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Create version 23.1.3

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This commit is contained in:
mvdbeek
2023-12-01 11:54:43 +01:00
parent 98dc9c9dd3
commit d7cc988979
39 changed files with 166 additions and 94 deletions
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lib/galaxy/version.py
+1 -1
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@@ -1,3 +1,3 @@
VERSION_MAJOR = "23.1"
VERSION_MINOR = "3.dev0"
VERSION_MINOR = "3"
VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else "")
packages/app/HISTORY.rst
+17 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
23.1.3.dev0
-----------
-------------------
23.1.3 (2023-12-01)
-------------------
No recorded changes since last release
-------------------
23.1.2 (2023-11-29)
@@ -42,6 +42,7 @@ Enhancements
Bug fixes
=========
*
* read job_conf directly from `config_dir` instead of computing it again from `config_file` by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#15596 <https://github.com/galaxyproject/galaxy/pull/15596>`_
* Fix some drs handling issues by `@nuwang <https://github.com/nuwang>`_ in `#15777 <https://github.com/galaxyproject/galaxy/pull/15777>`_
* Fix filesource file url support by `@nuwang <https://github.com/nuwang>`_ in `#15794 <https://github.com/galaxyproject/galaxy/pull/15794>`_
@@ -97,6 +98,7 @@ Bug fixes
Enhancements
============
*
* Empower Users to Select Storage Destination by `@jmchilton <https://github.com/jmchilton>`_ in `#14073 <https://github.com/galaxyproject/galaxy/pull/14073>`_
* External Login Flow: Redirect users if account already exists by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#15019 <https://github.com/galaxyproject/galaxy/pull/15019>`_
* Add slack error reporting plugin by `@hexylena <https://github.com/hexylena>`_ in `#15025 <https://github.com/galaxyproject/galaxy/pull/15025>`_
@@ -182,6 +184,7 @@ Other changes
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>`_
@@ -196,6 +199,7 @@ Bug fixes
Enhancements
============
*
*
* Update pulsar client library to 0.15.5 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16701 <https://github.com/galaxyproject/galaxy/pull/16701>`_
@@ -208,6 +212,7 @@ Enhancements
Bug fixes
=========
*
*
*
* Skip installing npm/yarn if available, fix conditional dependency parsing, create virtualenv via conda when conda active by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16403 <https://github.com/galaxyproject/galaxy/pull/16403>`_
@@ -226,6 +231,7 @@ 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>`_
@@ -242,12 +248,14 @@ 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>`_
============
Enhancements
============
*
*
*
* When importing tool data bundles, use the first loc file for the matching table by `@natefoo <https://github.com/natefoo>`_ in `#16247 <https://github.com/galaxyproject/galaxy/pull/16247>`_
@@ -256,6 +264,7 @@ Enhancements
Other changes
=============
*
*
* Forward port of slugify username received from oidc by `@nuwang <https://github.com/nuwang>`_ in `#16271 <https://github.com/galaxyproject/galaxy/pull/16271>`_
@@ -273,6 +282,7 @@ 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>`_
============
@@ -284,6 +294,7 @@ Enhancements
*
*
*
*
* Point release deps fixes and docs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16214 <https://github.com/galaxyproject/galaxy/pull/16214>`_
* Use galaxy-release-util to upload python packages by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16240 <https://github.com/galaxyproject/galaxy/pull/16240>`_
@@ -302,6 +313,7 @@ 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>`_
@@ -330,6 +342,7 @@ Other changes
*
*
*
*
* Startup fix when tool removed between reboot by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16175 <https://github.com/galaxyproject/galaxy/pull/16175>`_
-------------------
packages/app/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-app
url = https://github.com/galaxyproject/galaxy
version = 23.1.3.dev0
version = 23.1.3
[options]
include_package_data = True
packages/auth/HISTORY.rst
+4 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
23.1.3.dev0
-----------
-------------------
23.1.3 (2023-12-01)
-------------------
No recorded changes since last release
-------------------
23.1.2 (2023-11-29)
packages/auth/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-auth
url = https://github.com/galaxyproject/galaxy
version = 23.1.3.dev0
version = 23.1.3
[options]
include_package_data = True
packages/config/HISTORY.rst
+9 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
23.1.3.dev0
-----------
-------------------
23.1.3 (2023-12-01)
-------------------
No recorded changes since last release
-------------------
23.1.2 (2023-11-29)
@@ -36,6 +36,7 @@ Enhancements
Bug fixes
=========
*
* Fix some drs handling issues by `@nuwang <https://github.com/nuwang>`_ in `#15777 <https://github.com/galaxyproject/galaxy/pull/15777>`_
* Improve container resolver documentation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16280 <https://github.com/galaxyproject/galaxy/pull/16280>`_
* Limit tool document cache to tool configs with explicit cache path by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16537 <https://github.com/galaxyproject/galaxy/pull/16537>`_
@@ -46,6 +47,7 @@ Bug fixes
Enhancements
============
*
* External Login Flow: Redirect users if account already exists by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#15019 <https://github.com/galaxyproject/galaxy/pull/15019>`_
* Add slack error reporting plugin by `@hexylena <https://github.com/hexylena>`_ in `#15025 <https://github.com/galaxyproject/galaxy/pull/15025>`_
* Documents use of k8s_extra_job_envs in job_conf sample advanced by `@pcm32 <https://github.com/pcm32>`_ in `#15110 <https://github.com/galaxyproject/galaxy/pull/15110>`_
@@ -89,6 +91,7 @@ No recorded changes since last release
Bug fixes
=========
*
*
* Minor bug fix for default mail templates by `@neoformit <https://github.com/neoformit>`_ in `#16362 <https://github.com/galaxyproject/galaxy/pull/16362>`_
@@ -122,12 +125,14 @@ 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>`_
============
Enhancements
============
*
*
* Add ``ca_certs`` option for sentry client by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15943 <https://github.com/galaxyproject/galaxy/pull/15943>`_
packages/config/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-config
url = https://github.com/galaxyproject/galaxy
version = 23.1.3.dev0
version = 23.1.3
[options]
include_package_data = True
packages/data/HISTORY.rst
+13 -3
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@@ -3,11 +3,16 @@ History
.. to_doc
-----------
23.1.3.dev0
-----------
-------------------
23.1.3 (2023-12-01)
-------------------
=========
Bug fixes
=========
* Add missing optional description field, fixes ephemeris data library example by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17116 <https://github.com/galaxyproject/galaxy/pull/17116>`_
-------------------
23.1.2 (2023-11-29)
@@ -41,6 +46,7 @@ Enhancements
Bug fixes
=========
*
* Fix bad auto-merge of dev. by `@jmchilton <https://github.com/jmchilton>`_ in `#15386 <https://github.com/galaxyproject/galaxy/pull/15386>`_
* Merge conflicting db migration branches into one by `@jdavcs <https://github.com/jdavcs>`_ in `#15771 <https://github.com/galaxyproject/galaxy/pull/15771>`_
* Enable ``strict_equality`` mypy option by `@nsoranzo <https://github.com/nsoranzo>`_ in `#15808 <https://github.com/galaxyproject/galaxy/pull/15808>`_
@@ -71,6 +77,7 @@ Bug fixes
Enhancements
============
*
* Empower Users to Select Storage Destination by `@jmchilton <https://github.com/jmchilton>`_ in `#14073 <https://github.com/galaxyproject/galaxy/pull/14073>`_
* Add Storage Dashboard visualizations for histories by `@davelopez <https://github.com/davelopez>`_ in `#14820 <https://github.com/galaxyproject/galaxy/pull/14820>`_
* Towards decoupling datatypes and model by `@jdavcs <https://github.com/jdavcs>`_ in `#15186 <https://github.com/galaxyproject/galaxy/pull/15186>`_
@@ -129,6 +136,7 @@ Other changes
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>`_
@@ -142,6 +150,7 @@ Bug fixes
Bug fixes
=========
*
*
*
* Copy when_expression when copying workflow step by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16377 <https://github.com/galaxyproject/galaxy/pull/16377>`_
@@ -176,6 +185,7 @@ 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 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>`_
packages/data/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-data
url = https://github.com/galaxyproject/galaxy
version = 23.1.3.dev0
version = 23.1.3
[options]
include_package_data = True
packages/files/HISTORY.rst
+6 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
23.1.3.dev0
-----------
-------------------
23.1.3 (2023-12-01)
-------------------
No recorded changes since last release
-------------------
23.1.2 (2023-11-29)
@@ -29,6 +29,7 @@ Bug fixes
Bug fixes
=========
*
* Fix some drs handling issues by `@nuwang <https://github.com/nuwang>`_ in `#15777 <https://github.com/galaxyproject/galaxy/pull/15777>`_
* Fix filesource file url support by `@nuwang <https://github.com/nuwang>`_ in `#15794 <https://github.com/galaxyproject/galaxy/pull/15794>`_
* Fix unittest mocks to support us checking geturl() by `@dannon <https://github.com/dannon>`_ in `#16726 <https://github.com/galaxyproject/galaxy/pull/16726>`_
@@ -73,6 +74,7 @@ No recorded changes since last release
Bug fixes
=========
*
*
* Fix dropbox import to support newer versions by `@nuwang <https://github.com/nuwang>`_ in `#16239 <https://github.com/galaxyproject/galaxy/pull/16239>`_
packages/files/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-files
url = https://github.com/galaxyproject/galaxy
version = 23.1.3.dev0
version = 23.1.3
[options]
include_package_data = True
packages/job_execution/HISTORY.rst
+6 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
23.1.3.dev0
-----------
-------------------
23.1.3 (2023-12-01)
-------------------
No recorded changes since last release
-------------------
23.1.2 (2023-11-29)
@@ -31,6 +31,7 @@ Bug fixes
Bug fixes
=========
*
* Fix tags ownership by `@davelopez <https://github.com/davelopez>`_ in `#16339 <https://github.com/galaxyproject/galaxy/pull/16339>`_
* Push to object store even if ``set_meta`` fails by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16667 <https://github.com/galaxyproject/galaxy/pull/16667>`_
* Fix metadata setting in extended metadata + outputs_to_working_directory mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16678 <https://github.com/galaxyproject/galaxy/pull/16678>`_
@@ -59,6 +60,7 @@ Enhancements
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>`_
packages/job_execution/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-job-execution
url = https://github.com/galaxyproject/galaxy
version = 23.1.3.dev0
version = 23.1.3
[options]
include_package_data = True
packages/job_metrics/HISTORY.rst
+4 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
23.1.3.dev0
-----------
-------------------
23.1.3 (2023-12-01)
-------------------
No recorded changes since last release
-------------------
23.1.2 (2023-11-29)
packages/job_metrics/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-job-metrics
url = https://github.com/galaxyproject/galaxy
version = 23.1.3.dev0
version = 23.1.3
[options]
include_package_data = True
packages/navigation/HISTORY.rst
+4 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
23.1.3.dev0
-----------
-------------------
23.1.3 (2023-12-01)
-------------------
No recorded changes since last release
-------------------
23.1.2 (2023-11-29)
packages/navigation/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-navigation
url = https://github.com/galaxyproject/galaxy
version = 23.1.3.dev0
version = 23.1.3
[options]
include_package_data = True
packages/objectstore/HISTORY.rst
+5 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
23.1.3.dev0
-----------
-------------------
23.1.3 (2023-12-01)
-------------------
No recorded changes since last release
-------------------
23.1.2 (2023-11-29)
@@ -55,6 +55,7 @@ Other changes
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>`_
packages/objectstore/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-objectstore
url = https://github.com/galaxyproject/galaxy
version = 23.1.3.dev0
version = 23.1.3
[options]
include_package_data = True
packages/selenium/HISTORY.rst
+6 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
23.1.3.dev0
-----------
-------------------
23.1.3 (2023-12-01)
-------------------
No recorded changes since last release
-------------------
23.1.2 (2023-11-29)
@@ -80,6 +80,7 @@ No recorded changes since last release
Enhancements
============
*
*
* Port selenium setup to non-deprecated selenium options by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16215 <https://github.com/galaxyproject/galaxy/pull/16215>`_
@@ -98,6 +99,7 @@ Enhancements
*
*
*
*
* Add support for launching workflows via Tutorial Mode by `@hexylena <https://github.com/hexylena>`_ in `#15684 <https://github.com/galaxyproject/galaxy/pull/15684>`_
-------------------
packages/selenium/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-selenium
url = https://github.com/galaxyproject/galaxy
version = 23.1.3.dev0
version = 23.1.3
[options]
include_package_data = True
packages/test_api/HISTORY.rst
+8 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
23.1.3.dev0
-----------
-------------------
23.1.3 (2023-12-01)
-------------------
No recorded changes since last release
-------------------
23.1.2 (2023-11-29)
@@ -36,6 +36,7 @@ Enhancements
Bug fixes
=========
*
* Ensure session is request-scoped for legacy endpoints by `@jdavcs <https://github.com/jdavcs>`_ in `#16207 <https://github.com/galaxyproject/galaxy/pull/16207>`_
* allow anon access for api/datasets/get_content_as_text by `@martenson <https://github.com/martenson>`_ in `#16226 <https://github.com/galaxyproject/galaxy/pull/16226>`_
* qualify querying for an api-key by `@martenson <https://github.com/martenson>`_ in `#16320 <https://github.com/galaxyproject/galaxy/pull/16320>`_
@@ -57,6 +58,7 @@ Bug fixes
Enhancements
============
*
* Empower Users to Select Storage Destination by `@jmchilton <https://github.com/jmchilton>`_ in `#14073 <https://github.com/galaxyproject/galaxy/pull/14073>`_
* Outline Deployment Tests by `@jmchilton <https://github.com/jmchilton>`_ in `#15420 <https://github.com/galaxyproject/galaxy/pull/15420>`_
* Unify url handling with filesources by `@nuwang <https://github.com/nuwang>`_ in `#15497 <https://github.com/galaxyproject/galaxy/pull/15497>`_
@@ -109,6 +111,7 @@ 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>`_
@@ -120,6 +123,7 @@ Bug fixes
Enhancements
============
*
*
* Add support for launching workflows via Tutorial Mode by `@hexylena <https://github.com/hexylena>`_ in `#15684 <https://github.com/galaxyproject/galaxy/pull/15684>`_
* Allow setting auto_decompress property in staging interface by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16014 <https://github.com/galaxyproject/galaxy/pull/16014>`_
packages/test_api/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-test-api
url = https://github.com/galaxyproject/galaxy
version = 23.1.3.dev0
version = 23.1.3
[options]
include_package_data = True
packages/test_base/HISTORY.rst
+6 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
23.1.3.dev0
-----------
-------------------
23.1.3 (2023-12-01)
-------------------
No recorded changes since last release
-------------------
23.1.2 (2023-11-29)
@@ -29,6 +29,7 @@ Bug fixes
Bug fixes
=========
*
* Ensure session is request-scoped for legacy endpoints by `@jdavcs <https://github.com/jdavcs>`_ in `#16207 <https://github.com/galaxyproject/galaxy/pull/16207>`_
============
@@ -89,6 +90,7 @@ No recorded changes since last release
Bug fixes
=========
*
*
* Ensure history export contains all expected datasets by `@davelopez <https://github.com/davelopez>`_ in `#16013 <https://github.com/galaxyproject/galaxy/pull/16013>`_
* Fix extended metadata file size handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16109 <https://github.com/galaxyproject/galaxy/pull/16109>`_
packages/test_base/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-test-base
url = https://github.com/galaxyproject/galaxy
version = 23.1.3.dev0
version = 23.1.3
[options]
include_package_data = True
packages/test_driver/HISTORY.rst
+5 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
23.1.3.dev0
-----------
-------------------
23.1.3 (2023-12-01)
-------------------
No recorded changes since last release
-------------------
23.1.2 (2023-11-29)
@@ -29,6 +29,7 @@ Bug fixes
Bug fixes
=========
*
* Backport tool mem fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16601 <https://github.com/galaxyproject/galaxy/pull/16601>`_
* Fix allowlist deserialization in file sources by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16729 <https://github.com/galaxyproject/galaxy/pull/16729>`_
packages/test_driver/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-test-driver
url = https://github.com/galaxyproject/galaxy
version = 23.1.3.dev0
version = 23.1.3
[options]
include_package_data = True
packages/tool_util/HISTORY.rst
+13 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
23.1.3.dev0
-----------
-------------------
23.1.3 (2023-12-01)
-------------------
No recorded changes since last release
-------------------
23.1.2 (2023-11-29)
@@ -37,6 +37,7 @@ Enhancements
Bug fixes
=========
*
* Fixes for two framework test tools by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#15483 <https://github.com/galaxyproject/galaxy/pull/15483>`_
* add missing f for f-string by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#15584 <https://github.com/galaxyproject/galaxy/pull/15584>`_
* Fix call to `docker_cached_container_description` by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#15598 <https://github.com/galaxyproject/galaxy/pull/15598>`_
@@ -58,6 +59,7 @@ Bug fixes
Enhancements
============
*
* Decompress history data for testing assertions by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#15085 <https://github.com/galaxyproject/galaxy/pull/15085>`_
* OIDC tokens by `@SergeyYakubov <https://github.com/SergeyYakubov>`_ in `#15300 <https://github.com/galaxyproject/galaxy/pull/15300>`_
* Fix for new style conda packages by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#15446 <https://github.com/galaxyproject/galaxy/pull/15446>`_
@@ -94,6 +96,7 @@ Other changes
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>`_
@@ -107,6 +110,7 @@ Bug fixes
Bug fixes
=========
*
*
*
* Allow duplicate labels in linter if outputs contain filters by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#15933 <https://github.com/galaxyproject/galaxy/pull/15933>`_
@@ -132,6 +136,7 @@ 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>`_
@@ -139,6 +144,7 @@ Bug fixes
Enhancements
============
*
*
* When importing tool data bundles, use the first loc file for the matching table by `@natefoo <https://github.com/natefoo>`_ in `#16247 <https://github.com/galaxyproject/galaxy/pull/16247>`_
@@ -156,6 +162,7 @@ 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>`_
* Allow skipping ``expect_num_outputs`` when ``expect_failure`` is set in tool test by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16237 <https://github.com/galaxyproject/galaxy/pull/16237>`_
@@ -174,6 +181,7 @@ 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>`_
@@ -187,6 +195,7 @@ Enhancements
*
*
*
*
* Allow setting auto_decompress property in staging interface by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16014 <https://github.com/galaxyproject/galaxy/pull/16014>`_
-------------------
packages/tool_util/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-tool-util
url = https://github.com/galaxyproject/galaxy
version = 23.1.3.dev0
version = 23.1.3
[options]
include_package_data = True
packages/tours/HISTORY.rst
+4 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
23.1.3.dev0
-----------
-------------------
23.1.3 (2023-12-01)
-------------------
No recorded changes since last release
-------------------
23.1.2 (2023-11-29)
packages/tours/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-tours
url = https://github.com/galaxyproject/galaxy
version = 23.1.3.dev0
version = 23.1.3
[options]
include_package_data = True
packages/util/HISTORY.rst
+6 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
23.1.3.dev0
-----------
-------------------
23.1.3 (2023-12-01)
-------------------
No recorded changes since last release
-------------------
23.1.2 (2023-11-29)
@@ -43,6 +43,7 @@ Bug fixes
Enhancements
============
*
* Various Tool Shed Cleanup by `@jmchilton <https://github.com/jmchilton>`_ in `#15247 <https://github.com/galaxyproject/galaxy/pull/15247>`_
* Protection against problematic boolean parameters. by `@jmchilton <https://github.com/jmchilton>`_ in `#15493 <https://github.com/galaxyproject/galaxy/pull/15493>`_
* Unify url handling with filesources by `@nuwang <https://github.com/nuwang>`_ in `#15497 <https://github.com/galaxyproject/galaxy/pull/15497>`_
@@ -94,6 +95,7 @@ No recorded changes since last release
Bug fixes
=========
*
*
* Replace httpbin service with pytest-httpserver by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16042 <https://github.com/galaxyproject/galaxy/pull/16042>`_
packages/util/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-util
url = https://github.com/galaxyproject/galaxy
version = 23.1.3.dev0
version = 23.1.3
[options]
include_package_data = True
packages/web_apps/HISTORY.rst
+16 -3
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@@ -3,11 +3,16 @@ History
.. to_doc
-----------
23.1.3.dev0
-----------
-------------------
23.1.3 (2023-12-01)
-------------------
=========
Bug fixes
=========
* Add missing optional description field, fixes ephemeris data library example by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17116 <https://github.com/galaxyproject/galaxy/pull/17116>`_
-------------------
23.1.2 (2023-11-29)
@@ -36,6 +41,7 @@ Enhancements
Bug fixes
=========
*
* Create ToolSuccess route and refactor component by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#15484 <https://github.com/galaxyproject/galaxy/pull/15484>`_
* fix premature return in user API by `@martenson <https://github.com/martenson>`_ in `#15781 <https://github.com/galaxyproject/galaxy/pull/15781>`_
* Ensure session is request-scoped for legacy endpoints by `@jdavcs <https://github.com/jdavcs>`_ in `#16207 <https://github.com/galaxyproject/galaxy/pull/16207>`_
@@ -56,6 +62,7 @@ Bug fixes
Enhancements
============
*
* Empower Users to Select Storage Destination by `@jmchilton <https://github.com/jmchilton>`_ in `#14073 <https://github.com/galaxyproject/galaxy/pull/14073>`_
* Add Storage Dashboard visualizations for histories by `@davelopez <https://github.com/davelopez>`_ in `#14820 <https://github.com/galaxyproject/galaxy/pull/14820>`_
* External Login Flow: Redirect users if account already exists by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#15019 <https://github.com/galaxyproject/galaxy/pull/15019>`_
@@ -113,6 +120,7 @@ Other changes
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>`_
@@ -126,6 +134,7 @@ Bug fixes
Bug fixes
=========
*
*
*
* Fix active step display in workflow editor side panel by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16364 <https://github.com/galaxyproject/galaxy/pull/16364>`_
@@ -142,6 +151,7 @@ Bug fixes
*
*
*
*
* Fix folder access for anonymous user by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16330 <https://github.com/galaxyproject/galaxy/pull/16330>`_
-------------------
@@ -157,12 +167,14 @@ 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>`_
============
Enhancements
============
*
*
* When importing tool data bundles, use the first loc file for the matching table by `@natefoo <https://github.com/natefoo>`_ in `#16247 <https://github.com/galaxyproject/galaxy/pull/16247>`_
@@ -186,6 +198,7 @@ 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>`_
* Various fixes to path prefix handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16033 <https://github.com/galaxyproject/galaxy/pull/16033>`_
* Fix dataype_change not updating HDCA update_time by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16099 <https://github.com/galaxyproject/galaxy/pull/16099>`_
packages/web_apps/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-web-apps
url = https://github.com/galaxyproject/galaxy
version = 23.1.3.dev0
version = 23.1.3
[options]
include_package_data = True
packages/web_framework/HISTORY.rst
+9 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
23.1.3.dev0
-----------
-------------------
23.1.3 (2023-12-01)
-------------------
No recorded changes since last release
-------------------
23.1.2 (2023-11-29)
@@ -35,6 +35,7 @@ Enhancements
Bug fixes
=========
*
* Fix some drs handling issues by `@nuwang <https://github.com/nuwang>`_ in `#15777 <https://github.com/galaxyproject/galaxy/pull/15777>`_
* Ensure session is request-scoped for legacy endpoints by `@jdavcs <https://github.com/jdavcs>`_ in `#16207 <https://github.com/galaxyproject/galaxy/pull/16207>`_
@@ -42,6 +43,7 @@ Bug fixes
Enhancements
============
*
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#15435 <https://github.com/galaxyproject/galaxy/pull/15435>`_
* Don't error on missing parameters or unused parameters in UI controllers by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16246 <https://github.com/galaxyproject/galaxy/pull/16246>`_
@@ -54,6 +56,7 @@ Enhancements
Bug fixes
=========
*
*
* Don't read request body into memory by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16585 <https://github.com/galaxyproject/galaxy/pull/16585>`_
@@ -66,6 +69,7 @@ Bug fixes
Bug fixes
=========
*
*
*
* Media player fix issue 16415 by `@bdwheele <https://github.com/bdwheele>`_ in `#16443 <https://github.com/galaxyproject/galaxy/pull/16443>`_
@@ -101,6 +105,7 @@ Bug fixes
*
*
*
*
* Various fixes to path prefix handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16033 <https://github.com/galaxyproject/galaxy/pull/16033>`_
-------------------
packages/web_framework/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-web-framework
url = https://github.com/galaxyproject/galaxy
version = 23.1.3.dev0
version = 23.1.3
[options]
include_package_data = True
packages/web_stack/HISTORY.rst
+5 -4
View File
@@ -3,11 +3,11 @@ History
.. to_doc
-----------
23.1.3.dev0
-----------
-------------------
23.1.3 (2023-12-01)
-------------------
No recorded changes since last release
-------------------
23.1.2 (2023-11-29)
@@ -55,6 +55,7 @@ No recorded changes since last release
Bug fixes
=========
*
*
* Don't attempt to call a bool when using mem-self handler assignment. by `@natefoo <https://github.com/natefoo>`_ in `#16359 <https://github.com/galaxyproject/galaxy/pull/16359>`_
packages/web_stack/setup.cfg
+1 -1
View File
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-web-stack
url = https://github.com/galaxyproject/galaxy
version = 23.1.3.dev0
version = 23.1.3
[options]
include_package_data = True