From 671aa644f8ebc06b65fe060d43840ca432a1c833 Mon Sep 17 00:00:00 2001 From: Colin Date: Thu, 4 May 2023 20:28:06 +0000 Subject: [PATCH] Prepare for v2.5.0 release --- CHANGELOG.md | 128 +++++++++++++++++++ website/blog/2023-05-04-v2.5.0-release.md | 148 ++++++++++++++++++++++ website/docusaurus.config.json | 2 +- 3 files changed, 277 insertions(+), 1 deletion(-) create mode 100644 website/blog/2023-05-04-v2.5.0-release.md diff --git a/CHANGELOG.md b/CHANGELOG.md index 03f39b29c2..f19b102f11 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,131 @@ +## 2.5.0 (2023-05-04) + +
Packages in this release +

+ +| 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 | | + +

+
+ +#### :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) + ## 2.4.2 (2023-03-27)
Packages in this release diff --git a/website/blog/2023-05-04-v2.5.0-release.md b/website/blog/2023-05-04-v2.5.0-release.md new file mode 100644 index 0000000000..0ab72abcb8 --- /dev/null +++ b/website/blog/2023-05-04-v2.5.0-release.md @@ -0,0 +1,148 @@ +--- +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) + +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. + +## 2.5.0 (2023-05-04) + +
Packages in this release +

+ +| 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 | | + +

+
+ +#### :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) diff --git a/website/docusaurus.config.json b/website/docusaurus.config.json index bc3a4826c4..e07e37d032 100644 --- a/website/docusaurus.config.json +++ b/website/docusaurus.config.json @@ -9,7 +9,7 @@ "organizationName": "GMOD", "projectName": "jbrowse-components", "customFields": { - "currentVersion": "v2.4.2" + "currentVersion": "v2.5.0" }, "themeConfig": { "colorMode": {