diff --git a/doc/source/releases/17.05.rst b/doc/source/releases/17.05.rst index a343708e0742..1b95c065bab4 100644 --- a/doc/source/releases/17.05.rst +++ b/doc/source/releases/17.05.rst @@ -11,49 +11,49 @@ Enhancements .. major_feature -* Normalizes the handling of steps and missing tools for the workflow editor - `Pull Request 3181`_ .. feature -* added nrrd image datatype - (thanks to `@ThomasWollmann `__). - `Pull Request 3385`_ +* Allow direct uploading to collections. + `Pull Request 3696`_ * Overlay search for tools, wf, libraries and histories - (thanks to `@bgruening `__). + (thanks to `@anuprulez `__ and `@bgruening `__). `Pull Request 3460`_ +* Add Cytoscape as the Galaxy charts plugin + (thanks to `@anuprulez `__ and `@bgruening `__). + `Pull Request 3817`_ +* Ethercalc Interactive Environment + (thanks to `@shiltemann `__). + `Pull Request 3699`_ * Add a simple UI to manage tool dependencies (thanks to `@mvdbeek `__). `Pull Request 3479`_ +* Add nrrd image datatype + (thanks to `@ThomasWollmann `__). + `Pull Request 3385`_ * NGL Viewer for molecule representation - (thanks to `@bgruening `__). + (thanks to `@anuprulez `__ and `@bgruening `__). `Pull Request 3601`_ * Util to encode or decode values (thanks to `@erasche `__). `Pull Request 3622`_ * Support Docker Engine swarm mode for Interactive Environments `Pull Request 3666`_ -* Allow uploading to collections. - `Pull Request 3696`_ -* Ethercalc Interactive Environment - (thanks to `@shiltemann `__). - `Pull Request 3699`_ * Interactive Environment container waiting and swarm management `Pull Request 3740`_ * Webhook plugin: tool_list (thanks to `@blankclemens `__). `Pull Request 3753`_ -* Cytoscape as the Galaxy charts plugin - (thanks to `@bgruening `__). - `Pull Request 3817`_ * Phylocanvas as a BioJS component for the Galaxy charts - (thanks to `@bgruening `__). + (thanks to `@anuprulez `__ `@bgruening `__). `Pull Request 3850`_ * Container interface abstraction `Pull Request 3863`_ * Graphite support (thanks to `@erasche `__). `Pull Request 3964`_ +* Normalize the handling of steps and missing tools for the workflow editor + `Pull Request 3181`_ .. enhancement @@ -62,28 +62,12 @@ Enhancements `Pull Request 3104`_ * Workflow editor UI touch up `Pull Request 3407`_ -* Inline CSS in error report email - (thanks to `@erasche `__). - `Pull Request 3445`_ -* Improve routing for user preference views - `Pull Request 3446`_ -* Fix various transiently failing Selenium tests. - `Pull Request 3450`_ -* Tool Documentation and Testing Improvements - `Pull Request 3457`_ -* update readme badges - `Pull Request 3465`_ -* Lint some tools - (thanks to `@nsoranzo `__). - `Pull Request 3468`_ * Add an example group filter for displaying tool panel sections (thanks to `@gregvonkuster `__). `Pull Request 3484`_ * Python3: use @six.add_metaclass() decorator (thanks to `@nsoranzo `__). `Pull Request 3491`_ -* improve release issue docs - `Pull Request 3496`_ * Improvements to build sites configuration `Pull Request 3503`_ * Add compressed fastq peek and preview @@ -140,8 +124,6 @@ Enhancements `Pull Request 3619`_ * Usable slow query logging `Pull Request 3625`_ -* Fix kombu documentation link in galaxy.ini.sample - `Pull Request 3629`_ * Allow composite datatypes of type auto_primary_file to automatically generate dataset `Pull Request 3643`_ @@ -174,18 +156,10 @@ Enhancements * Add datatypes for soon coming PlantTribes Galaxy tools. (thanks to `@gregvonkuster `__). `Pull Request 3698`_ -* 'nametags' implementation - `Pull Request 3704`_ * Prefer versioned Conda dependencies to unversioned Galaxy ones `Pull Request 3708`_ * Touch up Galaxy testing documentation. `Pull Request 3715`_ -* Show tags in select search field - `Pull Request 3718`_ -* Use values for 'name'tags instead of child tags. - `Pull Request 3719`_ -* Fix tag escaping - `Pull Request 3720`_ * Add API and UI to remove requirements installed by Conda (thanks to `@mvdbeek `__). `Pull Request 3725`_ @@ -209,8 +183,6 @@ Enhancements `Pull Request 3752`_ * Abstract uWSGI handling into new galaxy.web.stack package `Pull Request 3759`_ -* Tagging tweaks to handle multiple 'name'/etc tags on a single object. - `Pull Request 3760`_ * i18n improvements and French localization `Pull Request 3762`_ * Should exit immediately to avoid index error @@ -237,8 +209,6 @@ Enhancements `Pull Request 3819`_ * Restrict workflow scheduling within a history to a fixed, random handler. `Pull Request 3820`_ -* Fix for EtherCalc IE image specification. - `Pull Request 3825`_ * Order processing evaluation of workflow invocations when scheduling. `Pull Request 3830`_ * Stricter checks for GFF/GFF3/GTF sniffing @@ -258,13 +228,9 @@ Enhancements * Small changes to links and add gitter (thanks to `@galaxyproject `__). `Pull Request 3861`_ -* Adding tagging to collections. - `Pull Request 3868`_ * Use detect_errors="exit_code" in Trim tool (thanks to `@nsoranzo `__). `Pull Request 3869`_ -* Allows to drag-and-drop history items into the content selector - `Pull Request 3871`_ * synchronise against latest UCSC versions (thanks to `@bgruening `__). `Pull Request 3874`_ @@ -290,16 +256,9 @@ Enhancements `Pull Request 3953`_ * change 'user' menu to login or register for anons `Pull Request 3955`_ -* Fix margin style values for color picker element - `Pull Request 3965`_ * Stats docs (thanks to `@erasche `__). `Pull Request 3968`_ -* 17.05 rstudio fixes / one small gie fix - (thanks to `@erasche `__). - `Pull Request 3975`_ -* Hashtags - `Pull Request 3979`_ * Enhance filenames with collection context when downloading datasets from GUI. `Pull Request 3985`_ @@ -309,46 +268,39 @@ Enhancements `Pull Request 4006`_ * Update Jupyter image to 17.05 `Pull Request 4007`_ +* Inline CSS in error report email + (thanks to `@erasche `__). + `Pull Request 3445`_ +* Improve routing for user preference views + `Pull Request 3446`_ +* Tool Documentation and Testing Improvements + `Pull Request 3457`_ +* update readme badges + `Pull Request 3465`_ +* Lint some tools + (thanks to `@nsoranzo `__). + `Pull Request 3468`_ +* improve release issue docs + `Pull Request 3496`_ .. small_enhancement -* Another fix for Selenium testing on Jenkins. - `Pull Request 3422`_ -* Fix most broken Selenium tests. - `Pull Request 3440`_ -* Various fixes for test image Docker user switching. - `Pull Request 3443`_ * Attempt work around for race-y sort of condition in Selenium sizzle checkers. `Pull Request 3451`_ * Webhooks: add tests (thanks to `@anatskiy `__). `Pull Request 3469`_ -* Fix selenium workflow tests broken with `#3181 - `__. - `Pull Request 3504`_ -* Fix integration test for default Conda mapping. - `Pull Request 3508`_ * Watch tool data table *.loc files, and reload if modified. (thanks to `@mvdbeek `__). `Pull Request 3533`_ -* Fix transiently failing Selenium upload test. - `Pull Request 3587`_ * Disable transiently failing tour test. `Pull Request 3599`_ -* Fix for transiently failing workflow test. - `Pull Request 3668`_ * Selenium Testing Improvements `Pull Request 3716`_ -* Fix webhook search overlay interfering with masthead load - `Pull Request 3731`_ * Merge ConfiguresGalaxyMixin.reload_toolbox() in _configure_toolbox() (thanks to `@nsoranzo `__). `Pull Request 3732`_ -* Assorted Fixes for Dockerized Test Setup - `Pull Request 3755`_ -* deduplicate obsolete API readme - `Pull Request 3777`_ * Abstraction for re-use between collection creators. `Pull Request 3781`_ * Merge ToolConfWatchers and separate from Toolbox @@ -357,10 +309,6 @@ Enhancements * Attempt to improve the robustness and verboseness of the test_sharing_valid Selenium test. `Pull Request 3841`_ -* Fix collection operations in workflows. - `Pull Request 3848`_ -* Remove old, unused search controller. - `Pull Request 3894`_ * Routes cleanup `Pull Request 3895`_ * Speedup startup and toolbox operations @@ -370,14 +318,9 @@ Enhancements `Pull Request 3933`_ * Followup to exception refactoring `Pull Request 3959`_ -* Small selenium hack to fix occasionally failing collection upload tests. - `Pull Request 3967`_ * Use container-based infrastructure (sudo: false) in TravisCI (thanks to `@nsoranzo `__). `Pull Request 3977`_ -* Fix Travix builds which use flake8-docstrings - (thanks to `@nsoranzo `__). - `Pull Request 3981`_ * Improve implicit workflow connection test case. `Pull Request 3991`_ @@ -390,6 +333,45 @@ Fixes .. bug +* Fix tag escaping + `Pull Request 3720`_ +* Fix kombu documentation link in galaxy.ini.sample + `Pull Request 3629`_ +* Fix for EtherCalc IE image specification. + `Pull Request 3825`_ +* Fix margin style values for color picker element + `Pull Request 3965`_ +* 17.05 rstudio fixes / one small gie fix + (thanks to `@erasche `__). + `Pull Request 3975`_ +* Fix transiently failing Selenium upload test. + `Pull Request 3587`_ +* Fix webhook search overlay interfering with masthead load + `Pull Request 3731`_ +* Fix collection operations in workflows. + `Pull Request 3848`_ +* Remove old, unused search controller. + `Pull Request 3894`_ +* deduplicate obsolete API readme + `Pull Request 3777`_ +* Assorted Fixes for Dockerized Test Setup + `Pull Request 3755`_ +* Another fix for Selenium testing on Jenkins. + `Pull Request 3422`_ +* Fix most broken Selenium tests. + `Pull Request 3440`_ +* Fix for transiently failing workflow test. + `Pull Request 3668`_ +* Fix selenium workflow tests broken with `#3181 + `__. + `Pull Request 3504`_ +* Fix integration test for default Conda mapping. + `Pull Request 3508`_ +* Various fixes for test image Docker user switching. + `Pull Request 3443`_ +* Fix Travix builds which use flake8-docstrings + (thanks to `@nsoranzo `__). + `Pull Request 3981`_ * Azure - Leasing container sometimes breaks things in docker galaxy (thanks to `@zfrenchee `__). `Pull Request 3263`_ @@ -398,6 +380,8 @@ Fixes `Pull Request 3322`_ * Fix cycle detection for single node workflows. `Pull Request 3374`_ +* Small selenium hack to fix occasionally failing collection upload tests. + `Pull Request 3967`_ * Bug fix in mulled.py (thanks to `@abdulrahmanazab `__). `Pull Request 3434`_ @@ -567,6 +551,8 @@ Fixes `Pull Request 4065`_ * Fix global grid action event handler `Pull Request 4068`_ +* Fix various transiently failing Selenium tests. + `Pull Request 3450`_ .. github_links .. _Pull Request 3104: https://github.com/galaxyproject/galaxy/pull/3104 diff --git a/doc/source/releases/17.05_announce.rst b/doc/source/releases/17.05_announce.rst index f257bff7ffe9..070fe6f1a028 100644 --- a/doc/source/releases/17.05_announce.rst +++ b/doc/source/releases/17.05_announce.rst @@ -11,11 +11,14 @@ Highlights **Feature1** Feature description. -**Feature2** - Feature description. - -**Feature3** - Feature description. +**Track your original datasets more easily** + When you add certain tags with a ``#`` in front (e.g. ``#sample_A``) to datasets they will be propagated + through toolruns to subsequent datasets helping you to better orientate within history. + Implemented in `Pull Request 3704`_ `Pull Request 3718`_ `Pull Request 3719`_ `Pull Request 3760`_ `Pull Request 3868`_ `Pull Request 3979`_ + +**Drag & Drop datasets into tool inputs** + Interface now allows dragging datasets from history panel into the content selectors of the tool form. + Implemented in `Pull Request 3871`_. Get Galaxy ==========