Merge branch 'release_23.1' into dev

# Conflicts: # packages/app/HISTORY.rst # packages/auth/HISTORY.rst # packages/config/HISTORY.rst # packages/data/HISTORY.rst # packages/files/HISTORY.rst # packages/job_execution/HISTORY.rst # packages/job_metrics/HISTORY.rst # packages/navigation/HISTORY.rst # packages/objectstore/HISTORY.rst # packages/selenium/HISTORY.rst # packages/test_api/HISTORY.rst # packages/test_base/HISTORY.rst # packages/test_driver/HISTORY.rst # packages/tool_util/HISTORY.rst # packages/tours/HISTORY.rst # packages/util/HISTORY.rst # packages/web_apps/HISTORY.rst # packages/web_framework/HISTORY.rst # packages/web_stack/HISTORY.rst
bgruening · Oct 23, 2023 · 5e2d094 · 5e2d094
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diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst
@@ -9,6 +9,30 @@ History
 
 
 
+-------------------
+23.0.6 (2023-10-23)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix upload paramfile handling (for real user setups) by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16504 <https://github.com/galaxyproject/galaxy/pull/16504>`_
+* Fix extra files path handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16541 <https://github.com/galaxyproject/galaxy/pull/16541>`_
+* Make sure job_wrapper uses a consistent metadata strategy by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16569 <https://github.com/galaxyproject/galaxy/pull/16569>`_
+* Fix conditional step evaluation with datasets in repeats by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16584 <https://github.com/galaxyproject/galaxy/pull/16584>`_
+* Don't read request body into memory by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16585 <https://github.com/galaxyproject/galaxy/pull/16585>`_
+* Fixes for extra files handling and cached object stores  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16595 <https://github.com/galaxyproject/galaxy/pull/16595>`_
+* Lazy load tool data tables in celery worker by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16640 <https://github.com/galaxyproject/galaxy/pull/16640>`_
+* Force `__DUPLICATE_FILE_TO_COLLECTION__` 'size' param to integer by `@simonbray <https://github.com/simonbray>`_ in `#16659 <https://github.com/galaxyproject/galaxy/pull/16659>`_
+
+============
+Enhancements
+============
+
+* Update pulsar client library to 0.15.5 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16701 <https://github.com/galaxyproject/galaxy/pull/16701>`_
+
 -------------------
 23.0.5 (2023-07-29)
 -------------------
@@ -31,6 +55,7 @@ Bug fixes
 Bug fixes
 =========
 
+* 
 * Fix default when statement evaluation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16332 <https://github.com/galaxyproject/galaxy/pull/16332>`_
 * Redact private role name and description when purging user by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16349 <https://github.com/galaxyproject/galaxy/pull/16349>`_
 
@@ -43,6 +68,7 @@ Bug fixes
 Bug fixes
 =========
 
+* 
 * 
 * Bump galaxy-release-util version to 0.1.2 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16241 <https://github.com/galaxyproject/galaxy/pull/16241>`_
 
@@ -67,6 +93,7 @@ Other changes
 Bug fixes
 =========
 
+* 
 * 
 * 
 * Fix ``Text File Busy`` errors at the source by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16212 <https://github.com/galaxyproject/galaxy/pull/16212>`_
@@ -75,6 +102,7 @@ Bug fixes
 Enhancements
 ============
 
+* 
 * 
 * 
 * Point release deps fixes and docs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16214 <https://github.com/galaxyproject/galaxy/pull/16214>`_
@@ -92,6 +120,7 @@ Bug fixes
 * 
 * 
 * 
+* 
 * Display DCE in job parameter component, allow rerunning with DCE input by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15744 <https://github.com/galaxyproject/galaxy/pull/15744>`_
 * Fix mixed outputs_to_working_directory pulsar destinations by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15927 <https://github.com/galaxyproject/galaxy/pull/15927>`_
 * Update Gravity to 1.0.3 by `@natefoo <https://github.com/natefoo>`_ in `#15939 <https://github.com/galaxyproject/galaxy/pull/15939>`_
@@ -115,6 +144,7 @@ Bug fixes
 Other changes
 =============
 
+* 
 * 
 * 
 * Startup fix when tool removed between reboot by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16175 <https://github.com/galaxyproject/galaxy/pull/16175>`_

diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst
@@ -9,6 +9,12 @@ History
 
 
 
+-------------------
+23.0.6 (2023-10-23)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 23.0.5 (2023-07-29)
 -------------------

diff --git a/packages/config/HISTORY.rst b/packages/config/HISTORY.rst
@@ -9,6 +9,12 @@ History
 
 
 
+-------------------
+23.0.6 (2023-10-23)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 23.0.5 (2023-07-29)
 -------------------
@@ -47,6 +53,7 @@ No recorded changes since last release
 Bug fixes
 =========
 
+* 
 * Change default watchdog inotify_buffer log level to info by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15967 <https://github.com/galaxyproject/galaxy/pull/15967>`_
 
 ============

diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst
@@ -9,6 +9,18 @@ History
 
 
 
+-------------------
+23.0.6 (2023-10-23)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix extra files path handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16541 <https://github.com/galaxyproject/galaxy/pull/16541>`_
+* Don't fail invocation message without dependent_workflow_step_id by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16628 <https://github.com/galaxyproject/galaxy/pull/16628>`_
+
 -------------------
 23.0.5 (2023-07-29)
 -------------------
@@ -47,6 +59,7 @@ No recorded changes since last release
 Bug fixes
 =========
 
+* 
 * Display DCE in job parameter component, allow rerunning with DCE input by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15744 <https://github.com/galaxyproject/galaxy/pull/15744>`_
 * Fix folder listing via file browser by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15950 <https://github.com/galaxyproject/galaxy/pull/15950>`_
 * Fix RO-crate invocation export with complex collections by `@davelopez <https://github.com/davelopez>`_ in `#15971 <https://github.com/galaxyproject/galaxy/pull/15971>`_

diff --git a/packages/files/HISTORY.rst b/packages/files/HISTORY.rst
@@ -9,6 +9,12 @@ History
 
 
 
+-------------------
+23.0.6 (2023-10-23)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 23.0.5 (2023-07-29)
 -------------------

diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst
@@ -9,6 +9,19 @@ History
 
 
 
+-------------------
+23.0.6 (2023-10-23)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix extra files path handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16541 <https://github.com/galaxyproject/galaxy/pull/16541>`_
+* Make sure job_wrapper uses a consistent metadata strategy by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16569 <https://github.com/galaxyproject/galaxy/pull/16569>`_
+* Fixes for extra files handling and cached object stores  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16595 <https://github.com/galaxyproject/galaxy/pull/16595>`_
+
 -------------------
 23.0.5 (2023-07-29)
 -------------------

diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst
@@ -9,6 +9,12 @@ History
 
 
 
+-------------------
+23.0.6 (2023-10-23)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 23.0.5 (2023-07-29)
 -------------------

diff --git a/packages/navigation/HISTORY.rst b/packages/navigation/HISTORY.rst
@@ -9,6 +9,12 @@ History
 
 
 
+-------------------
+23.0.6 (2023-10-23)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 23.0.5 (2023-07-29)
 -------------------

diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst
@@ -9,6 +9,18 @@ History
 
 
 
+-------------------
+23.0.6 (2023-10-23)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix extra files path handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16541 <https://github.com/galaxyproject/galaxy/pull/16541>`_
+* Fixes for extra files handling and cached object stores  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16595 <https://github.com/galaxyproject/galaxy/pull/16595>`_
+
 -------------------
 23.0.5 (2023-07-29)
 -------------------

diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst
@@ -9,6 +9,12 @@ History
 
 
 
+-------------------
+23.0.6 (2023-10-23)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 23.0.5 (2023-07-29)
 -------------------
@@ -50,6 +56,7 @@ Enhancements
 * 
 * 
 * 
+* 
 * Add support for launching workflows via Tutorial Mode by `@hexylena <https://github.com/hexylena>`_ in `#15684 <https://github.com/galaxyproject/galaxy/pull/15684>`_
 
 -------------------

diff --git a/packages/test_api/HISTORY.rst b/packages/test_api/HISTORY.rst
@@ -9,6 +9,12 @@ History
 
 
 
+-------------------
+23.0.6 (2023-10-23)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 23.0.5 (2023-07-29)
 -------------------

diff --git a/packages/test_base/HISTORY.rst b/packages/test_base/HISTORY.rst
@@ -9,6 +9,12 @@ History
 
 
 
+-------------------
+23.0.6 (2023-10-23)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 23.0.5 (2023-07-29)
 -------------------

diff --git a/packages/test_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst
@@ -9,6 +9,12 @@ History
 
 
 
+-------------------
+23.0.6 (2023-10-23)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 23.0.5 (2023-07-29)
 -------------------

diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst
@@ -9,6 +9,18 @@ History
 
 
 
+-------------------
+23.0.6 (2023-10-23)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fixes for extra files handling and cached object stores  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16595 <https://github.com/galaxyproject/galaxy/pull/16595>`_
+* Fix create/install commands for conda 23.9.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16831 <https://github.com/galaxyproject/galaxy/pull/16831>`_
+
 -------------------
 23.0.5 (2023-07-29)
 -------------------
@@ -38,6 +50,7 @@ No recorded changes since last release
 Bug fixes
 =========
 
+* 
 * xsd: add missing `sep` attribute for `has_n_columns` by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16262 <https://github.com/galaxyproject/galaxy/pull/16262>`_
 * Missing init prevents models.py being bundled into tool_util by `@nuwang <https://github.com/nuwang>`_ in `#16308 <https://github.com/galaxyproject/galaxy/pull/16308>`_
 
@@ -56,6 +69,7 @@ Enhancements
 Bug fixes
 =========
 
+* 
 * 
 * 
 * Don't fail CWL tool parsing when Cheetah not installed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16219 <https://github.com/galaxyproject/galaxy/pull/16219>`_
@@ -73,6 +87,7 @@ Bug fixes
 * 
 * 
 * 
+* 
 * Fix assertion linting to not fail on byte suffixes by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#15873 <https://github.com/galaxyproject/galaxy/pull/15873>`_
 * Fix ``get_test_from_anaconda()`` and ``base_image_for_targets()`` functions by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16125 <https://github.com/galaxyproject/galaxy/pull/16125>`_
 * Fix test search for mulled container hashes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16170 <https://github.com/galaxyproject/galaxy/pull/16170>`_
@@ -81,6 +96,7 @@ Bug fixes
 Enhancements
 ============
 
+* 
 * 
 * 
 * Allow setting auto_decompress property in staging interface by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16014 <https://github.com/galaxyproject/galaxy/pull/16014>`_

diff --git a/packages/tours/HISTORY.rst b/packages/tours/HISTORY.rst
@@ -9,6 +9,12 @@ History
 
 
 
+-------------------
+23.0.6 (2023-10-23)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 23.0.5 (2023-07-29)
 -------------------

diff --git a/packages/util/HISTORY.rst b/packages/util/HISTORY.rst
@@ -9,6 +9,12 @@ History
 
 
 
+-------------------
+23.0.6 (2023-10-23)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 23.0.5 (2023-07-29)
 -------------------

diff --git a/packages/web_apps/HISTORY.rst b/packages/web_apps/HISTORY.rst
@@ -9,6 +9,18 @@ History
 
 
 
+-------------------
+23.0.6 (2023-10-23)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix incorrect ASGI request host by `@davelopez <https://github.com/davelopez>`_ in `#16574 <https://github.com/galaxyproject/galaxy/pull/16574>`_
+* Allow the legacy DELETE dataset endpoint to accept any string for the history_id by `@assuntad23 <https://github.com/assuntad23>`_ in `#16593 <https://github.com/galaxyproject/galaxy/pull/16593>`_
+
 -------------------
 23.0.5 (2023-07-29)
 -------------------
@@ -29,6 +41,7 @@ Bug fixes
 Bug fixes
 =========
 
+* 
 * Fix folder access for anonymous user by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16330 <https://github.com/galaxyproject/galaxy/pull/16330>`_
 
 -------------------
@@ -40,6 +53,7 @@ Bug fixes
 Bug fixes
 =========
 
+* 
 * 
 * Fix converting Enum value to str for Python 3.11 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16284 <https://github.com/galaxyproject/galaxy/pull/16284>`_
 
@@ -64,6 +78,7 @@ No recorded changes since last release
 Bug fixes
 =========
 
+* 
 * 
 * 
 * Display DCE in job parameter component, allow rerunning with DCE input by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15744 <https://github.com/galaxyproject/galaxy/pull/15744>`_