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Create version 24.2.4

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Nate Coraor
2025-06-17 12:17:16 -04:00
parent e6a3dea50a
commit 7b1e4465bf
47 changed files with 340 additions and 117 deletions
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client/package.json
+1 -1
View File
@@ -1,6 +1,6 @@
{
"name": "@galaxyproject/galaxy-client",
"version": "24.0.0",
"version": "24.2.4",
"description": "Galaxy client application build system",
"keywords": [
"galaxy"
lib/galaxy/version.py
+1 -1
View File
@@ -1,3 +1,3 @@
VERSION_MAJOR = "24.2"
VERSION_MINOR = "4.dev0"
VERSION_MINOR = "4"
VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else "")
package.json
+1 -1
View File
@@ -1,6 +1,6 @@
{
"name": "@galaxyproject/galaxy",
"version": "24.0.0",
"version": "24.2.4",
"description": ".. figure:: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo.jpg :alt: Galaxy Logo",
"main": "index.js",
"scripts": {
packages/app/HISTORY.rst
+30 -3
View File
@@ -3,11 +3,38 @@ History
.. to_doc
-----------
24.2.4.dev0
-----------
-------------------
24.2.4 (2025-06-17)
-------------------
=========
Bug fixes
=========
* Reduce default framework tool test timeout to 60 seconds by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19819 <https://github.com/galaxyproject/galaxy/pull/19819>`_
* Fix various job concurrency limit issues by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19824 <https://github.com/galaxyproject/galaxy/pull/19824>`_
* Handle directories with percents directories with export_remote.xml. by `@jmchilton <https://github.com/jmchilton>`_ in `#19865 <https://github.com/galaxyproject/galaxy/pull/19865>`_
* Fix tabular metadata setting on pulsar with remote metadata by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19891 <https://github.com/galaxyproject/galaxy/pull/19891>`_
* Skip ``data_meta`` filter in run form by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19895 <https://github.com/galaxyproject/galaxy/pull/19895>`_
* Fix duplicate extensions for data inputs by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#19903 <https://github.com/galaxyproject/galaxy/pull/19903>`_
* Skip implicit HDA conversions in DataToolParameter options by `@davelopez <https://github.com/davelopez>`_ in `#19911 <https://github.com/galaxyproject/galaxy/pull/19911>`_
* Better interactive tool entry point query by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19942 <https://github.com/galaxyproject/galaxy/pull/19942>`_
* Drop unnecessary job cache job subquery by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19945 <https://github.com/galaxyproject/galaxy/pull/19945>`_
* Fix attempt restriction on multiple connections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19948 <https://github.com/galaxyproject/galaxy/pull/19948>`_
* Fix various parameter validation issues. by `@jmchilton <https://github.com/jmchilton>`_ in `#19949 <https://github.com/galaxyproject/galaxy/pull/19949>`_
* Sort intersected options by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19953 <https://github.com/galaxyproject/galaxy/pull/19953>`_
* Do not print OIDC access tokens to the logs by `@kysrpex <https://github.com/kysrpex>`_ in `#19966 <https://github.com/galaxyproject/galaxy/pull/19966>`_
* Renew OIDC access tokens using valid refresh tokens by `@kysrpex <https://github.com/kysrpex>`_ in `#19967 <https://github.com/galaxyproject/galaxy/pull/19967>`_
* Add missing job state history entry for queued state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19977 <https://github.com/galaxyproject/galaxy/pull/19977>`_
* Restrict job cache to terminal jobs (and other fixes) by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19978 <https://github.com/galaxyproject/galaxy/pull/19978>`_
* Fix dynamic filter option access when building command line by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19982 <https://github.com/galaxyproject/galaxy/pull/19982>`_
* Renew access tokens from PSA using valid refresh tokens by `@kysrpex <https://github.com/kysrpex>`_ in `#20040 <https://github.com/galaxyproject/galaxy/pull/20040>`_
* Job cache backports by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20078 <https://github.com/galaxyproject/galaxy/pull/20078>`_
* Skip ``param_value`` filter if ref value is runtime value by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20144 <https://github.com/galaxyproject/galaxy/pull/20144>`_
* Fix invocation failure dataset reference by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20200 <https://github.com/galaxyproject/galaxy/pull/20200>`_
* Fall back to name in job summary if no input label given by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20258 <https://github.com/galaxyproject/galaxy/pull/20258>`_
* Skip validation of expression.json input in workflow parameter validator by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20412 <https://github.com/galaxyproject/galaxy/pull/20412>`_
-------------------
24.2.3 (2025-03-16)
packages/app/setup.cfg
+2 -2
View File
@@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-app
url = https://github.com/galaxyproject/galaxy
version = 24.2.4.dev0
version = 24.2.4
[options]
include_package_data = True
@@ -88,4 +88,4 @@ console_scripts =
[options.packages.find]
exclude =
galaxy.tools.bundled*
tests*
tests*
packages/auth/HISTORY.rst
+4 -4
View File
@@ -3,11 +3,11 @@ History
.. to_doc
-----------
24.2.4.dev0
-----------
-------------------
24.2.4 (2025-06-17)
-------------------
No recorded changes since last release
-------------------
24.2.3 (2025-03-16)
packages/auth/setup.cfg
+2 -2
View File
@@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-auth
url = https://github.com/galaxyproject/galaxy
version = 24.2.4.dev0
version = 24.2.4
[options]
include_package_data = True
@@ -40,4 +40,4 @@ python_requires = >=3.8
[options.packages.find]
exclude =
tests*
tests*
packages/config/HISTORY.rst
+8 -3
View File
@@ -3,11 +3,16 @@ History
.. to_doc
-----------
24.2.4.dev0
-----------
-------------------
24.2.4 (2025-06-17)
-------------------
=========
Bug fixes
=========
* Reduce default framework tool test timeout to 60 seconds by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19819 <https://github.com/galaxyproject/galaxy/pull/19819>`_
-------------------
24.2.3 (2025-03-16)
packages/config/setup.cfg
+2 -2
View File
@@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-config
url = https://github.com/galaxyproject/galaxy
version = 24.2.4.dev0
version = 24.2.4
[options]
include_package_data = True
@@ -47,4 +47,4 @@ console_scripts =
[options.packages.find]
exclude =
tests*
tests*
packages/data/HISTORY.rst
+25 -3
View File
@@ -3,11 +3,33 @@ History
.. to_doc
-----------
24.2.4.dev0
-----------
-------------------
24.2.4 (2025-06-17)
-------------------
=========
Bug fixes
=========
* Reduce default framework tool test timeout to 60 seconds by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19819 <https://github.com/galaxyproject/galaxy/pull/19819>`_
* Try to recover from recurring activation link error by `@jdavcs <https://github.com/jdavcs>`_ in `#19844 <https://github.com/galaxyproject/galaxy/pull/19844>`_
* Check if index exists before creating by `@jdavcs <https://github.com/jdavcs>`_ in `#19873 <https://github.com/galaxyproject/galaxy/pull/19873>`_
* Let pysam use extra threads available in job by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19917 <https://github.com/galaxyproject/galaxy/pull/19917>`_
* Handle special charater in raw SQL by `@jdavcs <https://github.com/jdavcs>`_ in `#19925 <https://github.com/galaxyproject/galaxy/pull/19925>`_
* Use ``make_fast_zipfile`` directly by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19947 <https://github.com/galaxyproject/galaxy/pull/19947>`_
* Job cache backports by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20078 <https://github.com/galaxyproject/galaxy/pull/20078>`_
* Conditionally import from `galaxy.config` in `galaxy.model.mapping` if `TYPE_CHECKING` by `@natefoo <https://github.com/natefoo>`_ in `#20209 <https://github.com/galaxyproject/galaxy/pull/20209>`_
* Refactor display_as URL generation for UCSC links and fix to remove double slashes in URL by `@natefoo <https://github.com/natefoo>`_ in `#20239 <https://github.com/galaxyproject/galaxy/pull/20239>`_
* Make response header values strings by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20475 <https://github.com/galaxyproject/galaxy/pull/20475>`_
* Link workflow invocation outputs upon importing invocation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20485 <https://github.com/galaxyproject/galaxy/pull/20485>`_
* Make optional edam-ontology in datatypes registry optional by `@natefoo <https://github.com/natefoo>`_ in `#20492 <https://github.com/galaxyproject/galaxy/pull/20492>`_
============
Enhancements
============
* Bump up max_peek_size to 50MB by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19823 <https://github.com/galaxyproject/galaxy/pull/19823>`_
-------------------
24.2.3 (2025-03-16)
packages/data/setup.cfg
+1 -1
View File
@@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-data
url = https://github.com/galaxyproject/galaxy
version = 24.2.4.dev0
version = 24.2.4
[options]
include_package_data = True
packages/files/HISTORY.rst
+8 -3
View File
@@ -3,11 +3,16 @@ History
.. to_doc
-----------
24.2.4.dev0
-----------
-------------------
24.2.4 (2025-06-17)
-------------------
============
Enhancements
============
* Fix Invenio file source downloads not working with some Invenio instances by `@davelopez <https://github.com/davelopez>`_ in `#19930 <https://github.com/galaxyproject/galaxy/pull/19930>`_
-------------------
24.2.3 (2025-03-16)
packages/files/setup.cfg
+2 -2
View File
@@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-files
url = https://github.com/galaxyproject/galaxy
version = 24.2.4.dev0
version = 24.2.4
[options]
include_package_data = True
@@ -41,4 +41,4 @@ python_requires = >=3.8
[options.packages.find]
exclude =
tests*
tests*
packages/job_execution/HISTORY.rst
+8 -3
View File
@@ -3,11 +3,16 @@ History
.. to_doc
-----------
24.2.4.dev0
-----------
-------------------
24.2.4 (2025-06-17)
-------------------
=========
Bug fixes
=========
* Don't collect unnamed outputs twice in extended metadata mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19868 <https://github.com/galaxyproject/galaxy/pull/19868>`_
-------------------
24.2.3 (2025-03-16)
packages/job_execution/setup.cfg
+2 -2
View File
@@ -28,7 +28,7 @@ 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 = 24.2.4.dev0
version = 24.2.4
[options]
include_package_data = True
@@ -50,4 +50,4 @@ console_scripts =
[options.packages.find]
exclude =
tests*
tests*
packages/job_metrics/HISTORY.rst
+4 -4
View File
@@ -3,11 +3,11 @@ History
.. to_doc
-----------
24.2.4.dev0
-----------
-------------------
24.2.4 (2025-06-17)
-------------------
No recorded changes since last release
-------------------
24.2.3 (2025-03-16)
packages/job_metrics/setup.cfg
+2 -2
View File
@@ -29,7 +29,7 @@ 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 = 24.2.4.dev0
version = 24.2.4
[options]
include_package_data = True
@@ -40,4 +40,4 @@ python_requires = >=3.7
[options.packages.find]
exclude =
tests*
tests*
packages/meta/HISTORY.rst
+86 -4
View File
@@ -3,12 +3,94 @@ History
.. to_doc
-----------
24.2.4.dev0
-----------
-------------------
24.2.4 (2025-06-17)
-------------------
=========
Bug fixes
=========
* Fix #19515 - invalid citation handling changed with 24.2. by `@jmchilton <https://github.com/jmchilton>`_ in `#19716 <https://github.com/galaxyproject/galaxy/pull/19716>`_
* Fix collection builder input states by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19797 <https://github.com/galaxyproject/galaxy/pull/19797>`_
* Reduce default framework tool test timeout to 60 seconds by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19819 <https://github.com/galaxyproject/galaxy/pull/19819>`_
* Backport #19810: Fix workflow param tests not updating param type. by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19820 <https://github.com/galaxyproject/galaxy/pull/19820>`_
* Fix various job concurrency limit issues by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19824 <https://github.com/galaxyproject/galaxy/pull/19824>`_
* Do not reorder options in FormSelect component when multiselect disabled by `@jdavcs <https://github.com/jdavcs>`_ in `#19837 <https://github.com/galaxyproject/galaxy/pull/19837>`_
* Decode/encode FormDirectory paths to allow spaces (and other characters) by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#19841 <https://github.com/galaxyproject/galaxy/pull/19841>`_
* Try to recover from recurring activation link error by `@jdavcs <https://github.com/jdavcs>`_ in `#19844 <https://github.com/galaxyproject/galaxy/pull/19844>`_
* Add spacing between workflow author and invocation count by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#19849 <https://github.com/galaxyproject/galaxy/pull/19849>`_
* Fix default ordering of items sorted by name by `@jdavcs <https://github.com/jdavcs>`_ in `#19853 <https://github.com/galaxyproject/galaxy/pull/19853>`_
* Handle directories with percents directories with export_remote.xml. by `@jmchilton <https://github.com/jmchilton>`_ in `#19865 <https://github.com/galaxyproject/galaxy/pull/19865>`_
* Fix drag and drop for dataset collection elements by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#19866 <https://github.com/galaxyproject/galaxy/pull/19866>`_
* Don't collect unnamed outputs twice in extended metadata mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19868 <https://github.com/galaxyproject/galaxy/pull/19868>`_
* Check if index exists before creating by `@jdavcs <https://github.com/jdavcs>`_ in `#19873 <https://github.com/galaxyproject/galaxy/pull/19873>`_
* Lazy-load invocation step jobs as needed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19877 <https://github.com/galaxyproject/galaxy/pull/19877>`_
* Fix tabular metadata setting on pulsar with remote metadata by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19891 <https://github.com/galaxyproject/galaxy/pull/19891>`_
* Skip ``data_meta`` filter in run form by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19895 <https://github.com/galaxyproject/galaxy/pull/19895>`_
* Drop unused alembic-utils from galaxy-data package requirements by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19896 <https://github.com/galaxyproject/galaxy/pull/19896>`_
* Fix duplicate extensions for data inputs by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#19903 <https://github.com/galaxyproject/galaxy/pull/19903>`_
* Skip implicit HDA conversions in DataToolParameter options by `@davelopez <https://github.com/davelopez>`_ in `#19911 <https://github.com/galaxyproject/galaxy/pull/19911>`_
* Fix duplicate entries when using drag and drop in multiple mode by `@davelopez <https://github.com/davelopez>`_ in `#19913 <https://github.com/galaxyproject/galaxy/pull/19913>`_
* Let pysam use extra threads available in job by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19917 <https://github.com/galaxyproject/galaxy/pull/19917>`_
* Handle special charater in raw SQL by `@jdavcs <https://github.com/jdavcs>`_ in `#19925 <https://github.com/galaxyproject/galaxy/pull/19925>`_
* Report TestCaseValidation as linter error for 24.2 and above by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19928 <https://github.com/galaxyproject/galaxy/pull/19928>`_
* Better interactive tool entry point query by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19942 <https://github.com/galaxyproject/galaxy/pull/19942>`_
* Drop unnecessary job cache job subquery by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19945 <https://github.com/galaxyproject/galaxy/pull/19945>`_
* Use ``make_fast_zipfile`` directly by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19947 <https://github.com/galaxyproject/galaxy/pull/19947>`_
* Fix attempt restriction on multiple connections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19948 <https://github.com/galaxyproject/galaxy/pull/19948>`_
* Fix various parameter validation issues. by `@jmchilton <https://github.com/jmchilton>`_ in `#19949 <https://github.com/galaxyproject/galaxy/pull/19949>`_
* Sort intersected options by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19953 <https://github.com/galaxyproject/galaxy/pull/19953>`_
* Do not print OIDC access tokens to the logs by `@kysrpex <https://github.com/kysrpex>`_ in `#19966 <https://github.com/galaxyproject/galaxy/pull/19966>`_
* Renew OIDC access tokens using valid refresh tokens by `@kysrpex <https://github.com/kysrpex>`_ in `#19967 <https://github.com/galaxyproject/galaxy/pull/19967>`_
* Fix bug in psa-authnz redirect handling by `@dannon <https://github.com/dannon>`_ in `#19968 <https://github.com/galaxyproject/galaxy/pull/19968>`_
* Add missing job state history entry for queued state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19977 <https://github.com/galaxyproject/galaxy/pull/19977>`_
* Restrict job cache to terminal jobs (and other fixes) by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19978 <https://github.com/galaxyproject/galaxy/pull/19978>`_
* Do not display default labels obscuring selectable options in a vue-multiselect component by `@jdavcs <https://github.com/jdavcs>`_ in `#19981 <https://github.com/galaxyproject/galaxy/pull/19981>`_
* Fix dynamic filter option access when building command line by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19982 <https://github.com/galaxyproject/galaxy/pull/19982>`_
* Always set copy_elements to true by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19985 <https://github.com/galaxyproject/galaxy/pull/19985>`_
* ChatGXY Error Handling by `@dannon <https://github.com/dannon>`_ in `#19987 <https://github.com/galaxyproject/galaxy/pull/19987>`_
* Ensure job states are fetched in invocation view by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#20010 <https://github.com/galaxyproject/galaxy/pull/20010>`_
* Renew access tokens from PSA using valid refresh tokens by `@kysrpex <https://github.com/kysrpex>`_ in `#20040 <https://github.com/galaxyproject/galaxy/pull/20040>`_
* Fix edit permission for datasets delete button in storage dashboard overview by location by `@itisAliRH <https://github.com/itisAliRH>`_ in `#20066 <https://github.com/galaxyproject/galaxy/pull/20066>`_
* Job cache backports by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20078 <https://github.com/galaxyproject/galaxy/pull/20078>`_
* Fix `mulled-search --destination quay`, add index reuse by `@natefoo <https://github.com/natefoo>`_ in `#20107 <https://github.com/galaxyproject/galaxy/pull/20107>`_
* Fix edam selenium test by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20134 <https://github.com/galaxyproject/galaxy/pull/20134>`_
* Skip ``param_value`` filter if ref value is runtime value by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20144 <https://github.com/galaxyproject/galaxy/pull/20144>`_
* Fix ``DataCollectionParameterModel`` factory by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20164 <https://github.com/galaxyproject/galaxy/pull/20164>`_
* Fix invocation failure dataset reference by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20200 <https://github.com/galaxyproject/galaxy/pull/20200>`_
* Conditionally import from `galaxy.config` in `galaxy.model.mapping` if `TYPE_CHECKING` by `@natefoo <https://github.com/natefoo>`_ in `#20209 <https://github.com/galaxyproject/galaxy/pull/20209>`_
* Refactor display_as URL generation for UCSC links and fix to remove double slashes in URL by `@natefoo <https://github.com/natefoo>`_ in `#20239 <https://github.com/galaxyproject/galaxy/pull/20239>`_
* Fall back to name in job summary if no input label given by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20258 <https://github.com/galaxyproject/galaxy/pull/20258>`_
* Fix WF Run RO-Crate logo width in Firefox by `@davelopez <https://github.com/davelopez>`_ in `#20305 <https://github.com/galaxyproject/galaxy/pull/20305>`_
* Fix searching roles in admin UI by `@jdavcs <https://github.com/jdavcs>`_ in `#20394 <https://github.com/galaxyproject/galaxy/pull/20394>`_
* Skip validation of expression.json input in workflow parameter validator by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20412 <https://github.com/galaxyproject/galaxy/pull/20412>`_
* Fix unit tests returning values by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20413 <https://github.com/galaxyproject/galaxy/pull/20413>`_
* Fix ``mull_targets()`` with mamba 2.x by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20416 <https://github.com/galaxyproject/galaxy/pull/20416>`_
* Make response header values strings by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20475 <https://github.com/galaxyproject/galaxy/pull/20475>`_
* Fix legacy get_metadata_file controller route by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20477 <https://github.com/galaxyproject/galaxy/pull/20477>`_
* Prevent running datatype autodetect on purged datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20479 <https://github.com/galaxyproject/galaxy/pull/20479>`_
* Link workflow invocation outputs upon importing invocation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20485 <https://github.com/galaxyproject/galaxy/pull/20485>`_
* Make optional edam-ontology in datatypes registry optional by `@natefoo <https://github.com/natefoo>`_ in `#20492 <https://github.com/galaxyproject/galaxy/pull/20492>`_
============
Enhancements
============
* Bump up max_peek_size to 50MB by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19823 <https://github.com/galaxyproject/galaxy/pull/19823>`_
* Point install_requires at requirements.txt file by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19864 <https://github.com/galaxyproject/galaxy/pull/19864>`_
* Fix Invenio file source downloads not working with some Invenio instances by `@davelopez <https://github.com/davelopez>`_ in `#19930 <https://github.com/galaxyproject/galaxy/pull/19930>`_
* Update selectable object stores after adding or editing them by `@davelopez <https://github.com/davelopez>`_ in `#19992 <https://github.com/galaxyproject/galaxy/pull/19992>`_
=============
Other changes
=============
* Backport parts of #19659 by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19805 <https://github.com/galaxyproject/galaxy/pull/19805>`_
* Remove unused client route for standalone wizard interface by `@dannon <https://github.com/dannon>`_ in `#19836 <https://github.com/galaxyproject/galaxy/pull/19836>`_
* Publish pre-built client with (point-)release by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19879 <https://github.com/galaxyproject/galaxy/pull/19879>`_
* Update dev package version in meta package by `@natefoo <https://github.com/natefoo>`_ in `#20159 <https://github.com/galaxyproject/galaxy/pull/20159>`_
-------------------
19.9.0 (2019-11-21)
packages/meta/setup.cfg
+1 -1
View File
@@ -30,7 +30,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy
url = https://github.com/galaxyproject/galaxy
version = 24.2.4.dev0
version = 24.2.4
[options]
include_package_data = True
packages/navigation/HISTORY.rst
+4 -4
View File
@@ -3,11 +3,11 @@ History
.. to_doc
-----------
24.2.4.dev0
-----------
-------------------
24.2.4 (2025-06-17)
-------------------
No recorded changes since last release
-------------------
24.2.3 (2025-03-16)
packages/navigation/setup.cfg
+2 -2
View File
@@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-navigation
url = https://github.com/galaxyproject/galaxy
version = 24.2.4.dev0
version = 24.2.4
[options]
include_package_data = True
@@ -40,4 +40,4 @@ python_requires = >=3.8
[options.packages.find]
exclude =
tests*
tests*
packages/objectstore/HISTORY.rst
+8 -3
View File
@@ -3,11 +3,16 @@ History
.. to_doc
-----------
24.2.4.dev0
-----------
-------------------
24.2.4 (2025-06-17)
-------------------
=========
Bug fixes
=========
* Handle special charater in raw SQL by `@jdavcs <https://github.com/jdavcs>`_ in `#19925 <https://github.com/galaxyproject/galaxy/pull/19925>`_
-------------------
24.2.3 (2025-03-16)
packages/objectstore/setup.cfg
+2 -2
View File
@@ -29,7 +29,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-objectstore
url = https://github.com/galaxyproject/galaxy
version = 24.2.4.dev0
version = 24.2.4
[options]
include_package_data = True
@@ -42,4 +42,4 @@ python_requires = >=3.7
[options.packages.find]
exclude =
tests*
tests*
packages/schema/HISTORY.rst
+8 -3
View File
@@ -3,11 +3,16 @@ History
.. to_doc
-----------
24.2.4.dev0
-----------
-------------------
24.2.4 (2025-06-17)
-------------------
=========
Bug fixes
=========
* ChatGXY Error Handling by `@dannon <https://github.com/dannon>`_ in `#19987 <https://github.com/galaxyproject/galaxy/pull/19987>`_
-------------------
24.2.3 (2025-03-16)
packages/schema/setup.cfg
+2 -2
View File
@@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-schema
url = https://github.com/galaxyproject/galaxy
version = 24.2.4.dev0
version = 24.2.4
[options]
include_package_data = True
@@ -40,4 +40,4 @@ python_requires = >=3.8
[options.packages.find]
exclude =
tests*
tests*
packages/selenium/HISTORY.rst
+8 -3
View File
@@ -3,11 +3,16 @@ History
.. to_doc
-----------
24.2.4.dev0
-----------
-------------------
24.2.4 (2025-06-17)
-------------------
=========
Bug fixes
=========
* Always set copy_elements to true by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19985 <https://github.com/galaxyproject/galaxy/pull/19985>`_
-------------------
24.2.3 (2025-03-16)
packages/selenium/setup.cfg
+2 -2
View File
@@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-selenium
url = https://github.com/galaxyproject/galaxy
version = 24.2.4.dev0
version = 24.2.4
[options]
include_package_data = True
@@ -48,4 +48,4 @@ console_scripts =
[options.packages.find]
exclude =
tests*
tests*
packages/test_api/HISTORY.rst
+11 -3
View File
@@ -3,11 +3,19 @@ History
.. to_doc
-----------
24.2.4.dev0
-----------
-------------------
24.2.4 (2025-06-17)
-------------------
=========
Bug fixes
=========
* Skip ``data_meta`` filter in run form by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19895 <https://github.com/galaxyproject/galaxy/pull/19895>`_
* Restrict job cache to terminal jobs (and other fixes) by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19978 <https://github.com/galaxyproject/galaxy/pull/19978>`_
* Job cache backports by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20078 <https://github.com/galaxyproject/galaxy/pull/20078>`_
* Skip ``param_value`` filter if ref value is runtime value by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20144 <https://github.com/galaxyproject/galaxy/pull/20144>`_
-------------------
24.2.3 (2025-03-16)
packages/test_api/setup.cfg
+2 -2
View File
@@ -28,7 +28,7 @@ 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 = 24.2.4.dev0
version = 24.2.4
[options]
include_package_data = True
@@ -47,4 +47,4 @@ driver =
[options.packages.find]
exclude =
tests*
tests*
packages/test_base/HISTORY.rst
+9 -3
View File
@@ -3,11 +3,17 @@ History
.. to_doc
-----------
24.2.4.dev0
-----------
-------------------
24.2.4 (2025-06-17)
-------------------
=========
Bug fixes
=========
* Restrict job cache to terminal jobs (and other fixes) by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19978 <https://github.com/galaxyproject/galaxy/pull/19978>`_
* Job cache backports by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20078 <https://github.com/galaxyproject/galaxy/pull/20078>`_
-------------------
24.2.3 (2025-03-16)
packages/test_base/setup.cfg
+2 -2
View File
@@ -28,7 +28,7 @@ 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 = 24.2.4.dev0
version = 24.2.4
[options]
include_package_data = True
@@ -46,4 +46,4 @@ python_requires = >=3.8
[options.packages.find]
exclude =
tests*
tests*
packages/test_driver/HISTORY.rst
+8 -3
View File
@@ -3,11 +3,16 @@ History
.. to_doc
-----------
24.2.4.dev0
-----------
-------------------
24.2.4 (2025-06-17)
-------------------
=========
Bug fixes
=========
* Reduce default framework tool test timeout to 60 seconds by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19819 <https://github.com/galaxyproject/galaxy/pull/19819>`_
-------------------
24.2.3 (2025-03-16)
packages/test_driver/setup.cfg
+2 -2
View File
@@ -28,7 +28,7 @@ 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 = 24.2.4.dev0
version = 24.2.4
[options]
include_package_data = True
@@ -46,4 +46,4 @@ python_requires = >=3.8
[options.packages.find]
exclude =
tests*
tests*
packages/tool_shed/HISTORY.rst
+8 -3
View File
@@ -3,11 +3,16 @@ History
.. to_doc
-----------
24.2.4.dev0
-----------
-------------------
24.2.4 (2025-06-17)
-------------------
=========
Bug fixes
=========
* Fix unit tests returning values by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20413 <https://github.com/galaxyproject/galaxy/pull/20413>`_
-------------------
24.2.3 (2025-03-16)
packages/tool_shed/setup.cfg
+2 -2
View File
@@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-tool-shed
url = https://github.com/galaxyproject/galaxy
version = 24.2.4.dev0
version = 24.2.4
[options]
include_package_data = True
@@ -65,4 +65,4 @@ python_requires = >=3.8
[options.packages.find]
exclude =
tests*
tests*
packages/tool_util/HISTORY.rst
+14 -3
View File
@@ -3,11 +3,22 @@ History
.. to_doc
-----------
24.2.4.dev0
-----------
-------------------
24.2.4 (2025-06-17)
-------------------
=========
Bug fixes
=========
* Fix #19515 - invalid citation handling changed with 24.2. by `@jmchilton <https://github.com/jmchilton>`_ in `#19716 <https://github.com/galaxyproject/galaxy/pull/19716>`_
* Drop unused alembic-utils from galaxy-data package requirements by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19896 <https://github.com/galaxyproject/galaxy/pull/19896>`_
* Report TestCaseValidation as linter error for 24.2 and above by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19928 <https://github.com/galaxyproject/galaxy/pull/19928>`_
* Fix various parameter validation issues. by `@jmchilton <https://github.com/jmchilton>`_ in `#19949 <https://github.com/galaxyproject/galaxy/pull/19949>`_
* Fix `mulled-search --destination quay`, add index reuse by `@natefoo <https://github.com/natefoo>`_ in `#20107 <https://github.com/galaxyproject/galaxy/pull/20107>`_
* Fix ``DataCollectionParameterModel`` factory by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20164 <https://github.com/galaxyproject/galaxy/pull/20164>`_
* Fix ``mull_targets()`` with mamba 2.x by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20416 <https://github.com/galaxyproject/galaxy/pull/20416>`_
-------------------
24.2.3 (2025-03-16)
packages/tool_util/setup.cfg
+2 -2
View File
@@ -29,7 +29,7 @@ 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 = 24.2.4.dev0
version = 24.2.4
[options]
include_package_data = True
@@ -78,4 +78,4 @@ extended-assertions =
[options.packages.find]
exclude =
tests*
tests*
packages/tours/HISTORY.rst
+4 -4
View File
@@ -3,11 +3,11 @@ History
.. to_doc
-----------
24.2.4.dev0
-----------
-------------------
24.2.4 (2025-06-17)
-------------------
No recorded changes since last release
-------------------
24.2.3 (2025-03-16)
packages/tours/setup.cfg
+2 -2
View File
@@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-tours
url = https://github.com/galaxyproject/galaxy
version = 24.2.4.dev0
version = 24.2.4
[options]
include_package_data = True
@@ -45,4 +45,4 @@ console_scripts =
[options.packages.find]
exclude =
tests*
tests*
packages/util/HISTORY.rst
+8 -3
View File
@@ -3,11 +3,16 @@ History
.. to_doc
-----------
24.2.4.dev0
-----------
-------------------
24.2.4 (2025-06-17)
-------------------
=========
Bug fixes
=========
* Use ``make_fast_zipfile`` directly by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19947 <https://github.com/galaxyproject/galaxy/pull/19947>`_
-------------------
24.2.3 (2025-03-16)
packages/util/setup.cfg
+2 -2
View File
@@ -29,7 +29,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-util
url = https://github.com/galaxyproject/galaxy
version = 24.2.4.dev0
version = 24.2.4
[options]
include_package_data = True
@@ -63,4 +63,4 @@ config_template =
[options.packages.find]
exclude =
tests*
tests*
packages/web_apps/HISTORY.rst
+20 -3
View File
@@ -3,11 +3,28 @@ History
.. to_doc
-----------
24.2.4.dev0
-----------
-------------------
24.2.4 (2025-06-17)
-------------------
=========
Bug fixes
=========
* Try to recover from recurring activation link error by `@jdavcs <https://github.com/jdavcs>`_ in `#19844 <https://github.com/galaxyproject/galaxy/pull/19844>`_
* Fix bug in psa-authnz redirect handling by `@dannon <https://github.com/dannon>`_ in `#19968 <https://github.com/galaxyproject/galaxy/pull/19968>`_
* ChatGXY Error Handling by `@dannon <https://github.com/dannon>`_ in `#19987 <https://github.com/galaxyproject/galaxy/pull/19987>`_
* Job cache backports by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20078 <https://github.com/galaxyproject/galaxy/pull/20078>`_
* Fix searching roles in admin UI by `@jdavcs <https://github.com/jdavcs>`_ in `#20394 <https://github.com/galaxyproject/galaxy/pull/20394>`_
* Fix legacy get_metadata_file controller route by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20477 <https://github.com/galaxyproject/galaxy/pull/20477>`_
* Prevent running datatype autodetect on purged datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20479 <https://github.com/galaxyproject/galaxy/pull/20479>`_
=============
Other changes
=============
* Remove unused client route for standalone wizard interface by `@dannon <https://github.com/dannon>`_ in `#19836 <https://github.com/galaxyproject/galaxy/pull/19836>`_
-------------------
24.2.3 (2025-03-16)
packages/web_apps/setup.cfg
+2 -2
View File
@@ -28,7 +28,7 @@ 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 = 24.2.4.dev0
version = 24.2.4
[options]
include_package_data = True
@@ -76,4 +76,4 @@ console_scripts =
[options.packages.find]
exclude =
tests*
tool_shed.test*
tool_shed.test*
packages/web_framework/HISTORY.rst
+8 -3
View File
@@ -3,11 +3,16 @@ History
.. to_doc
-----------
24.2.4.dev0
-----------
-------------------
24.2.4 (2025-06-17)
-------------------
=========
Bug fixes
=========
* Fix default ordering of items sorted by name by `@jdavcs <https://github.com/jdavcs>`_ in `#19853 <https://github.com/galaxyproject/galaxy/pull/19853>`_
-------------------
24.2.3 (2025-03-16)
packages/web_framework/setup.cfg
+2 -2
View File
@@ -28,7 +28,7 @@ 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 = 24.2.4.dev0
version = 24.2.4
[options]
include_package_data = True
@@ -49,4 +49,4 @@ python_requires = >=3.8
[options.packages.find]
exclude =
tests*
tests*
packages/web_stack/HISTORY.rst
+4 -4
View File
@@ -3,11 +3,11 @@ History
.. to_doc
-----------
24.2.4.dev0
-----------
-------------------
24.2.4 (2025-06-17)
-------------------
No recorded changes since last release
-------------------
24.2.3 (2025-03-16)
packages/web_stack/setup.cfg
+2 -2
View File
@@ -28,7 +28,7 @@ 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 = 24.2.4.dev0
version = 24.2.4
[options]
include_package_data = True
@@ -41,4 +41,4 @@ python_requires = >=3.8
[options.packages.find]
exclude =
tests*
tests*