From 86b75b90c79d9f916f9822b7ca936067f656f021 Mon Sep 17 00:00:00 2001 From: Robert Buels Date: Tue, 13 Feb 2018 17:57:22 -0800 Subject: [PATCH] updated release notes for all issues and pulls in the 1.12.4 milestone --- release-notes.txt | 57 +++++++++++++++++++++++++++++++++++++++-------- 1 file changed, 48 insertions(+), 9 deletions(-) diff --git a/release-notes.txt b/release-notes.txt index 557be4c0e6..bbc10ba74e 100644 --- a/release-notes.txt +++ b/release-notes.txt @@ -4,7 +4,7 @@ * Fixed SEVERE performance regression that basically made flatfile-to-json.pl unusable on Perl 5.18 and higher. Huge thanks to Colin Diesh for tracking - this down. (issue #470, @cmdcolin) + this down. (issue #470, pull #912, @cmdcolin) * setup.sh now uses npm instead of Bower (which is deprecated) to install dependencies. @enuggetry @@ -12,20 +12,23 @@ * Removed legacy `wig-to-json.pl` and `bam-to-json.pl` scripts. @rbuels * Added a `--trackConfig` option to `prepare-refseqs.pl` to allow injecting - refseq configuration variables at format time. @erasche + refseq configuration variables at format time. (pull #884, @erasche) * Added trackLabels: "no-block" config feature. Moves track labels/menus above the features so as not to obscure the features. (issue #901, #490) - * Make jbrowse npm installable. thanks to @cmdcolin & @enuggetry. + * Added a `--category` option to `add-bw-track.pl` and `add-bam-track.pl` to + set the new track's category. Thanks to @loraine-gueguen for the implementation! + (pull #911, @loraine-gueguen) - * Change "Length on ref" to "Seq length on ref" in Alignments feature detail boxes, - so that the length on the reference appears next to the sequence length. Thanks to - @colindaven for the suggestion! + * Made jbrowse installable using `npm`. @cmdcolin and @enuggetry. - * implement express server for jbrowse for quick launch (jb_run.js). @enuggetry. + * Implemented a built-in node.js Express server `jb_run.js` for quick JBrowse launching. + @enuggetry - * jb_setup.js @enuggetry. + * Added an `--unsorted` option to `prepare-refseqs.pl` that formats reference sequences + in the same order in which they appear in the input sequence file. Thanks to + @dsenalik for the suggestion and implementation! (pull #924, @dsenalik) * Allows for dot-notation instead of JSON (pull #952) for addTracks, addBookmarks, and addStores. https://github.com/GMOD/jbrowse/pull/952. Address security concerns @@ -33,7 +36,7 @@ * If a track has no `key` set in its track configuration, JBrowse will now look for a `key` in its track metadata, and use that if it is present. Thanks to Loraine - Guéguen for the idea (issue #957). @rbuels + Guéguen for the idea (issue #957, pull #958). @rbuels * Suppress execution of biodb-to-json.pl on sample data while running setup.sh on MacOS High Sierra with stock Perl due to an issue with the stock Perl having @@ -58,6 +61,42 @@ * Upgraded to use new Google Analytics API for usage reporting. (@rdhayes) + * Fixed bug in which start/stop codons were sometimes not displayed in the sequence + track at certain zoom levels (issue #858, pull req #859, @cmdcolin) + + * Fixed a regression in which the `defaultTracks` configuration variable was no longer + respected when set to a comma-separated list. (issue #892, pull #896, @rdhayes) + + * Made a cosmetic change to Alignments track detail popups, changing "Length on ref" to + be displayed as "Seq length on ref", so that it is displayed more usefully next to + "Seq length". Thanks to @colindaven for the suggestion and implementation! + (pull #939, @colindaven) + + * Improved the error messages displayed when a JBrowse glyph class fails to load. Thanks + to @scottcain and @cmdcolin for tracking down the issue and improving the error + handling! (issue #968, @cmdcolin) + + * Added support for an `addFeatures` URL query parameter that can inject features from + the URL query string. (issue #976, @nathandunn) + + * Changed the project's `git` workflow to utilize a `dev` branch that is separate from + `master`, with `master` only being updated when a new release of JBrowse is published. + (issue #975, @enuggetry) + + * Implemented automated deployment of JBrowse releases to GitHub releases and `npm`. + Thanks to @abretaud, @nathandunn, @erasche, and @cmdcolin for valuable discussions. + (issue #822, pull #979, pull #984, @rbuels) + + * Added a `--bigwigCoverage` option to `add-bam-track.pl` to support configuring pregenerated + coverage histograms from the command line. Thanks to @loraine-gueguen for the suggestion + and implementation! (pull #972, @loraine-gueguen) + + * Improved documentation of the `CategoryURL` plugin. (pull #985, @enuggetry) + + * Re-enabled and improved documentation and configurability of the gradient colors in the + `NeatCanvasFeatures` plugin. (issue #982, pull #985, @enuggetry) + + # Release 1.12.3 2017-05-02 19:20:01 America/Los_Angeles ## Minor improvements