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More progress on release notes for 21.01.

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John Chilton
2021-02-16 11:44:33 -05:00
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@@ -16,10 +16,13 @@ Enhancements
* Add workflow invocation detail component.
`Pull Request 10976`_
* History panel rewrite (available in the UI as a beta option).
`Pull Request 8441`_
`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
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 10204`_, `Pull Request 11099`_,
@@ -74,7 +77,7 @@ Enhancements
* 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 11027`_, `Pull Request 11039`_
* Allow setting file download filename_pattern by client.
`Pull Request 11108`_
* Add FastAPI migration of licenses endpoints
@@ -83,8 +86,10 @@ Enhancements
* Improvements to workflow imports from GA4GH TRS servers
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 10805`_, `Pull Request 10619`_
* Enhancements for galaxy-tool-test script.
`Pull Request 10620`_, `Pull Request 10779`_
* 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`_
* Speedup xml replacement when loading tools.
`Pull Request 10804`_
* Update askomics interactive tool to 4.1.1
@@ -99,10 +104,6 @@ Enhancements
* Implement expression tool for picking non-null values for CWL-style merging of
conditional branches in native Galaxy workflows.
`Pull Request 10712`_
* Add workflow tests for some newer workflow features.
`Pull Request 10478`_, `Pull Request 10669`_
* wait_for_invocation should take in an assert_ok flag like other wait methods.
`Pull Request 10668`_
* Add and document API for publishing and tagging workflows
(thanks to `@simonbray <https://github.com/simonbray>`__).
`Pull Request 10748`_
@@ -112,7 +113,8 @@ Enhancements
* 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 10769`_, `Pull Request 11036`_, `Pull Request 11042`_,
`Pull Request 11041`_, `Pull Request 10580`_
* Replace StreamBall, replace tarballs with zip
`Pull Request 10919`_
* Simplify JobInformation and DatasetInformation components
@@ -143,14 +145,14 @@ Enhancements
`Pull Request 11078`_
* Implement backend quota interface - with better logic isolation and unit tests.
`Pull Request 10212`_
* When compiling dynamic installation confs, ensure location is actually writeable
* 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
* Display user disk usage in admin user panel.
`Pull Request 10666`_
* Allow TRS servers to not be defined
* 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.
@@ -160,7 +162,7 @@ Enhancements
`Pull Request 11067`
* Allow InteractiveTools to use path-based proxying when ``requires_domain=False``.
`Pull Request 8596`_
* Add warning for non-existing tool version
* Add warning for non-existing tool versions on tool form
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
`Pull Request 10139`_
* Set up confirmation page for new Custos/oidc users.
@@ -206,56 +208,56 @@ Enhancements
`Pull Request 10499`_
* Use dataset selector in rules input dialog.
`Pull Request 10505`_
* Add enumeration restriction to detect_errors
* Add enumeration restriction to ``detect_errors`` in tool XML schema
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 10510`_
* Simpler API for getting user API key.
`Pull Request 10522`_
* Add S3 plugin for remote files browser.
`Pull Request 10523`_
* informative error message on /api/authenticate/baseauth
* 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.
* More comments for rapid testing optional ``galaxy.files`` stuff.
`Pull Request 10526`_
* 'copy to clipboard' button on datasets
* 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
* 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
* Improve performance of copying HDAs and HDCAs.
`Pull Request 10549`_
* Update to new LTS nodejs version
* Update to new LTS nodejs version.
`Pull Request 10565`_
* Document data manager repository layout
(thanks to `@brinkmanlab <https://github.com/brinkmanlab>`__).
(thanks to `@innovate-invent <https://github.com/innovate-invent>`__).
`Pull Request 10573`_
* Set uwsgi's honour-stdin option when in debug mode
* Set uwsgi's honour-stdin option when in debug mode.
`Pull Request 10577`_
* Make extract wf action more visible
* Make primary extract workflow action button more visible
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 10583`_
* pgcleanup can redirect logging to stdout
* 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 `@brinkmanlab <https://github.com/brinkmanlab>`__).
(thanks to `@innovate-invent <https://github.com/innovate-invent>`__).
`Pull Request 10633`_
* Rev cwltool to 3.0.20201109103151
`Pull Request 10658`_
* 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`_
* Migrate API tests to GitHub workflow
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 10674`_
@@ -322,23 +324,17 @@ Enhancements
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 10861`_
* Allow build_list inputs to be optional
(thanks to `@brinkmanlab <https://github.com/brinkmanlab>`__).
(thanks to `@innovate-invent <https://github.com/innovate-invent>`__).
`Pull Request 10863`_
* Report galaxy URL in tool test script, optionally publish history
`Pull Request 10879`_
* Dynamic select parameters: also allow to choose legal options by name
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 10880`_
* More improvements to tool test scripting.
`Pull Request 10908`_
* 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`_
* API support for history import/export from/to galaxy.files plugins
`Pull Request 10993`_
* Check Python typing for galaxy-containers and galaxy-tool-util during CI.
`Pull Request 11000`_
* Update locale.js
@@ -354,44 +350,36 @@ Enhancements
`Pull Request 11030`_
* Remove migration logic that will never be used now.
`Pull Request 11038`_
* More type annotation fixes.
`Pull Request 11039`_
* Support complex markers in `run_tests.sh`
* 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`_
* Revise user experience for history import and export.
`Pull Request 11054`_
* Move framework tests to GitHub workflows + lint test tools
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 11055`_
* add validation for collection parameters
* 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.
* 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`_
* Documentation for Writing Tests
`Pull Request 11088`_
* Update coverage documentation in run_tests.sh
`Pull Request 11102`_
* Make minor improvements, add ToC
`Pull Request 11104`_
* Persist scroll/url information, in chrome, firefox
* Major overhaul and expansion of documentation for writing tests in Galaxy.
`Pull Request 11088`_, `Pull Request 11102`_, `Pull Request 11104`_
* Persist scroll/url information for GTN webhook
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 11290`_
* Improve API test for datatype change
* Improve API test for datatype changing
(thanks to `@simonbray <https://github.com/simonbray>`__).
`Pull Request 10272`_
* Datatypes refactoring
* Various datatype code structure improvements
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 10279`_
* Drop unnecessary list casting in Anndata datatype
* Drop unnecessary list casting in ``Anndata`` datatype.
`Pull Request 10296`_
* Drop unused helpers in web.framework.helpers
* Drop unused helpers in ``web.framework.helpers``
`Pull Request 10345`_
* Drop support for retired Python 3.5
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
@@ -402,48 +390,44 @@ Enhancements
* Typos and semantic fixes for iRODS object store
(thanks to `@trel <https://github.com/trel>`__).
`Pull Request 10423`_
* K8s runner typo: job_destinantion->job_destination
* Fix K8s job runner typo
(thanks to `@almahmoud <https://github.com/almahmoud>`__).
`Pull Request 10501`_
* Drop communication server
* Drop communication server.
`Pull Request 10514`_
* Worfklow typo fix in styling
`Pull Request 10580`_
* Refactor logic for workflow_step.input_type into model.
* Add workflow tests for some newer workflow features.
`Pull Request 10478`_, `Pull Request 10669`_
* Improve helper code ``wait_for_invocation``.
`Pull Request 10668`_
* Refactor logic for ``workflow_step.input_type`` into model.
`Pull Request 10657`_
* Rename flake8 ignorelist
* Rename flake8 ignorelist.
`Pull Request 10702`_
* Refactor more generally useful Selenium code into reusable library code.
`Pull Request 10783`_
* 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.
* Convert ``datasets.set_edit`` to modern decorator, reuse manager.
`Pull Request 10854`_
* Make model somewhat compatible with sqlalchemy-1.4
* 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
* 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
* Use ``email_from`` value from schema for tool error report email.
`Pull Request 10956`_
* Beta History initial load optimization (a.k.a. Added many data providers)
`Pull Request 10971`_
* drop migration hack from htcondor
* Drop migration hack for htcondor
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 10991`_
* Remove unused tag_outputs workflow controller action.
* Remove unused ``tag_outputs`` workflow controller action.
`Pull Request 11040`_
* Drop 'unreachable'-ish showWarnings method in workflow editor.
`Pull Request 11041`_
* Sync vuex to galaxy
`Pull Request 11071`_
* Build FastAPI app in a single location
`Pull Request 11074`_
@@ -496,11 +480,11 @@ Fixes
`Pull Request 11029`_
* Maintain expanded state of JobStep during polling
`Pull Request 11144`_
* Fix tool version switch in workflow editor
* Fix tool version switch in workflow editor.
`Pull Request 11257`_
* Fix populated state for empty collections
* Fix populated state for empty collections.
`Pull Request 11312`_
* Fix Workflow report markdown lost upon renaming the workflow
* Fix Workflow report markdown lost upon renaming the workflow.
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 11317`_
* Bump client axios dependency from 0.19.2 to 0.21.1.