From ab8a645bec15a9ff0baf36bbcd4bebbb51aee5da Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Fri, 22 Sep 2023 09:57:38 -0400 Subject: [PATCH] Remaining PRs reconciled. --- doc/source/releases/23.1.rst | 174 +++++++++++++++++++++ doc/source/releases/23.1_announce_user.rst | 9 ++ doc/source/releases/23.1_prs.rst | 61 ++++++++ 3 files changed, 244 insertions(+) diff --git a/doc/source/releases/23.1.rst b/doc/source/releases/23.1.rst index 7af1f35f933..ea7f4f58923 100644 --- a/doc/source/releases/23.1.rst +++ b/doc/source/releases/23.1.rst @@ -118,11 +118,23 @@ Enhancements `Pull Request 16179`_ .. enhancement_tag_workflows +* Include workflow invocations in default activity + (thanks to `@mvdbeek `__). + `Pull Request 16338`_ +* Improve help text for conditional workflow step + (thanks to `@mvdbeek `__). + `Pull Request 16355`_ +* Hide conditionally skipped output + (thanks to `@mvdbeek `__). + `Pull Request 16356`_ * e2e test for workflow license selector (thanks to `@jmchilton `__). `Pull Request 16243`_ .. enhancement_tag_ui +* Disable console instead of dropping + (thanks to `@ElectronicBlueberry `__). + `Pull Request 16372`_ * Stricter typescript config (thanks to `@ElectronicBlueberry `__). `Pull Request 15311`_ @@ -186,6 +198,15 @@ Enhancements `Pull Request 16045`_ .. enhancement +* Add message showing console disable/enable, along with instructions o… + (thanks to `@dannon `__). + `Pull Request 16401`_ +* Add missing archived filter in saved histories + (thanks to `@davelopez `__). + `Pull Request 16475`_ +* Bump bx-python to 0.10.0 + (thanks to `@mvdbeek `__). + `Pull Request 16484`_ * Add Storage Dashboard visualizations for histories (thanks to `@davelopez `__). `Pull Request 14820`_ @@ -494,6 +515,12 @@ Enhancements `Pull Request 16473`_ .. small_enhancement +* Filter deleted keys from api_keys relationship + (thanks to `@dannon `__). + `Pull Request 16321`_ +* Drop expunge_all() call in WebTransactionRequest + (thanks to `@mvdbeek `__). + `Pull Request 16606`_ * Towards decoupling datatypes and model (thanks to `@jdavcs `__). `Pull Request 15186`_ @@ -639,6 +666,12 @@ Fixes .. bug_tag_viz +* H5web updates + (thanks to `@dannon `__). + `Pull Request 16509`_ +* Update galaxyproject/charts utilizing visualizations + (thanks to `@dannon `__). + `Pull Request 16674`_ * Fixes the parcel2 build for hdf5 viz when using node18. (thanks to `@dannon `__). `Pull Request 16047`_ @@ -652,11 +685,35 @@ Fixes `Pull Request 16092`_ .. bug_tag_tools +* Remove render.py script from iSEE + (thanks to `@neoformit `__). + `Pull Request 16616`_ * FileInput no longer accept 'U' in the file mode (thanks to `@bgruening `__). `Pull Request 16704`_ .. bug_tag_workflows +* Fixes for conditional subworkflow steps + (thanks to `@mvdbeek `__). + `Pull Request 16632`_ +* Fix invocation progress bar for skipped and deleted jobs + (thanks to `@mvdbeek `__). + `Pull Request 16365`_ +* Fix workflow invocation detail reactivity + (thanks to `@mvdbeek `__). + `Pull Request 16369`_ +* Fix replacement parameters for subworkflows + (thanks to `@jmchilton `__). + `Pull Request 16592`_ +* Backport tool mem fixes + (thanks to `@mvdbeek `__). + `Pull Request 16601`_ +* Fix expression evaluation for nested state + (thanks to `@mvdbeek `__). + `Pull Request 16656`_ +* Push to object store even if ``set_meta`` fails + (thanks to `@mvdbeek `__). + `Pull Request 16667`_ * Add missing join condition in job search (thanks to `@mvdbeek `__). `Pull Request 16710`_ @@ -682,6 +739,27 @@ Fixes `Pull Request 16166`_ .. bug_tag_jobs +* Add missing singularity_no_mount prop parsing + (thanks to `@mvdbeek `__). + `Pull Request 16367`_ +* Job cache fixes for DCEs + (thanks to `@mvdbeek `__). + `Pull Request 16384`_ +* Run through tmp_dir_creation_statement only once + (thanks to `@mvdbeek `__). + `Pull Request 16529`_ +* Ignore errors with user-set job resources + (thanks to `@mvdbeek `__). + `Pull Request 16579`_ +* make sure that TMP, TEMP, and TMPDIR are set + (thanks to `@bernt-matthias `__). + `Pull Request 16594`_ +* Ensure Job belongs to current SA session + (thanks to `@mvdbeek `__). + `Pull Request 16655`_ +* Fix metadata setting in extended metadata + outputs_to_working_directory mode + (thanks to `@mvdbeek `__). + `Pull Request 16678`_ * Fix closed transaction error on galaxy startup/check jobs (thanks to `@jdavcs `__). `Pull Request 16687`_ @@ -696,11 +774,107 @@ Fixes `Pull Request 16096`_ .. bug_tag_admin +* Reload toolbox after forking when using `--preload` + (thanks to `@mvdbeek `__). + `Pull Request 16620`_ * Improve container resolver documentation (thanks to `@mvdbeek `__). `Pull Request 16280`_ .. bug +* Update 23.1 release tags for migration scripts + (thanks to `@jdavcs `__). + `Pull Request 16294`_ +* Remove pin on ``packaging`` in packages + (thanks to `@nsoranzo `__). + `Pull Request 16322`_ +* Fix 'news' webhook to account for the RC one more time. + (thanks to `@dannon `__). + `Pull Request 16328`_ +* Fix disk usage recalculation for distributed object stores + (thanks to `@mvdbeek `__). + `Pull Request 16380`_ +* Fix histories count + (thanks to `@davelopez `__). + `Pull Request 16400`_ +* Fix toolform creator + (thanks to `@dannon `__). + `Pull Request 16419`_ +* For display (only) allow control+click for new window opening + (thanks to `@dannon `__). + `Pull Request 16432`_ +* Swap datatype&convert tab to a static 'datatypes' tab. + (thanks to `@dannon `__). + `Pull Request 16466`_ +* Fix tagging component for anonymous users + (thanks to `@mvdbeek `__). + `Pull Request 16481`_ +* Fix up unit tests for local use + (thanks to `@mvdbeek `__). + `Pull Request 16483`_ +* Fix history item states help display to apply same styling attributes + (thanks to `@dannon `__). + `Pull Request 16500`_ +* fix font-weight disparity between browsers + (thanks to `@hujambo-dunia `__). + `Pull Request 16515`_ +* Fix for Accessibility, on Workflows List page Tooltip + (thanks to `@hujambo-dunia `__). + `Pull Request 16520`_ +* Fix double-encoding notification content + (thanks to `@mvdbeek `__). + `Pull Request 16530`_ +* Exclude selenium version with broken type hints + (thanks to `@mvdbeek `__). + `Pull Request 16531`_ +* Limit tool document cache to tool configs with explicit cache path + (thanks to `@mvdbeek `__). + `Pull Request 16537`_ +* Fix `multiple` remote test data + (thanks to `@davelopez `__). + `Pull Request 16542`_ +* Don't use ``docker run`` --user flag on OSX + (thanks to `@mvdbeek `__). + `Pull Request 16573`_ +* Fix shared item notification link + (thanks to `@davelopez `__). + `Pull Request 16581`_ +* Make datatype edit default value a string instead of list of strings + (thanks to `@mvdbeek `__). + `Pull Request 16591`_ +* Bump minimum tpv version to 2.3.2 + (thanks to `@mvdbeek `__). + `Pull Request 16597`_ +* Optimize getting current user session + (thanks to `@mvdbeek `__). + `Pull Request 16604`_ +* Drop RecursiveMiddleware + (thanks to `@mvdbeek `__). + `Pull Request 16605`_ +* Only reindex tool search once after forking + (thanks to `@mvdbeek `__). + `Pull Request 16611`_ +* Account for expires/expires_in when refreshing token + (thanks to `@mvdbeek `__). + `Pull Request 16621`_ +* Fix nested conditional workflow steps + (thanks to `@mvdbeek `__). + `Pull Request 16641`_ +* Login/Register fixes + (thanks to `@dannon `__). + `Pull Request 16652`_ +* Make sort_collection tool require terminal datasets + (thanks to `@mvdbeek `__). + `Pull Request 16661`_ +* xsd: allow name attribute of test collections + (thanks to `@bernt-matthias `__). + `Pull Request 16663`_ +* Only show 'edit' on published pages when viewer is the owner. + (thanks to `@dannon `__). + `Pull Request 16680`_ +* Fix regex validation for global inline flags + (thanks to `@mvdbeek `__). + `Pull Request 16683`_ * Fix legend not scrollable in storage overview charts (thanks to `@davelopez `__). `Pull Request 16703`_ diff --git a/doc/source/releases/23.1_announce_user.rst b/doc/source/releases/23.1_announce_user.rst index 5dea9d96e8b..9b2d66f821d 100644 --- a/doc/source/releases/23.1_announce_user.rst +++ b/doc/source/releases/23.1_announce_user.rst @@ -76,6 +76,12 @@ New Visualizations =========================================================== .. visualizations +* H5web updates + (thanks to `@dannon `__). + `Pull Request 16509`_ +* Update galaxyproject/charts utilizing visualizations + (thanks to `@dannon `__). + `Pull Request 16674`_ * Add support for visualizing HDF5 datasets (thanks to `@jarrah42 `__). `Pull Request 15394`_ @@ -149,6 +155,9 @@ Builtin Tool Updates =========================================================== .. tools +* Remove render.py script from iSEE + (thanks to `@neoformit `__). + `Pull Request 16616`_ * FileInput no longer accept 'U' in the file mode (thanks to `@bgruening `__). `Pull Request 16704`_ diff --git a/doc/source/releases/23.1_prs.rst b/doc/source/releases/23.1_prs.rst index d5ecb20c46c..902a672fa0c 100644 --- a/doc/source/releases/23.1_prs.rst +++ b/doc/source/releases/23.1_prs.rst @@ -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