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Merge pull request #9194 from hexylena/user-rename

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Update github username @erasche to @hexylena and correct inconsistencies
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Martin Cech
2020-01-09 11:32:53 -05:00
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parent aa17c91be3 1c27a3021e
commit 075212937f
23 changed files with 142 additions and 142 deletions
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CONTRIBUTORS.md
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@@ -124,7 +124,7 @@ The following individuals have contributed code to Galaxy:
* Chinmay Rao <chinmay@bx.psu.edu>
* Matt Ralston <mrals89@gmail.com>
* ramezrawas <ramezrawas@gmail.com>
* Eric Rasche <esr@tamu.edu> <rasche.eric@gmail.com> <rasche.eric@yandex.ru>
* Helena Rasche <helena.rasche@gmail.com>
* Athos Ribeiro <athoscr@fedoraproject.org>
* Andrew Robinson <Andrew.Robinson@latrobe.edu.au>
* Devon Ryan <dpryan79@gmail.com>
doc/source/admin/special_topics/interactive_environments.svg
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@@ -484,7 +484,7 @@
<dc:title>Galaxy Jupyter Graphic</dc:title>
<dc:creator>
<cc:Agent>
<dc:title>Björn Grüning, Torsten Houwaart, Eric Rasche</dc:title>
<dc:title>Björn Grüning, Torsten Houwaart, Helena Rasche</dc:title>
</cc:Agent>
</dc:creator>
<dc:language>en_US</dc:language>
Side by Side Swipe Overlay

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doc/source/dev/interactive_environments.rst
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@@ -545,4 +545,4 @@ If everything went well, at this point you should see a directory listing show u
.. image:: interactive_environments_success.png
If you find yourself encountering difficulties, the "Hello, World" IE is
available in a `GitHub repo <https://github.com/erasche/hello-world-interactive-environment/releases/tag/v15.10>`__, and there are people on the IRC channel who can help debug.
available in a `GitHub repo <https://github.com/hexylena/hello-world-interactive-environment/releases/tag/v15.10>`__, and there are people on the IRC channel who can help debug.
doc/source/releases/15.05.rst
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@@ -55,10 +55,10 @@ Enhancements
`Pull Request 143`_
* Add NCBI SRA datatype - thanks to Matt Shirley. `Pull Request 87`_
* Stronger toolbox filtering. `Pull Request 119`_
* Allow updating Tool Shed repositories via the API - thanks to Eric Rasche.
* Allow updating Tool Shed repositories via the API - thanks to Helena Rasche.
`Pull Request 30`_
* Expose category list in show call for Tool Shed repositories - thanks to
Eric Rasche. `Pull Request 29`_
Helena Rasche. `Pull Request 29`_
* Add API endpoint to create Tool Shed repositories. `Pull Request 2`_
* Do not configure Galaxy to use the test Tool Shed by default.
`Pull Request 38`_
@@ -67,7 +67,7 @@ Enhancements
* Enhance multi-selection widgets to allow key combinations ``Ctrl-A``
and ``Ctrl-X``. e8564d7_, `Trello <https://trello.com/c/3QhD5l5h>`__
* New, consistent button for displaying citation BibTeX. `Pull Request 19`_
* Improved ``README`` reflecting move to Github - thanks in part to Eric
* Improved ``README`` reflecting move to Github - thanks in part to Helena
Rasche. `PR #2 (old repo)
<https://github.com/galaxyproject/galaxy-beta1/pull/2>`__,
226e826_, 2650d09_, 7d5dde8_
@@ -87,14 +87,14 @@ Enhancements
* Preserve spaces in ``Count1`` tool (``tools/filters/uniq.xml``) - thanks to
Peter Cock. `Pull Request 13`_
* `Interactive Environments`_ improvements and fixes from multiple
developers including Eric Rasche and Björn Grüning. `Pull Request 69`_,
developers including Helena Rasche and Björn Grüning. `Pull Request 69`_,
`Pull Request 73`_, `Pull Request 131`_, `Pull Request 135`_,
`Pull Request 152`_, `Pull Request 197`_
* Enable multi-part upload for exporting files with the GenomeSpace export
* Enable multi-part upload for exporting files with the GenomeSpace export
tool. `Pull Request 74`_, `Trello <https://trello.com/c/28O46iln>`__
* Large refactoring, expansion, and increase in test coverage for "managers".
`Pull Request 76`_
* Improved display of headers in tool help. 157eba6_,
* Improved display of headers in tool help. 157eba6_,
`Biostar <https://biostar.usegalaxy.org/p/11211/>`__
* Uniform configuration of "From" field for sent emails - thanks to Nicola
Soranzo. `Pull Request 23`_
@@ -112,8 +112,8 @@ Enhancements
* Add test tool demonstrating citing a Github repository. 65def71_
* Add option to track all automated changes to the integrated tool panel.
10bb492_
* Make tool version explicit in all distribution tool - thanks to Peter Cock.
`Pull Request 14`_.
* Make tool version explicit in all distribution tool - thanks to Peter Cock.
`Pull Request 14`_.
* Relocate the external metadata setting script. `Pull Request 7`_
* Parameterize script used to pull new builds from the UCSC Browser.
e4e5df0_
@@ -141,7 +141,7 @@ Fixes
properly. `Pull Request 198`_, `Trello <https://trello.com/c/WVlaLsOh>`__
* Fix scatter plot API communications for certain proxied Galaxy instances -
thanks to @yhoogstrate. `Pull Request 89`_
* Fix bug in collectl_ job metrics plugin - thanks to Carrie Ganote.
* Fix bug in collectl_ job metrics plugin - thanks to Carrie Ganote.
`Pull Request 231`_
* Fix late validation of tool parameters. `Pull Request 115`_
* Fix ``fasta_to_tabular_converter.py`` (for implicit conversion) - thanks to
@@ -161,7 +161,7 @@ Fixes
* Fix to remove redundant version ids in tool version selector.
`Pull Request 244`_
* Fix for downloading metadata files. `Pull Request 234`_
* Fix for history failing to render if it contains more exotic dataset
* Fix for history failing to render if it contains more exotic dataset
collection types. `Pull Request 196`_
* Fixes for BaseURLToolParameter. `Pull Request 247`_
* Fix to suppress pysam binary incompatibility warning when using datatypes
doc/source/releases/15.07.rst
+12 -12
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@@ -12,7 +12,7 @@ Enhancements
.. enhancements
* Interactive environment (IE) framework updates including a new IE for RStudio.
(Thanks to a team effort spearheaded by `@erasche <https://github.com/erasche>`__.)
(Thanks to a team effort spearheaded by `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 229`_, `Pull Request 230`_
* Rework workflow editor to use newer tool form components and allow construction
of workflows with tools explicitly producing output collections.
@@ -27,8 +27,8 @@ Enhancements
focus on the API documentation. (Thanks to `@nsoranzo
<https://github.com/nsoranzo>`__.)
`Pull Request 399`_, `Pull Request 405`_
* Add EDAM IDs to Galaxy datatypes. (Thanks to a team effort initiated by `@erasche
<https://github.com/erasche>`__.)
* Add EDAM IDs to Galaxy datatypes. (Thanks to a team effort initiated by `@hexylena
<https://github.com/hexylena>`__.)
`Pull Request 80`_, `Pull Request 342`_
* Improved reports app sorting and bug fixes thanks to
Daniel Bouchard (`@Airistotal <https://github.com/Airistotal>`__). Even more
@@ -66,11 +66,11 @@ Enhancements
<https://github.com/Christian-B>`__.) `Pull Request 441`_
* Add emboss datatypes (previously migrated to Tool Shed). (Thanks to `@bgruening
<https://github.com/bgruening>`__.) `Pull Request 148`_
* Add new Hmmer & Stockholm datatypes. (Thanks to `@erasche
<https://github.com/erasche>`__.) `Pull Request 218`_
* Add an RData datatype. (Thanks to `@erasche
<https://github.com/erasche>`__.) `Pull Request 239`_
* Add mauve XMFA datatype (Thanks to `@erasche <https://github.com/erasche>`__.)
* Add new Hmmer & Stockholm datatypes. (Thanks to `@hexylena
<https://github.com/hexylena>`__.) `Pull Request 218`_
* Add an RData datatype. (Thanks to `@hexylena
<https://github.com/hexylena>`__.) `Pull Request 239`_
* Add mauve XMFA datatype (Thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 270`_
* Add ConnectivityTable (\*.ct) (RNA 2D structure format) datatype.
(Thanks to `@yhoogstrate <https://github.com/yhoogstrate>`__.)
@@ -114,10 +114,10 @@ Enhancements
`Pull Request 186`_
* Switch visualizations registry to entry_point config definition for
built-in visualizations. `Pull Request 243`_
* Set default value for IE sig proxy (Thanks to `@erasche
<https://github.com/erasche>`__.) `Pull Request 197`_
* Set default value for IE sig proxy (Thanks to `@hexylena
<https://github.com/hexylena>`__.) `Pull Request 197`_
* Other smaller interactive environment updates. (Thanks to
`@erasche <https://github.com/erasche>`__.)
`@hexylena <https://github.com/hexylena>`__.)
`Pull Request 412`_
* Refuse to load interactive debugging middleware under uwsgi.
`Pull Request 200`_
@@ -179,7 +179,7 @@ Enhancements
* Add configurable Docker hostname (Thanks to `@bgruening
<https://github.com/bgruening>`__.) `Pull Request 356`_
* Improve XML styling of display applications.
(Thanks to `@erasche <https://github.com/erasche>`__.)
(Thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 364`_
* README improvements including - adding shields for Biostar, IRC, and Travis.
`Pull Request 368`_, `Pull Request 369`_
doc/source/releases/15.07_announce.rst
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@@ -10,7 +10,7 @@ Highlights
**Interactive Environments**
The interactive environments (IE) framework features several updates this release
and Galaxy is now distributed with a new IE for RStudio implemented by Eric Rasche.
and Galaxy is now distributed with a new IE for RStudio implemented by Helena Rasche.
**Workflow Editor Enhancements**
The workflow editor has been significantly revamped - it now uses newer tool form
@@ -18,9 +18,9 @@ Highlights
output collections.
**Policies for Committers and Pull Requests**
The process for adding committers to the project and fielding pull requests has
The process for adding committers to the project and fielding pull requests has
been formalized and documented in the source code. Three new committers have been
added to the project - Björn Grüning, Nicola Soranzo, and Eric Rasche.
added to the project - Björn Grüning, Nicola Soranzo, and Helena Rasche.
`Github <https://github.com/galaxyproject/galaxy>`__
@@ -28,17 +28,17 @@ Highlights
New
.. code-block:: shell
% git clone -b master https://github.com/galaxyproject/galaxy.git
Update to latest stable release
.. code-block:: shell
% git checkout master && pull --ff-only origin master
Update to exact version
.. code-block:: shell
% git checkout v15.07
@@ -47,8 +47,8 @@ Update to exact version
Upgrade
.. code-block:: shell
% hg pull
% hg pull
% hg update latest_15.07
doc/source/releases/15.10.rst
+12 -12
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@@ -32,10 +32,10 @@ Enhancements
* Add ``regex_replace`` tool dependency install action.
`Pull Request 457`_
* Document Galaxy interactive environments (GIEs).
(Thanks to `@erasche <https://github.com/erasche>`__.)
(Thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 803`_
* Explicit project procedure language on reversions and WIP. (Thanks to `@erasche
<https://github.com/erasche>`__.)
* Explicit project procedure language on reversions and WIP. (Thanks to `@hexylena
<https://github.com/hexylena>`__.)
`Pull Request 556`_
* Readme improvemenets - GitHub issues, security email contact and CI testing
(Thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
@@ -97,7 +97,7 @@ Enhancements
* Expose tool config file path to admins via the API.
`Pull Request 652`_
* Add Galaxy developer documentation section to docs.
(Thanks to `@erasche <https://github.com/erasche>`__.)
(Thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 654`_
* Password reset improvements.
`Pull Request 655`_
@@ -115,7 +115,7 @@ Enhancements
* Set a default value for copy history dialog radio input (to copy *all*).
`Pull Request 693`_
* Remove various code duplication.
(Thanks to `@erasche <https://github.com/erasche>`__.)
(Thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 694`_
* Use ``setup.py`` for Python all installations during dependency installation.
(Thanks to `@bgruening <https://github.com/bgruening>`__.)
@@ -163,13 +163,13 @@ Enhancements
<https://github.com/scholtalbers>`__.)
`Pull Request 777`_
* Unify the docker command, command_inject, and command_wrapper (Thanks to
`@erasche <https://github.com/erasche>`__.)
`@hexylena <https://github.com/hexylena>`__.)
`Pull Request 782`_
* Test case to prevent regression of `#753
<https://github.com/galaxyproject/galaxy/issues/753>`__.
`Pull Request 784`_
* Refactor interactive environment launching to use Docker's ``-P`` option.
(Thanks to `@erasche <https://github.com/erasche>`__.)
(Thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 790`_
* Print ``has_metrics`` class name instead of object memory address. (Thanks to
`@nsoranzo <https://github.com/nsoranzo>`__.)
@@ -205,7 +205,7 @@ Enhancements
`Pull Request 847`_
* Remove unused ``echo`` tool
`Pull Request 848`_
* Update interactive environments for this release. (Thanks to `@erasche <https://github.com/erasche>`__.)
* Update interactive environments for this release. (Thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 849`_
* Enhancements for IPython interactive environment allowing it run in certain
deployments.
@@ -296,10 +296,10 @@ Fixes
(Thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
`Pull Request 596`_
* Fix bug in reload API where id wasn't recognised.
(Thanks to `@erasche <https://github.com/erasche>`__.)
(Thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 619`_
* Correct typo in tool shed action handler code.
(Thanks to `@erasche <https://github.com/erasche>`__.)
(Thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 561`_
* Small fixes for UI functional tests.
`Pull Request 485`_, `Pull Request 487`_
@@ -404,7 +404,7 @@ Fixes
* Tool form error messages and rerun fixes.
`Pull Request 766`_
* Quote value to fix configparser error in interactive environments.
(Thanks to `@erasche <https://github.com/erasche>`__.)
(Thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 775`_
* Fix upload event binding.
`Pull Request 778`_
@@ -425,7 +425,7 @@ Fixes
(Thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
`Pull Request 838`_
* Expose all API keys to admins under ``REMOTE_USER``.
(Thanks to `@erasche <https://github.com/erasche>`__.)
(Thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 873`_
* Various fixes for data libraries.
`Pull Request 878`_
doc/source/releases/16.01.rst
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@@ -58,7 +58,7 @@ Enhancements
`Pull Request 1405`_
* Add search on username/any for API calls to user and use Select2 for sharing
workflows/pages/histories
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 1111`_
* Improve masthead and scratchbook UI and architecture.
`Pull Request 1407`_, `Pull Request 1424`_
@@ -113,7 +113,7 @@ Enhancements
environment variables.
`Pull Request 564`_, `Pull Request 889`_
* Reorganize history menu
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 985`_
* Look up installed tools from different toolshed(s)
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
@@ -141,7 +141,7 @@ Enhancements
(thanks to `@scholtalbers <https://github.com/scholtalbers>`__.)
`Pull Request 912`_
* Add an API script to upload directory as a data library
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 918`_
* Enable dockerized toolshed tests.
`Pull Request 942`_
@@ -197,7 +197,7 @@ Enhancements
* Use common exceptions in tools.
`Pull Request 874`_
* Refactor the remote user middleware for complexity
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 875`_
* Allowed for capitalized package names such as R in unlinked tool shed
dependency resolver
@@ -221,7 +221,7 @@ Enhancements
* Add Workflow editor UI for step labels.
`Pull Request 1251`_
* Ease the grunt uglify process
(Thanks to `@erasche <https://github.com/erasche>`__.)
(Thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 1238`_
* Add beta run workflow form based on the newer tool form code.
`Pull Request 1249`_
@@ -260,7 +260,7 @@ Enhancements
* Unify and abstract code for checking if file looks like a tool definition.
`Pull Request 1368`_
* Added hashes to pip requirements file
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 1393`_
* Interactive environment updates
(thanks to `@bgruening <https://github.com/bgruening>`__.)
@@ -376,10 +376,10 @@ Fixes
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
`Pull Request 863`_
* Bump version of sqlite3 in nodejs proxy
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 866`_
* Expose API keys to admins under ``REMOTE_USER``
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 872`_
* Bug fix for tool shed repository API
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
@@ -394,7 +394,7 @@ Fixes
error.
`Pull Request 908`_
* Bug fix for condor runner changes made this release cycle
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 909`_
* Change user preference datatype to text.
`Pull Request 916`_
@@ -404,14 +404,14 @@ Fixes
* Revise tool URL building.
`Pull Request 947`_
* Fix for code checking if a file seems to a tool definition file
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 949`_
* Fix base panels to include scripts as the last element of the body.
`Pull Request 969`_
* Grid batch operation fixes.
`Pull Request 971`_
* Fix extra files path URL problem.
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 991`_
* Fixes broken env-var declarations for tools with weird chars in their names
(thanks to `@yhoogstrate <https://github.com/yhoogstrate>`__.)
@@ -485,7 +485,7 @@ Fixes
* Fix for creating workflow outputs on initial workflow upload.
`Pull Request 1330`_
* Don't query on unencoded IDs for error form
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 1340`_
* If ``GALAXY_SLOTS`` is defined in the environment, use it for the local runner.
`Pull Request 1346`_
doc/source/releases/16.04.rst
+7 -7
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@@ -38,7 +38,7 @@ Enhancements
* disable 'hg push' to TS repositories
`Pull Request 2033`_
* Generic GIE Launcher, GIE Image Chooser, multiple datasets
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 1403`_
* The entire Python source code is now continuously checked with flake8 for
PEP-8 style consistency and common errors. The last 3500 errors were fixed in
@@ -49,7 +49,7 @@ Enhancements
.. enhancement
* Implement new GIE proxy
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 1807`_
* Workflow editor overview click navigation
`Pull Request 1843`_
@@ -58,7 +58,7 @@ Enhancements
* datalibs: introduce folder management; fix various glitches; refactor
`Pull Request 1562`_
* Add makefile target for release process
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 1433`_
* libraries: provide select all/none options when importing
`Pull Request 1970`_
@@ -152,7 +152,7 @@ Enhancements
* Implement dataset empty input validator.
`Pull Request 1808`_
* Makefile help target + formatting
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 1824`_
* Add license and repository information to package.json.
`Pull Request 1829`_
@@ -228,7 +228,7 @@ Enhancements
* make new beta TS tools installation via API configurable
`Pull Request 2088`_
* Patch in visual separation of section parameters
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 2091`_
* Add sample supervisor config
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__.)
@@ -447,7 +447,7 @@ Fixes
* Fix farbtastic's use of deprecated jquery fns by loading jq-migrate in galaxy.panels.mako .
`Pull Request 1972`_
* Remove duplicate help target
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 1980`_
* Fix booleans in workflow editor
`Pull Request 1990`_
@@ -477,7 +477,7 @@ Fixes
* Show sections in workflow run
`Pull Request 2087`_
* Workflow section fix backport
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 2092`_
* Run external local set_metadata jobs in the job's working directory
`Pull Request 2094`_
doc/source/releases/16.07.rst
+9 -9
View File
@@ -35,7 +35,7 @@ Highlighted Enhancements
(thanks to `@BalthazarPavot <https://github.com/BalthazarPavot>`__.)
`Pull Request 2664`_
* Nicer bug report emails
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 2143`_
* Tools with auto_format='true' now connectable in workflow editor
(thanks to `@yhoogstrate <https://github.com/yhoogstrate>`__.)
@@ -160,7 +160,7 @@ Enhancements
* Remove backported importlib and ordereddict.
`Pull Request 2380`_
* Note on updating tool testing
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 2381`_
* Docker swarm support for Galaxy Interactive Environments (GIEs)
`Pull Request 2386`_, `Pull Request 2392`_
@@ -238,7 +238,7 @@ Enhancements
* Allow users to purge datasets by default.
`Pull Request 2553`_
* Add Jupyter IE to the allowed visualizations for BAM datasets
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 2572`_
* Python3: port 215 files
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__, `@tshtatland <https://github.com/tshtatland>`__, `@xiaoqian1984 <https://github.com/xiaoqian1984>`__, `@alanryanwang <https://github.com/alanryanwang>`__ and `@ericenns <https://github.com/ericenns>`__.)
@@ -392,14 +392,14 @@ Fixes
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
`Pull Request 2223`_
* Sanitize poorly escaped input value in run workflow form
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 2231`_
* Multi-data collection reductions in repeat blocks are broken.
`Pull Request 2233`_
* Encode collection reduce in serializable fashion
`Pull Request 2241`_
* Cast everything to a string
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 2252`_
* Use standard model.orm.now for toolshed's password reset token datetime math
`Pull Request 2261`_
@@ -426,7 +426,7 @@ Fixes
* Build: remove redundant webpack step in makefile
`Pull Request 2327`_
* Unicodify has different semantics to str, causing bug reporter bug
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 2336`_
* Wrap statsd timing middleware more closely around the core application
`Pull Request 2342`_
@@ -441,7 +441,7 @@ Fixes
(thanks to `@bgruening <https://github.com/bgruening>`__.)
`Pull Request 2394`_
* Check variable's presence before calling str methods
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 2408`_
* UI, history: correctly handle index API defaults
`Pull Request 2413`_
@@ -482,10 +482,10 @@ Fixes
* Initialize objectstore for fix_set_dataset_sizes script
`Pull Request 2544`_
* Fix old bug in non-allowed_images.yml GIEs
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 2548`_
* More defensive GIE Proxying
(thanks to `@erasche <https://github.com/erasche>`__.)
(thanks to `@hexylena <https://github.com/hexylena>`__.)
`Pull Request 2552`_
* Fixes for showing min/max labels in Trackster.
`Pull Request 2555`_
doc/source/releases/16.10.rst
+3 -3
View File
@@ -221,7 +221,7 @@ Enhancements
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 3033`_
* Remove outdated warning on ID_SECRET
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 3046`_
* Add Galaxy architecture slides documentation to project.
`Pull Request 3060`_, `Pull Request 3091`_
@@ -330,10 +330,10 @@ Fixes
(thanks to `@sszakony <https://github.com/sszakony>`__).
`Pull Request 2808`_
* Allow NodeJS proxy to do reverse proxying
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 2817`_
* Fixes for the RStudio interactive environment
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 2818`_
* Acquire lock before attempting to install conda
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
doc/source/releases/17.01.rst
+7 -7
View File
@@ -50,20 +50,20 @@ Enhancements
`Pull Request 3217`_
* Many improvements to the job information page - including
exposing certain job metrics to non-admin users
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 3344`_, `Pull Request 3256`_,
`Pull Request 3340`_
* Formalize decision to increase time between releases to four months. The next release
will be 17.05.
`Pull Request 3271`_
* Add API endpoint to determine who the current user is
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 3423`_
* Extend API version information for Docker-based Galaxy instances
(thanks to `@manabuishii <https://github.com/manabuishii>`__).
`Pull Request 3411`_
* Implement a more complete Genbank datatype with sniffer
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 3339`_
* Add additional image datatypes
(thanks to `@ThomasWollmann <https://github.com/ThomasWollmann>`__).
@@ -114,7 +114,7 @@ Enhancements
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 3328`_
* Allow admins to see API keys under when using remote user authentication from proxies.
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 3338`_
* Limit adjusting Galaxy's Python environment to legacy tools
(discussed in Deprecation Notices section of release notes).
@@ -149,7 +149,7 @@ Fixes
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 3215`_
* Fix user table header in admin view
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 3200`_
* Fix to adjust masthead and tool search.
`Pull Request 3055`_
@@ -193,10 +193,10 @@ Fixes
(thanks to `@manabuishii <https://github.com/manabuishii>`__).
`Pull Request 3409`_
* Fix login functionality for RStudio IEs
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 3414`_
* Fix accidental email exposure during history sharing
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 3417`_
* Fix UX problem when sharing objects with users.
`Pull Request 3373`_
doc/source/releases/17.05.rst
+9 -9
View File
@@ -38,7 +38,7 @@ Enhancements
(thanks to `@anuprulez <https://github.com/anuprulez>`__ and `@bgruening <https://github.com/bgruening>`__).
`Pull Request 3601`_
* Add script to encode or decode the IDs that Galaxy exposes to users and admins
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 3622`_
* Support Docker Engine swarm mode for Interactive Environments.
`Pull Request 3666`_
@@ -50,7 +50,7 @@ Enhancements
* Container interface abstraction.
`Pull Request 3863`_
* Graphite support
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 3964`_
* Normalize the handling of steps and missing tools for the workflow editor.
`Pull Request 3181`_
@@ -187,7 +187,7 @@ Enhancements
* i18n improvements and French localization.
`Pull Request 3762`_
* Should exit immediately to avoid index error
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 3770`_
* Made collection operations help sections slightly more readable.
`Pull Request 3784`_
@@ -258,7 +258,7 @@ Enhancements
* Change 'User' menu to 'Login or Register' for anonymous users.
`Pull Request 3955`_
* Stats docs
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 3968`_
* Enhance filenames with collection context when downloading datasets from
GUI.
@@ -270,7 +270,7 @@ Enhancements
* Update Jupyter image to 17.05 .
`Pull Request 4007`_
* Inline CSS in error report email
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 3445`_
* Improve routing for user preference views.
`Pull Request 3446`_
@@ -340,7 +340,7 @@ Fixes
* Fix margin style values for color picker element.
`Pull Request 3965`_
* 17.05 rstudio fixes / one small GIE fix
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 3975`_
* Fix transiently failing Selenium upload test.
`Pull Request 3587`_
@@ -480,7 +480,7 @@ Fixes
* Fix multiple collection reductions on multiple data parameters.
`Pull Request 3875`_
* Fix inability for viz to raise loading with non-ascii messages
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 3881`_
* Fix new history endpoint providing custom builds metadata.
`Pull Request 3887`_
@@ -525,7 +525,7 @@ Fixes
* Use the configured tool_path when loading data managers.
`Pull Request 3989`_
* Typo in remote user / user preferences exception
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4015`_
* Fix setting up explicit container resolution from a container resolution
config file.
@@ -546,7 +546,7 @@ Fixes
* Fix for S3ObjectStore _clean_cache method.
`Pull Request 4055`_
* Correct webhooks to use Galaxy.root and be compatible with proxy_prefix
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4065`_
* Fix global grid action event handler.
`Pull Request 4068`_
doc/source/releases/17.09.rst
+16 -16
View File
@@ -80,7 +80,7 @@ Enhancements
`Pull Request 4466`_
* Refactor tool error reporting into plugins and implement a new
plugin for `influxdb <https://www.influxdata.com/>`__
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4305`_, `Pull Request 4533`_
* Implement second toolshed installation UX targetting the API.
`Pull Request 3626`_
@@ -120,10 +120,10 @@ Enhancements
(thanks to `@arbernard <https://github.com/arbernard>`__).
`Pull Request 4489`_
* Nicer tool click targets for toolbox
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4470`_
* Implement a "plain" bootstrap theme for the UX
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4470`_
* Add Selenium tests for the "saved histories", "published histories", and
"custom builds"
@@ -136,7 +136,7 @@ Enhancements
`Pull Request 4576`_, `Pull Request 4561`_, `Pull Request 4531`_, `Pull Request 4564`_,
`Pull Request 4582`_, `Pull Request 4586`_, `Pull Request 4592`_, `Pull Request 4042`_
* Prevent graphite from dying loudly
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4036`_
* Updated parameters check for OpenID
(thanks to `@VJalili <https://github.com/VJalili>`__).
@@ -164,12 +164,12 @@ Enhancements
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 4096`_
* Security policy
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4113`_
* Improved styling of workflow list.
`Pull Request 4138`_
* Swap over all URLs to new wiki location
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4141`_
* Documentation fixes and improvements
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
@@ -238,10 +238,10 @@ Enhancements
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4271`_
* More uniform backend code for generating page titles
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4272`_, `Pull Request 4578`_
* Fix blockquote>p sizing
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4273`_
* Expose more user properties to admins via the API.
`Pull Request 4274`_
@@ -256,7 +256,7 @@ Enhancements
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 4284`_
* Improve security via local network access restrictions
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4289`_
* Enhancement for Phyloviz viz plugin
(thanks to `@bgruening <https://github.com/bgruening>`__).
@@ -288,7 +288,7 @@ Enhancements
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4368`_, `Pull Request 4380`_
* Galactic Radio Telescope Update
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4376`_
* Show minimum required galaxy version in tool shed and galaxy installation
process
@@ -308,7 +308,7 @@ Enhancements
* Generalize allow_library_path_paste to allow_path_paste.
`Pull Request 4404`_
* Small GRT bugfixes
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4408`_
* Update conda channel order to sync with Bioconda
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
@@ -335,7 +335,7 @@ Enhancements
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 4456`_
* Improvements to `Sentry <https://sentry.io/welcome/>`__ integration
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4457`_, `Pull Request 4471`_
* Fix for GIEs to not automatically uppercase environment variables
(thanks to `@xgaia <https://github.com/xgaia>`__).
@@ -359,7 +359,7 @@ Enhancements
* Minor copy datasets dialog improvement.
`Pull Request 4486`_
* 41% reduction in freiburg galaxy startup time
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4495`_
* Allow paramiko cli to recover from ssh timeout
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
@@ -473,7 +473,7 @@ Enhancements
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4598`_
* Remove various unreachable statements
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4603`_
* Refactored a dataset variable to HDA
(thanks to `@VJalili <https://github.com/VJalili>`__).
@@ -583,7 +583,7 @@ Fixes
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 4420`_
* Some unicoding for local runner
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4426`_
* Break connection in workflow editor if necessary
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
@@ -603,7 +603,7 @@ Fixes
* Fix drag and drop from history for Firefox
`Pull Request 4496`_
* 2017-08 Security Patch
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4501`_
* Fix history import if using symlink in database directory
(thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
doc/source/releases/17.09_announce.rst
+1 -1
View File
@@ -141,7 +141,7 @@ Cross site scripting and session fixation
Disclosed on the `mailing list <https://lists.galaxyproject.org/pipermail/galaxy-dev/2017-August/025938.html>`__ in August 2017.
Vulnerabilities were found by Eric Rasche and Manabu Ishii respectively. Detailed descriptions of these categories of vulnerabilities can be found at:
Vulnerabilities were found by Helena Rasche and Manabu Ishii respectively. Detailed descriptions of these categories of vulnerabilities can be found at:
- `<https://www.owasp.org/index.php/Cross-site_Scripting_(XSS)>`__
- https://www.owasp.org/index.php/Session_fixation
doc/source/releases/18.01.rst
+9 -9
View File
@@ -45,7 +45,7 @@ Enhancements
(thanks to `@xgaia <https://github.com/xgaia>`__).
`Pull Request 4737`_
* Implement a Github error report backend for
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4765`_
* Add maintenance script to simplify setting up a cleanup cron job
(thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
@@ -136,7 +136,7 @@ Enhancements
* Allow multiple simultaneous uploads via single POST.
`Pull Request 4563`_
* Various bits of proactive security-related hardening
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4604`_
* Move test helper ``wait_for_dataset_collection`` for reuse
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
@@ -157,14 +157,14 @@ Enhancements
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 4688`_
* Nicer logging message for sentry
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4693`_
* Use enumeration to provide history input index names.
`Pull Request 4700`_
* Cleanup delayed action in ``history-view.js``.
`Pull Request 4704`_
* Add logging during for script integrity exceptions
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4720`_
* Fix to respect ``galaxy.json`` supplied metadata for empty outputs.
`Pull Request 4722`_
@@ -187,7 +187,7 @@ Enhancements
(thanks to `@pcm32 <https://github.com/pcm32>`__ and the `@phnmnl <https://github.com/phnmnl>`__ project).
`Pull Request 4751`_
* Send all influxdb stats to a single bucket
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 4758`_
* PEP-8 fixes in random doctests.
`Pull Request 4764`_
@@ -274,7 +274,7 @@ Enhancements
* Document fastest way to iterate on client & client tests together.
`Pull Request 5051`_
* Support separate DSN for job sentry error reports
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 5056`_
* Build endpoint separation
`Pull Request 5058`_
@@ -531,7 +531,7 @@ Fixes
`Pull Request 5045`_
* Safely handle possible ``None`` value encountered in processing and execution of
post-job action arguments
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 5050`_
* Restore admin form routes.
`Pull Request 5065`_
@@ -563,7 +563,7 @@ Fixes
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5121`_
* Fix attribute error that was missed during refactor of sentry
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 5122`_
* Fix connecting non-input modules to subworkflow inputs.
`Pull Request 5140`_
@@ -664,7 +664,7 @@ Fixes
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5357`_
* Handle ``None`` in job owner in API
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 5358`_
* Fix form logic in deactivate or uninstall.
`Pull Request 5363`_
doc/source/releases/18.05.rst
+6 -6
View File
@@ -50,7 +50,7 @@ Enhancements
`Pull Request 5479`_
* Allow formatting `StatsD <https://github.com/etsy/statsd>`__ data for
`InfluxDB <https://github.com/influxdata/influxdb>`__
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 5742`_
* Tool versions should follow `PEP 440 <https://www.python.org/dev/peps/pep-0440/>`__
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
@@ -145,10 +145,10 @@ Enhancements
* Various improvements for API tests.
`Pull Request 5697`_, `Pull Request 5699`_
* Small log level improvement
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 5715`_
* Swap password checking for the constant time comparison algorithm
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 5719`_
* Upgrade clone failure logging to error
(thanks to `@pvanheus <https://github.com/pvanheus>`__).
@@ -201,7 +201,7 @@ Enhancements
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5924`_
* Document Github bug reporter
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 5928`_
* Rewrite history structure display in `VueJS <https://vuejs.org/>`__
(thanks to `@anuprulez <https://github.com/anuprulez>`__).
@@ -295,7 +295,7 @@ Fixes
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 5718`_
* `Sentry <https://sentry.io/>`__ bug reports working for anonymous users
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 5721`_
* Add Galaxy `lib` directory to Python path for 2 scripts
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
@@ -366,7 +366,7 @@ Fixes
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 5917`_
* Correct signal number in admin documentation
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 5921`_
* Fix error with data managers when trying to move_merge nonexistent
extra_files dir
doc/source/releases/18.05_announce.rst
+1 -1
View File
@@ -45,7 +45,7 @@ Highlights
**GDPR Beta Mode**
We introduce beta GDPR privacy mode. Admins can enable it to help them comply with the European Union law
known as `General Data Protection Regulation <http://eur-lex.europa.eu/legal-content/en/TXT/?uri=CELEX:32016R0679>`__,
which goes into effect on May 25, 2018. Thanks to `@erasche <https://github.com/erasche>`__.
which goes into effect on May 25, 2018. Thanks to `@hexylena <https://github.com/hexylena>`__.
`Pull Request 6069`_
doc/source/releases/18.09.rst
+7 -7
View File
@@ -54,7 +54,7 @@ Enhancements
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6013`_
* Add hostname metric
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 6021`_
* Pause jobs with invalid inputs
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
@@ -88,7 +88,7 @@ Enhancements
* Common dataset selector
`Pull Request 6195`_
* Permit numeric values of GRT instance ID in config
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 6200`_
* Add the newick extension for the Newick datatype,
(thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
@@ -100,7 +100,7 @@ Enhancements
* Charts filename download fix
`Pull Request 6216`_
* Wrap inputs in labels
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 6221`_
* Workflow submit text links
`Pull Request 6240`_
@@ -209,14 +209,14 @@ Enhancements
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6469`_
* Fix bug noticed in sentry
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 6474`_
* Rulebuilder: Special case auto URL schema detection for SRA inputs.
`Pull Request 6476`_
* GRT: fix the upload logging init
`Pull Request 6478`_
* Add more information to the dataset template
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 6480`_
* Use bootstrap vue classes for workflow import form
`Pull Request 6489`_
@@ -344,7 +344,7 @@ Enhancements
.. small_enhancement
* Remove duplicate metric sending
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 6011`_
* This strips the graphite-specific middleware
`Pull Request 6018`_
@@ -670,7 +670,7 @@ Fixes
* Redirect unidentified routes in admin panel
`Pull Request 6551`_
* Remove the sharing of toolbox in GRT
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 6553`_
* Restore ``log_destination = stdout`` configuration option.
`Pull Request 6555`_
doc/source/releases/19.01.rst
+2 -2
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@@ -310,7 +310,7 @@ Fixes
.. bug
* Fixes to allow config schema to validate
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 5919`_
* Patch `update.sh` to address dependency update issues on a macOS.
`Pull Request 6694`_
@@ -414,7 +414,7 @@ Fixes
* Fix resubmission on tool error detection.
`Pull Request 7040`_
* GRT: Rip out all parameters, round file sizes
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 7041`_
* Pass through ``--daemon`` option to gunicorn
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
doc/source/releases/19.01_announce.rst
+1 -1
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@@ -21,7 +21,7 @@ Highlights
**More Colorful Tags**
Use consistently hashed randomized colors for history dataset name tags to increase visual
distinction between tags, making it easier to track data flow in complex histories.
Thanks to `@erasche <https://github.com/erasche>`__.
Thanks to `@hexylena <https://github.com/hexylena>`__.
`Pull Request 7072`_, `Pull Request 7081`_
**Extensive Workflow Enhancements (continued)**
doc/source/releases/19.05.rst
+6 -6
View File
@@ -46,7 +46,7 @@ Enhancements
`Pull Request 7193`_, `Pull Request 7192`_, `Pull Request 7537`_,
`Pull Request 7540`_, `Pull Request 7684`_, `Pull Request 7704`_
* User facing release notes
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 7527`_
* Implement dataset source and hash tracking.
`Pull Request 7487`_, `Pull Request 4659`_, `Pull Request 7549`_
@@ -223,10 +223,10 @@ Enhancements
* Automatically set ``cookie_path`` using ``url_for()``.
`Pull Request 7404`_
* Allow configuration location of user preferences extra configuration
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 7428`_
* Add hover styling to target tool in tool panel
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 7437`_
* Update Docker testing image
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
@@ -260,7 +260,7 @@ Enhancements
* Refactor XSD output elements to share common output attributes.
`Pull Request 7555`_
* Improve linking between job conf handler assignment and documentation
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 7558`_
* Refactor ``galaxy.web.security`` into ``galaxy.security.idencoding``.
`Pull Request 7560`_
@@ -537,7 +537,7 @@ Fixes
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 7547`_
* Correct db-self handler assignment method
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 7561`_
* Fix database config doctests when env vars are in use for dburi
`Pull Request 7562`_
@@ -549,7 +549,7 @@ Fixes
* Update cloud imports to adhere with cloudbridge interface changes.
`Pull Request 7586`_
* Fix RStudio GIE
(thanks to `@erasche <https://github.com/erasche>`__).
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 7590`_, `Pull Request 7925`_
* Fix styleguide.
`Pull Request 7602`_
doc/source/releases/19.05_announce.rst
+1 -1
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@@ -14,7 +14,7 @@ Highlights
oriented but will likely be even more so now. Features such as favoriting tools,
improved workflow editor feedback, and an exciting new cellxgene GIE may have
been featured in these release notes in the past but are now featured in the
user release notes instead. A huge thanks to `@erasche <https://github.com/erasche>`__
user release notes instead. A huge thanks to `@hexylena <https://github.com/hexylena>`__
for getting the ball rolling on this initiative.
Check out the `19.05 user release notes <https://docs.galaxyproject.org/en/release_19.05/releases/19.05_announce_user.html>`__.