diff --git a/doc/source/releases/17.09.rst b/doc/source/releases/17.09.rst index 87fcb327abce..da30a7417c6e 100644 --- a/doc/source/releases/17.09.rst +++ b/doc/source/releases/17.09.rst @@ -29,10 +29,11 @@ Enhancements `Pull Request 3611`_ * Add job runner for `Chronos `__ (thanks to `@theosotr `__). - `Pull Request 3946`_ -* Paramiko based shell job runner + `Pull Request 3946`_, `Pull Request 4120`_ +* Many improvements to the shell job runner (including a new Paramiko based + runner with retry support) (thanks to `@mvdbeek `__). - `Pull Request 4358`_ + `Pull Request 4358`_, `Pull Request 4599`_, `Pull Request 4343`_ * Add entry for ``empty_extra_files_path`` validator (thanks to `@gregvonkuster `__). `Pull Request 3994`_ @@ -94,10 +95,13 @@ Enhancements `Pull Request 3179`_ * Speed up and optimize the process of identifying public libraries. `Pull Request 4640`_ -* Various data libraries improvements. - `Pull Request 4512`_ -* Enhance workflow import API endpoint to allow admins to install repositories corresponding to a supplied - workflow (thanks to `@manabuishii `__). +* Numerous data library fixes and improvements - both to the frontend and backend. + `Pull Request 4568`_, `Pull Request 4595`_, + `Pull Request 4594`_, `Pull Request 4579`_, `Pull Request 4560`_ + `Pull Request 4512`_, `Pull Request 4621`_, `Pull Request 4752`_ +* 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 `__). @@ -188,11 +192,9 @@ Enhancements `Pull Request 4163`_, `Pull Request 4101`_ * Set content type to application/json for JSON text types. `Pull Request 4160`_ -* Improved Mulled Containers - `Pull Request 4173`_ -* Allow Galaxy to use cached mulled containers for Singularity. - `Pull Request 4179`_ -* Build mulled images for Singularity on demand... +* Assorted enhancements for container support (both for mulled container generation + and fetching as well as to new Singularity support). + `Pull Request 4173`_, `Pull Request 4179`_, `Pull Request 4180`_, `Pull Request 4185`_ * Make updateucsc.sh.sample usable without any change (thanks to `@nsoranzo `__). @@ -214,7 +216,7 @@ Enhancements * "Join two Datasets" (join1) preserve column headers (thanks to `@lecorguille `__). `Pull Request 4229`_ -* add public-only filter for data libraries +* Add public-only filter for data libraries (thanks to `@pvanheus `__). `Pull Request 4232`_ * Fix import order and Python3 compatibility for 51 files @@ -467,16 +469,9 @@ Enhancements * Check user roles only once if user has no roles (thanks to `@mvdbeek `__). `Pull Request 4546`_ -* Fix data library collection import. - `Pull Request 4568`_ -* Various fixes for data libraries. - `Pull Request 4595`_ * Remove unused bam to bai converter (thanks to `@mvdbeek `__). `Pull Request 4598`_ -* Retry job submissions in ShellJobRunner - (thanks to `@mvdbeek `__). - `Pull Request 4599`_ * Remove various unreachable statements (thanks to `@erasche `__). `Pull Request 4603`_ @@ -492,186 +487,152 @@ Fixes .. major_bug - .. bug +* Various hashtag (or name tag) fixes (also backported to 17.05). + `Pull Request 4139`_, `Pull Request 4188`_ * Simplify RC creation in Makefile. `Pull Request 4011`_ -* Do not recurse in ensure_installed() +* Do not recurse in ``ensure_installed()`` (thanks to `@bernt-matthias `__). `Pull Request 4049`_ * Minor fixes for new locales, rebuild of client. `Pull Request 4050`_ -* French error +* French translation error (thanks to `@yvanlebras `__). `Pull Request 4051`_ -* Very minor history tour tweaks +* Minor history tour tweaks. `Pull Request 4061`_ -* conditional postclick execution onNext +* Improve tour button logic (thanks to `@bagnacan `__). `Pull Request 4062`_ -* Don't try to get the file name of purged files +* Bug fix to prevent fetching the file path of purged files (thanks to `@dpryan79 `__). `Pull Request 4066`_ -* Rebuild to provide new localization. - `Pull Request 4081`_ * ToolShed tool dependency install fixes (thanks to `@nsoranzo `__). `Pull Request 4105`_ -* Fix failed merge for populate model - `Pull Request 4112`_ * Fix legacy Python path for genome diversity tools from miller lab. `Pull Request 4117`_ -* Fix chronos client initialization - (thanks to `@theosotr `__). - `Pull Request 4120`_ * Avoid locale specific string.letters for job_name (thanks to `@peterjc `__). `Pull Request 4121`_ -* New workflow menu message fix - `Pull Request 4124`_ -* Fix typo +* Fix typo in job_conf.xml.sample (thanks to `@manabuishii `__). `Pull Request 4126`_ -* Tag fixes - `Pull Request 4139`_ * Hide error highlighting if user interacts with highlighted field `Pull Request 4147`_ -* fix webhooks loading url +* Fix webhooks loading URL. `Pull Request 4158`_ * Fix older GIE config sample description. `Pull Request 4164`_ -* Improve default handling of Singularity volumes. - `Pull Request 4180`_ * Fix `#3990 `__, don't chown non-galaxy files (thanks to `@dpryan79 `__). `Pull Request 4186`_ -* Hashtags w/ workflow-defined tags fix - `Pull Request 4188`_ * Debug of script library_upload_dir.py (thanks to `@FredericBGA `__). `Pull Request 4199`_ * Correct name of neo4j datatype class (thanks to `@pvanheus `__). `Pull Request 4223`_ -* Fix Registry.get_datatype_by_extension() to return None if ext is unknown +* Fix ``Registry.get_datatype_by_extension()`` to return ``None`` if ``ext`` is unknown (thanks to `@nsoranzo `__). `Pull Request 4224`_ -* avoids broken version of mercurial in conda +* Avoid broken version of Mercurial in conda (thanks to `@bwlang `__). `Pull Request 4227`_ * Fix empty tabular output error when using discover_datasets. (thanks to `@pkrog `__). `Pull Request 4240`_ -* Importing old exported histories failing +* Fix importing old exported histories. (thanks to `@cche `__). `Pull Request 4268`_ -* Update tool_conf.xml.main to reflect main's current state. +* Update ``tool_conf.xml.main`` to reflect usegalaxy.org's current state. `Pull Request 4295`_ -* Fix TypeError when uploading large files from ftp to s3 +* Fix ``TypeError`` when uploading large files from FTP to S3. (thanks to `@jlhg `__). `Pull Request 4315`_ -* Fix for loading tools when tool.lineage is None. +* Fix for loading tools when ``tool.lineage is None``. `Pull Request 4317`_ * Fix for the caching of location filenames when they are broken symlinks. `Pull Request 4318`_ * Remove print debug option from toolshed. `Pull Request 4332`_ -* Prevent early dataset state changes in the ShellJobRunner - (thanks to `@mvdbeek `__). - `Pull Request 4343`_ * Fix default output labels for subworkflows (thanks to `@mvdbeek `__). `Pull Request 4346`_ -* Search Overlay plugin bug fix +* Search overlay plugin bug fix (thanks to `@bgruening `__). `Pull Request 4348`_ -* Patch bug preventing creation of dataset library folders - (thanks to `@galaxyproject `__). - `Pull Request 4357`_ * Tool version and lineage fixes (thanks to `@mvdbeek `__). `Pull Request 4375`_ -* Bugfix: Ensure task splitting handles before job resolution. +* Fix bug in ``scripts/extract_dataset_part.py`` during task splitting. `Pull Request 4383`_ -* Fix get_tool returning list when it shouldn't. +* Fix ``get_tool`` returning list when it shouldn't. `Pull Request 4390`_ -* Bugfix for loading subworkflows from workflow descriptions. +* Bug fix for loading subworkflows from workflow descriptions. `Pull Request 4394`_ -* Bugfix: __str__ method on tool parsers would throw an Exception. +* Bug fix ``__str__`` method on tool parsers that previously would throw an ``Exception``. `Pull Request 4395`_ -* Add missing chemical formats to datatypes_conf.xml.sample +* Add missing chemical formats to ``datatypes_conf.xml.sample`` (thanks to `@nsoranzo `__). `Pull Request 4413`_ -* Don't cast tool_version to string if tool_version is None-type +* Don't cast ``tool_version`` to string if ``tool_version`` is None-type (thanks to `@mvdbeek `__). `Pull Request 4420`_ -* some unicoding for local runner +* Some unicoding for local runner (thanks to `@erasche `__). `Pull Request 4426`_ * Break connection in workflow editor if necessary (thanks to `@mvdbeek `__). `Pull Request 4431`_ -* Fix private role validation +* Fix private role validation. `Pull Request 4432`_ * Remove print of non-existent attribute 'content' (thanks to `@chambm `__). `Pull Request 4439`_ -* Fix API tests broken in `#4434 - `__ - (thanks to `@nsoranzo `__). - `Pull Request 4445`_ -* Fix E201 errors (spaces in parens) in new memepsp datatype - `Pull Request 4446`_ * Fix quota function name `Pull Request 4469`_ * Fixes for VCF/BCF datatypes (thanks to `@nsoranzo `__). `Pull Request 4477`_ -* Validate workflow step after step argument injection +* Validate workflow step after step argument injection. `Pull Request 4483`_ * Fix drag and drop from history for Firefox `Pull Request 4496`_ * 2017-08 Security Patch (thanks to `@erasche `__). `Pull Request 4501`_ -* import of history works even if we use symlink in database directory +* Fix history import if using symlink in database directory (thanks to `@FredericBGA `__). `Pull Request 4511`_ -* Fix missing tools wf editor alternative +* Fix missing tools in the workflow editor (thanks to `@mvdbeek `__). `Pull Request 4552`_ * Prevent unbound variable error history controller. `Pull Request 4557`_ -* improve docs and access checks in datalibs manager/api - `Pull Request 4560`_ * Backport uwsgi fix from `#2836 `__. `Pull Request 4565`_ -* Bug: Fix startup of galaxy when webhooks dir is empty +* Bug fix startup of galaxy when webhooks dir is empty (thanks to `@mvdbeek `__). `Pull Request 4570`_ -* Fix delete option in history menu +* Fix delete option in history menu. `Pull Request 4574`_ -* datalibs: fix two bugs, refactor - `Pull Request 4579`_ * Cancel workflow invocations when histories are deleted. `Pull Request 4580`_ -* Fix datalib search pagination - `Pull Request 4594`_ * Multiview missing histories fix `Pull Request 4610`_ * Fix virtualenv activation for some scripts (thanks to `@nsoranzo `__). `Pull Request 4616`_ -* replace separators in library sharing role names - `Pull Request 4621`_ * Pulsar remote metadata fixes `Pull Request 4622`_ * Swap sanitize whitelist form to use a post. `Pull Request 4625`_ -* Misc. spelling/grammatical error fixes. +* Fix various spelling and grammatical error fixes. `Pull Request 4626`_ * Typo fix (thanks to `@VJalili `__). @@ -687,7 +648,6 @@ Fixes * Explicitly write registry.xml when creating a job for the upload tool (thanks to `@mvdbeek `__). `Pull Request 4644`_, `Pull Request 4600`_ - * Fix links on workflow, history items. `Pull Request 4656`_ * Fix for modules resolver. @@ -706,9 +666,9 @@ Fixes * Add message (error and info) display to workflows display list. `Pull Request 4716`_ * If the newest version of a tool is hidden, load the newest older version, if - any, into the tool panel + any, into the tool panel. `Pull Request 4726`_ -* Fix missing support for command_inject when using containers lib in GIEs +* Fix missing support for command_inject when using containers lib in GIEs. `Pull Request 4740`_ * Fix t, a, g, s returned in to_dict() method (thanks to `@mvdbeek `__). @@ -720,8 +680,6 @@ Fixes `Pull Request 4748`_ * Force onload webhooks to wait for Galaxy object (and root) resolution. `Pull Request 4750`_ -* replace selector for selecting selected rows - `Pull Request 4752`_ * GIEs: Grandfather automatic uppercasing of some env_override variables `Pull Request 4760`_