@jbrowse/cli - npm Package Versions

2.10.1 (2024-01-09)

:rocket: Enhancement

• core
  • #4155 Remove react-svg-tooltip library (@cmdcolin)
• Other
  • #4152 Add directional feet to breakends in linear arc display (@cmdcolin)
  • #4143 Add webpack build for @jbrowse/react-app (@cmdcolin)

:bug: Bug Fix

• Other
  • #4158 Fix subfeature refNames on BED and BEDTabix parsers (@cmdcolin)
  • #4154 Fix metadata facet filters being blank (@cmdcolin)
• core
  • #4147 Fix bad svg output in v2.10.0 in cases where feature names have angle brackets (@cmdcolin)

:memo: Documentation

• #4142 Update 03_assemblies.md (@dtdoering)

Committers: 2

• Colin Diesh (@cmdcolin)
• Drew T. Doering (@dtdoering) Done in 3.10s.

yarn run v1.22.19 $ lerna-changelog --silent --silent --next-version 2.10.0

2.10.0 (2023-12-15)

:rocket: Enhancement

• core
  • #4138 Speed up large FromConfigAdapter usages with alternative adapter id calculation (@cmdcolin)
  • #4114 Improve pluginManager.jexl typescript definition (@cmdcolin)
• Other
  • #4135 Split "recently used tracks" local storage keys by view assemblies (@cmdcolin)
  • #4003 Adds the ability to highlight regions using the bookmarks widget (@carolinebridge-oicr)
  • #4123 Remove session.notify after using the Add track workflow (@cmdcolin)
  • #3859 Add new pairwise indexed PAF adapter format with CLI creation workflow (@cmdcolin)
  • #4109 Allow right clicking synteny features (@cmdcolin)
  • #4110 Scroll both panels of the linear synteny view when side scrolling the middle panel (@cmdcolin)
  • #4108 Convert to floating-ui for tooltips for small speedup (@cmdcolin)
  • #4107 Refactors and bundle size improvements (@cmdcolin)
• app-core, core
  • #4134 Add ability to click and drag synteny area of synteny view to side scroll (@cmdcolin)

:bug: Bug Fix

• Other
  • #4137 Fix dotplot axis ticks going out of bounds (@cmdcolin)
• core
  • #4136 Fix "Export SVG" feature in next 14 (@cmdcolin)
  • #4125 Fix internet accounts not being shown in file selector after page refresh and hide HTTP basic internet accounts (@cmdcolin)
• app-core, embedded-core
  • #4121 Fix view menu checkboxes not responding in some cases (@cmdcolin)

:memo: Documentation

• app-core, product-core, web-core
  • #4106 Add links between autogen docs (@cmdcolin)

:house: Internal

• #4103 Add mastodon account to website links (@cmdcolin)

Committers: 2

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin) Done in 2.06s.

yarn run v1.22.19 $ lerna-changelog --silent --silent --next-version 2.9.0

2.9.0 (2023-11-30)

:rocket: Enhancement

• Other
  • #4070 Add support for single file hubs (@cmdcolin)
  • #4096 Allow searching by gene name using linear synteny view (@cmdcolin)
  • #4068 Allow searching the text-index by gene name from the URL bar (@cmdcolin)
  • #3948 Make the default setting for the dotplot/synteny views use 'Existing tracks' by default (@cmdcolin)
  • #4039 Adds "Favorites" and "Recently used" track categories to the track selector (@carolinebridge-oicr)
  • #4067 Add arc plugin to @jbrowse/react-linear-genome-view core plugins (@cmdcolin)
• core, product-core
  • #4091 Allow hiding subfeatures in the feature details panel (@cmdcolin)

:bug: Bug Fix

• core
  • #4094 Refactor faceted track selector to use more MST state (@cmdcolin)
  • #4086 Fix issue where --load inPlace and --force can sometimes remove file unexpectedly (@cmdcolin)
  • #4059 Fix missing icons on some cascading menus (@carolinebridge-oicr)
• Other
  • #4095 Fix faceted metadata header names colliding with non-metadata header names (@cmdcolin)
  • #4071 Fix Mac auto-updates fetching non-existent zip (@cmdcolin)
  • #4062 Fix duplicate key error in hierarchical track selector from using connections (@cmdcolin)

Committers: 2

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin) Done in 1.41s.

yarn run v1.22.19 $ lerna-changelog --silent --next-version 2.8.0

2.8.0 (2023-11-09)

:rocket: Enhancement

• Other
  • #4045 Create multi-region arc display type for variant tracks (@cmdcolin)
  • #4050 Allow specifying alternative config.json path via global variable (@cmdcolin)
  • #4046 Show last autosave on jbrowse-web start screen (@cmdcolin)
  • #4044 Speed up "multi-region" navigation in search box (@cmdcolin)
  • #4032 Add jbrowse sort-gff subcommand (@cmdcolin)
• product-core
  • #4040 Strip baseUri in 'About track' copy config (@cmdcolin)
• core
  • #4035 Prompt to horizontally flip view when launching linear synteny view on inverted feature (@cmdcolin)
• app-core
  • #4024 Add right-handed arrow to view title to emphasize the focused view (@carolinebridge-oicr)

:bug: Bug Fix

• #4052 Fix browser back button behavior in jbrowse-web (@cmdcolin)
• #4043 Fix crash in "Open session" widget for sessions that have 'track-less views' (@cmdcolin)

:memo: Documentation

• #4027 Add office hours and community meetings (@cmdcolin)

Committers: 2

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin) Done in 2.23s.

yarn run v1.22.19 $ lerna-changelog --silent --next-version 2.7.2

2.7.2 (2023-10-27)

:rocket: Enhancement

• core
  • #3923 Proposal: Add "extendWorker" extension point (@garrettjstevens)
• Other
  • #4020 Allow configuring LGV trackLabels setting via config (@cmdcolin)
  • #3999 Example of using customElement + ShadowDOM for @jbrowse/react-linear-genome-view (@AcaDemIQ)
  • #4015 Create MacOS universal build of jbrowse-desktop to help M1 macs (@cmdcolin)
• core, product-core
  • #4013 Create concept of global hovered state (@cmdcolin)

:bug: Bug Fix

• #4016 Fix mouseover tooltip getting stuck after region select popup in dotplot (@cmdcolin)
• #4007 Update cram-js for bzip2 fix (@cmdcolin)

:house: Internal

• core
  • #4005 Refactors and typescript improvements for jbrowse-web loader (@cmdcolin)
• app-core, core
  • #3994 Refactors for app-core view container (@cmdcolin)

Committers: 3

• Alexey Mukhin (@AcaDemIQ)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens) Done in 1.56s.

yarn run v1.22.19 $ lerna-changelog --silent --next-version 2.7.1

2.7.1 (2023-10-18)

:rocket: Enhancement

• Other
  • #3986 Allow editing step size and window size of GC content adapter (@cmdcolin)
• core
  • #3982 Allow rendering semi-circles in the arc renderer + SVG rendering of arcs (@cmdcolin)
• __mocks__, core
  • #3981 Auto-create HTML links for URLs, and strip HTML tags where they can't be rendered (@cmdcolin)

:bug: Bug Fix

• Other
  • #3991 Remove some non-functioning options from top level menu in @jbrowse/react-app (@cmdcolin)
  • #3980 Downgrade electron 26->25 to fix screen blanking (@cmdcolin)
• core
  • #3971 Fix rendering multi-quantitative tracks when blank data is present (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin) Done in 1.65s.

yarn run v1.22.18 $ lerna-changelog --next-version 2.7.0

2.7.0 (2023-10-04)

:rocket: Enhancement

• Other
  • #3956 Make faceted track selector facet filters responsive to adjacent filter selections (@cmdcolin)
  • #3953 Report JSON parse error when failing to load JSON file on desktop (@cmdcolin)
  • #3951 Add jobs widget to jbrowse-web (@carolinebridge-oicr)
  • #3900 Make bookmarks persistent across sessions with local storage (@carolinebridge-oicr)
  • #3896 Upgrade oclif to v3 to avoid deprecation warnings (@garrettjstevens)
  • #3907 Change the config.json missing screen to an "It worked!" message (@cmdcolin)
  • #3901 Use shortened VCF feature description for some types of insertions and deletions (@cmdcolin)
  • #3840 Adds custom filtering option to alignments tracks (@carolinebridge-oicr)
  • #3832 Adds keyboard shortcuts for panning and zooming on a focused view (@carolinebridge-oicr)
• core
  • #3954 Add column resizing for jbrowse-desktop start screen recent sessions panel (@cmdcolin)
  • #3938 Adds code improvements to GridBookmarkWidget (@carolinebridge-oicr)
  • #3914 Swap out NPM color library for colord library (@cmdcolin)
• app-core, core, embedded-core
  • #3931 Add eslint-plugin-fast-refresh (@cmdcolin)
• app-core
  • #3916 Use theme.secondary.main instead of theme.secondary.light on focusedView (@cmdcolin)
• app-core, core, embedded-core, product-core, text-indexing, web-core
  • #3502 Update to react v18, mobx-react v9 (@cmdcolin)
  • #3885 Eject react-script config from jbrowse-web and jbrowse-desktop (@cmdcolin)
• app-core, core, web-core
  • #3831 Adds session model reference to view in focus (@carolinebridge-oicr)

:bug: Bug Fix

• app-core, core
  • #3959 Remove type any from return value of getContainingView, getSession (@cmdcolin)
• Other
  • #3946 Fix setting multiple hierarchical defaultCollapsed config options at initialization (@cmdcolin)
  • #3937 Fix dev mode error from LGV overview scalebar (@cmdcolin)
  • #3925 Reduce amount of canvas commands issued to the dotplot renderer (@cmdcolin)
  • #3924 Fix incorrect tick mark label on dotplot axes happening in some cases (@cmdcolin)
  • #3921 Fix hydration warning by only rendering the SvgFeature "selected feature" and "mouseover" client side (@cmdcolin)
  • #3910 Fix feature label offsets in SVG exports with main thread RPC (@cmdcolin)
  • #3905 Fix alignments track infinite loading when applying same "Color by" or "Sort by" setting twice (@cmdcolin)
  • #3904 Fix "Color by"->"Mapping quality" for CRAM files (@cmdcolin)
  • #3902 Fix ability to use plaintext bed in add-track CLI (@cmdcolin)
• core
  • #3929 Fix mouse getting out of sync while dragging resize handle (@cmdcolin)
  • #3912 Avoid undefined getConf on assembly.configuration safeReference (@cmdcolin)
  • #3887 Add forwardRef to wrapped re-exported lazy components (@garrettjstevens)
  • #3866 Fix calculation of width of "view container title" (@cmdcolin)
  • #3865 Strip alpha from colors for improved SVG export compatibility (@cmdcolin)

:memo: Documentation

• #3957 Add error handler example for embedded components (@cmdcolin)
• #3913 Add color scheme for pathogenicity for ClinVar config_demo track (@scottcain)
• #3881 Improve some of the extension point documentation (@cmdcolin)

:house: Internal

• app-core, core, embedded-core
  • #3931 Add eslint-plugin-fast-refresh (@cmdcolin)
• core
  • #3920 Remove some unused "renameReference" code in static/dynamic blocks (@cmdcolin)
• Other
  • #3882 Minor refactors and typescripting improvements (@cmdcolin)
• app-core, core, embedded-core, product-core, web-core
  • #3855 Replace shortid with vendored nanoid (@cmdcolin)

Committers: 4

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Scott Cain (@scottcain) Done in 2.80s.

yarn run v1.22.18 $ lerna-changelog 2.6.3

:rocket: Enhancement

• Other
  • #3830 Refactors LGV synteny and pileup with shared mixins (@carolinebridge-oicr)
  • #3811 Add ability to show/hide all tracks in category (@cmdcolin)
• app-core
  • #3810 Add sorting and collapsing options to the hierarchical track selector (@cmdcolin)
  • #3827 Add check for document.activeElement == INPUT before undo/redo (@cmdcolin)

:bug: Bug Fix

• #3839 Fix bug where multi-quantitative tracks plotted incorrectly for some bigwigs with empty regions (@cmdcolin)
• #3837 Fix text layout in dotplots with long coordinate strings (@cmdcolin)
• #3825 Fix SVG export compatibility by removing rgba strings (@cmdcolin)
• #3814 Fix suspense fallback to track container for lazy loaded display components (@cmdcolin)
• #3808 Fix track ordering of hierarchical track selector to more closely match the config.json (@cmdcolin)
• #3806 Fix a bug on the BookmarkWidget mui data grid where labels were not saving (@carolinebridge-oicr)
• #3804 Fix version missing from about menu in @jbrowse/react-app (@cmdcolin)

:house: Internal

• #3818 Miscellaneous plugin store code refactoring (@cmdcolin)

Committers: 3

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Robert Buels (@rbuels) Done in 1.50s.

yarn run v1.22.18 $ lerna-changelog 2.6.2

:rocket: Enhancement

• #3796 Allow workers to load CJS plugins (@garrettjstevens)
• #3783 Add ability for track selector button in synteny view to select individual views (@cmdcolin)
• #3452 Use notarytool for macOS desktop signing (@cmdcolin)
• #3766 Add nextjs circular genome view demo (@cmdcolin)

:bug: Bug Fix

• Other
  • #3798 Fix VCF feature starting at 1-based 1 (@cmdcolin)
  • #3775 Fix stranded RNA-seq rendering and rename option Color by -> "First-of-pair strand" (@cmdcolin)
  • #3758 Adds safety checks on AlignmentsDisplay properties to avoid undefined rendering (@carolinebridge-oicr)
  • #3770 Fix potential issue with display searchFeatureByID being undefined (@cmdcolin)
• core
  • #3784 Fix synteny rubberband tooltips when views are exactly the same (@cmdcolin)
  • #3782 Fix crash on color picker component using debounce on color property (@carolinebridge-oicr)
  • #3767 Check session tracks for text search adapters (@garrettjstevens)
• app-core, core, embedded-core, product-core, text-indexing, web-core
  • #3771 Use inlineSourceMaps for tsc builds and other misc changes (@cmdcolin)

:house: Internal

• Other
  • #3794 Move embedded demos to individual repos (@cmdcolin)
• core, product-core
  • #3786 Centralize rpcWorker in product-core (@cmdcolin)

Committers: 3

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens) Done in 1.55s.

yarn run v1.22.18 $ lerna-changelog 2.6.1

:rocket: Enhancement

• Other
  • #3743 Create mixin for shared code between LinearWiggleDisplay and MultiWiggleLinearDisplay (@cmdcolin)
  • #3711 Allow synteny data adapters to open files larger than 512Mb (@cmdcolin)
  • #3639 Add button to bookmark in jbrowse-web share dialog (@cmdcolin)
  • #3631 Add BEDPE add track workflow, avoid showing "Add track" when disabled (@carolinebridge-oicr)
  • #3700 Render alignment track arcs instantly after bpPerPx change (@cmdcolin)
  • #3695 Reduce re-drawing on alignments track paired read arcs/cloud display types (@cmdcolin)
• core
  • #3725 Filter tracks that match all view.assemblyNames in multi-assembly track selector modes (@cmdcolin)
  • #3531 Add @jbrowse/react-app embedded component (@cmdcolin)
  • #3653 Evaluate extension point on track config pre-process snapshot (@cmdcolin)
  • #3706 Miscellaneous alignments arc/cloud fixes (@cmdcolin)
  • #3698 Add column resizers to the variant ANN/CSQ panels (@cmdcolin)
• app-core, product-core, web-core
  • #3531 Add @jbrowse/react-app embedded component (@cmdcolin)
• __mocks__
  • #3707 Improved read cloud display for long reads with inversions (@cmdcolin)

:bug: Bug Fix

• core
  • #3749 Avoid re-prompting a user login when refresh token is processed (@cmdcolin)
  • #3572 Add OAuth and HTTP BasicAuth servers for local testing, fix some OAuth flows (@garrettjstevens)
  • #3708 Add removable-media to jbrowse desktop snap (@cmdcolin)
  • #3687 Take into account ML tag when showing MM tag on alignments, misc refactoring (@cmdcolin)
• Other
  • #3747 Fix blank lines in GFF crashing text-index (@cmdcolin)
  • #3739 Fix specifying the assemblyNames config slot on add-connection CLI (@cmdcolin)
  • #3631 Add BEDPE add track workflow, avoid showing "Add track" when disabled (@carolinebridge-oicr)
  • #3667 Fix horizontal flip functionality for Hi-C display (@studentshivang)
  • #3703 Fix rendering error in alignments tracks when filtering by tag in CRAM file (@Lilas-w)
  • #3694 Fix ability to filter certain fields in BAM/CRAM files (@cmdcolin)
  • #3691 Fix breakpoint split view alignment connections not pointing at right position in v2.5.0 (@cmdcolin)
  • #3686 Fix jbrowse create/jbrowse upgrade CLI intermittent failures (@cmdcolin)
• product-core, web-core
  • #3738 Don't throw on UCSC connection containing assemblies not matching connection->assemblyNames config (@cmdcolin)
• app-core, core, embedded-core
  • #3731 Fix view menu going off screen in some cases (@cmdcolin)
• app-core
  • #3713 Fix centering of the ImportForm on SV inspector (@cmdcolin)

:memo: Documentation

• Other
  • #3752 Add storybook example for fetching features currently in view (@cmdcolin)
  • #3732 Add JBrowse R shiny app demo (@carolinebridge-oicr)
  • #3693 Remove package table from release blogposts (@cmdcolin)
• core, embedded-core, product-core
  • #3704 Organize autogenerated docs into categories (@cmdcolin)

:house: Internal

• app-core, core, product-core, text-indexing
  • #3740 Bump electron, proxy-agent, fontsource-roboto, etc. and update SnackbarMessage from typed array to object (@cmdcolin)
• core
  • #3741 Distinguish between SessionWithConnections and SessionWithConnectionEditing (@cmdcolin)
• Other
  • #3734 PileupRenderer refactor (@cmdcolin)
• app-core, core, product-core, web-core
  • #3717 More modularizing of shared app code (@cmdcolin)
• product-core
  • #3709 Silence console warn in CopyAndDelete test (@cmdcolin)
• app-core, core, embedded-core, product-core, text-indexing
  • #3701 Create app-core and embedded-core packages (@cmdcolin)
• core, product-core
  • #3661 Create packages/product-core containing shared code between the various products (@rbuels)

Committers: 6

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Robert Buels (@rbuels)
• Shivang Dwivedi (@studentshivang)
• @Lilas-w Done in 2.84s.