing | | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | https://www.npmjs.com/package/@jbrowse/plugin-authentication | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gccontent | https://www.npmjs.com/package/@jbrowse/plugin-gccontent | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-text-indexing | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

</p> </details>
:rocket: Enhancement
  • Other
    • #3403 Reduce overplotting on dotplot grid lines and other misc improvements (@cmdcolin)
    • #3381 Add method for cache busting requests to the config file in jbrowse-web (@cmdcolin)
    • #3384 Add method to more easily create compact view of alignments (@cmdcolin)
  • core
    • #3391 Allow arc display to connect to "unpaired" positions using RNEXT/PNEXT or SA tag (@cmdcolin)
    • #3387 Small UI tweaks for add track workflow (@cmdcolin)
    • #3358 Create new "arc" display type to show long range connections between paired-end and split-reads (@cmdcolin)
  • text-indexing
    • #3385 Optimize prefix size for text indexing automatically (@cmdcolin)
:bug: Bug Fix
  • Other
    • #3407 Remove trackhub registry plugin from core plugins, moved to plugin store (@cmdcolin)
    • #3406 Fix loading connection tracks from connections that don't specify assemblyNames in config (@cmdcolin)
    • #3390 Fix positioning within large alignments for query->target LGV synteny navigation (@cmdcolin)
    • #3388 Fix search result that matches synonyms that matches multiple locations (@cmdcolin)
  • core
    • #3404 Fix double-render of some synteny features (@cmdcolin)
    • #3401 Remove y-scalebar rendering placeholder values in blank and loading states (@cmdcolin)
    • #3389 Fix issue where snackbar would not show up when same error message is triggered multiple times (@cmdcolin)
:memo: Documentation
  • core
  • Other
    • #3383 Add note to user guide about variant callers that can be used for SV inspector (@cmdcolin)
:house: Internal
  • __mocks__, core, text-indexing
    • #3400 Reduce peerDependency warnings from installing dev environment (@cmdcolin)
  • core
Committers: 1
cmdcolin
published 2.2.2 •

Changelog

Source

2.2.2 (2022-12-06)

<details><summary>Packages in this release</summary> <p>

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/text-indexing | | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | https://www.npmjs.com/package/@jbrowse/plugin-authentication | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gccontent | https://www.npmjs.com/package/@jbrowse/plugin-gccontent | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-lollipop | | | @jbrowse/plugin-menus | | | @jbrowse/plugin-protein | | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-text-indexing | | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

</p> </details>
:rocket: Enhancement
  • Other
    • #3350 Retain feature labels in compact display mode for SVG features, and allow turning off keeping feature description without feature label (@cmdcolin)
    • #3357 Allow holding shift key to create rubberband selection on LGV (@cmdcolin)
    • #3363 Create remove-track CLI command (@cmdcolin)
    • #3341 Add BEDPE adapter type (@cmdcolin)
  • core
:bug: Bug Fix
  • Other
    • #3377 Fix rendering and clicking synteny features when using MainThreadRpc (@cmdcolin)
    • #3375 Fix jbrowse upgrade CLI command overwriting config.json with --branch or --nightly options (@cmdcolin)
    • #3370 Fix error with SNPCoverage not rendering MM tag modifications in some cases (@cmdcolin)
    • #3366 Fix ability to use LGV synteny track on inverted alignments (@cmdcolin)
    • #3348 Fix for breakpoint split view and circular view issues with <TRA> type entries in v2.2.1 (@cmdcolin)
  • core
    • #3369 Fix uncaught promise errors and add lint rule for catching these (@cmdcolin)
:memo: Documentation
:house: Internal
  • core
    • #3368 Create base "Dialog" component to standardize dialogs across codebase (@cmdcolin)
  • text-indexing
Committers: 2
cmdcolin
published 2.2.1 •

Changelog

Source

2.2.1 (2022-11-21)

<details><summary>Packages in this release</summary> <p>

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-authentication | https://www.npmjs.com/package/@jbrowse/plugin-authentication | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-view | | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gccontent | https://www.npmjs.com/package/@jbrowse/plugin-gccontent | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

</p> </details>
:rocket: Enhancement
  • Other
    • #3277 Create new "Add track workflow" that allows pasting JSON track configs (@cmdcolin)
    • #3328 Add GC content display type to the reference sequence track (@cmdcolin)
    • #3316 Add LGV typescripting to @jbrowse/react-linear-genome-view (@cmdcolin)
  • core
    • #3298 Add authentication plugin to embedded components (@garrettjstevens)
    • #3329 Add ability to minimize/collapse tracks and views and move views up/down in view stack (@cmdcolin)
    • #3308 Add ability to display synteny track in a normal LGV showing regions of synteny as features (@cmdcolin)
    • #3317 Move ErrorBoundary so that tracks/views that have crashed can be closed more easily (@cmdcolin)
:bug: Bug Fix
  • Other
    • #3342 Fix CRAM mismatches calculation regression in v2.2.0 (@cmdcolin)
    • #3319 Fix pileup "sort by" setting being lost on zoom level change (@cmdcolin)
  • core
    • #3340 Fix linear genome view import form going into infinite loading state changing assemblies with same refnames (@cmdcolin)
    • #3339 Fix force flag for drawing large regions and node-fetch polyfill for node 18 fix in @jbrowse/img (@cmdcolin)
Committers: 2
cmdcolin
published 2.2.0 •

Changelog

Source

2.2.0 (2022-11-04)

<details><summary>Packages in this release</summary> <p>

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/text-indexing | | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-arc | | | @jbrowse/plugin-authentication | https://www.npmjs.com/package/@jbrowse/plugin-authentication | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | @jbrowse/plugin-comparative-adapters | | | @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config | | @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @jbrowse/plugin-jobs-management | | | @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse | | @jbrowse/plugin-linear-comparative-view | | | @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | @jbrowse/plugin-menus | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @jbrowse/plugin-text-indexing | | | @jbrowse/plugin-trackhub-registry | | | @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix | | @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants | | @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img | | @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view | | @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | @jbrowse/web | |

</p> </details>
:rocket: Enhancement
  • Other
  • core
    • #3299 Add ability to open a synteny track directly from the dotplot/linear synteny view import forms (@cmdcolin)
    • #3287 Lazy-load assemblies on demand instead of all at app startup (@cmdcolin)
    • #3279 Remove unnecessary expanded region query and small refactors (@cmdcolin)
:bug: Bug Fix
  • core
    • #3309 Fix animated "Loading..." message keyframes (@cmdcolin)
    • #3306 Fix the RefNameAutocomplete displaying a stale value for chromosome names (@cmdcolin)
    • #3302 Improve rubberband zooming across elided regions (@cmdcolin)
  • Other
    • #3293 Fix CRAM plotting for data files that encode insertions in uncommon way (@cmdcolin)
:memo: Documentation
:house: Internal
Committers: 3
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