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.. to_doc
21.01
===============================
.. announce_start
Enhancements
-------------------------------
* Galaxy Markdown enhancements including integration of visualizations - allow embedding
visualizations in Galaxy Markdown (workflow invocation reports and pages) with
Markdown editor support and allow exporting workflow reports directly to Galaxy Pages.
`Pull Request 10241`_, `Pull Request 10288`_, `Pull Request 10404`_
* Add workflow invocation detail component.
`Pull Request 10976`_
* History panel rewrite (available in the UI as a beta option).
`Pull Request 8441`_, `Pull Request 11071`_, `Pull Request 10971`_
* Allow organizing the panel via EDAM ontology annotations.
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 10592`_
* Large overhaul over history import and export - including improved user experience, APIs, and allowing importing and exporting
to file sources plugins (including FTP).
`Pull Request 11054`_, `Pull Request 10993`_
* Various substantial improvements to data library user interface and performance
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 10204`_, `Pull Request 11099`_,
`Pull Request 10557`_, `Pull Request 10558`_,
`Pull Request 10807`_
* Script for finding missing db indexes
`Pull Request 10350`_
* Implement Galaxy database model schema rendering script.
`Pull Request 10571`_
* Allow configuration of activation email message.
`Pull Request 10959`_
* UI & API for Supporting Best Practice Workflows
`Pull Request 10988`_, `Pull Request 11025`_
* Implement edit & upgrade subworkflow buttons in workflow editor.
`Pull Request 11032`_
* Implement user-facing objectstore metadata.
`Pull Request 10233`_
* Fixes and improvements to favorited tools in the tool panel.
`Pull Request 10955`_, `Pull Request 9873`_
* Move upload button below Tool panel header, increase size, add label.
`Pull Request 10499`_, `Pull Request 10696`_
* Fix upload button tooltip.
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 11541`_
* Fix markdown tag for history dataset collections.
`Pull Request 11587`_
* Add author and license metadata and corresponding web microdata annotations for tools
and workflows.
`Pull Request 10408`_
* iRODS data migration script
(thanks to `@kxk302 <https://github.com/kxk302>`__).
`Pull Request 10125`_
* Integrate NORA's image viewer - a medical image viewer and annotation tool.
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 11035`_
* Add the OpenSeadragon viewer and extend datatypes for deep zoom images
(thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
`Pull Request 10756`_, `Pull Request 11017`_, `Pull Request 10546`_
* Add gfa2 datatype
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 10270`_
* Add nifti1 and nifti2 datatype
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 11020`_
* Add tck and trk datatype
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 11021`_
* Add gifti datatype
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 11028`_
* Add cmap datatype
(thanks to `@jaidevjoshi83 <https://github.com/jaidevjoshi83>`__).
`Pull Request 11471`_
* Expand image formats for viewing in OpenSeadragon
(thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
`Pull Request 11017`_
* add ome.tiff datatype
(thanks to `@qiagu <https://github.com/qiagu>`__).
`Pull Request 10349`_
* Add datatype converters for various MD filetypes
(thanks to `@simonbray <https://github.com/simonbray>`__).
`Pull Request 10757`_
* Add Apache Parquet datatype
`Pull Request 11047`_
* Add msf datatype
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 11084`_
* Allow the "Apply Rules" tool to attach tags to output datasets.
`Pull Request 10382`_
* Implement mypy type checking for the Galaxy Python backend.
`Pull Request 11009`_, `Pull Request 11037`_,
`Pull Request 11022`_, `Pull Request 11007`_,
`Pull Request 11027`_, `Pull Request 11039`_,
`Pull Request 11000`_, `Pull Request 10992`_,
`Pull Request 11013`_, `Pull Request 11019`_
* Allow setting file download filename_pattern by client.
`Pull Request 11108`_
* Add FastAPI migration of licenses endpoints
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 11056`_
* Improvements to workflow imports from GA4GH TRS servers
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 10805`_, `Pull Request 10619`_
* Major enhancements for the ``galaxy-tool-test`` script (installed as part of the PyPI
package ``galaxy-tool-util``).
`Pull Request 10620`_, `Pull Request 10779`_,
`Pull Request 10908`_, `Pull Request 10879`_,
`Pull Request 10725`_, `Pull Request 10735`_
`Pull Request 10767`_
* Add ffindex and ffdata database file types
`Pull Request 11218`_
* Add compressed paf datatype
(thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
`Pull Request 11567`_
* Speedup xml replacement
`Pull Request 10804`_
* Allow build_list tool inputs to be optional
`Pull Request 10871`_
(thanks to `@abretaud <https://github.com/abretaud>`__).
`Pull Request 10878`_
* Revise tool inputs to allow nested parameters and allow ``build_for_rerun`` and other
(thanks to `@simonbray <https://github.com/simonbray>`__).
`Pull Request 11332`_, `Pull Request 10720`_
* Allow empty file uploads
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 11079`_
* Convert collection creator user interface components to Vue.
`Pull Request 10240`_
* Disable dataset edit button after the dataset has been deleted
(thanks to `@simonbray <https://github.com/simonbray>`__).
`Pull Request 10589`_
* update the cellxgene IT container
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 11546`_
* Implement expression tool for picking non-null values for CWL-style merging of
conditional branches in native Galaxy workflows.
`Pull Request 10712`_
* Add and document API for publishing and tagging workflows
(thanks to `@simonbray <https://github.com/simonbray>`__).
`Pull Request 10748`_
* Allow relative paths when staging jobs (e.g. with planemo run)
(thanks to `@simonbray <https://github.com/simonbray>`__).
`Pull Request 10886`_
* Various small cleanups and improvements to the workflow editor and migrations toward
Vue.
`Pull Request 10999`_, `Pull Request 11001`_, `Pull Request 11024`_,
`Pull Request 10769`_, `Pull Request 11036`_, `Pull Request 11042`_,
`Pull Request 11041`_, `Pull Request 10580`_, `Pull Request 11046`_
* Add FastAPI as backend and start porting backend to an ASGI webapp to
enable modern programming features such a message queues and web sockets.
`Pull Request 10823`_, `Pull Request 11074`_
* Follow-up on best practice workflow linting user interface component
`Pull Request 11140`_
* Bug fix - cannot set dbkeys in workflow tests.
`Pull Request 11543`_
* Replace StreamBall, replace tarballs with zip
`Pull Request 10919`_
* Move upload button below Tool panel header, increase size, add label.
`Pull Request 10499`_
* Convert dataset and job information displays to Vue
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 10327`_, `Pull Request 10353`_, `Pull Request 10980`_
* Simpler API for getting user API key.
`Pull Request 10522`_
* Add S3 plugin for remote files browser.
`Pull Request 10523`_
* Fixed sync between legacy galaxy variable and Vuex current history
`Pull Request 11172`_
* Set undesired execution hosts to avoid in LSF
(thanks to `@pcm32 <https://github.com/pcm32>`__).
`Pull Request 10260`_
* Limit CPUs used in docker containers
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 10373`_
* Adding nodeSelector to K8S runner job pod spec
(thanks to `@almahmoud <https://github.com/almahmoud>`__).
`Pull Request 10380`_
* Cache container resolution during job execution
`Pull Request 10451`_
* Support stopping Interactive Tools without deleting their outputs
`Pull Request 10497`_
* Override some k8s runner params with destination params
(thanks to `@almahmoud <https://github.com/almahmoud>`__).
`Pull Request 10520`_
* Improve database operation job submission performance
`Pull Request 10539`_
* Don't specify default bind type for singularity
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 10625`_
* Allow extra job metadata to be specified for k8s
(thanks to `@nuwang <https://github.com/nuwang>`__).
`Pull Request 11078`_
* Implement backend quota interface - with better logic isolation and unit tests.
`Pull Request 10212`_
* When compiling dynamic installation tool conf files, ensure location is actually writeable.
`Pull Request 10387`_
* Display minutes in admin jobs cutoff
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 10493`_
* Display user disk usage in admin user panel.
`Pull Request 10666`_
* Allow GA4GH TRS servers configuration to not be undefined/empty
(thanks to `@selten <https://github.com/selten>`__).
`Pull Request 10817`_
* Drop ``legacy_eager_objectstore_initialization`` config option.
`Pull Request 10828`_
* Clarify ``master_api_key`` intended use
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 11067`
* Allow InteractiveTools to use path-based proxying when ``requires_domain=False``.
`Pull Request 8596`_
* Add setting that lets admins enable/disable the tool document cache
`Pull Request 11186`_
* Add warning for non-existing tool versions on tool form
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 10139`_
* Add default dbkey when collecting builds.
`Pull Request 10667`_
* Fix running subworkflows with parameter input steps.
`Pull Request 10722`_
* Fix workflow runs with data_column runtime parameter changes.
`Pull Request 11596`_
* Various fixes for copying workflow nodes.
`Pull Request 11602`_
* Fix optional workflow parameter inputs not recovered when setting step outputs.
`Pull Request 11626`_
* Drop API Key listings from admin user list.
`Pull Request 10745`_
* Render OpenEBench link in new consolidated tool metadata.
`Pull Request 10789`_
* Rework arguments to a couple model security operations to allow greater reuse.
`Pull Request 10835`_
* Add cancel option to workflow create form.
`Pull Request 10953`_
* Cleanup client unit test removing jquery and mocking ajax calls.
`Pull Request 10904`_
* Add tooltip to workflow node output checkbox.
`Pull Request 10957`_
* More structured workflow create and update parameter handling.
`Pull Request 11016`_
* Drop temporary hacks for upgrading export jobs from Galaxy 19.01 to 19.05.
`Pull Request 10990`_
* Make Selenium BibTeX rendering test more robust.
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 10809`_
* Implement select all box on admin "Manage Dependencies" page.
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 10758`_
* Add link to view dataset in dataset params.
(thanks to `@simonbray <https://github.com/simonbray>`__).
`Pull Request 10752`_
* Set up confirmation page for new Custos/oidc users.
`Pull Request 10198`_, `Pull Request 10952`_
* Add script to diff two release config files.
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 10258`_
* Small optimization for uploads.
`Pull Request 10316`_
* More convenient syntax for configuring file source plugins.
`Pull Request 10326`_
* Allow ``planemo run`` to stage in existing datasets without re-uploading
(thanks to `@simonbray <https://github.com/simonbray>`__).
`Pull Request 10334`_
* Auto-focus upload name in upload dialog.
`Pull Request 10487`_
* Revise style of radio button groups to improve visibility.
`Pull Request 10489`_
* Add update time to workflow version selector in workflow editor.
`Pull Request 10492`_
* Update authnz to include Azure as IDP
(thanks to `@cginmn <https://github.com/cginmn>`__).
`Pull Request 10413`_
* Let ``python-irodsclient`` session manage connections.
`Pull Request 10437`_
* Document workflow model classes
(thanks to `@innovate-invent <https://github.com/innovate-invent>`__).
`Pull Request 10471`_
* Update link for Galaxy configuration file in Galaxy debug document.
`Pull Request 10488`_
* Add missing documentation for macro elements in XSD
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 10495`_
* Update developer guidelines with instructions for proper commit messages.
`Pull Request 10498`_
* Use dataset selector in rules input dialog.
`Pull Request 10505`_
* List tool functionality/compatiblity changes with profile version in tool schema
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 10798`_
* Add enumeration restriction to ``detect_errors`` in tool XML schema
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 10510`_
* More informative error message for ``/api/authenticate/baseauth``
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 10524`_
* Add more tags to Github.
`Pull Request 10525`_
* More comments for rapid testing optional ``galaxy.files`` stuff.
`Pull Request 10526`_
* Add ``copy to clipboard`` button to datasets
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 10529`_
* Add awesome-galaxy repo link to docs
(thanks to `@innovate-invent <https://github.com/innovate-invent>`__).
`Pull Request 10530`_
* Generate path resolution note for sample file, docs.
`Pull Request 10537`_
* Allow admins to add an additional custom logo to the masthead
`Pull Request 10540`_
* Improve performance of copying HDAs and HDCAs.
`Pull Request 10549`_
* Update to new LTS nodejs version.
`Pull Request 10565`_
* Document data manager repository layout
(thanks to `@innovate-invent <https://github.com/innovate-invent>`__).
`Pull Request 10573`_
* Set uwsgi's honour-stdin option when in debug mode.
`Pull Request 10577`_
* Make primary extract workflow action button more visible
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 10583`_
* Allow ``pgcleanup`` to redirect logging to stdout
(thanks to `@gmauro <https://github.com/gmauro>`__).
`Pull Request 10594`_
* Remove IUC conda channel from default configuration
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 10608`_
* Document toolshed repository response object
(thanks to `@innovate-invent <https://github.com/innovate-invent>`__).
`Pull Request 10633`_
* Full Python dependencies update
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 10660`_
* Rev Python cwltool dependency to ``3.0.20201109103151``.
`Pull Request 10658`_
* Add AnVILFS conditional dependency.
(thanks to `@almahmoud <https://github.com/almahmoud>`__).
`Pull Request 11569`_
* Migrate API tests to GitHub workflow
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 10674`_
* Fix ``metadata_bcf`` framework test
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 11603`
* Added dockerfile [biohackathon]
(thanks to `@nuwang <https://github.com/nuwang>`__).
`Pull Request 10681`_
* Harden, formalize 'null' handling around boolean tool parameters
`Pull Request 10694`_
* Allow expression tools to output copies of input HDAs.
`Pull Request 10700`_
* Update ftp document for rounds=100000
(thanks to `@linnil1 <https://github.com/linnil1>`__).
`Pull Request 10701`_
* Implement and test proper null handling and optional values for integers, floats,
and text parameters in tools and workflows.
`Pull Request 10703`_
* Re-sync ``galaxy.tool_util.cwl`` with CWL branch of Galaxy.
`Pull Request 10716`_
* Upgrade syntax using ``pyupgrade --py36-plus``
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 10751`_
* Revision of sharing component, adds url copy to clipboard feature
`Pull Request 10754`_
* Don't cancel other selenium steps, if one step fails
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 10801`_
* Extension lookup with lower case extension
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 10803`_
* Retry failing selenium test once
`Pull Request 10806`_
* Add GitHub workflow to build docs
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 10811`_
* Maintainance Bot with GithubActions
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 10813`_
* document optional default for multiple in xsd
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 10819`_
* Implement read-only conda resolver (alternative)
`Pull Request 10822`_
* Improved error handling in API Interactor
`Pull Request 10833`_
* Add ``<filter>`` inline python example for ``select`` type in tool schema docs
(thanks to `@tensionhead <https://github.com/tensionhead>`__).
`Pull Request 10838`_
* Use `github-script` action for maintenance_bot job too
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 10844`_
* Unit testing and optimization for creating private roles and dataset sharing.
`Pull Request 10845`_
* Always expand tool about section if metadata is available
`Pull Request 10847`_
* Fix tag image in UI for consistency.
`Pull Request 10853`_
* Run CI labeler on reopened PRs, but skip if area labels are present
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 10861`_
* Allow ``build_list`` tool inputs to be optional
(thanks to `@innovate-invent <https://github.com/innovate-invent>`__).
`Pull Request 10863`_, `Pull Request 10871`_
* Allow selecting dynamic select parameters by name in the API and tool tests
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 10880`_
* Add screenshot decorators to selenium tests
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 10911`_
* Add version tab which links to release notes to help tab.
(thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
`Pull Request 10960`_
* Update locale.js
(thanks to `@shenweiyan <https://github.com/shenweiyan>`__).
`Pull Request 11011`_
* Document how parameters in sections are referenced
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 11026`_
* Upload test results as artifact in case of failure
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 11030`_
* Remove migration logic that will never be used now.
`Pull Request 11038`_
* Support complex markers in ``run_tests.sh``
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 11045`_
* Optimized binary datatype sniffing for various binary datatypes.
`Pull Request 11049`_
* Move framework tests to GitHub workflows + lint test tools
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 11055`_
* Allow setting filename_pattern by client
(thanks to `@brinkmanlab <https://github.com/brinkmanlab>`__).
`Pull Request 11058`_
* Add validation for tool ``data_collection`` parameters
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 11063`_
* Verify behavior of non-existent ``from_work_dir`` outputs.
`Pull Request 11073`_
* Show OpenAPI documentation for API tags
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 11083`_
* Major overhaul and expansion of documentation for writing tests in Galaxy.
`Pull Request 11088`_, `Pull Request 11102`_, `Pull Request 11104`_
* Parallelize client and server builds in dockerfile
(thanks to `@nuwang <https://github.com/nuwang>`__).
`Pull Request 11161`_
* add more markers for screenshooting
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 11171`_
* Don't flush for each failed output dataset
`Pull Request 11282`_
* Don't check if item is in list, use set subtraction
`Pull Request 11284`_
* Persist scroll/url information for GTN webhook
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 11290`_
* Add tracking code to webhook for GTN stats
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 11387`_
* Sort tool versions from newest to oldest in tool form
(thanks to `@cat-bro <https://github.com/cat-bro>`__).
`Pull Request 11490`_
* Improve API test for changing datatype
(thanks to `@simonbray <https://github.com/simonbray>`__).
`Pull Request 10272`_
* Various datatype code structure improvements
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 10279`_
* Drop unnecessary list casting in ``Anndata`` datatype.
`Pull Request 10296`_
* Drop unused helpers in ``web.framework.helpers``
`Pull Request 10345`_
* Drop support for retired Python 3.5
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 10368`_
* Make ``MetadataCollection`` a proper mapping
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 10374`_
* Typos and semantic fixes for iRODS object store
(thanks to `@trel <https://github.com/trel>`__).
`Pull Request 10423`_
* Fix K8s job runner typo
(thanks to `@almahmoud <https://github.com/almahmoud>`__).
`Pull Request 10501`_
* Drop communication server.
`Pull Request 10514`_
* Add workflow tests for some newer workflow features.
`Pull Request 10478`_, `Pull Request 10669`_
* Various small changes to test helper code.
`Pull Request 10668`_, `Pull Request 10783`_
* Refactor logic for ``workflow_step.input_type`` into model.
`Pull Request 10657`_
* Rename flake8 ignorelist.
`Pull Request 10702`_
* Rely on emails to determine GitLab users.
(thanks to `@selten <https://github.com/selten>`__).
`Pull Request 10830`_
* Convert ``datasets.set_edit`` to modern decorator, reuse manager.
`Pull Request 10854`_
* Make model somewhat compatible with sqlalchemy-1.4.
`Pull Request 10856`_
* Run maintenance bot only once
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 10858`_
* Replace usage of ``mkstemp`` with ``NamedTemporaryFile``.
`Pull Request 10862`_
* Small edits objectstore code.
`Pull Request 10867`_
* Remove ``trans`` from ``stream_dataset_collection()``
`Pull Request 10907`_
* Use ``email_from`` value from schema for tool error report email.
`Pull Request 10956`_
* Drop migration hack for htcondor.
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 10991`_
* Remove unused ``tag_outputs`` workflow controller action.
`Pull Request 11040`_
* Fix workflow terminals not updating appropriately.
`Pull Request 11542`_
Fixes
-------------------------------
* Hide purged datasets from visualizations
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 10483`_
* Fix reference error in MVP client application
(thanks to `@tmcgowan <https://github.com/tmcgowan>`__).
`Pull Request 10782`_
* Nora visualization version bump incorporating a few upstream bugfixes.
`Pull Request 11475`_
* Cleanup the supported filestypes for Nora.
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 11544`_
* Fix for GTF sniffer
(thanks to `@mtekman <https://github.com/mtekman>`__).
`Pull Request 10588`_
* Fix AnnData datatype peek
(thanks to `@mtekman <https://github.com/mtekman>`__).
`Pull Request 10986`_
* Remove mutatable arguments from Pythn function calls
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 10998`_, `Pull Request 11003`_, `Pull Request 11006`_
* Fix mtx unbound error.
`Pull Request 11368`_
* Fix sniffers of interval datatypes for files starting with many comments
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 11416`_
* Avoid false positives in Phylip sniffer.
`Pull Request 11595`_
* Add display_in_upload for protobuf datatypes.
`Pull Request 11555`_
* Don't display obs_names in select list.
`Pull Request 11574`_
* Disable tool cache if there is a problem.
`Pull Request 10808`_
* Put new toolshed tools in existing tool panel sections if the ID matches.
`Pull Request 10984`_
* Make hash selection mandatory in hash tool.
`Pull Request 11427`_
* Various Pyiron interactive tool fixes.
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 11545`_
* Allow using Openrefine without data inputs.
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 11547`_
* Set $HOME for interactive tools that require a specific directory.
(thanks to `@abretaud <https://github.com/abretaud>`__).
`Pull Request 11577`_
* Add checks to workflow toolbox, avoid displaying empty sections.
`Pull Request 10363`_
* Filter duplicate workflow output labels when initializing workflow step outputs.
`Pull Request 10432`_
* Properly scale workflow node coordinates before saving workflow.
`Pull Request 10511`_
* Fix changing versions in workflow editor.
`Pull Request 10516`_
* Fix currently failing Selenium tests, move to GitHub workflow.
`Pull Request 10755`_
* Don't preload editor mako with hidden workflows.
`Pull Request 10759`_
* Fix generation of BCO `object_id` and `etag`
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 10964`_
* Record invocation_step outputs as appropriate.
`Pull Request 10970`_
* Fix workflow parameter text value restriction when connected to select and text parameter.
`Pull Request 10975`_
* Convert deprecated `log.warn()`` calls to ``log.warning()``
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 10996`_
* Misc fixes
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 11029`_
* Maintain expanded state of JobStep during polling
`Pull Request 11144`_
* Fix tool version switch in workflow editor.
`Pull Request 11257`_
* Fix populated state for empty collections.
`Pull Request 11312`_
* Fix Workflow report markdown lost upon renaming the workflow.
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 11317`_
* Fix TypeError in WorkflowsAPIController.get_versions()
(thanks to `@rikeshi <https://github.com/rikeshi>`__).
`Pull Request 11373`_
* Wrap core of workflow monitor thread in try/except.
`Pull Request 11434`_
* Fix random-ish workflow error with maximum_workflow_jobs_per_scheduling_iteration.
`Pull Request 11513`_
* Mark workflow as changed when editing step label or annotation.
`Pull Request 11533`_
* Add input step data label when extracting workflow.
`Pull Request 11532`_
* Fix saving FileSource parameter in a workflow.
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 11605`_
* Fix collection mapping over filtered output problem.
`Pull Request 11621`_
* Bump client axios dependency from 0.19.2 to 0.21.1.
`Pull Request 11053`_
* Improved exception handling for missing job parameter field.
`Pull Request 10298`_
* Ensure `requirements` in a `DependenciesDescription` is a `ToolRequirements`
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 11044`_
* Allow specifying remote Pulsar app configuration external to job destination
attributes to prevent persisting connection secrets.
`Pull Request 11254`_, `Pull Request 11256`_, `Pull Request 11261`_
* Fix history import job done before import complete.
`Pull Request 11170`_
* Allow specifying remote pulsar app config by path.
`Pull Request 11191`_
* Fix jobs finishing after update to 21.01
`Pull Request 11330`_
* Add server name, PID and thread name to each handler log message.
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 11609`_, `Pull Request 11598`_
* Don't log handled exceptions when filling cheetah template.
`Pull Request 11355`_
* Update Pulsar client to 0.14.2
`Pull Request 11381`_
* Always mount a writable $_JOB_TMP_DIR when running tools in containers.
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 11448`_
* Restore the ability to pull containers from admin menu.
`Pull Request 10814`_
* Fix error in admin panel when creating new quota
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 11277`_
* Fix error on Admin panel when creating or editing Forms
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 11388`_
* Fix DefaultQuotaAssociation access to Enum values
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 11511`_
* Add logging if installable tool config file not found
`Pull Request 11515`_
* Fix ToolShed link in Admin->Local Data
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 11548`_
* Properly log out of oidc on galaxy logout
(thanks to `@juleengraham <https://github.com/juleengraham>`__).
`Pull Request 10108`_
* Fix quota meter style.
`Pull Request 10299`_
* Fix pytest breakage in package testing.
`Pull Request 10320`_
* Update documentation for proftpd configuration
(thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
`Pull Request 10351`_
* Add test for ``data_column`` parameter referring to non-tabular data (bed) and fix bug.
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 10365`_
* Fix assigning default value to variables in ``run_test_wrapper.sh``
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 10381`_
* Fix issues with copying tags and collections.
`Pull Request 10761`_
* Fix various style issues with rule builder.
`Pull Request 10766`_
* Fix certain classes of workflow extraction on copied objects.
`Pull Request 11151`_
* Fix Pulsar client to add tool environment variables to remote jobs.
`Pull Request 11349`_
* Fix workflow preview for tool repeat blocks without ``title``.
`Pull Request 10851`_
* Fix various issues with the sharing user interface component.
`Pull Request 11305`_
* Fix various issues with the admin jobs user interface component.
`Pull Request 11205`_
* Fix handling of collection element identifiers in history panel.
`Pull Request 10427`_
* Fix report's library function call in ``dataset_info.mako``.
`Pull Request 10476`_
* Fix drag and drop highlighting in tool form for data inputs.
`Pull Request 10494`_
* Display consistent format for job runtime
(thanks to `@kxk302 <https://github.com/kxk302>`__).
`Pull Request 10504`_
* Modified list-of-pairs to copy datasets as hidden
(thanks to `@assuntad23 <https://github.com/assuntad23>`__).
`Pull Request 10508`_
* Fix search info popup to become hidden on click away
(thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
`Pull Request 10512`_
* Disable upload option in default data dialog since history panel is not always available
`Pull Request 10533`_
* Fix ``ObjectUploadTarget`` handling in tool util staging code.
`Pull Request 10650`_
* Fix link to job config sample in docs
(thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
`Pull Request 10673`_
* Produce a clean list of dataset instances if not datasets in collection.
`Pull Request 10676`_
* Add ``refresh_time`` to iRODS configuration, so that connections older than refresh_time are re-created.
(thanks to `@kxk302 <https://github.com/kxk302>`__).
`Pull Request 10698`_
* Fix typo in filter_failed_collection help section
`Pull Request 10717`_
* Cleanup announce samples.
`Pull Request 10762`_
* Fix admin job configuration example links
(thanks to `@RichardJActon <https://github.com/RichardJActon>`__).
`Pull Request 10771`_
* Fix collectl plugin for Python 3.
`Pull Request 10775`_
* Improve update handling for switches, use es6 and listento functions.
`Pull Request 10785`_
* Fix list of cached Docker images not getting updated.
`Pull Request 10796`_
* Small fixes to history panel.
`Pull Request 10802`_
* Fix vue-unit test in toolsview.test.js
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 10812`_
* Various bugfixes for reloading the toolbox.
`Pull Request 10818`_
* Cast ``ncores`` to str for ``subprocess.call()``
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 10825`_
* Test cases and fix for config option ``new_user_dataset_access_role_default_private``.
`Pull Request 10834`_
* Fix label verifier in Github Maintenance Bot
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 10836`_
* Move new config files samples to `lib/galaxy/config/sample/`
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 10842`_
* Fix mulled unit test.
`Pull Request 10857`_
* Fixes to Github action for building documentation
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 10866`_
* Import `Mapping` from `collection.abc`
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 10872`_
* Update lxml for CVE-2020-27783
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 10882`_
* Update ``Makefile`` target and verbiage for Jest.
`Pull Request 10910`_
* Allow YAML list format for config options.
`Pull Request 10945`_
* Bump tensorflow Python dependency from 2.3.1 to 2.4.0.
`Pull Request 10946`_
* Added handler for history options menu webhook
(thanks to `@kjetilkl <https://github.com/kjetilkl>`__).
`Pull Request 10949`_
* Various documentation fixes
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 10963`_
* Fix tool validation for empty files in certain scenarios.
`Pull Request 10981`_
* Overwrite uwsgi default py-call-osafterfork.
`Pull Request 10983`_
* Small improvements to package structure to try to get ``galaxy-app`` closer to working.
`Pull Request 11010`_
* Fix change feed.
`Pull Request 11018`_
* Pass ``job`` to ``setup_external_metadata()`` in ``SetMetadataToolAction.execute_via_app()``
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 11031`_
* Document min, max, and optional for data parameters
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 11061`_
* Add empty preferences attribute to BootstrapAdminUser
(thanks to `@simonbray <https://github.com/simonbray>`__).
`Pull Request 11062`_
* Make YAML tool parser parse ``expect_failure``.
`Pull Request 11072`_
* Fix type column in library folder.
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 11093`_
* Fix exporting datasets from library as collection.
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 11623`_, `Pull Request 11625`_
* Fix spurious "Select" button in upload.
`Pull Request 11096`_
* Cleanup a variety of sphinx warnings and update lib structure.
`Pull Request 11097`_, `Pull Request 11103`_
* Don't use copy when serializing JSON in ``safe_dumps``.
`Pull Request 11169`_
* Reduce authnz exception exposure.
`Pull Request 11212`_
* Fix arguments in ``create_api_key``
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 11243`_
* Routing fixes for username path components and username validation fixes.
`Pull Request 11260`_
* Decrease verbosity of urllib connectionpool logging
`Pull Request 11266`_
* Set correct status code in old history route
`Pull Request 11269`_
* Update Python dependency pulsar-galaxy-lib to 0.14.1.
`Pull Request 11279`_
* Use nested state tracking with sqlalchemy-mutable
`Pull Request 11288`_
* Fix /u/username/* routes.
`Pull Request 11289`_
* Raise correct exceptions in `MetadataCollection`
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 11293`_
* Unpin pulsar-galaxy-lib in packages
`Pull Request 11294`_
`Pull Request 11314`_
* Multi-character strings shouldn't be split
(thanks to `@selten <https://github.com/selten>`__).
`Pull Request 11341`_
* Fix command line building when using interpreter
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 11343`_
* Fix job_destination display if job has no destination params yet.
`Pull Request 11354`_
* Only attempt to resolve loc file fallback if path is relative path.
`Pull Request 11361`_
* Fix setCurrentHistoryId in legacy history panel context.
`Pull Request 11369`_
* Fix rule-based screenshots.
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 11389`_
* Fix CircleCI unit tests.
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 11391`_
* Fix interactivetools_proxy_host typo.
(thanks to `@almahmoud <https://github.com/almahmoud>`__).
`Pull Request 11441`_
* Disable tool document cache by default.
`Pull Request 11447`_
* Fix typo in folder search.
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 11463`_
* List most common Galaxy file plugins at the top.
`Pull Request 11491`_
* Fix OIDC logout and redirection.
`Pull Request 11520`_
* Fix markdown tag visualizations.
`Pull Request 11534`_
* Fix unhandled error when creating tags with multiple dots.
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 11535`_
* Allow format attribute in output collections.
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 11536`_
* Fix remote user logout redirect.
`Pull Request 11540`_
* Fix various Rule Builder issues.
`Pull Request 11553`_
* Fix upload button tooltip blocking tool search field.
`Pull Request 11572`_
* Fix name and hid when selecting uploaded datasets.
`Pull Request 11576`_
* Improve feedback for remote file listing exceptions.
`Pull Request 11581`_
.. include:: 21.01_prs.rst
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