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@dannon
dannon committed Sep 22, 2023
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174 changes: 174 additions & 0 deletions doc/source/releases/23.1.rst
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Expand Up @@ -118,11 +118,23 @@ Enhancements
`Pull Request 16179`_
.. enhancement_tag_workflows
* Include workflow invocations in default activity
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16338`_
* Improve help text for conditional workflow step
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16355`_
* Hide conditionally skipped output
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16356`_
* e2e test for workflow license selector
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 16243`_
.. enhancement_tag_ui
* Disable console instead of dropping
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
`Pull Request 16372`_
* Stricter typescript config
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
`Pull Request 15311`_
Expand Down Expand Up @@ -186,6 +198,15 @@ Enhancements
`Pull Request 16045`_
.. enhancement
* Add message showing console disable/enable, along with instructions o…
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 16401`_
* Add missing archived filter in saved histories
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 16475`_
* Bump bx-python to 0.10.0
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16484`_
* Add Storage Dashboard visualizations for histories
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 14820`_
Expand Down Expand Up @@ -494,6 +515,12 @@ Enhancements
`Pull Request 16473`_
.. small_enhancement
* Filter deleted keys from api_keys relationship
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 16321`_
* Drop expunge_all() call in WebTransactionRequest
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16606`_
* Towards decoupling datatypes and model
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
`Pull Request 15186`_
Expand Down Expand Up @@ -639,6 +666,12 @@ Fixes
.. bug_tag_viz
* H5web updates
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 16509`_
* Update galaxyproject/charts utilizing visualizations
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 16674`_
* Fixes the parcel2 build for hdf5 viz when using node18.
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 16047`_
Expand All @@ -652,11 +685,35 @@ Fixes
`Pull Request 16092`_
.. bug_tag_tools
* Remove render.py script from iSEE
(thanks to `@neoformit <https://github.com/neoformit>`__).
`Pull Request 16616`_
* FileInput no longer accept 'U' in the file mode
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 16704`_
.. bug_tag_workflows
* Fixes for conditional subworkflow steps
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16632`_
* Fix invocation progress bar for skipped and deleted jobs
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16365`_
* Fix workflow invocation detail reactivity
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16369`_
* Fix replacement parameters for subworkflows
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 16592`_
* Backport tool mem fixes
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16601`_
* Fix expression evaluation for nested state
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16656`_
* Push to object store even if ``set_meta`` fails
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16667`_
* Add missing join condition in job search
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16710`_
Expand All @@ -682,6 +739,27 @@ Fixes
`Pull Request 16166`_
.. bug_tag_jobs
* Add missing singularity_no_mount prop parsing
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16367`_
* Job cache fixes for DCEs
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16384`_
* Run through tmp_dir_creation_statement only once
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16529`_
* Ignore errors with user-set job resources
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16579`_
* make sure that TMP, TEMP, and TMPDIR are set
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 16594`_
* Ensure Job belongs to current SA session
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16655`_
* Fix metadata setting in extended metadata + outputs_to_working_directory mode
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16678`_
* Fix closed transaction error on galaxy startup/check jobs
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
`Pull Request 16687`_
Expand All @@ -696,11 +774,107 @@ Fixes
`Pull Request 16096`_
.. bug_tag_admin
* Reload toolbox after forking when using `--preload`
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16620`_
* Improve container resolver documentation
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16280`_
.. bug
* Update 23.1 release tags for migration scripts
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
`Pull Request 16294`_
* Remove pin on ``packaging`` in packages
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 16322`_
* Fix 'news' webhook to account for the RC one more time.
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 16328`_
* Fix disk usage recalculation for distributed object stores
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16380`_
* Fix histories count
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 16400`_
* Fix toolform creator
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 16419`_
* For display (only) allow control+click for new window opening
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 16432`_
* Swap datatype&convert tab to a static 'datatypes' tab.
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 16466`_
* Fix tagging component for anonymous users
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16481`_
* Fix up unit tests for local use
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16483`_
* Fix history item states help display to apply same styling attributes
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 16500`_
* fix font-weight disparity between browsers
(thanks to `@hujambo-dunia <https://github.com/hujambo-dunia>`__).
`Pull Request 16515`_
* Fix for Accessibility, on Workflows List page Tooltip
(thanks to `@hujambo-dunia <https://github.com/hujambo-dunia>`__).
`Pull Request 16520`_
* Fix double-encoding notification content
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16530`_
* Exclude selenium version with broken type hints
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16531`_
* Limit tool document cache to tool configs with explicit cache path
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16537`_
* Fix `multiple` remote test data
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 16542`_
* Don't use ``docker run`` --user flag on OSX
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16573`_
* Fix shared item notification link
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 16581`_
* Make datatype edit default value a string instead of list of strings
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16591`_
* Bump minimum tpv version to 2.3.2
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16597`_
* Optimize getting current user session
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16604`_
* Drop RecursiveMiddleware
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16605`_
* Only reindex tool search once after forking
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16611`_
* Account for expires/expires_in when refreshing token
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16621`_
* Fix nested conditional workflow steps
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16641`_
* Login/Register fixes
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 16652`_
* Make sort_collection tool require terminal datasets
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16661`_
* xsd: allow name attribute of test collections
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 16663`_
* Only show 'edit' on published pages when viewer is the owner.
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 16680`_
* Fix regex validation for global inline flags
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16683`_
* Fix legend not scrollable in storage overview charts
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 16703`_
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9 changes: 9 additions & 0 deletions doc/source/releases/23.1_announce_user.rst
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Expand Up @@ -76,6 +76,12 @@ New Visualizations
===========================================================

.. visualizations
* H5web updates
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 16509`_
* Update galaxyproject/charts utilizing visualizations
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 16674`_
* Add support for visualizing HDF5 datasets
(thanks to `@jarrah42 <https://github.com/jarrah42>`__).
`Pull Request 15394`_
Expand Down Expand Up @@ -149,6 +155,9 @@ Builtin Tool Updates
===========================================================

.. tools
* Remove render.py script from iSEE
(thanks to `@neoformit <https://github.com/neoformit>`__).
`Pull Request 16616`_
* FileInput no longer accept 'U' in the file mode
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 16704`_
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61 changes: 61 additions & 0 deletions doc/source/releases/23.1_prs.rst
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@@ -1,5 +1,66 @@

.. github_links
.. _Pull Request 16632: https://github.com/galaxyproject/galaxy/pull/16632
.. _Pull Request 16294: https://github.com/galaxyproject/galaxy/pull/16294
.. _Pull Request 16299: https://github.com/galaxyproject/galaxy/pull/16299
.. _Pull Request 16321: https://github.com/galaxyproject/galaxy/pull/16321
.. _Pull Request 16322: https://github.com/galaxyproject/galaxy/pull/16322
.. _Pull Request 16328: https://github.com/galaxyproject/galaxy/pull/16328
.. _Pull Request 16338: https://github.com/galaxyproject/galaxy/pull/16338
.. _Pull Request 16355: https://github.com/galaxyproject/galaxy/pull/16355
.. _Pull Request 16356: https://github.com/galaxyproject/galaxy/pull/16356
.. _Pull Request 16365: https://github.com/galaxyproject/galaxy/pull/16365
.. _Pull Request 16367: https://github.com/galaxyproject/galaxy/pull/16367
.. _Pull Request 16369: https://github.com/galaxyproject/galaxy/pull/16369
.. _Pull Request 16372: https://github.com/galaxyproject/galaxy/pull/16372
.. _Pull Request 16380: https://github.com/galaxyproject/galaxy/pull/16380
.. _Pull Request 16384: https://github.com/galaxyproject/galaxy/pull/16384
.. _Pull Request 16400: https://github.com/galaxyproject/galaxy/pull/16400
.. _Pull Request 16401: https://github.com/galaxyproject/galaxy/pull/16401
.. _Pull Request 16419: https://github.com/galaxyproject/galaxy/pull/16419
.. _Pull Request 16432: https://github.com/galaxyproject/galaxy/pull/16432
.. _Pull Request 16465: https://github.com/galaxyproject/galaxy/pull/16465
.. _Pull Request 16466: https://github.com/galaxyproject/galaxy/pull/16466
.. _Pull Request 16475: https://github.com/galaxyproject/galaxy/pull/16475
.. _Pull Request 16481: https://github.com/galaxyproject/galaxy/pull/16481
.. _Pull Request 16483: https://github.com/galaxyproject/galaxy/pull/16483
.. _Pull Request 16484: https://github.com/galaxyproject/galaxy/pull/16484
.. _Pull Request 16500: https://github.com/galaxyproject/galaxy/pull/16500
.. _Pull Request 16509: https://github.com/galaxyproject/galaxy/pull/16509
.. _Pull Request 16515: https://github.com/galaxyproject/galaxy/pull/16515
.. _Pull Request 16520: https://github.com/galaxyproject/galaxy/pull/16520
.. _Pull Request 16529: https://github.com/galaxyproject/galaxy/pull/16529
.. _Pull Request 16530: https://github.com/galaxyproject/galaxy/pull/16530
.. _Pull Request 16531: https://github.com/galaxyproject/galaxy/pull/16531
.. _Pull Request 16533: https://github.com/galaxyproject/galaxy/pull/16533
.. _Pull Request 16537: https://github.com/galaxyproject/galaxy/pull/16537
.. _Pull Request 16542: https://github.com/galaxyproject/galaxy/pull/16542
.. _Pull Request 16573: https://github.com/galaxyproject/galaxy/pull/16573
.. _Pull Request 16579: https://github.com/galaxyproject/galaxy/pull/16579
.. _Pull Request 16581: https://github.com/galaxyproject/galaxy/pull/16581
.. _Pull Request 16591: https://github.com/galaxyproject/galaxy/pull/16591
.. _Pull Request 16592: https://github.com/galaxyproject/galaxy/pull/16592
.. _Pull Request 16594: https://github.com/galaxyproject/galaxy/pull/16594
.. _Pull Request 16597: https://github.com/galaxyproject/galaxy/pull/16597
.. _Pull Request 16601: https://github.com/galaxyproject/galaxy/pull/16601
.. _Pull Request 16604: https://github.com/galaxyproject/galaxy/pull/16604
.. _Pull Request 16605: https://github.com/galaxyproject/galaxy/pull/16605
.. _Pull Request 16606: https://github.com/galaxyproject/galaxy/pull/16606
.. _Pull Request 16611: https://github.com/galaxyproject/galaxy/pull/16611
.. _Pull Request 16616: https://github.com/galaxyproject/galaxy/pull/16616
.. _Pull Request 16620: https://github.com/galaxyproject/galaxy/pull/16620
.. _Pull Request 16621: https://github.com/galaxyproject/galaxy/pull/16621
.. _Pull Request 16641: https://github.com/galaxyproject/galaxy/pull/16641
.. _Pull Request 16652: https://github.com/galaxyproject/galaxy/pull/16652
.. _Pull Request 16655: https://github.com/galaxyproject/galaxy/pull/16655
.. _Pull Request 16656: https://github.com/galaxyproject/galaxy/pull/16656
.. _Pull Request 16661: https://github.com/galaxyproject/galaxy/pull/16661
.. _Pull Request 16663: https://github.com/galaxyproject/galaxy/pull/16663
.. _Pull Request 16667: https://github.com/galaxyproject/galaxy/pull/16667
.. _Pull Request 16674: https://github.com/galaxyproject/galaxy/pull/16674
.. _Pull Request 16678: https://github.com/galaxyproject/galaxy/pull/16678
.. _Pull Request 16680: https://github.com/galaxyproject/galaxy/pull/16680
.. _Pull Request 16683: https://github.com/galaxyproject/galaxy/pull/16683
.. _Pull Request 16687: https://github.com/galaxyproject/galaxy/pull/16687
.. _Pull Request 16703: https://github.com/galaxyproject/galaxy/pull/16703
.. _Pull Request 16704: https://github.com/galaxyproject/galaxy/pull/16704
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