Create version 24.0.3

galaxyproject · Jun 28, 2024 · d947481 · d947481
1 parent 8a52443
commit d947481
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diff --git a/lib/galaxy/version.py b/lib/galaxy/version.py
@@ -1,3 +1,3 @@
 VERSION_MAJOR = "24.0"
-VERSION_MINOR = "3.dev0"
+VERSION_MINOR = "3"
 VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else "")
diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst
@@ -3,11 +3,55 @@ History
 
 .. to_doc
 
------------
-24.0.3.dev0
------------
+-------------------
+24.0.3 (2024-06-28)
+-------------------
+
 
+=========
+Bug fixes
+=========
+
+* Raise exception if collection elements missing during download by `@jdavcs <https://github.com/jdavcs>`_ in `#18094 <https://github.com/galaxyproject/galaxy/pull/18094>`_
+* Allow purge query param, deprecate purge body param by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18105 <https://github.com/galaxyproject/galaxy/pull/18105>`_
+* Backport OIDC schema fix by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18111 <https://github.com/galaxyproject/galaxy/pull/18111>`_
+* Don't log exception if cancelled slurm job doesn't have stderr file by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18121 <https://github.com/galaxyproject/galaxy/pull/18121>`_
+* Downgrade missing output file in working directory to warning for failed jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18123 <https://github.com/galaxyproject/galaxy/pull/18123>`_
+* Fix data default values not getting added to history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18132 <https://github.com/galaxyproject/galaxy/pull/18132>`_
+* Drop redundant error message by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18156 <https://github.com/galaxyproject/galaxy/pull/18156>`_
+* Emit warning when user-cancelled job already complete by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18178 <https://github.com/galaxyproject/galaxy/pull/18178>`_
+* Avoid object store path lookup when constructing JobState object by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18190 <https://github.com/galaxyproject/galaxy/pull/18190>`_
+* Add string cast for dbkey / genome_build by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18207 <https://github.com/galaxyproject/galaxy/pull/18207>`_
+* Check dataset state when attempting to acces dataset contents by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18214 <https://github.com/galaxyproject/galaxy/pull/18214>`_
+* Don't set dataset peek for errored jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18231 <https://github.com/galaxyproject/galaxy/pull/18231>`_
+* Raise exception when extracting dataset from collection without datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18249 <https://github.com/galaxyproject/galaxy/pull/18249>`_
+* Skip tests if toolshed, dx.doi not responding by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18250 <https://github.com/galaxyproject/galaxy/pull/18250>`_
+* Don't attempt to download purged datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18278 <https://github.com/galaxyproject/galaxy/pull/18278>`_
+* Check various preconditions in FeatureLocationIndexDataProvider by `@davelopez <https://github.com/davelopez>`_ in `#18283 <https://github.com/galaxyproject/galaxy/pull/18283>`_
+* Don't serialize display application links for deleted datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18307 <https://github.com/galaxyproject/galaxy/pull/18307>`_
+* Downgrade doi fetch error to debug by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18330 <https://github.com/galaxyproject/galaxy/pull/18330>`_
+* Fix authentication error for anonymous users querying jobs by `@davelopez <https://github.com/davelopez>`_ in `#18333 <https://github.com/galaxyproject/galaxy/pull/18333>`_
+* Fix seek in slurm memory check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18338 <https://github.com/galaxyproject/galaxy/pull/18338>`_
+* Do not copy purged outputs to object store by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18342 <https://github.com/galaxyproject/galaxy/pull/18342>`_
+* Kill pulsar job if job stopped on galaxy side by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18348 <https://github.com/galaxyproject/galaxy/pull/18348>`_
+* Allow DCE as outer input to to_cwl by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18349 <https://github.com/galaxyproject/galaxy/pull/18349>`_
+* Fix anonymous user job retrieval logic by `@davelopez <https://github.com/davelopez>`_ in `#18358 <https://github.com/galaxyproject/galaxy/pull/18358>`_
+* Fix update group API payload model by `@davelopez <https://github.com/davelopez>`_ in `#18374 <https://github.com/galaxyproject/galaxy/pull/18374>`_
+* Fix user's private role can be missing by `@davelopez <https://github.com/davelopez>`_ in `#18381 <https://github.com/galaxyproject/galaxy/pull/18381>`_
+* Fix null inputs in database operation tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18385 <https://github.com/galaxyproject/galaxy/pull/18385>`_
+* Assign default ``data`` extension on discovered collection output  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18389 <https://github.com/galaxyproject/galaxy/pull/18389>`_
+* Fix ``get_accessible_job`` if called without session by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18400 <https://github.com/galaxyproject/galaxy/pull/18400>`_
+* Fix invocation step_job_summary for new collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18402 <https://github.com/galaxyproject/galaxy/pull/18402>`_
+* Really allow in-range validator for txt by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18411 <https://github.com/galaxyproject/galaxy/pull/18411>`_
+* Fix collection map over status for dragged collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18416 <https://github.com/galaxyproject/galaxy/pull/18416>`_
+* Serialize purged flag for datasets in collections by `@davelopez <https://github.com/davelopez>`_ in `#18420 <https://github.com/galaxyproject/galaxy/pull/18420>`_
+
+=============
+Other changes
+=============
 
+* Minor linting cleanup by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18421 <https://github.com/galaxyproject/galaxy/pull/18421>`_
+* Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18428 <https://github.com/galaxyproject/galaxy/pull/18428>`_
 
 -------------------
 24.0.2 (2024-05-07)

diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg
@@ -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 = 24.0.3.dev0
+version = 24.0.3
 
 [options]
 include_package_data = True

diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst
@@ -3,11 +3,11 @@ History
 
 .. to_doc
 
------------
-24.0.3.dev0
------------
-
+-------------------
+24.0.3 (2024-06-28)
+-------------------
 
+No recorded changes since last release
 
 -------------------
 24.0.2 (2024-05-07)

diff --git a/packages/auth/setup.cfg b/packages/auth/setup.cfg
@@ -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 = 24.0.3.dev0
+version = 24.0.3
 
 [options]
 include_package_data = True

diff --git a/packages/config/HISTORY.rst b/packages/config/HISTORY.rst
@@ -3,11 +3,23 @@ History
 
 .. to_doc
 
------------
-24.0.3.dev0
------------
+-------------------
+24.0.3 (2024-06-28)
+-------------------
+
 
+=========
+Bug fixes
+=========
+
+* Backport OIDC schema fix by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18111 <https://github.com/galaxyproject/galaxy/pull/18111>`_
+* Minor fix to enable external hgweb process by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18256 <https://github.com/galaxyproject/galaxy/pull/18256>`_
+
+=============
+Other changes
+=============
 
+* Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18428 <https://github.com/galaxyproject/galaxy/pull/18428>`_
 
 -------------------
 24.0.2 (2024-05-07)

diff --git a/packages/config/setup.cfg b/packages/config/setup.cfg
@@ -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 = 24.0.3.dev0
+version = 24.0.3
 
 [options]
 include_package_data = True

diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst
@@ -3,11 +3,30 @@ History
 
 .. to_doc
 
------------
-24.0.3.dev0
------------
+-------------------
+24.0.3 (2024-06-28)
+-------------------
+
 
+=========
+Bug fixes
+=========
+
+* Downgrade count lines error to warning by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18175 <https://github.com/galaxyproject/galaxy/pull/18175>`_
+* Don't set dataset peek for errored jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18231 <https://github.com/galaxyproject/galaxy/pull/18231>`_
+* Transparently open compressed files in DatasetDataProvider by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18248 <https://github.com/galaxyproject/galaxy/pull/18248>`_
+* Raise exception when extracting dataset from collection without datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18249 <https://github.com/galaxyproject/galaxy/pull/18249>`_
+* Set page importable to false when serializing by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18263 <https://github.com/galaxyproject/galaxy/pull/18263>`_
+* Fix first_dataset_element type hint by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18284 <https://github.com/galaxyproject/galaxy/pull/18284>`_
+* Do not copy purged outputs to object store by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18342 <https://github.com/galaxyproject/galaxy/pull/18342>`_
+* Fix user's private role can be missing by `@davelopez <https://github.com/davelopez>`_ in `#18381 <https://github.com/galaxyproject/galaxy/pull/18381>`_
+* Assign default ``data`` extension on discovered collection output  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18389 <https://github.com/galaxyproject/galaxy/pull/18389>`_
+
+=============
+Other changes
+=============
 
+* Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18428 <https://github.com/galaxyproject/galaxy/pull/18428>`_
 
 -------------------
 24.0.2 (2024-05-07)

diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg
@@ -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 = 24.0.3.dev0
+version = 24.0.3
 
 [options]
 include_package_data = True

diff --git a/packages/files/HISTORY.rst b/packages/files/HISTORY.rst
@@ -3,11 +3,20 @@ History
 
 .. to_doc
 
------------
-24.0.3.dev0
------------
+-------------------
+24.0.3 (2024-06-28)
+-------------------
+
 
+=========
+Bug fixes
+=========
 
+* Fix listing possibly untitled records in Invenio Plugin by `@davelopez <https://github.com/davelopez>`_ in `#18130 <https://github.com/galaxyproject/galaxy/pull/18130>`_
+* Raise ``RequestParameterInvalidException`` when url is invalid by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18155 <https://github.com/galaxyproject/galaxy/pull/18155>`_
+* Fix error message when accessing restricted Zenodo records by `@davelopez <https://github.com/davelopez>`_ in `#18169 <https://github.com/galaxyproject/galaxy/pull/18169>`_
+* Raise ``RequestParameterInvalidException`` if url can't be verified by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18230 <https://github.com/galaxyproject/galaxy/pull/18230>`_
+* Fix Invenio credentials handling by `@davelopez <https://github.com/davelopez>`_ in `#18255 <https://github.com/galaxyproject/galaxy/pull/18255>`_
 
 -------------------
 24.0.2 (2024-05-07)

diff --git a/packages/files/setup.cfg b/packages/files/setup.cfg
@@ -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 = 24.0.3.dev0
+version = 24.0.3
 
 [options]
 include_package_data = True

diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst
@@ -3,11 +3,20 @@ History
 
 .. to_doc
 
------------
-24.0.3.dev0
------------
+-------------------
+24.0.3 (2024-06-28)
+-------------------
+
 
+=========
+Bug fixes
+=========
 
+* Include traceback when logging email PJA exception by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18122 <https://github.com/galaxyproject/galaxy/pull/18122>`_
+* Don't commit in ``DeleteIntermediatesAction`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18131 <https://github.com/galaxyproject/galaxy/pull/18131>`_
+* Don't fail metadata if we only have an extra output files dir by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18179 <https://github.com/galaxyproject/galaxy/pull/18179>`_
+* Don't set dataset peek for errored jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18231 <https://github.com/galaxyproject/galaxy/pull/18231>`_
+* Do not copy purged outputs to object store by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18342 <https://github.com/galaxyproject/galaxy/pull/18342>`_
 
 -------------------
 24.0.2 (2024-05-07)

diff --git a/packages/job_execution/setup.cfg b/packages/job_execution/setup.cfg
@@ -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 = 24.0.3.dev0
+version = 24.0.3
 
 [options]
 include_package_data = True

diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst
@@ -3,11 +3,11 @@ History
 
 .. to_doc
 
------------
-24.0.3.dev0
------------
-
+-------------------
+24.0.3 (2024-06-28)
+-------------------
 
+No recorded changes since last release
 
 -------------------
 24.0.2 (2024-05-07)

diff --git a/packages/job_metrics/setup.cfg b/packages/job_metrics/setup.cfg
@@ -28,7 +28,7 @@ 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 = 24.0.3.dev0
+version = 24.0.3
 
 [options]
 include_package_data = True

diff --git a/packages/navigation/HISTORY.rst b/packages/navigation/HISTORY.rst
@@ -3,11 +3,11 @@ History
 
 .. to_doc
 
------------
-24.0.3.dev0
------------
-
+-------------------
+24.0.3 (2024-06-28)
+-------------------
 
+No recorded changes since last release
 
 -------------------
 24.0.2 (2024-05-07)

diff --git a/packages/navigation/setup.cfg b/packages/navigation/setup.cfg
@@ -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 = 24.0.3.dev0
+version = 24.0.3
 
 [options]
 include_package_data = True

diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst
@@ -3,11 +3,18 @@ History
 
 .. to_doc
 
------------
-24.0.3.dev0
------------
+-------------------
+24.0.3 (2024-06-28)
+-------------------
+
 
+=========
+Bug fixes
+=========
 
+* Include stack when reporting delete error by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18208 <https://github.com/galaxyproject/galaxy/pull/18208>`_
+* Only log error if deleting directory really failed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18236 <https://github.com/galaxyproject/galaxy/pull/18236>`_
+* Do not copy purged outputs to object store by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18342 <https://github.com/galaxyproject/galaxy/pull/18342>`_
 
 -------------------
 24.0.2 (2024-05-07)

diff --git a/packages/objectstore/setup.cfg b/packages/objectstore/setup.cfg
@@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-objectstore
 url = https://github.com/galaxyproject/galaxy
-version = 24.0.3.dev0
+version = 24.0.3
 
 [options]
 include_package_data = True

diff --git a/packages/schema/HISTORY.rst b/packages/schema/HISTORY.rst
@@ -3,11 +3,21 @@ History
 
 .. to_doc
 
------------
-24.0.3.dev0
------------
+-------------------
+24.0.3 (2024-06-28)
+-------------------
+
 
+=========
+Bug fixes
+=========
 
+* do not expand datasets that are known to be inaccessible by `@martenson <https://github.com/martenson>`_ in `#17818 <https://github.com/galaxyproject/galaxy/pull/17818>`_
+* Allow purge query param, deprecate purge body param by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18105 <https://github.com/galaxyproject/galaxy/pull/18105>`_
+* Fix deprecated `deprecated` argument by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18119 <https://github.com/galaxyproject/galaxy/pull/18119>`_
+* Fix users API serialization when listing users by `@davelopez <https://github.com/davelopez>`_ in `#18329 <https://github.com/galaxyproject/galaxy/pull/18329>`_
+* Fix update group API payload model by `@davelopez <https://github.com/davelopez>`_ in `#18374 <https://github.com/galaxyproject/galaxy/pull/18374>`_
+* Serialize purged flag for datasets in collections by `@davelopez <https://github.com/davelopez>`_ in `#18420 <https://github.com/galaxyproject/galaxy/pull/18420>`_
 
 -------------------
 24.0.2 (2024-05-07)

diff --git a/packages/schema/setup.cfg b/packages/schema/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-schema
 url = https://github.com/galaxyproject/galaxy
-version = 24.0.3.dev0
+version = 24.0.3
 
 [options]
 include_package_data = True

diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst
@@ -3,11 +3,11 @@ History
 
 .. to_doc
 
------------
-24.0.3.dev0
------------
-
+-------------------
+24.0.3 (2024-06-28)
+-------------------
 
+No recorded changes since last release
 
 -------------------
 24.0.2 (2024-05-07)

diff --git a/packages/selenium/setup.cfg b/packages/selenium/setup.cfg
@@ -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 = 24.0.3.dev0
+version = 24.0.3
 
 [options]
 include_package_data = True