mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Release notes for 19.09.
This commit is contained in:
John Chilton
@@ -0,0 +1,632 @@
|
||||
|
||||
.. to_doc
|
||||
|
||||
19.09
|
||||
===============================
|
||||
|
||||
.. announce_start
|
||||
|
||||
Enhancements
|
||||
-------------------------------
|
||||
|
||||
* Add InteractiveTools.
|
||||
`Pull Request 7494`_, `Pull Request 8506`_, `Pull Request 8574`_,
|
||||
`Pull Request 8589`_
|
||||
* Implement workflow invocation reports.
|
||||
`Pull Request 8543`_, `Pull Request 8664`_, `Pull Request 8683`_
|
||||
* VueJS rewrite of Toolshed install interface - with substantial API extensions to enable this.
|
||||
`Pull Request 7402`_, `Pull Request 8090`_, `Pull Request 8621`_,
|
||||
`Pull Request 8635`_, `Pull Request 8681`_, `Pull Request 7825`_
|
||||
`Pull Request 8638`_, `Pull Request 8035`_, `Pull Request 8076`_,
|
||||
`Pull Request 8585`_, `Pull Request 8622`_
|
||||
* VueJS rewrite of admin jobs page
|
||||
(thanks to `@scrathat <https://github.com/scrathat>`__).
|
||||
`Pull Request 7790`_
|
||||
* VueJS rewrite of tools panel (resolves `#8262
|
||||
<https://github.com/galaxyproject/galaxy/issues/8262>`__)
|
||||
(thanks to `@inkuzmin <https://github.com/inkuzmin>`__).
|
||||
`Pull Request 8368`_
|
||||
* VueJS rewrite of dataset job properties tables - with API extensions to enable this.
|
||||
`Pull Request 8022`_, `Pull Request 8044`_
|
||||
* VueJS rewrite of Page management components - with API extensions to enable this.
|
||||
`Pull Request 8047`_
|
||||
* New visualization - free style image annotation
|
||||
(thanks to `@anuprulez <https://github.com/anuprulez>`__).
|
||||
`Pull Request 6891`_
|
||||
* New visualization - OpenLayers maps.
|
||||
(thanks to `@anuprulez <https://github.com/anuprulez>`__).
|
||||
`Pull Request 7888`_
|
||||
* New visualization - hyphy-vision
|
||||
(thanks to `@veg <https://github.com/veg>`__).
|
||||
`Pull Request 8227`_
|
||||
* Implement frameworks for datatype validation and tool-based QC.
|
||||
`Pull Request 7913`_
|
||||
* New Pulsar runner for Kubernetes allowing file staging with Kubernetes.
|
||||
`Pull Request 7835`_, `Pull Request 8195`_
|
||||
* Implement option to delete or preserve Kubernetes pods after completion
|
||||
(thanks to `@nuwang <https://github.com/nuwang>`__).
|
||||
`Pull Request 8091`_
|
||||
* Implement ``walltime_limit`` option for the Kuberentes jobs
|
||||
(thanks to `@telukir <https://github.com/telukir>`__).
|
||||
`Pull Request 8311`_
|
||||
* Implement UI for Authnz API.
|
||||
`Pull Request 7665`_
|
||||
* Extend dataset search and add search API endpoint
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7745`_
|
||||
* Add Matthias Bernt to the committers group.
|
||||
`Pull Request 8446`_
|
||||
* Add filtering and sorting for folders in data libraries
|
||||
(with help from `@bwlang <https://github.com/bwlang>`__).
|
||||
`Pull Request 8281`_, `Pull Request 8287`_, `Pull Request 8277`_
|
||||
* Implement ``xref`` tag on the tool structure (with visualization)
|
||||
(thanks to `@ValentinMarcon <https://github.com/ValentinMarcon>`__).
|
||||
`Pull Request 7905`_
|
||||
* Substantial progress toward refactoring and decomposing Galaxy into properly
|
||||
installable packages.
|
||||
(with help from `@dglaetzer <https://github.com/dglaetzer>`__ and
|
||||
`@nsoranzo <https://github.com/nsoranzo>`__ and `@gmauro <https://github.com/gmauro>`__).
|
||||
`Pull Request 921`_, `Pull Request 7992`_, `Pull Request 8114`_,
|
||||
`Pull Request 8234`_, `Pull Request 8241`_, `Pull Request 8266`_,
|
||||
`Pull Request 8276`_, `Pull Request 8284`_, `Pull Request 8293`_,
|
||||
`Pull Request 8306`_, `Pull Request 8305`_, `Pull Request 8307`_,
|
||||
`Pull Request 8308`_, `Pull Request 7971`_, `Pull Request 8051`_,
|
||||
`Pull Request 8062`_, `Pull Request 8280`_, `Pull Request 8310`_,
|
||||
`Pull Request 8302`_, `Pull Request 8298`_, `Pull Request 8098`_,
|
||||
`Pull Request 8208`_, `Pull Request 8235`_, `Pull Request 8365`_,
|
||||
`Pull Request 8357`_, `Pull Request 8342`_, `Pull Request 8345`_,
|
||||
`Pull Request 8431`_, `Pull Request 8269`_, `Pull Request 8314`_,
|
||||
`Pull Request 8687`_, `Pull Request 8702`_, `Pull Request 8610`_,
|
||||
`Pull Request 8315`_
|
||||
* Enable dynamic reloading of select config options.
|
||||
`Pull Request 8475`_
|
||||
* Improved architecture for Galaxy's configuration object
|
||||
`Pull Request 8502`_, `Pull Request 8526`_,
|
||||
`Pull Request 8462`_, `Pull Request 8433`_,
|
||||
`Pull Request 8545`_
|
||||
* Allow YAML/JSON job configuration - including embedding right in Galaxy config, validation, better defaults,
|
||||
and better section naming.
|
||||
`Pull Request 7854`_, `Pull Request 8616`_, `Pull Request 7882`_
|
||||
`Pull Request 8609`_
|
||||
* Allow declaring dependency resolvers right in Galaxy config, validation, and serialization.
|
||||
`Pull Request 8118`_, `Pull Request 8152`_
|
||||
* Add external display application plugin for iCn3D.
|
||||
`Pull Request 8347`_
|
||||
* Enable external display application plugin parameters to declare ``allow_cors="true"``.
|
||||
`Pull Request 8539`_
|
||||
* Add XML Schema Definition (XSD) for Galaxy External Dispaly Applications (GEDAs).
|
||||
`Pull Request 8461`_
|
||||
* Adding Shapefile composite datatype
|
||||
(thanks to `@Alanamosse <https://github.com/Alanamosse>`__).
|
||||
`Pull Request 7615`_
|
||||
* Add mcool datatype and extend h5 tool output testing
|
||||
(thanks to `@msauria <https://github.com/msauria>`__).
|
||||
`Pull Request 7993`_
|
||||
* Add hyphy_results.json datatype
|
||||
(thanks to `@veg <https://github.com/veg>`__).
|
||||
`Pull Request 8186`_
|
||||
* Add pgp and osw datatypes as used in OpenSWATH experiments
|
||||
(thanks to `@bgruening <https://github.com/bgruening>`__).
|
||||
`Pull Request 8458`_
|
||||
* Add ckpt datatype
|
||||
(thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
|
||||
`Pull Request 8086`_
|
||||
* Add dada2 datatypes
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 7895`_
|
||||
* Add rDock active site datatype
|
||||
(thanks to `@bgruening <https://github.com/bgruening>`__).
|
||||
`Pull Request 8727`_
|
||||
* Add Kallistobus datatypes
|
||||
(thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
|
||||
`Pull Request 8229`_
|
||||
* Sniff fastqsanger more aggressively
|
||||
(thanks to `@wm75 <https://github.com/wm75>`__).
|
||||
`Pull Request 8322`_
|
||||
* Various collection operation tool improvements
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8038`_
|
||||
* Enhance unzip/zip collection collection operation to annotate output format properly
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 8239`_
|
||||
* Implement option to strip whitespace from tool ``environment_variables``.
|
||||
`Pull Request 8296`_
|
||||
* Add tool output test assertion for ``n_lines``
|
||||
(thanks to `@bgruening <https://github.com/bgruening>`__).
|
||||
`Pull Request 8440`_
|
||||
* Add zoom reset feature for workflows
|
||||
(thanks to `@juleengraham <https://github.com/juleengraham>`__).
|
||||
`Pull Request 8301`_
|
||||
* Fix tool run output to display more data.
|
||||
`Pull Request 8018`_
|
||||
* Track basename at the time of creation for datasets.
|
||||
`Pull Request 7670`_
|
||||
* Remove GFF headers during conversion (backported to 19.05).
|
||||
`Pull Request 7808`_
|
||||
* Enable mulled containers by default for 19.09.
|
||||
`Pull Request 8569`_
|
||||
* Enhanced GitLab integration
|
||||
(thanks to `@selten <https://github.com/selten>`__).
|
||||
`Pull Request 8455`_, `Issue #8183 <https://github.com/galaxyproject/galaxy/issues/8183>`__
|
||||
* Make admin users grid filter on purged
|
||||
`Pull Request 8303`_
|
||||
* Add links to admin entry page.
|
||||
`Pull Request 8351`_
|
||||
* Add ELIXIR OIDC backend, upgrade social-auth-core requirement version
|
||||
(thanks to `@kidanem <https://github.com/kidanem>`__).
|
||||
`Pull Request 7852`_
|
||||
* Run futurize for python2 cheetah templates, fix scope issue for Python 3
|
||||
comprehensions
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7867`_
|
||||
* Improve look and feel for data libraries
|
||||
(thanks to `@inkuzmin <https://github.com/inkuzmin>`__).
|
||||
`Pull Request 7878`_
|
||||
* Raise detailed exception for broken citation
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7891`_
|
||||
* Remove ``file`` attribute of bibtex citation
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7911`_
|
||||
* Use transparent background in default welcome page.
|
||||
`Pull Request 7929`_
|
||||
* Cellxgene GIE - use API to get datasets.
|
||||
`Pull Request 7945`_
|
||||
* Change "username" to "public name" throughout the user interface.
|
||||
`Pull Request 8009`_
|
||||
* History menu (cog) UI updates.
|
||||
`Pull Request 8024`_
|
||||
* Delegate config file watching to single handler
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8078`_
|
||||
* Allow admins to disable the visualizations tab in the masthead.
|
||||
`Pull Request 8450`_
|
||||
* Pin SQLAlchemy to ``<1.3`` and update all dependencies
|
||||
`Pull Request 8120`_
|
||||
* Enable authorization to Google Cloud Platform
|
||||
`Pull Request 8123`_
|
||||
* Update Python dependencies, unpin SQLAlchemy
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 8126`_
|
||||
* Update requirements and use pyuwsgi
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8489`_
|
||||
* Update ``cloudauthz`` dependency to v0.4.0.
|
||||
`Pull Request 8155`_
|
||||
* Improve accessibility of certain UI elements.
|
||||
`Pull Request 8133`_
|
||||
* Round-off the time taken for CPU execution
|
||||
(thanks to `@janani-prasad <https://github.com/janani-prasad>`__).
|
||||
`Pull Request 8144`_
|
||||
* Add API to tag library datasets
|
||||
(thanks to `@abretaud <https://github.com/abretaud>`__).
|
||||
`Pull Request 8530`_
|
||||
* Improve API docs.
|
||||
`Pull Request 8541`_
|
||||
* Update repository issue handling text in docs.
|
||||
`Pull Request 8542`_
|
||||
* Improved tool parameter error reporting
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 8163`_
|
||||
* Configuration API cleanup.
|
||||
`Pull Request 8206`_
|
||||
* New regular expression filter, and efficient sort filter
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 8211`_
|
||||
* Data managers - allow removal of entries
|
||||
(thanks to `@selten <https://github.com/selten>`__).
|
||||
`Pull Request 8250`_, `Pull Request 8503`_
|
||||
* Adjust minimum tag length.
|
||||
`Pull Request 8256`_
|
||||
* Some improvements to tool menu styles.
|
||||
`Pull Request 8285`_
|
||||
* Make styleguide work for VueJS components.
|
||||
`Pull Request 8291`_
|
||||
* Library date propagate
|
||||
(thanks to `@bwlang <https://github.com/bwlang>`__).
|
||||
`Pull Request 8294`_
|
||||
* Skip database migrations on entirely clean new databases
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8300`_
|
||||
* Implement undelete and purge API for users
|
||||
(thanks to `@cganote <https://github.com/cganote>`__).
|
||||
`Pull Request 8309`_
|
||||
* Use lowercase true/false in config_schema.yml
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 8319`_
|
||||
* Check correct permission for allowing a user to modify lib folder
|
||||
(thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
|
||||
`Pull Request 8326`_
|
||||
* Issue`#8105 <https://github.com/galaxyproject/galaxy/issues/8105>`__: Make
|
||||
tool favourite query a toggle
|
||||
(thanks to `@janani-prasad <https://github.com/janani-prasad>`__).
|
||||
`Pull Request 8331`_
|
||||
* Update anchor tags and enhance navigation cues for screen readers
|
||||
`Pull Request 8334`_
|
||||
* Better config isolation for integration tests.
|
||||
`Pull Request 8355`_
|
||||
* catch exceptions occuring in expression validators
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 8359`_
|
||||
* Update RST files to reflect code structure changes.
|
||||
`Pull Request 8363`_
|
||||
* make cleanup script use logging instead of print
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 8394`_
|
||||
* Mention IGB in the docs
|
||||
`Pull Request 8404`_
|
||||
* Automatically replace dashes by underscores for ``argument`` attribute on tool parameters.
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 8409`_
|
||||
* Add basic unit test for lint_inputs
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8410`_
|
||||
* Various improvements designed to optimize ToolBox loading time.
|
||||
`Pull Request 8421`_, `Pull Request 8422`_, `Pull Request 8426`_
|
||||
* Fix authentication provider exception not logged
|
||||
(thanks to `@BioinformaticsPlatformWIV-ISP <https://github.com
|
||||
/BioinformaticsPlatformWIV-ISP>`__).
|
||||
`Pull Request 8424`_
|
||||
* Optimize unrestricted library dataset permission checks.
|
||||
`Pull Request 8430`_
|
||||
* Change 'a when tag has not been defined for' level to debug
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8439`_
|
||||
* Fix database migrations for MySQL but mention it is unsupported in the docs
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 8640`_, `Pull Request 8407`_, `Pull Request 8473`_
|
||||
* Auto convert python 2 code files using 2to3
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8499`_
|
||||
* Update sass version to support node 12.
|
||||
`Pull Request 8507`_
|
||||
* Integration test for ``outputs_to_working_directory`` with Pulsar.
|
||||
`Pull Request 8335`_
|
||||
* Fix 'postgres' dialect name has been renamed to 'postgresql' deprecat…
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7804`_
|
||||
* Use ``markupsafe.escape`` instead of ``cgi.escape``
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7837`_
|
||||
* Use ``getfullargspec`` on Python 3
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7838`_
|
||||
* Align popup/dropdown menu templating.
|
||||
`Pull Request 7871`_
|
||||
* Change keyboard input for floats and switch to ES6 features
|
||||
`Pull Request 7927`_
|
||||
* Tool output_checker - fix superficial condition
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 7980`_
|
||||
* Enhance ``galaxy.js`` and entry folder for ES6.
|
||||
`Pull Request 8025`_, `Pull Request 8034`_
|
||||
* Switch ``var`` to ``let`` and ``const`` for VueJS components
|
||||
`Pull Request 8028`_, `Pull Request 8036`_
|
||||
* es6 upgrades in entry folder
|
||||
* Remove unresolved function causing console error.
|
||||
`Pull Request 8101`_
|
||||
* Swap out ``galaxy.util.odict`` for core python ``collections.OrderedDict`` objects.
|
||||
`Pull Request 8104`_
|
||||
* Enhance ``make config-rebuild`` to update config/docs.
|
||||
`Pull Request 8220`_
|
||||
* Refactor ``setup_user_get_key`` method to return the created test user and its
|
||||
API key.
|
||||
`Pull Request 8233`_
|
||||
* Fix various small UI issues.
|
||||
`Pull Request 8275`_
|
||||
* Replace in-python quota calc with a SQL query
|
||||
(thanks to `@erasche <https://github.com/erasche>`__).
|
||||
`Pull Request 8452`_
|
||||
* Remove deprecated scripts
|
||||
(thanks to `@erasche <https://github.com/erasche>`__).
|
||||
`Pull Request 8465`_
|
||||
* Fix markup in ToolEntryPoints, format client
|
||||
`Pull Request 8549`_
|
||||
* Allow specifying ``maxseconds`` in ``verify_tool``
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7828`_
|
||||
* Call tool_script.sh with shell
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8077`_
|
||||
* Drop "Manage" from admin workflow Invocation link.
|
||||
`Pull Request 8693`_
|
||||
* Record Galaxy version a job is created with.
|
||||
`Pull Request 8414`_
|
||||
* Git ignore files in ``database/shed_tools`` directory
|
||||
(thanks to `@ashvark <https://github.com/ashvark>`__).
|
||||
`Pull Request 8268`_
|
||||
* Added unit testing section to the client README
|
||||
`Pull Request 7890`_
|
||||
* Update Sphinx RST files for ``lib/``.
|
||||
`Pull Request 8270`_
|
||||
* Allow re-populating objectstore from ``to_dict`` form.
|
||||
`Pull Request 8213`_
|
||||
* Testing framework fixes
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 8147`_
|
||||
* Extend ObjectStore integration tests.
|
||||
`Pull Request 8042`_
|
||||
* Fix link formats for mulled_containers.rst, minor rewording.
|
||||
`Pull Request 8075`_
|
||||
* Add missing files from galaxy-lib
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 8113`_
|
||||
|
||||
Fixes
|
||||
-------------------------------
|
||||
|
||||
* Add file extensions when downloading from data libraries
|
||||
(thanks to `@selten <https://github.com/selten>`__).
|
||||
`Pull Request 8456`_
|
||||
* Fix tool ``assert_command`` tag test not executed
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 7730`_
|
||||
* Fix inconsistent defaults for cleanup scripts - fixing `#975 <https://github.com/galaxyproject/galaxy/issues/975>`__
|
||||
(thanks to `@erasche <https://github.com/erasche>`__).
|
||||
`Pull Request 8470`_
|
||||
* Allow missing H5 groups in Loom files
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 8560`_
|
||||
* Document undocumented ``workflow_schedulers_config_file``
|
||||
(thanks to `@erasche <https://github.com/erasche>`__).
|
||||
`Pull Request 8437`_
|
||||
* Use bootstrap classes to fix form css issue.
|
||||
`Pull Request 8371`_
|
||||
* Fix Pulsar job files API to allow transferring directory content.
|
||||
`Pull Request 8124`_
|
||||
* Fix gops_intersect_1 importing galaxy
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7805`_
|
||||
* Quit gsummary script with non-zero exit code upon error
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8214`_
|
||||
* Sort Collection - add missing when tags
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 8366`_
|
||||
* Remove gops from venv list
|
||||
(thanks to `@bgruening <https://github.com/bgruening>`__).
|
||||
`Pull Request 8492`_
|
||||
* Don't let ``parameter_input`` steps be workflow outputs
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7799`_
|
||||
* Fix column assign bug
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8023`_
|
||||
* Quick hack to allow delayed invocations followed by step that consumes an
|
||||
input parameter
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8249`_
|
||||
* Expression tool fix - include workdir path when reading env var from file
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8253`_
|
||||
* Fix workflow tags lost on save
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8398`_
|
||||
* Fix failure in resubmitting job more than once
|
||||
(thanks to `@pcm32 <https://github.com/pcm32>`__).
|
||||
`Pull Request 7832`_
|
||||
* Add file missing from `#7694
|
||||
<https://github.com/galaxyproject/galaxy/issues/7694>`__
|
||||
`Pull Request 7873`_
|
||||
* Strip unicode control characters from TEXT before entering the database
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7889`_
|
||||
* Fix Kubernetes test for job I/O separation.
|
||||
`Pull Request 7892`_
|
||||
* In output_checker, fixed wrong comparison.
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 7966`_
|
||||
* Fix typo grap -> grab.
|
||||
`Pull Request 8061`_
|
||||
* Fix wording for pod retries while maintaining backward compatibility
|
||||
(thanks to `@nuwang <https://github.com/nuwang>`__).
|
||||
`Pull Request 8082`_
|
||||
* Kubernetes / CLI runner integration test fixes
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8154`_
|
||||
* Fail job if queueing job fails
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8161`_
|
||||
* Fix job wrapper fail for queued jobs
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8179`_
|
||||
* Fix failure to fail job when tool is unavailable
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8181`_
|
||||
* Fix external_metadata_set_successfully when metadata file doesn't exist
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8182`_
|
||||
* Fix portable metadata datatypes config.
|
||||
`Pull Request 8207`_
|
||||
* Fix cancelling jobs with a message from the admin panel
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8231`_
|
||||
* Fix Kubernetes runner on Python 3
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8321`_
|
||||
* Fix univa runner check for drmaa python module
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 8385`_
|
||||
* Fix memory statement for drmaa (SGE/UNIVA)
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 8451`_
|
||||
* Fix setting metadata externally
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8497`_
|
||||
* Fix Pulsar version checking logic.
|
||||
`Pull Request 8524`_
|
||||
* Hack to fix Pulsar for containerized jobs.
|
||||
`Pull Request 8533`_
|
||||
* Improve and refactor process group handling in the local job runners
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 8538`_
|
||||
* Fix container property parsing for Singularity.
|
||||
`Pull Request 8614`_
|
||||
* Data Manager interface - fix to use standard card header styles without extra
|
||||
markup.
|
||||
`Pull Request 7811`_
|
||||
* Allow looking up tool section using label
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8225`_
|
||||
* Backport tool shed and data manager fixes
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
* Create repository clone path if it doesn't exist.
|
||||
`Pull Request 7770`_
|
||||
* Remove unused requirejs imports from templates.
|
||||
`Pull Request 7810`_
|
||||
* Small bugfix to GRT for ancient data, deprecated params table
|
||||
(thanks to `@erasche <https://github.com/erasche>`__).
|
||||
`Pull Request 7830`_
|
||||
* Fix help text in ftp-uploader dialog.
|
||||
`Pull Request 7908`_
|
||||
* Update instructions on conda upgrade
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7918`_
|
||||
* Remove view button, fix library flag in data dialog.
|
||||
`Pull Request 7935`_
|
||||
* Fix non-eager object store with nested object stores
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7939`_
|
||||
* Fix extra newlines in peek code.
|
||||
`Pull Request 7952`_
|
||||
* Fix populators.py workflow testing for non-text inputs.
|
||||
`Pull Request 7953`_
|
||||
* Only show colon when a port exists in URL.
|
||||
`Pull Request 7985`_
|
||||
* Remove href from a tag to prevent backbone page reload and change sometimes.
|
||||
`Pull Request 7991`_
|
||||
* Various datatype I/O fixes
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7995`_
|
||||
* Don't close popup menu if header item is clicked.
|
||||
`Pull Request 8001`_
|
||||
* Refactor comments in sample object stores to remove nested comments.
|
||||
(thanks to `@simpsonw <https://github.com/simpsonw>`__).
|
||||
`Pull Request 8016`_
|
||||
* Fix Selenium DatasetPopulator for more interesting uploads.
|
||||
`Pull Request 8046`_
|
||||
* Fix ``stream_to_open_named_file`` for non-utf8 text (backported to 19.05)
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8050`_
|
||||
* Small testing Dockerfile fixes
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 8094`_
|
||||
* Report a lint error if a citation is empty
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 8112`_
|
||||
* Ensure ``DEFAULT_TOOL_TEST_WAIT`` is an integer
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8136`_
|
||||
* Fix for tool test data in sub directories
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 8162`_
|
||||
* Increase default font size to 0.85rem. Unify default welcome page fonts.
|
||||
`Pull Request 8168`_
|
||||
* Use ``IdEncodingHelper`` to encode/decode user ids
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 8201`_
|
||||
* Fix prefix usage in history copy dialog.
|
||||
`Pull Request 8205`_
|
||||
* Fix UnicodeEncodeError when verifying test results
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8221`_
|
||||
* Fix migration if ``WorkflowStepConnection`` index not present
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8247`_
|
||||
* Fix regex rule count
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8254`_
|
||||
* Fix and unify search bar handling.
|
||||
`Pull Request 8257`_
|
||||
* Typo fix comunity -> community
|
||||
(thanks to `@yochannah <https://github.com/yochannah>`__).
|
||||
`Pull Request 8267`_
|
||||
* Fix typo in run_tests.sh help text.
|
||||
`Pull Request 8289`_
|
||||
* Don't show the pip progress bar when installing under CI
|
||||
`Pull Request 8290`_
|
||||
* Use temporary file for sniff tests
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 8304`_
|
||||
* Adjustments for panel spacing changes
|
||||
`Pull Request 8316`_
|
||||
* Restore docs building
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 8323`_
|
||||
* Updates interactor to not ignore numbers in user email address
|
||||
`Pull Request 8324`_
|
||||
* Test removing uwsgi weird python package from circleci
|
||||
`Pull Request 8337`_
|
||||
* Fix use of ``PIP_PROGRESS_BAR`` env variable
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 8343`_
|
||||
* Startup fixes
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 8346`_
|
||||
* Fix default involucro path
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8360`_
|
||||
* Fix autodetection of zip file format (including xlsx)
|
||||
(thanks to `@wm75 <https://github.com/wm75>`__).
|
||||
`Pull Request 8362`_
|
||||
* Hide references card if array is empty.
|
||||
`Pull Request 8373`_
|
||||
* Fix exception thrown with invalid session key
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8377`_
|
||||
* Better isolation of embedded Pulsar tests.
|
||||
`Pull Request 8386`_
|
||||
* Fix absolutely positioned elements and children from displaying off-screen.
|
||||
`Pull Request 8466`_
|
||||
* Don't cleanup integration tests twice.
|
||||
`Pull Request 8468`_
|
||||
* Try separate amqp connection from database for integration testing.
|
||||
`Pull Request 8469`_
|
||||
* Fix for NodeJS executable being called ``nodejs`` in Conda.
|
||||
(thanks to `@bgruening <https://github.com/bgruening>`__).
|
||||
`Pull Request 8474`_
|
||||
* Fix startup checks when using a Conda env
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 8477`_
|
||||
* Use default backdrop color for modals.
|
||||
`Pull Request 8479`_
|
||||
* Fix shed_tool_conf isolated tool (not in section) removal
|
||||
`Pull Request 8485`_
|
||||
* Do not warn for not configured ``user_preferences_extra_conf_path``
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 8494`_
|
||||
* Use default background for scratchbook.
|
||||
`Pull Request 8527`_
|
||||
* Explicitly declare ``expression`` as ``sql.text``.
|
||||
`Pull Request 8544`_
|
||||
* Update ``calculate_or_set_disk_usage`` to support sqlite
|
||||
(thanks to `@qiagu <https://github.com/qiagu>`__).
|
||||
`Pull Request 8552`_
|
||||
* Fix menu option classes (and thus event bindings) for histories in th…
|
||||
`Pull Request 8575`_
|
||||
* Modify tool panel section text color, size and margin to improve readability.
|
||||
`Pull Request 8579`_
|
||||
* Replaces tabs with spaces in apache.md
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 8590`_
|
||||
* Capture missing log messages
|
||||
`Pull Request 8605`_
|
||||
* Regenerate ts search indexes in tmp directory.
|
||||
`Pull Request 8611`_
|
||||
* Only schedule file watching if an observer exists
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8629`_
|
||||
* Fix issue with xml comment handling on python 3
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8643`_
|
||||
* Fix tool JSON wrapper fail to wrap paths
|
||||
(thanks to `@qiagu <https://github.com/qiagu>`__).
|
||||
`Pull Request 8647`_
|
||||
* Bugfix - kill testing container when test script is killed.
|
||||
`Pull Request 8679`_
|
||||
* Build dependency manager only for galaxy app
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 8696`_
|
||||
|
||||
|
||||
.. include:: 19.09_prs.rst
|
||||
@@ -3,8 +3,60 @@
|
||||
September 2019 Galaxy Release (v 19.09)
|
||||
===========================================================
|
||||
|
||||
.. include:: _header.rst
|
||||
|
||||
Schedule
|
||||
Highlights
|
||||
===========================================================
|
||||
* Planned Freeze Date: 2019-09-02
|
||||
* Planned Release Date: 2019-09-23
|
||||
|
||||
**Interactive Tools**
|
||||
A new type of Galaxy tool has been implemented that allow interactive experiences like
|
||||
Galaxy Interactive Environments (via a proxy and Docker containers) but using plugins defined with
|
||||
Galaxy's XML tool syntax. Dan Blankenberg's slides on these new features from Galaxy
|
||||
Community Conference can be found `here <https://static.sched.com/hosted_files/gcc2019/c1/S8A-4__Dan_Blankenberg_Tools.pdf>`__.
|
||||
More information can be found in the original pull request including interactive tool
|
||||
versions of all of Galaxy's bundled interactive environments `Pull Request 7494`_.
|
||||
|
||||
**Workflow Invocation Reports**
|
||||
Workflows may now define Markdown templates with Galaxy specific embedded syntax extensions
|
||||
that can tie together workflow inputs, outputs, jobs, and metadata into rich reports.
|
||||
More information on the motivation for these reports can be found in `these slides <bit.ly/gxreports19>`__,
|
||||
implementation details and GUI enhancements are described in the original pull request
|
||||
(`#8030 <https://github.com/galaxyproject/galaxy/pull/8030>`__), and details on the final
|
||||
syntax selected for embedded Galaxy objects can be found in the pull request that was ultimately
|
||||
merged (`#8543 <https://github.com/galaxyproject/galaxy/pull/8543>`__).
|
||||
|
||||
**New Toolshed Client Interface**
|
||||
The march toward replacing templated backend generated HTML with modern, reactive
|
||||
components continued in Galaxy 19.09. Galaxy's tool panel, job properties tables,
|
||||
job management controls, and "Pages" infrastructure were all replaced with VueJS
|
||||
components (with huge help from `@scrathat <https://github.com/scrathat>`__
|
||||
and `@inkuzmin <https://github.com/inkuzmin>`__). Most notably, Galaxy's interface
|
||||
to the Toolshed was also rewritten in VueJS and is now completely API driven.
|
||||
This project drove numerous enhancements to the Toolshed API including vastly improved
|
||||
search functionality. This interface has been completely re-imagined and feels much
|
||||
more interactive.
|
||||
|
||||
Get Galaxy
|
||||
==========
|
||||
|
||||
The code lives at `GitHub <https://github.com/galaxyproject/galaxy>`__ and you should have `Git <https://git-scm.com/>`__ to obtain it.
|
||||
|
||||
To get a new Galaxy repository run:
|
||||
.. code-block:: shell
|
||||
|
||||
$ git clone -b release_19.09 https://github.com/galaxyproject/galaxy.git
|
||||
|
||||
To update an existing Galaxy repository run:
|
||||
.. code-block:: shell
|
||||
|
||||
$ git fetch origin && git checkout release_19.09 && git pull --ff-only origin release_19.09
|
||||
|
||||
See the `community hub <https://galaxyproject.org/develop/source-code/>`__ for additional details regarding the source code locations.
|
||||
|
||||
Release Notes
|
||||
===========================================================
|
||||
|
||||
.. include:: 19.09.rst
|
||||
:start-after: announce_start
|
||||
|
||||
.. include:: _thanks.rst
|
||||
|
||||
@@ -0,0 +1,86 @@
|
||||
|
||||
===========================================================
|
||||
September 2019 Galaxy Release (v 19.09)
|
||||
===========================================================
|
||||
|
||||
.. include:: _header.rst
|
||||
|
||||
Highlights
|
||||
===========================================================
|
||||
|
||||
**Feature1**
|
||||
Feature description.
|
||||
|
||||
**Feature2**
|
||||
Feature description.
|
||||
|
||||
**Feature3**
|
||||
Feature description.
|
||||
|
||||
|
||||
New Visualizations
|
||||
===========================================================
|
||||
|
||||
.. visualizations
|
||||
* New visualization - free style image annotation
|
||||
(thanks to `@anuprulez <https://github.com/anuprulez>`__).
|
||||
`Pull Request 6891`_
|
||||
* New visualization - OpenLayers maps.
|
||||
(thanks to `@anuprulez <https://github.com/anuprulez>`__).
|
||||
`Pull Request 7888`_
|
||||
* New visualization - hyphy-vision
|
||||
(thanks to `@veg <https://github.com/veg>`__).
|
||||
`Pull Request 8227`_
|
||||
* Add external display application plugin for iCn3D.
|
||||
`Pull Request 8347`_
|
||||
|
||||
New Datatypes
|
||||
===========================================================
|
||||
|
||||
.. datatypes
|
||||
|
||||
* Adding Shapefile composite datatype
|
||||
(thanks to `@Alanamosse <https://github.com/Alanamosse>`__).
|
||||
`Pull Request 7615`_
|
||||
* Add mcool datatype and extend h5 tool output testing
|
||||
(thanks to `@msauria <https://github.com/msauria>`__).
|
||||
`Pull Request 7993`_
|
||||
* Add hyphy_results.json datatype
|
||||
(thanks to `@veg <https://github.com/veg>`__).
|
||||
`Pull Request 8186`_
|
||||
* Add pgp and osw datatypes as used in OpenSWATH experiments
|
||||
(thanks to `@bgruening <https://github.com/bgruening>`__).
|
||||
`Pull Request 8458`_
|
||||
* Add ckpt datatype
|
||||
(thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
|
||||
`Pull Request 8086`_
|
||||
* Add dada2 datatypes
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 7895`_
|
||||
* Add rDock active site datatype
|
||||
(thanks to `@bgruening <https://github.com/bgruening>`__).
|
||||
`Pull Request 8727`_
|
||||
* Add Kallistobus datatypes
|
||||
(thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
|
||||
`Pull Request 8229`_
|
||||
|
||||
Builtin Tool Updates
|
||||
===========================================================
|
||||
|
||||
.. tools
|
||||
|
||||
* Various collection operation tool improvements
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8038`_
|
||||
* Enhance unzip/zip collection collection operation to annotate output format properly
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 8239`_
|
||||
|
||||
Release Notes
|
||||
===========================================================
|
||||
|
||||
Please see the `full release notes <19.09_announce.html>`_ for more details.
|
||||
|
||||
.. include:: 19.09_prs.rst
|
||||
|
||||
.. include:: _thanks.rst
|
||||
@@ -0,0 +1,334 @@
|
||||
|
||||
.. github_links
|
||||
.. _Pull Request 921: https://github.com/galaxyproject/galaxy/pull/921
|
||||
.. _Pull Request 6891: https://github.com/galaxyproject/galaxy/pull/6891
|
||||
.. _Pull Request 7402: https://github.com/galaxyproject/galaxy/pull/7402
|
||||
.. _Pull Request 7494: https://github.com/galaxyproject/galaxy/pull/7494
|
||||
.. _Pull Request 7615: https://github.com/galaxyproject/galaxy/pull/7615
|
||||
.. _Pull Request 7665: https://github.com/galaxyproject/galaxy/pull/7665
|
||||
.. _Pull Request 7670: https://github.com/galaxyproject/galaxy/pull/7670
|
||||
.. _Pull Request 7730: https://github.com/galaxyproject/galaxy/pull/7730
|
||||
.. _Pull Request 7745: https://github.com/galaxyproject/galaxy/pull/7745
|
||||
.. _Pull Request 7770: https://github.com/galaxyproject/galaxy/pull/7770
|
||||
.. _Pull Request 7772: https://github.com/galaxyproject/galaxy/pull/7772
|
||||
.. _Pull Request 7790: https://github.com/galaxyproject/galaxy/pull/7790
|
||||
.. _Pull Request 7799: https://github.com/galaxyproject/galaxy/pull/7799
|
||||
.. _Pull Request 7804: https://github.com/galaxyproject/galaxy/pull/7804
|
||||
.. _Pull Request 7805: https://github.com/galaxyproject/galaxy/pull/7805
|
||||
.. _Pull Request 7808: https://github.com/galaxyproject/galaxy/pull/7808
|
||||
.. _Pull Request 7810: https://github.com/galaxyproject/galaxy/pull/7810
|
||||
.. _Pull Request 7811: https://github.com/galaxyproject/galaxy/pull/7811
|
||||
.. _Pull Request 7825: https://github.com/galaxyproject/galaxy/pull/7825
|
||||
.. _Pull Request 7828: https://github.com/galaxyproject/galaxy/pull/7828
|
||||
.. _Pull Request 7829: https://github.com/galaxyproject/galaxy/pull/7829
|
||||
.. _Pull Request 7830: https://github.com/galaxyproject/galaxy/pull/7830
|
||||
.. _Pull Request 7832: https://github.com/galaxyproject/galaxy/pull/7832
|
||||
.. _Pull Request 7835: https://github.com/galaxyproject/galaxy/pull/7835
|
||||
.. _Pull Request 7837: https://github.com/galaxyproject/galaxy/pull/7837
|
||||
.. _Pull Request 7838: https://github.com/galaxyproject/galaxy/pull/7838
|
||||
.. _Pull Request 7843: https://github.com/galaxyproject/galaxy/pull/7843
|
||||
.. _Pull Request 7852: https://github.com/galaxyproject/galaxy/pull/7852
|
||||
.. _Pull Request 7854: https://github.com/galaxyproject/galaxy/pull/7854
|
||||
.. _Pull Request 7867: https://github.com/galaxyproject/galaxy/pull/7867
|
||||
.. _Pull Request 7871: https://github.com/galaxyproject/galaxy/pull/7871
|
||||
.. _Pull Request 7873: https://github.com/galaxyproject/galaxy/pull/7873
|
||||
.. _Pull Request 7878: https://github.com/galaxyproject/galaxy/pull/7878
|
||||
.. _Pull Request 7882: https://github.com/galaxyproject/galaxy/pull/7882
|
||||
.. _Pull Request 7885: https://github.com/galaxyproject/galaxy/pull/7885
|
||||
.. _Pull Request 7888: https://github.com/galaxyproject/galaxy/pull/7888
|
||||
.. _Pull Request 7889: https://github.com/galaxyproject/galaxy/pull/7889
|
||||
.. _Pull Request 7890: https://github.com/galaxyproject/galaxy/pull/7890
|
||||
.. _Pull Request 7891: https://github.com/galaxyproject/galaxy/pull/7891
|
||||
.. _Pull Request 7892: https://github.com/galaxyproject/galaxy/pull/7892
|
||||
.. _Pull Request 7895: https://github.com/galaxyproject/galaxy/pull/7895
|
||||
.. _Pull Request 7897: https://github.com/galaxyproject/galaxy/pull/7897
|
||||
.. _Pull Request 7905: https://github.com/galaxyproject/galaxy/pull/7905
|
||||
.. _Pull Request 7908: https://github.com/galaxyproject/galaxy/pull/7908
|
||||
.. _Pull Request 7911: https://github.com/galaxyproject/galaxy/pull/7911
|
||||
.. _Pull Request 7913: https://github.com/galaxyproject/galaxy/pull/7913
|
||||
.. _Pull Request 7918: https://github.com/galaxyproject/galaxy/pull/7918
|
||||
.. _Pull Request 7927: https://github.com/galaxyproject/galaxy/pull/7927
|
||||
.. _Pull Request 7929: https://github.com/galaxyproject/galaxy/pull/7929
|
||||
.. _Pull Request 7935: https://github.com/galaxyproject/galaxy/pull/7935
|
||||
.. _Pull Request 7939: https://github.com/galaxyproject/galaxy/pull/7939
|
||||
.. _Pull Request 7945: https://github.com/galaxyproject/galaxy/pull/7945
|
||||
.. _Pull Request 7952: https://github.com/galaxyproject/galaxy/pull/7952
|
||||
.. _Pull Request 7953: https://github.com/galaxyproject/galaxy/pull/7953
|
||||
.. _Pull Request 7966: https://github.com/galaxyproject/galaxy/pull/7966
|
||||
.. _Pull Request 7971: https://github.com/galaxyproject/galaxy/pull/7971
|
||||
.. _Pull Request 7980: https://github.com/galaxyproject/galaxy/pull/7980
|
||||
.. _Pull Request 7985: https://github.com/galaxyproject/galaxy/pull/7985
|
||||
.. _Pull Request 7986: https://github.com/galaxyproject/galaxy/pull/7986
|
||||
.. _Pull Request 7991: https://github.com/galaxyproject/galaxy/pull/7991
|
||||
.. _Pull Request 7992: https://github.com/galaxyproject/galaxy/pull/7992
|
||||
.. _Pull Request 7993: https://github.com/galaxyproject/galaxy/pull/7993
|
||||
.. _Pull Request 7995: https://github.com/galaxyproject/galaxy/pull/7995
|
||||
.. _Pull Request 8001: https://github.com/galaxyproject/galaxy/pull/8001
|
||||
.. _Pull Request 8009: https://github.com/galaxyproject/galaxy/pull/8009
|
||||
.. _Pull Request 8016: https://github.com/galaxyproject/galaxy/pull/8016
|
||||
.. _Pull Request 8018: https://github.com/galaxyproject/galaxy/pull/8018
|
||||
.. _Pull Request 8022: https://github.com/galaxyproject/galaxy/pull/8022
|
||||
.. _Pull Request 8023: https://github.com/galaxyproject/galaxy/pull/8023
|
||||
.. _Pull Request 8024: https://github.com/galaxyproject/galaxy/pull/8024
|
||||
.. _Pull Request 8025: https://github.com/galaxyproject/galaxy/pull/8025
|
||||
.. _Pull Request 8028: https://github.com/galaxyproject/galaxy/pull/8028
|
||||
.. _Pull Request 8034: https://github.com/galaxyproject/galaxy/pull/8034
|
||||
.. _Pull Request 8035: https://github.com/galaxyproject/galaxy/pull/8035
|
||||
.. _Pull Request 8036: https://github.com/galaxyproject/galaxy/pull/8036
|
||||
.. _Pull Request 8038: https://github.com/galaxyproject/galaxy/pull/8038
|
||||
.. _Pull Request 8042: https://github.com/galaxyproject/galaxy/pull/8042
|
||||
.. _Pull Request 8044: https://github.com/galaxyproject/galaxy/pull/8044
|
||||
.. _Pull Request 8045: https://github.com/galaxyproject/galaxy/pull/8045
|
||||
.. _Pull Request 8046: https://github.com/galaxyproject/galaxy/pull/8046
|
||||
.. _Pull Request 8047: https://github.com/galaxyproject/galaxy/pull/8047
|
||||
.. _Pull Request 8050: https://github.com/galaxyproject/galaxy/pull/8050
|
||||
.. _Pull Request 8051: https://github.com/galaxyproject/galaxy/pull/8051
|
||||
.. _Pull Request 8061: https://github.com/galaxyproject/galaxy/pull/8061
|
||||
.. _Pull Request 8062: https://github.com/galaxyproject/galaxy/pull/8062
|
||||
.. _Pull Request 8070: https://github.com/galaxyproject/galaxy/pull/8070
|
||||
.. _Pull Request 8075: https://github.com/galaxyproject/galaxy/pull/8075
|
||||
.. _Pull Request 8076: https://github.com/galaxyproject/galaxy/pull/8076
|
||||
.. _Pull Request 8077: https://github.com/galaxyproject/galaxy/pull/8077
|
||||
.. _Pull Request 8078: https://github.com/galaxyproject/galaxy/pull/8078
|
||||
.. _Pull Request 8082: https://github.com/galaxyproject/galaxy/pull/8082
|
||||
.. _Pull Request 8086: https://github.com/galaxyproject/galaxy/pull/8086
|
||||
.. _Pull Request 8090: https://github.com/galaxyproject/galaxy/pull/8090
|
||||
.. _Pull Request 8091: https://github.com/galaxyproject/galaxy/pull/8091
|
||||
.. _Pull Request 8094: https://github.com/galaxyproject/galaxy/pull/8094
|
||||
.. _Pull Request 8098: https://github.com/galaxyproject/galaxy/pull/8098
|
||||
.. _Pull Request 8101: https://github.com/galaxyproject/galaxy/pull/8101
|
||||
.. _Pull Request 8104: https://github.com/galaxyproject/galaxy/pull/8104
|
||||
.. _Pull Request 8112: https://github.com/galaxyproject/galaxy/pull/8112
|
||||
.. _Pull Request 8113: https://github.com/galaxyproject/galaxy/pull/8113
|
||||
.. _Pull Request 8114: https://github.com/galaxyproject/galaxy/pull/8114
|
||||
.. _Pull Request 8118: https://github.com/galaxyproject/galaxy/pull/8118
|
||||
.. _Pull Request 8120: https://github.com/galaxyproject/galaxy/pull/8120
|
||||
.. _Pull Request 8123: https://github.com/galaxyproject/galaxy/pull/8123
|
||||
.. _Pull Request 8124: https://github.com/galaxyproject/galaxy/pull/8124
|
||||
.. _Pull Request 8126: https://github.com/galaxyproject/galaxy/pull/8126
|
||||
.. _Pull Request 8133: https://github.com/galaxyproject/galaxy/pull/8133
|
||||
.. _Pull Request 8136: https://github.com/galaxyproject/galaxy/pull/8136
|
||||
.. _Pull Request 8137: https://github.com/galaxyproject/galaxy/pull/8137
|
||||
.. _Pull Request 8138: https://github.com/galaxyproject/galaxy/pull/8138
|
||||
.. _Pull Request 8144: https://github.com/galaxyproject/galaxy/pull/8144
|
||||
.. _Pull Request 8147: https://github.com/galaxyproject/galaxy/pull/8147
|
||||
.. _Pull Request 8152: https://github.com/galaxyproject/galaxy/pull/8152
|
||||
.. _Pull Request 8154: https://github.com/galaxyproject/galaxy/pull/8154
|
||||
.. _Pull Request 8155: https://github.com/galaxyproject/galaxy/pull/8155
|
||||
.. _Pull Request 8161: https://github.com/galaxyproject/galaxy/pull/8161
|
||||
.. _Pull Request 8162: https://github.com/galaxyproject/galaxy/pull/8162
|
||||
.. _Pull Request 8163: https://github.com/galaxyproject/galaxy/pull/8163
|
||||
.. _Pull Request 8168: https://github.com/galaxyproject/galaxy/pull/8168
|
||||
.. _Pull Request 8179: https://github.com/galaxyproject/galaxy/pull/8179
|
||||
.. _Pull Request 8181: https://github.com/galaxyproject/galaxy/pull/8181
|
||||
.. _Pull Request 8182: https://github.com/galaxyproject/galaxy/pull/8182
|
||||
.. _Pull Request 8186: https://github.com/galaxyproject/galaxy/pull/8186
|
||||
.. _Pull Request 8195: https://github.com/galaxyproject/galaxy/pull/8195
|
||||
.. _Pull Request 8201: https://github.com/galaxyproject/galaxy/pull/8201
|
||||
.. _Pull Request 8205: https://github.com/galaxyproject/galaxy/pull/8205
|
||||
.. _Pull Request 8206: https://github.com/galaxyproject/galaxy/pull/8206
|
||||
.. _Pull Request 8207: https://github.com/galaxyproject/galaxy/pull/8207
|
||||
.. _Pull Request 8208: https://github.com/galaxyproject/galaxy/pull/8208
|
||||
.. _Pull Request 8211: https://github.com/galaxyproject/galaxy/pull/8211
|
||||
.. _Pull Request 8212: https://github.com/galaxyproject/galaxy/pull/8212
|
||||
.. _Pull Request 8213: https://github.com/galaxyproject/galaxy/pull/8213
|
||||
.. _Pull Request 8214: https://github.com/galaxyproject/galaxy/pull/8214
|
||||
.. _Pull Request 8220: https://github.com/galaxyproject/galaxy/pull/8220
|
||||
.. _Pull Request 8221: https://github.com/galaxyproject/galaxy/pull/8221
|
||||
.. _Pull Request 8225: https://github.com/galaxyproject/galaxy/pull/8225
|
||||
.. _Pull Request 8227: https://github.com/galaxyproject/galaxy/pull/8227
|
||||
.. _Pull Request 8229: https://github.com/galaxyproject/galaxy/pull/8229
|
||||
.. _Pull Request 8231: https://github.com/galaxyproject/galaxy/pull/8231
|
||||
.. _Pull Request 8233: https://github.com/galaxyproject/galaxy/pull/8233
|
||||
.. _Pull Request 8234: https://github.com/galaxyproject/galaxy/pull/8234
|
||||
.. _Pull Request 8235: https://github.com/galaxyproject/galaxy/pull/8235
|
||||
.. _Pull Request 8239: https://github.com/galaxyproject/galaxy/pull/8239
|
||||
.. _Pull Request 8241: https://github.com/galaxyproject/galaxy/pull/8241
|
||||
.. _Pull Request 8246: https://github.com/galaxyproject/galaxy/pull/8246
|
||||
.. _Pull Request 8247: https://github.com/galaxyproject/galaxy/pull/8247
|
||||
.. _Pull Request 8249: https://github.com/galaxyproject/galaxy/pull/8249
|
||||
.. _Pull Request 8250: https://github.com/galaxyproject/galaxy/pull/8250
|
||||
.. _Pull Request 8253: https://github.com/galaxyproject/galaxy/pull/8253
|
||||
.. _Pull Request 8254: https://github.com/galaxyproject/galaxy/pull/8254
|
||||
.. _Pull Request 8256: https://github.com/galaxyproject/galaxy/pull/8256
|
||||
.. _Pull Request 8257: https://github.com/galaxyproject/galaxy/pull/8257
|
||||
.. _Pull Request 8266: https://github.com/galaxyproject/galaxy/pull/8266
|
||||
.. _Pull Request 8267: https://github.com/galaxyproject/galaxy/pull/8267
|
||||
.. _Pull Request 8268: https://github.com/galaxyproject/galaxy/pull/8268
|
||||
.. _Pull Request 8269: https://github.com/galaxyproject/galaxy/pull/8269
|
||||
.. _Pull Request 8270: https://github.com/galaxyproject/galaxy/pull/8270
|
||||
.. _Pull Request 8275: https://github.com/galaxyproject/galaxy/pull/8275
|
||||
.. _Pull Request 8276: https://github.com/galaxyproject/galaxy/pull/8276
|
||||
.. _Pull Request 8277: https://github.com/galaxyproject/galaxy/pull/8277
|
||||
.. _Pull Request 8280: https://github.com/galaxyproject/galaxy/pull/8280
|
||||
.. _Pull Request 8281: https://github.com/galaxyproject/galaxy/pull/8281
|
||||
.. _Pull Request 8284: https://github.com/galaxyproject/galaxy/pull/8284
|
||||
.. _Pull Request 8285: https://github.com/galaxyproject/galaxy/pull/8285
|
||||
.. _Pull Request 8287: https://github.com/galaxyproject/galaxy/pull/8287
|
||||
.. _Pull Request 8289: https://github.com/galaxyproject/galaxy/pull/8289
|
||||
.. _Pull Request 8290: https://github.com/galaxyproject/galaxy/pull/8290
|
||||
.. _Pull Request 8291: https://github.com/galaxyproject/galaxy/pull/8291
|
||||
.. _Pull Request 8293: https://github.com/galaxyproject/galaxy/pull/8293
|
||||
.. _Pull Request 8294: https://github.com/galaxyproject/galaxy/pull/8294
|
||||
.. _Pull Request 8296: https://github.com/galaxyproject/galaxy/pull/8296
|
||||
.. _Pull Request 8298: https://github.com/galaxyproject/galaxy/pull/8298
|
||||
.. _Pull Request 8300: https://github.com/galaxyproject/galaxy/pull/8300
|
||||
.. _Pull Request 8301: https://github.com/galaxyproject/galaxy/pull/8301
|
||||
.. _Pull Request 8302: https://github.com/galaxyproject/galaxy/pull/8302
|
||||
.. _Pull Request 8303: https://github.com/galaxyproject/galaxy/pull/8303
|
||||
.. _Pull Request 8304: https://github.com/galaxyproject/galaxy/pull/8304
|
||||
.. _Pull Request 8305: https://github.com/galaxyproject/galaxy/pull/8305
|
||||
.. _Pull Request 8306: https://github.com/galaxyproject/galaxy/pull/8306
|
||||
.. _Pull Request 8307: https://github.com/galaxyproject/galaxy/pull/8307
|
||||
.. _Pull Request 8308: https://github.com/galaxyproject/galaxy/pull/8308
|
||||
.. _Pull Request 8309: https://github.com/galaxyproject/galaxy/pull/8309
|
||||
.. _Pull Request 8310: https://github.com/galaxyproject/galaxy/pull/8310
|
||||
.. _Pull Request 8311: https://github.com/galaxyproject/galaxy/pull/8311
|
||||
.. _Pull Request 8314: https://github.com/galaxyproject/galaxy/pull/8314
|
||||
.. _Pull Request 8315: https://github.com/galaxyproject/galaxy/pull/8315
|
||||
.. _Pull Request 8316: https://github.com/galaxyproject/galaxy/pull/8316
|
||||
.. _Pull Request 8319: https://github.com/galaxyproject/galaxy/pull/8319
|
||||
.. _Pull Request 8320: https://github.com/galaxyproject/galaxy/pull/8320
|
||||
.. _Pull Request 8321: https://github.com/galaxyproject/galaxy/pull/8321
|
||||
.. _Pull Request 8322: https://github.com/galaxyproject/galaxy/pull/8322
|
||||
.. _Pull Request 8323: https://github.com/galaxyproject/galaxy/pull/8323
|
||||
.. _Pull Request 8324: https://github.com/galaxyproject/galaxy/pull/8324
|
||||
.. _Pull Request 8326: https://github.com/galaxyproject/galaxy/pull/8326
|
||||
.. _Pull Request 8329: https://github.com/galaxyproject/galaxy/pull/8329
|
||||
.. _Pull Request 8331: https://github.com/galaxyproject/galaxy/pull/8331
|
||||
.. _Pull Request 8334: https://github.com/galaxyproject/galaxy/pull/8334
|
||||
.. _Pull Request 8335: https://github.com/galaxyproject/galaxy/pull/8335
|
||||
.. _Pull Request 8337: https://github.com/galaxyproject/galaxy/pull/8337
|
||||
.. _Pull Request 8342: https://github.com/galaxyproject/galaxy/pull/8342
|
||||
.. _Pull Request 8343: https://github.com/galaxyproject/galaxy/pull/8343
|
||||
.. _Pull Request 8345: https://github.com/galaxyproject/galaxy/pull/8345
|
||||
.. _Pull Request 8346: https://github.com/galaxyproject/galaxy/pull/8346
|
||||
.. _Pull Request 8347: https://github.com/galaxyproject/galaxy/pull/8347
|
||||
.. _Pull Request 8351: https://github.com/galaxyproject/galaxy/pull/8351
|
||||
.. _Pull Request 8355: https://github.com/galaxyproject/galaxy/pull/8355
|
||||
.. _Pull Request 8357: https://github.com/galaxyproject/galaxy/pull/8357
|
||||
.. _Pull Request 8359: https://github.com/galaxyproject/galaxy/pull/8359
|
||||
.. _Pull Request 8360: https://github.com/galaxyproject/galaxy/pull/8360
|
||||
.. _Pull Request 8362: https://github.com/galaxyproject/galaxy/pull/8362
|
||||
.. _Pull Request 8363: https://github.com/galaxyproject/galaxy/pull/8363
|
||||
.. _Pull Request 8365: https://github.com/galaxyproject/galaxy/pull/8365
|
||||
.. _Pull Request 8366: https://github.com/galaxyproject/galaxy/pull/8366
|
||||
.. _Pull Request 8368: https://github.com/galaxyproject/galaxy/pull/8368
|
||||
.. _Pull Request 8371: https://github.com/galaxyproject/galaxy/pull/8371
|
||||
.. _Pull Request 8373: https://github.com/galaxyproject/galaxy/pull/8373
|
||||
.. _Pull Request 8377: https://github.com/galaxyproject/galaxy/pull/8377
|
||||
.. _Pull Request 8385: https://github.com/galaxyproject/galaxy/pull/8385
|
||||
.. _Pull Request 8386: https://github.com/galaxyproject/galaxy/pull/8386
|
||||
.. _Pull Request 8394: https://github.com/galaxyproject/galaxy/pull/8394
|
||||
.. _Pull Request 8398: https://github.com/galaxyproject/galaxy/pull/8398
|
||||
.. _Pull Request 8404: https://github.com/galaxyproject/galaxy/pull/8404
|
||||
.. _Pull Request 8405: https://github.com/galaxyproject/galaxy/pull/8405
|
||||
.. _Pull Request 8407: https://github.com/galaxyproject/galaxy/pull/8407
|
||||
.. _Pull Request 8409: https://github.com/galaxyproject/galaxy/pull/8409
|
||||
.. _Pull Request 8410: https://github.com/galaxyproject/galaxy/pull/8410
|
||||
.. _Pull Request 8414: https://github.com/galaxyproject/galaxy/pull/8414
|
||||
.. _Pull Request 8421: https://github.com/galaxyproject/galaxy/pull/8421
|
||||
.. _Pull Request 8422: https://github.com/galaxyproject/galaxy/pull/8422
|
||||
.. _Pull Request 8424: https://github.com/galaxyproject/galaxy/pull/8424
|
||||
.. _Pull Request 8426: https://github.com/galaxyproject/galaxy/pull/8426
|
||||
.. _Pull Request 8430: https://github.com/galaxyproject/galaxy/pull/8430
|
||||
.. _Pull Request 8431: https://github.com/galaxyproject/galaxy/pull/8431
|
||||
.. _Pull Request 8433: https://github.com/galaxyproject/galaxy/pull/8433
|
||||
.. _Pull Request 8437: https://github.com/galaxyproject/galaxy/pull/8437
|
||||
.. _Pull Request 8439: https://github.com/galaxyproject/galaxy/pull/8439
|
||||
.. _Pull Request 8440: https://github.com/galaxyproject/galaxy/pull/8440
|
||||
.. _Pull Request 8446: https://github.com/galaxyproject/galaxy/pull/8446
|
||||
.. _Pull Request 8450: https://github.com/galaxyproject/galaxy/pull/8450
|
||||
.. _Pull Request 8451: https://github.com/galaxyproject/galaxy/pull/8451
|
||||
.. _Pull Request 8452: https://github.com/galaxyproject/galaxy/pull/8452
|
||||
.. _Pull Request 8455: https://github.com/galaxyproject/galaxy/pull/8455
|
||||
.. _Pull Request 8456: https://github.com/galaxyproject/galaxy/pull/8456
|
||||
.. _Pull Request 8457: https://github.com/galaxyproject/galaxy/pull/8457
|
||||
.. _Pull Request 8458: https://github.com/galaxyproject/galaxy/pull/8458
|
||||
.. _Pull Request 8461: https://github.com/galaxyproject/galaxy/pull/8461
|
||||
.. _Pull Request 8462: https://github.com/galaxyproject/galaxy/pull/8462
|
||||
.. _Pull Request 8465: https://github.com/galaxyproject/galaxy/pull/8465
|
||||
.. _Pull Request 8466: https://github.com/galaxyproject/galaxy/pull/8466
|
||||
.. _Pull Request 8468: https://github.com/galaxyproject/galaxy/pull/8468
|
||||
.. _Pull Request 8469: https://github.com/galaxyproject/galaxy/pull/8469
|
||||
.. _Pull Request 8470: https://github.com/galaxyproject/galaxy/pull/8470
|
||||
.. _Pull Request 8473: https://github.com/galaxyproject/galaxy/pull/8473
|
||||
.. _Pull Request 8474: https://github.com/galaxyproject/galaxy/pull/8474
|
||||
.. _Pull Request 8475: https://github.com/galaxyproject/galaxy/pull/8475
|
||||
.. _Pull Request 8477: https://github.com/galaxyproject/galaxy/pull/8477
|
||||
.. _Pull Request 8479: https://github.com/galaxyproject/galaxy/pull/8479
|
||||
.. _Pull Request 8485: https://github.com/galaxyproject/galaxy/pull/8485
|
||||
.. _Pull Request 8489: https://github.com/galaxyproject/galaxy/pull/8489
|
||||
.. _Pull Request 8490: https://github.com/galaxyproject/galaxy/pull/8490
|
||||
.. _Pull Request 8492: https://github.com/galaxyproject/galaxy/pull/8492
|
||||
.. _Pull Request 8494: https://github.com/galaxyproject/galaxy/pull/8494
|
||||
.. _Pull Request 8495: https://github.com/galaxyproject/galaxy/pull/8495
|
||||
.. _Pull Request 8497: https://github.com/galaxyproject/galaxy/pull/8497
|
||||
.. _Pull Request 8499: https://github.com/galaxyproject/galaxy/pull/8499
|
||||
.. _Pull Request 8502: https://github.com/galaxyproject/galaxy/pull/8502
|
||||
.. _Pull Request 8503: https://github.com/galaxyproject/galaxy/pull/8503
|
||||
.. _Pull Request 8506: https://github.com/galaxyproject/galaxy/pull/8506
|
||||
.. _Pull Request 8507: https://github.com/galaxyproject/galaxy/pull/8507
|
||||
.. _Pull Request 8510: https://github.com/galaxyproject/galaxy/pull/8510
|
||||
.. _Pull Request 8521: https://github.com/galaxyproject/galaxy/pull/8521
|
||||
.. _Pull Request 8524: https://github.com/galaxyproject/galaxy/pull/8524
|
||||
.. _Pull Request 8526: https://github.com/galaxyproject/galaxy/pull/8526
|
||||
.. _Pull Request 8527: https://github.com/galaxyproject/galaxy/pull/8527
|
||||
.. _Pull Request 8530: https://github.com/galaxyproject/galaxy/pull/8530
|
||||
.. _Pull Request 8532: https://github.com/galaxyproject/galaxy/pull/8532
|
||||
.. _Pull Request 8533: https://github.com/galaxyproject/galaxy/pull/8533
|
||||
.. _Pull Request 8536: https://github.com/galaxyproject/galaxy/pull/8536
|
||||
.. _Pull Request 8537: https://github.com/galaxyproject/galaxy/pull/8537
|
||||
.. _Pull Request 8538: https://github.com/galaxyproject/galaxy/pull/8538
|
||||
.. _Pull Request 8539: https://github.com/galaxyproject/galaxy/pull/8539
|
||||
.. _Pull Request 8541: https://github.com/galaxyproject/galaxy/pull/8541
|
||||
.. _Pull Request 8542: https://github.com/galaxyproject/galaxy/pull/8542
|
||||
.. _Pull Request 8543: https://github.com/galaxyproject/galaxy/pull/8543
|
||||
.. _Pull Request 8544: https://github.com/galaxyproject/galaxy/pull/8544
|
||||
.. _Pull Request 8545: https://github.com/galaxyproject/galaxy/pull/8545
|
||||
.. _Pull Request 8549: https://github.com/galaxyproject/galaxy/pull/8549
|
||||
.. _Pull Request 8552: https://github.com/galaxyproject/galaxy/pull/8552
|
||||
.. _Pull Request 8560: https://github.com/galaxyproject/galaxy/pull/8560
|
||||
.. _Pull Request 8561: https://github.com/galaxyproject/galaxy/pull/8561
|
||||
.. _Pull Request 8569: https://github.com/galaxyproject/galaxy/pull/8569
|
||||
.. _Pull Request 8574: https://github.com/galaxyproject/galaxy/pull/8574
|
||||
.. _Pull Request 8575: https://github.com/galaxyproject/galaxy/pull/8575
|
||||
.. _Pull Request 8579: https://github.com/galaxyproject/galaxy/pull/8579
|
||||
.. _Pull Request 8585: https://github.com/galaxyproject/galaxy/pull/8585
|
||||
.. _Pull Request 8589: https://github.com/galaxyproject/galaxy/pull/8589
|
||||
.. _Pull Request 8590: https://github.com/galaxyproject/galaxy/pull/8590
|
||||
.. _Pull Request 8605: https://github.com/galaxyproject/galaxy/pull/8605
|
||||
.. _Pull Request 8608: https://github.com/galaxyproject/galaxy/pull/8608
|
||||
.. _Pull Request 8609: https://github.com/galaxyproject/galaxy/pull/8609
|
||||
.. _Pull Request 8610: https://github.com/galaxyproject/galaxy/pull/8610
|
||||
.. _Pull Request 8611: https://github.com/galaxyproject/galaxy/pull/8611
|
||||
.. _Pull Request 8613: https://github.com/galaxyproject/galaxy/pull/8613
|
||||
.. _Pull Request 8614: https://github.com/galaxyproject/galaxy/pull/8614
|
||||
.. _Pull Request 8616: https://github.com/galaxyproject/galaxy/pull/8616
|
||||
.. _Pull Request 8621: https://github.com/galaxyproject/galaxy/pull/8621
|
||||
.. _Pull Request 8622: https://github.com/galaxyproject/galaxy/pull/8622
|
||||
.. _Pull Request 8623: https://github.com/galaxyproject/galaxy/pull/8623
|
||||
.. _Pull Request 8629: https://github.com/galaxyproject/galaxy/pull/8629
|
||||
.. _Pull Request 8630: https://github.com/galaxyproject/galaxy/pull/8630
|
||||
.. _Pull Request 8635: https://github.com/galaxyproject/galaxy/pull/8635
|
||||
.. _Pull Request 8638: https://github.com/galaxyproject/galaxy/pull/8638
|
||||
.. _Pull Request 8640: https://github.com/galaxyproject/galaxy/pull/8640
|
||||
.. _Pull Request 8643: https://github.com/galaxyproject/galaxy/pull/8643
|
||||
.. _Pull Request 8647: https://github.com/galaxyproject/galaxy/pull/8647
|
||||
.. _Pull Request 8650: https://github.com/galaxyproject/galaxy/pull/8650
|
||||
.. _Pull Request 8654: https://github.com/galaxyproject/galaxy/pull/8654
|
||||
.. _Pull Request 8658: https://github.com/galaxyproject/galaxy/pull/8658
|
||||
.. _Pull Request 8663: https://github.com/galaxyproject/galaxy/pull/8663
|
||||
.. _Pull Request 8664: https://github.com/galaxyproject/galaxy/pull/8664
|
||||
.. _Pull Request 8679: https://github.com/galaxyproject/galaxy/pull/8679
|
||||
.. _Pull Request 8681: https://github.com/galaxyproject/galaxy/pull/8681
|
||||
.. _Pull Request 8683: https://github.com/galaxyproject/galaxy/pull/8683
|
||||
.. _Pull Request 8687: https://github.com/galaxyproject/galaxy/pull/8687
|
||||
.. _Pull Request 8693: https://github.com/galaxyproject/galaxy/pull/8693
|
||||
.. _Pull Request 8696: https://github.com/galaxyproject/galaxy/pull/8696
|
||||
.. _Pull Request 8698: https://github.com/galaxyproject/galaxy/pull/8698
|
||||
.. _Pull Request 8702: https://github.com/galaxyproject/galaxy/pull/8702
|
||||
.. _Pull Request 8703: https://github.com/galaxyproject/galaxy/pull/8703
|
||||
.. _Pull Request 8719: https://github.com/galaxyproject/galaxy/pull/8719
|
||||
.. _Pull Request 8721: https://github.com/galaxyproject/galaxy/pull/8721
|
||||
.. _Pull Request 8727: https://github.com/galaxyproject/galaxy/pull/8727
|
||||
@@ -0,0 +1,10 @@
|
||||
|
||||
===========================================================
|
||||
January 2020 Galaxy Release (v 20.01)
|
||||
===========================================================
|
||||
|
||||
|
||||
Schedule
|
||||
===========================================================
|
||||
* Planned Freeze Date: 2020-01-06
|
||||
* Planned Release Date: 2020-01-27
|
||||
@@ -4,6 +4,7 @@ Releases
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
|
||||
19.09_announce
|
||||
19.05_announce
|
||||
19.01_announce
|
||||
18.09_announce
|
||||
|
||||
@@ -295,6 +295,7 @@ OPTION_ACTIONS = {
|
||||
'allow_library_path_paste': _RenameAction("allow_path_paste"),
|
||||
'trust_ipython_notebook_conversion': _RenameAction("trust_jupyter_notebook_conversion"),
|
||||
'enable_beta_tool_command_isolation': _DeprecatedAndDroppedAction(),
|
||||
'enable_beta_ts_api_install': _DeprecatedAndDroppedAction(),
|
||||
'single_user': _ProductionUnsafe(True),
|
||||
'tool_submission_burst_threads': _DeprecatedAndDroppedAction(),
|
||||
'tool_submission_burst_at': _DeprecatedAndDroppedAction(),
|
||||
|
||||
@@ -11,6 +11,7 @@ import re
|
||||
import string
|
||||
import sys
|
||||
import textwrap
|
||||
from collections import OrderedDict
|
||||
|
||||
try:
|
||||
import requests
|
||||
@@ -38,10 +39,11 @@ DEVTEAM = [
|
||||
"davebx", "martenson", "jmchilton",
|
||||
"tnabtaf", "natefoo", "jgoecks",
|
||||
"guerler", "jennaj", "nekrut", "jxtx",
|
||||
"VJalili", "WilliamHolden", "Nerdinacan"
|
||||
"VJalili", "WilliamHolden", "Nerdinacan",
|
||||
"ic4f",
|
||||
]
|
||||
|
||||
TEMPLATE = string.Template("""
|
||||
TEMPLATE = """
|
||||
.. to_doc
|
||||
|
||||
${release}
|
||||
@@ -57,10 +59,8 @@ Enhancements
|
||||
|
||||
.. feature
|
||||
|
||||
|
||||
.. enhancement
|
||||
|
||||
|
||||
.. small_enhancement
|
||||
|
||||
|
||||
@@ -76,7 +76,7 @@ Fixes
|
||||
|
||||
.. include:: ${release}_prs.rst
|
||||
|
||||
""")
|
||||
"""
|
||||
|
||||
ANNOUNCE_TEMPLATE = string.Template("""
|
||||
===========================================================
|
||||
@@ -286,6 +286,16 @@ RELEASE_ISSUE_TEMPLATE = string.Template("""
|
||||
- [ ] Close this issue.
|
||||
""")
|
||||
|
||||
GROUPPED_TAGS = OrderedDict([
|
||||
('area/visualizations', 'viz'),
|
||||
('area/datatypes', 'datatypes'),
|
||||
('area/tools', 'tools'),
|
||||
('area/workflows', 'workflows'),
|
||||
('area/client', 'ui'),
|
||||
('area/jobs', 'jobs'),
|
||||
('area/admin', 'admin'),
|
||||
])
|
||||
|
||||
# https://api.github.com/repos/galaxyproject/galaxy/pulls?base=dev&state=closed
|
||||
# https://api.github.com/repos/galaxyproject/galaxy/pulls?base=release_15.07&state=closed
|
||||
# https://api.github.com/repos/galaxyproject/galaxy/compare/release_15.05...dev
|
||||
@@ -334,7 +344,12 @@ def release_issue(argv):
|
||||
def do_release(argv):
|
||||
release_name = argv[2]
|
||||
release_file = _release_file(release_name + ".rst")
|
||||
release_info = TEMPLATE.safe_substitute(release=release_name)
|
||||
enhancement_targets = "\n\n".join([".. enhancement_tag_%s" % a for a in GROUPPED_TAGS.values()])
|
||||
bug_targets = "\n\n".join([".. bug_tag_%s" % a for a in GROUPPED_TAGS.values()])
|
||||
template = TEMPLATE
|
||||
template = template.replace(".. enhancement", "%s\n\n.. enhancement" % enhancement_targets)
|
||||
template = template.replace(".. bug", "%s\n\n.. bug" % bug_targets)
|
||||
release_info = string.Template(template).safe_substitute(release=release_name)
|
||||
open(release_file, "w").write(release_info.encode("utf-8"))
|
||||
month = int(release_name.split(".")[1])
|
||||
month_name = calendar.month_name[month]
|
||||
@@ -533,6 +548,8 @@ def main(argv):
|
||||
|
||||
def extend_target(target, line, source=history):
|
||||
from_str = ".. %s\n" % target
|
||||
if target not in source:
|
||||
raise Exception("Failed to find target [%s] in source [%s]" % (target, source))
|
||||
return source.replace(from_str, from_str + line + "\n")
|
||||
|
||||
ident = argv[1]
|
||||
@@ -596,7 +613,8 @@ def main(argv):
|
||||
to_doc += "{0}_".format(short_rev)
|
||||
|
||||
to_doc = wrap(to_doc)
|
||||
history = extend_target(text_target, to_doc, history)
|
||||
if text_target is not None:
|
||||
history = extend_target(text_target, to_doc, history)
|
||||
if req and 'labels' in req:
|
||||
labels = req['labels']
|
||||
if 'area/datatypes' in labels:
|
||||
@@ -671,13 +689,23 @@ def _text_target(github, pull_request, labels=None):
|
||||
elif is_feature:
|
||||
text_target = "feature"
|
||||
elif is_enhancement:
|
||||
text_target = "enhancement"
|
||||
for group_name in GROUPPED_TAGS.keys():
|
||||
if group_name in labels:
|
||||
text_target = "enhancement_tag_%s" % GROUPPED_TAGS[group_name]
|
||||
break
|
||||
else:
|
||||
text_target = "enhancement"
|
||||
elif is_some_kind_of_enhancement:
|
||||
text_target = "small_enhancement"
|
||||
elif is_major:
|
||||
text_target = "major_bug"
|
||||
elif is_bug:
|
||||
text_target = "bug"
|
||||
for group_name in GROUPPED_TAGS.keys():
|
||||
if group_name in labels:
|
||||
text_target = "bug_tag_%s" % GROUPPED_TAGS[group_name]
|
||||
break
|
||||
else:
|
||||
text_target = "bug"
|
||||
else:
|
||||
print("Logic problem, cannot determine section for %s" % _pr_to_str(pull_request))
|
||||
text_target = None
|
||||
|
||||
Reference in New Issue
Block a user