From 5bde1d1c3a0239ef37369f59e90ceca863d6821f Mon Sep 17 00:00:00 2001 From: John Chilton Date: Mon, 16 Oct 2017 14:04:39 -0400 Subject: [PATCH] Small progress on 17.09 release notes. --- doc/source/releases/17.09.rst | 102 +++++++++---------------- doc/source/releases/17.09_announce.rst | 7 +- 2 files changed, 43 insertions(+), 66 deletions(-) diff --git a/doc/source/releases/17.09.rst b/doc/source/releases/17.09.rst index 5cdd4b96ab0..8e617ba6459 100644 --- a/doc/source/releases/17.09.rst +++ b/doc/source/releases/17.09.rst @@ -15,29 +15,33 @@ Enhancements .. feature * Galaxy Workflow support for GenomeSpace - (thanks to `@gvlproject `__). + (thanks to `@nuwang `__ and + `@gvlproject `__). `Pull Request 1814`_ +* Support tags (including new "name" tags) in data libraries. + (thanks to `@bwlang `__). + `Pull Request 4262`_ * HiCBrowser as Galaxy IE (thanks to `@bgruening `__). `Pull Request 3330`_ * Synnefo/Pithos+ object store backend (thanks to `@saxtouri `__). `Pull Request 3611`_ -* Add job runner for Chronos +* Add job runner for `Chronos `__ (thanks to `@theosotr `__). `Pull Request 3946`_ -* Add entry for empty_extra_files_path validator +* Paramiko based shell job runner + (thanks to `@mvdbeek `__). + `Pull Request 4358`_ +* Add entry for ``empty_extra_files_path`` validator (thanks to `@gregvonkuster `__). `Pull Request 3994`_ -* Async update: support to collections +* Extend async data sources to support dataset collections (thanks to `@fabio-cumbo `__). `Pull Request 4198`_ -* Add API repository uninstall endpoint +* Add a repository uninstall endpoint to the tool dependency API (thanks to `@mvdbeek `__). `Pull Request 4248`_ -* Data Library tags support - (thanks to `@bwlang `__). - `Pull Request 4262`_ * Display preview feature for Bam datatype (thanks to `@ashvark `__). `Pull Request 4279`_ @@ -47,13 +51,10 @@ Enhancements * Created alphabetic and numerical sort tool for collection operations (thanks to `@glormph `__). `Pull Request 4329`_ -* Paramiko based shell runner - (thanks to `@mvdbeek `__). - `Pull Request 4358`_ -* Stop loading tools that require a newer galaxy +* Prevent loading tools that require a newer galaxy (thanks to `@mvdbeek `__). `Pull Request 4382`_ -* Vcf gz datatype +* Add explicit support for gzipped VCF files (thanks to `@ffinfo `__). `Pull Request 4254`_ * Add ptkscmp datatype @@ -68,25 +69,26 @@ Enhancements * Add support for the MEME psp format (thanks to `@gregvonkuster `__). `Pull Request 4430`_ -* add biom2 datatype +* Add biom2 datatype (thanks to `@shiltemann `__). `Pull Request 4519`_ * Add Excel97 Datatype `Pull Request 4410`_ -* add mz5 datatype +* Add mz5 datatype (thanks to `@bgruening `__). `Pull Request 4466`_ .. enhancement -* Configuration & Server Overhaul - Tool Shed and Reports +* Revamp configuration and default server for tool shed and Galaxy reports application + (these now use a uwsgi server by default configured with a YAML configuration file). `Pull Request 3179`_ * Speed up and optimize the process of identifying public libraries. `Pull Request 4640`_ -* A round of data libraries improvements. +* Various data libraries improvements. `Pull Request 4512`_ -* Install tools and workflow - (thanks to `@manabuishii `__). +* Enhance workflow import API endpoint to allow admins to install repositories corresponding to a supplied + workflow (thanks to `@manabuishii `__). `Pull Request 3064`_ * GFF3 support in filter by attribute (thanks to `@peterjc `__). @@ -94,18 +96,28 @@ Enhancements * Add extension point for user preferences (thanks to `@bgruening `__). `Pull Request 3383`_ -* respect expose_user_email configuration in datalibraries permissions list +* Respect ``expose_user_email`` configuration in data libraries permissions list. `Pull Request 4611`_ -* Explicitly include PyPI as an --extra-index-url to pip +* Explicitly include PyPI as an ``--extra-index-url`` to pip. `Pull Request 4674`_ -* Kubernetes runner: Non-privileged filesystem access, updated k8s Job version +* Improved Kubernetes support (non-privileged filesystem access, updated k8s Job API target) (thanks to `@phnmnl `__). `Pull Request 3972`_ -* Nicer tool click targets for base + "plain" theme +* Nicer tool click targets for toolbox (thanks to `@erasche `__). `Pull Request 4470`_ -* Setup framework for retrying failed Selenium tests. - `Pull Request 3993`_ +* Implement a "plain" bootstrap theme for the UX + (thanks to `@erasche `__). + `Pull Request 4470`_ +* Add Selenium tests for the "saved histories" and "published histories" + (thanks to `@anatskiy `__). + `Pull Request 4587`_, `Pull Request 4502`_ +* Dozens of Selenium functional test enhancements and fixes + `Pull Request 3993`_, `Pull Request 4523`_, `Pull Request 4524`_, `Pull Request 4549`_, + `Pull Request 4588`_, `Pull Request 4589`_, `Pull Request 4647`_, + `Pull Request 3992`_, `Pull Request 4003`_, `Pull Request 4053`_, + `Pull Request 4576`_, `Pull Request 4561`_, `Pull Request 4531`_, `Pull Request 4564`_, + `Pull Request 4582`_, `Pull Request 4586`_, `Pull Request 4592`_ * Tool-Describing-Tours (thanks to `@anatskiy `__). `Pull Request 4019`_ @@ -375,10 +387,6 @@ Enhancements `Pull Request 4514`_ * Display d3 hierarchy datatype in upload interface `Pull Request 4522`_ -* Selenium test fixes and improvements. - `Pull Request 4523`_ -* Fix workflow run Selenium test and make it more robust. - `Pull Request 4524`_ * Implement influxdb error reporter (thanks to `@erasche `__). `Pull Request 4533`_ @@ -389,8 +397,6 @@ Enhancements `Pull Request 4542`_ * allow linking, posix and spaces conversions in datalib imports `Pull Request 4547`_ -* Assorted Selenium test fixes - `Pull Request 4549`_ * Allow exporting workflows when tool is uninstalled (thanks to `@mvdbeek `__). `Pull Request 4553`_ @@ -404,10 +410,6 @@ Enhancements * Add show/hide deleted/hidden links when history is filtered... (thanks to `@chambm `__). `Pull Request 4581`_ -* Make history sharing Selenium tests more robust and informative. - `Pull Request 4588`_ -* Improve error reporting in Selenium tests when ``wait_for_logged_in`` fails. - `Pull Request 4589`_ * Python 3 fixes for set_metadata.py `Pull Request 4607`_ * Allow adding new data tables without restart @@ -416,8 +418,6 @@ Enhancements * remove .git and .hg from recursive file search (thanks to `@bgruening `__). `Pull Request 4636`_ -* Improved state handling for @anatskiy-style Selenium tests. - `Pull Request 4647`_ * Better handling of long id secrets when generating per-kind encryption keys. `Pull Request 4713`_ @@ -428,17 +428,11 @@ Enhancements * Add test case clarifying datasets do get "renamed" by rename PJA in collections. `Pull Request 3983`_ -* Fixes for Selenium workflow run test case. - `Pull Request 3992`_ -* Fix handling main_panel switching in various Selenium tests. - `Pull Request 4003`_ * One more fix for main_panel fix in `#3992 `__. `Pull Request 4042`_ * Add some test tools for collection job failures. `Pull Request 4044`_ -* Reset Selenium test connection between test retries. - `Pull Request 4053`_ * Add admin app `Pull Request 4067`_ * Preparation for grids mako removal @@ -497,15 +491,10 @@ Enhancements * Workflow loading speedup (thanks to `@mvdbeek `__). `Pull Request 4500`_ -* Published History Grid tests - (thanks to `@anatskiy `__). - `Pull Request 4502`_ * Prevent transient job state test failures from failing the build. `Pull Request 4510`_ * More robust workflow invocation testing. `Pull Request 4530`_ -* Another fix for Selenium worklow tests. - `Pull Request 4531`_ * Refactor history import/export tests to allow collection testing. `Pull Request 4534`_ * Refactor test modules toward cleaner dependencies @@ -520,27 +509,10 @@ Enhancements * Check user roles only once if user has no roles (thanks to `@mvdbeek `__). `Pull Request 4546`_ -* Revert "Remove Selenium test that is broken because Galaxy is broken." - (thanks to `@mvdbeek `__). - `Pull Request 4561`_ -* Increase the robustness of Selenium workflow management tests. - `Pull Request 4564`_ * Fix datalib collection import `Pull Request 4568`_ -* Make submitting logins for Selenium tests a bit more robust. - `Pull Request 4576`_ * Delegate displaying of page titles to Layout.display() `Pull Request 4578`_ -* Retry failed clicks more aggressively for Selenium tests. - `Pull Request 4582`_ -* Fix another issue with sorting by owner for published histories Selenium - test. - `Pull Request 4586`_ -* Add Selenium tests for the Saved Histories - (thanks to `@anatskiy `__). - `Pull Request 4587`_ -* Small improvements to workflow editor Selenium tests. - `Pull Request 4592`_ * Datalibs various fixes `Pull Request 4595`_ * Remove bam to bai converter diff --git a/doc/source/releases/17.09_announce.rst b/doc/source/releases/17.09_announce.rst index 36b8ea58df2..62c63764ecf 100644 --- a/doc/source/releases/17.09_announce.rst +++ b/doc/source/releases/17.09_announce.rst @@ -9,7 +9,12 @@ Highlights =========================================================== **Singularity** - `Pull Request 4175`_ + Tool execution using the HPC-friendly container technology `Singularity `__ + is now supported. Custom containers can be specified by the Galaxy admin on a per job destination basis + or standardized containers can be built or downloaded corresponding to Conda requirements automatically + using the mulled toolkit built into Galaxy (just like is possible for Docker). For more information + checkout `this presentation `__ from the 2017 Galaxy Community Conference. + `Pull Request 4175`_ **Download entire collection** Downloading whole colections is now possible from the history interface. `Pull Request 4098`_