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| Original file line number | Diff line number | Diff line change |
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| --- | ||
| title: v2.5.0 Release | ||
| date: 2023-05-04 20:27:20 | ||
| tags: ['release', 'jbrowse 2'] | ||
| --- | ||
|
|
||
| This release includes some small bugfixes. It also renames some internal APIs, | ||
| if you are a plugin developer, take note of the new naming. | ||
|
|
||
| ## Downloads | ||
|
|
||
| - [v2.5.0](https://github.com/GMOD/jbrowse-components/releases/tag/v2.5.0) | ||
|
|
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| To install JBrowse 2 for the web, you can download the link above, or you can | ||
| use the JBrowse CLI to automatically download the latest version. See the | ||
| [JBrowse web quick start](https://jbrowse.org/jb2/docs/quickstart_web) for more | ||
| details. | ||
|
|
||
| See "Packages in this release" in the changelog for links to packages published | ||
| on NPM. | ||
|
|
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| ## 2.5.0 (2023-05-04) | ||
|
|
||
| <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-arc | | | ||
| | @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | ||
| | @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-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-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-rdf | | | ||
| | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | ||
| | @jbrowse/plugin-spreadsheet-view | | | ||
| | @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 | ||
| - [#3675](https://github.com/GMOD/jbrowse-components/pull/3675) Use | ||
| react-popper for tooltips in DotplotView | ||
| ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3637](https://github.com/GMOD/jbrowse-components/pull/3637) Fix | ||
| renderDelay not being applied to dynamicBlocks | ||
| ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - `core` | ||
| - [#3677](https://github.com/GMOD/jbrowse-components/pull/3677) Adjust | ||
| RefNameAutocomplete width calculation to avoid ellipses | ||
| ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3660](https://github.com/GMOD/jbrowse-components/pull/3660) Bump | ||
| x-data-grid dependency, refactors for BaseFeatureDetails, add GridToolbar | ||
| ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3626](https://github.com/GMOD/jbrowse-components/pull/3626) Update to mui | ||
| x-data-grid 6 ([@cmdcolin](https://github.com/cmdcolin)) | ||
|
|
||
| #### :bug: Bug Fix | ||
|
|
||
| - `core` | ||
| - [#3681](https://github.com/GMOD/jbrowse-components/pull/3681) Guard against | ||
| undefined in CoreGetFeatureDetails | ||
| ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3662](https://github.com/GMOD/jbrowse-components/pull/3662) Fix empty | ||
| feature sequence on top-level gene feature | ||
| ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3666](https://github.com/GMOD/jbrowse-components/pull/3666) Fix text boxes | ||
| being too small in Dialog boxes ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3642](https://github.com/GMOD/jbrowse-components/pull/3642) Fix error | ||
| handling of feature detail formatter jexl callbacks | ||
| ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3621](https://github.com/GMOD/jbrowse-components/pull/3621) Update plugin | ||
| rollup polyfill package | ||
| ([@garrettjstevens](https://github.com/garrettjstevens)) | ||
| - [#3620](https://github.com/GMOD/jbrowse-components/pull/3620) Fix potential | ||
| crashes where alignment SEQ field may be empty, simplify some display model | ||
| code ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - Other | ||
| - [#3670](https://github.com/GMOD/jbrowse-components/pull/3670) Only | ||
| double-click zoom if not clicking on feature | ||
| ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3652](https://github.com/GMOD/jbrowse-components/pull/3652) Fix text being | ||
| invisible on overview scalebar when cytobands shown | ||
| ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3632](https://github.com/GMOD/jbrowse-components/pull/3632) Fix mouse | ||
| click-and-drag behavior in the alternative "cursor mode" for the dotplot | ||
| view ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3625](https://github.com/GMOD/jbrowse-components/pull/3625) Fix UCSC | ||
| trackhub assembly aliases matching | ||
| ([@andrzejgrzelak](https://github.com/andrzejgrzelak)) | ||
| - `__mocks__`, `core` | ||
| - [#3630](https://github.com/GMOD/jbrowse-components/pull/3630) Fix flakyness | ||
| of connection test ([@cmdcolin](https://github.com/cmdcolin)) | ||
|
|
||
| #### :memo: Documentation | ||
|
|
||
| - Other | ||
| - [#3676](https://github.com/GMOD/jbrowse-components/pull/3676) Refactor | ||
| circular genome view storybook ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3671](https://github.com/GMOD/jbrowse-components/pull/3671) Fix website | ||
| documentation sidebar on browsers with prefers-reduced-motion | ||
| ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3654](https://github.com/GMOD/jbrowse-components/pull/3654) Add some docs | ||
| for configuring defaultSession ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - `core` | ||
| - [#3646](https://github.com/GMOD/jbrowse-components/pull/3646) Refactor | ||
| linear genome view storybook ([@cmdcolin](https://github.com/cmdcolin)) | ||
|
|
||
| #### :house: Internal | ||
|
|
||
| - `core` | ||
| - [#3647](https://github.com/GMOD/jbrowse-components/pull/3647) Refactoring | ||
| navToMultiple, navToLocString, and related | ||
| ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3629](https://github.com/GMOD/jbrowse-components/pull/3629) Typescript | ||
| checking for config slot names ([@rbuels](https://github.com/rbuels)) | ||
| - [#3618](https://github.com/GMOD/jbrowse-components/pull/3618) Rename APIs | ||
| for feature density stats and quantitative stats | ||
| ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - [#3615](https://github.com/GMOD/jbrowse-components/pull/3615) Add check for | ||
| default export to plugin loader ([@rbuels](https://github.com/rbuels)) | ||
|
|
||
| #### Committers: 4 | ||
|
|
||
| - Colin Diesh ([@cmdcolin](https://github.com/cmdcolin)) | ||
| - Garrett Stevens ([@garrettjstevens](https://github.com/garrettjstevens)) | ||
| - Robert Buels ([@rbuels](https://github.com/rbuels)) | ||
| - [@andrzejgrzelak](https://github.com/andrzejgrzelak) |
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