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