diff --git a/doc/source/releases/17.09.rst b/doc/source/releases/17.09.rst index 41b4e08d3d4..87fcb327abc 100644 --- a/doc/source/releases/17.09.rst +++ b/doc/source/releases/17.09.rst @@ -77,6 +77,15 @@ Enhancements * Add mz5 datatype (thanks to `@bgruening `__). `Pull Request 4466`_ +* Refactor tool error reporting into plugins and implement a new + plugin for `influxdb `__ + (thanks to `@erasche `__). + `Pull Request 4305`_, `Pull Request 4533`_ +* Implement second toolshed installation UX targetting the API. + `Pull Request 3626`_ +* Tool-Describing-Tours + (thanks to `@anatskiy `__). + `Pull Request 4019`_ .. enhancement @@ -121,10 +130,7 @@ Enhancements `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`_ + `Pull Request 4582`_, `Pull Request 4586`_, `Pull Request 4592`_, `Pull Request 4042`_ * Prevent graphite from dying loudly (thanks to `@erasche `__). `Pull Request 4036`_ @@ -172,7 +178,8 @@ Enhancements * Replace various mako templates with client side JavaScript rendering. `Pull Request 4157`_, `Pull Request 4167`_, `Pull Request 4169`_, `Pull Request 4201`_, `Pull Request 4311`_, `Pull Request 4377`_, - `Pull Request 4411`_, `Pull Request 4334`_ + `Pull Request 4411`_, `Pull Request 4334`_, `Pull Request 4305`_, + `Pull Request 4067`_, `Pull Request 4327`_ * Related to the above mako transition, rework various "grid" rendering code to do more on the client side as well. `Pull Request 4302`_, `Pull Request 4291`_, `Pull Request 4293`_, @@ -228,46 +235,40 @@ Enhancements * Keep tool parameters when rerunning a job (thanks to `@mvdbeek `__). `Pull Request 4271`_ -* Uniform titles +* More uniform backend code for generating page titles (thanks to `@erasche `__). - `Pull Request 4272`_ + `Pull Request 4272`_, `Pull Request 4578`_ * Fix blockquote>p sizing (thanks to `@erasche `__). `Pull Request 4273`_ * Expose more user properties to admins via the API. `Pull Request 4274`_ -* Ensure tags are copied and presented when moving Collections +* Ensure tags are copied and presented when moving collections (thanks to `@pvanheus `__). `Pull Request 4277`_ -* Add test_errors to .gitignore. +* Add ``test_errors`` to .gitignore. `Pull Request 4278`_ -* Package locking for node modules. +* Implement package locking for node modules. `Pull Request 4283`_ * Enhancement for Phylocanvas plugin (thanks to `@bgruening `__). `Pull Request 4284`_ -* Local network access restrictions +* Improve security via local network access restrictions (thanks to `@erasche `__). `Pull Request 4289`_ * Enhancement for Phyloviz viz plugin (thanks to `@bgruening `__). `Pull Request 4292`_ -* Submitting the galaxy jobs as a predefined system user: using - 'real_system_username' +* Allow submitting the galaxy jobs as a predefined system user using + ``real_system_username`` (thanks to `@ashvark `__). `Pull Request 4294`_ * Update Japanese translation (thanks to `@manabuishii `__). `Pull Request 4304`_ -* Refactor bug reporting into plugins / Remove bug report mako - (thanks to `@erasche `__). - `Pull Request 4305`_ -* Localization support for Tool Help +* Allow localization of more UI strings (thanks to `@manabuishii `__). - `Pull Request 4306`_ -* Support Localization Scratchbook - (thanks to `@manabuishii `__). - `Pull Request 4307`_ + `Pull Request 4306`_, `Pull Request 4307`_ * Allow import of history archives via simple file upload (thanks to `@mvdbeek `__). `Pull Request 4326`_ @@ -277,12 +278,13 @@ Enhancements * Updated the version requirements (thanks to `@VJalili `__). `Pull Request 4342`_ -* CSRF protection for login, logout, and user registration. +* CSRF protection for login, logout, and user registration (most parts of the + Galaxy UI still don't have explicit CSRF protection). `Pull Request 4365`_, `Pull Request 4710`_ * Implement ``default_identifier_source`` for tool collection outputs and sort input keys by default (thanks to `@mvdbeek `__). - `Pull Request 4368`_ + `Pull Request 4368`_, `Pull Request 4380`_ * Galactic Radio Telescope Update (thanks to `@erasche `__). `Pull Request 4376`_ @@ -324,9 +326,6 @@ Enhancements * Add autopep8 script to help rebasing branches after `#4440 `__. `Pull Request 4447`_ -* Interactive Environment: possibility to don't uppercase env variables - (thanks to `@xgaia `__). - `Pull Request 4454`_ * Uniform indentation of multiline if conditionals (thanks to `@nsoranzo `__). `Pull Request 4455`_ @@ -338,7 +337,7 @@ Enhancements `Pull Request 4457`_, `Pull Request 4471`_ * Fix for GIEs to not automatically uppercase environment variables (thanks to `@xgaia `__). - `Pull Request 4458`_ + `Pull Request 4458`_, `Pull Request 4454`_ * Fix security checking of WorkflowInvocation for published workflows (thanks to `@mvdbeek `__). `Pull Request 4465`_ @@ -369,9 +368,6 @@ Enhancements `Pull Request 4514`_ * Display d3 hierarchy datatype in upload interface `Pull Request 4522`_ -* Implement influxdb error reporter - (thanks to `@erasche `__). - `Pull Request 4533`_ * Sync non-CWL galaxy-lib changes. `Pull Request 4535`_ * Add a small howto on profiling galaxy code @@ -405,66 +401,55 @@ Enhancements .. small_enhancement -* API installation of toolshed repositories. - `Pull Request 3626`_ * Add test case clarifying datasets do get "renamed" by rename PJA in collections. `Pull Request 3983`_ -* One more fix for main_panel fix in `#3992 - `__. - `Pull Request 4042`_ * Add some test tools for collection job failures. `Pull Request 4044`_ -* Add admin app - `Pull Request 4067`_ * Merge ShedToolLineage and StockLineage to ToolLineage (thanks to `@mvdbeek `__). `Pull Request 4119`_ * Move PlantTribes datatypes to a separate file with enhancements and fixes (thanks to `@gregvonkuster `__). `Pull Request 4137`_ -* Move galaxy.tools.toolbox.cache to galaxy.tools.cache. +* Move ``galaxy.tools.toolbox.cache`` to ``galaxy.tools.cache``. `Pull Request 4155`_ -* Spacing convention, -> util.asbool, atribute -> attribute +* Small code style and error message fixes for data library code (thanks to `@bwlang `__). `Pull Request 4250`_ -* refactors tag manager to use only what it needs… +* Refactors tag manager to not consume the unneeded ``app`` argument (thanks to `@bwlang `__). `Pull Request 4253`_ -* Use contextmanager when using compression_util.get_fileobj() +* Use contextmanager when using ``compression_util.get_fileobj()`` (thanks to `@mvdbeek `__). `Pull Request 4270`_ -* Swap the deprecated unescape() for decodeURIComponent +* Swap the deprecated ``unescape()`` for ``decodeURIComponent``. `Pull Request 4321`_ -* Separate admin controllers - `Pull Request 4327`_ -* Some formatting +* More consistent formatting for model mapping code (thanks to `@VJalili `__). `Pull Request 4333`_ -* Merging configure menu with main workflow view +* Merge configure menu with main workflow view (thanks to `@bgruening `__). `Pull Request 4353`_ -* Delete conda_exec_home instead of env['HOME'] +* Delete ``conda_exec_home`` instead of ``env['HOME']`` (thanks to `@mvdbeek `__). `Pull Request 4360`_ -* Add test tool for API tests - (thanks to `@mvdbeek `__). - `Pull Request 4380`_ -* Replace list with generator when iterating headers +* Replace list with generator when iterating headers in datatypes code (thanks to `@mvdbeek `__). `Pull Request 4388`_ -* Get tools with tool_version in more places +* Get tools with ``tool_version`` in more places (thanks to `@mvdbeek `__). `Pull Request 4391`_ -* Fix lgtm alerts +* Fix issues identified by the JavaScript linting application + `lgtm `__. (thanks to `@xiemaisi `__). `Pull Request 4421`_ -* Remove /mobile and associated templates +* Remove /mobile and associated templates (the code was unused and broken). `Pull Request 4494`_ * Workflow loading speedup (thanks to `@mvdbeek `__). `Pull Request 4500`_ -* Prevent transient job state test failures from failing the build. +* Prevent transient job state API test failures from failing the build. `Pull Request 4510`_ * More robust workflow invocation testing. `Pull Request 4530`_ @@ -482,28 +467,23 @@ Enhancements * Check user roles only once if user has no roles (thanks to `@mvdbeek `__). `Pull Request 4546`_ -* Fix datalib collection import +* Fix data library collection import. `Pull Request 4568`_ -* Delegate displaying of page titles to Layout.display() - `Pull Request 4578`_ -* Datalibs various fixes +* Various fixes for data libraries. `Pull Request 4595`_ -* Remove bam to bai converter +* Remove unused bam to bai converter (thanks to `@mvdbeek `__). `Pull Request 4598`_ * Retry job submissions in ShellJobRunner (thanks to `@mvdbeek `__). `Pull Request 4599`_ -* Write datatypes registry xml to working directory - (thanks to `@mvdbeek `__). - `Pull Request 4600`_ -* Remove unreachable statements +* Remove various unreachable statements (thanks to `@erasche `__). `Pull Request 4603`_ -* Refactored a dataset variable to hda +* Refactored a dataset variable to HDA (thanks to `@VJalili `__). `Pull Request 4630`_ -* disable MacOS CI on travis +* Disable MacOS tests on TravisCI. `Pull Request 4631`_ @@ -706,7 +686,8 @@ Fixes `Pull Request 4639`_ * Explicitly write registry.xml when creating a job for the upload tool (thanks to `@mvdbeek `__). - `Pull Request 4644`_ + `Pull Request 4644`_, `Pull Request 4600`_ + * Fix links on workflow, history items. `Pull Request 4656`_ * Fix for modules resolver.