Create version 24.1.3

lib/galaxy/version.py

@@ -1,3 +1,3 @@
 VERSION_MAJOR = "24.1"
-VERSION_MINOR = "3.dev0"
+VERSION_MINOR = "3"
 VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else "")

packages/app/HISTORY.rst

@@ -3,11 +3,68 @@ History
 
 .. to_doc
 
------------
-24.1.3.dev0
------------
+-------------------
+24.1.3 (2024-10-25)
+-------------------
 
 
+=========
+Bug fixes
+=========
+
+* 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>`_
+* Update mercurial to non-yanked 6.7.4 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18434 <https://github.com/galaxyproject/galaxy/pull/18434>`_
+* Fix dropped when_expression on step upgrade by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18446 <https://github.com/galaxyproject/galaxy/pull/18446>`_
+* Improve workflow-related exception reporting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18447 <https://github.com/galaxyproject/galaxy/pull/18447>`_
+* Fix subwofklow tags serialization type by `@arash77 <https://github.com/arash77>`_ in `#18456 <https://github.com/galaxyproject/galaxy/pull/18456>`_
+*  by `@laperlej <https://github.com/laperlej>`_ in `#18459 <https://github.com/galaxyproject/galaxy/pull/18459>`_
+* Add input extra files to `get_input_fnames` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18462 <https://github.com/galaxyproject/galaxy/pull/18462>`_
+* Return generic message for password reset email by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18479 <https://github.com/galaxyproject/galaxy/pull/18479>`_
+* Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18494 <https://github.com/galaxyproject/galaxy/pull/18494>`_
+* Prevent job submission if input collection element is deleted by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18517 <https://github.com/galaxyproject/galaxy/pull/18517>`_
+* Strip unicode null from tool stdio by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18527 <https://github.com/galaxyproject/galaxy/pull/18527>`_
+* Fix map over calculation for runtime inputs  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18535 <https://github.com/galaxyproject/galaxy/pull/18535>`_
+* Fix for not-null in 'column_list' object by `@hujambo-dunia <https://github.com/hujambo-dunia>`_ in `#18553 <https://github.com/galaxyproject/galaxy/pull/18553>`_
+* Also fail ``ensure_dataset_on_disk`` if dataset is in new state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18559 <https://github.com/galaxyproject/galaxy/pull/18559>`_
+* Fix sqlalchemy statement in tooltagmanager reset output by `@dannon <https://github.com/dannon>`_ in `#18591 <https://github.com/galaxyproject/galaxy/pull/18591>`_
+* Set minimum weasyprint version by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18606 <https://github.com/galaxyproject/galaxy/pull/18606>`_
+* Improve relabel identifiers message when number of columns is not 2 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18634 <https://github.com/galaxyproject/galaxy/pull/18634>`_
+* Fix extract workflow from history when implicit collection has no jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18661 <https://github.com/galaxyproject/galaxy/pull/18661>`_
+* Make sure we set file size also for purged outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18681 <https://github.com/galaxyproject/galaxy/pull/18681>`_
+* File source and object store instance api fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18685 <https://github.com/galaxyproject/galaxy/pull/18685>`_
+* Fix change datatype PJA on expression tool data outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18691 <https://github.com/galaxyproject/galaxy/pull/18691>`_
+* Fill in missing help for cross product tools. by `@jmchilton <https://github.com/jmchilton>`_ in `#18698 <https://github.com/galaxyproject/galaxy/pull/18698>`_
+* Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18731 <https://github.com/galaxyproject/galaxy/pull/18731>`_
+* Catch and display exceptions when importing malformatted yaml workflows by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18734 <https://github.com/galaxyproject/galaxy/pull/18734>`_
+* Fix infinitely delayed workflow scheduling if skipped step creates HDCA by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18751 <https://github.com/galaxyproject/galaxy/pull/18751>`_
+* Fix directory get or create logic by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18752 <https://github.com/galaxyproject/galaxy/pull/18752>`_
+* Fix job summary for optional unset job data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18754 <https://github.com/galaxyproject/galaxy/pull/18754>`_
+* Allow to change only the description of a quota by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18775 <https://github.com/galaxyproject/galaxy/pull/18775>`_
+* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
+* Fix unspecified ``oidc_endpoint`` variable overwriting specified ``redirect_url`` by `@bgruening <https://github.com/bgruening>`_ in `#18818 <https://github.com/galaxyproject/galaxy/pull/18818>`_
+* Fix wrong celery_app config on job and workflow handlers by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18819 <https://github.com/galaxyproject/galaxy/pull/18819>`_
+* Fix ``named cursor is not valid anymore`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18825 <https://github.com/galaxyproject/galaxy/pull/18825>`_
+* Tighten TRS url check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18841 <https://github.com/galaxyproject/galaxy/pull/18841>`_
+* Fix Workflow index bookmark filter by `@itisAliRH <https://github.com/itisAliRH>`_ in `#18842 <https://github.com/galaxyproject/galaxy/pull/18842>`_
+* Skip metric collection if job working directory doesn't exist by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18845 <https://github.com/galaxyproject/galaxy/pull/18845>`_
+* Extend on disk checks to running, queued and error states by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18846 <https://github.com/galaxyproject/galaxy/pull/18846>`_
+* Raise MessageException instead of assertions on rerun problems by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18858 <https://github.com/galaxyproject/galaxy/pull/18858>`_
+* Fix data_column ref to nested collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18875 <https://github.com/galaxyproject/galaxy/pull/18875>`_
+* Fix loading very old workflows with data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18876 <https://github.com/galaxyproject/galaxy/pull/18876>`_
+* Access tool data table filters in workflow building mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18900 <https://github.com/galaxyproject/galaxy/pull/18900>`_
+* Fix username used in invocation report by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18932 <https://github.com/galaxyproject/galaxy/pull/18932>`_
+* Disable locking when opening h5 files, add missing ``with`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18976 <https://github.com/galaxyproject/galaxy/pull/18976>`_
+* Fix job search statement building by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19010 <https://github.com/galaxyproject/galaxy/pull/19010>`_
+* Put cached jobs back into queue on handler restart by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19012 <https://github.com/galaxyproject/galaxy/pull/19012>`_
+
+============
+Enhancements
+============
+
+* Include workflow invocation id in exception logs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18594 <https://github.com/galaxyproject/galaxy/pull/18594>`_
+* Implemented the generic OIDC backend from python-social-auth into Gal… by `@Edmontosaurus <https://github.com/Edmontosaurus>`_ in `#18670 <https://github.com/galaxyproject/galaxy/pull/18670>`_
+* Collect job metrics also when job failed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18809 <https://github.com/galaxyproject/galaxy/pull/18809>`_
+* prevent "missing refresh_token" errors by supporting <extra_scopes> also with Keycloak backend by `@ljocha <https://github.com/ljocha>`_ in `#18826 <https://github.com/galaxyproject/galaxy/pull/18826>`_
 
 -------------------
 24.1.2 (2024-09-25)

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 = 24.1.3.dev0
+version = 24.1.3
 
 [options]
 include_package_data = True

packages/auth/HISTORY.rst

@@ -3,11 +3,11 @@ History
 
 .. to_doc
 
------------
-24.1.3.dev0
------------
-
+-------------------
+24.1.3 (2024-10-25)
+-------------------
 
+No recorded changes since last release
 
 -------------------
 24.1.2 (2024-09-25)

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 = 24.1.3.dev0
+version = 24.1.3
 
 [options]
 include_package_data = True

packages/config/HISTORY.rst

@@ -3,11 +3,33 @@ History
 
 .. to_doc
 
------------
-24.1.3.dev0
------------
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
 
+* 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>`_
+* Strip whitespace when listifying admin users by `@jdavcs <https://github.com/jdavcs>`_ in `#18656 <https://github.com/galaxyproject/galaxy/pull/18656>`_
+* Remove defaults channel for conda usage by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18859 <https://github.com/galaxyproject/galaxy/pull/18859>`_
 
+============
+Enhancements
+============
+
+* Make `default_panel_view` a `_by_host` option by `@natefoo <https://github.com/natefoo>`_ in `#18471 <https://github.com/galaxyproject/galaxy/pull/18471>`_
+* More datatype deprecation warnings by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18612 <https://github.com/galaxyproject/galaxy/pull/18612>`_
+* Implemented the generic OIDC backend from python-social-auth into Gal… by `@Edmontosaurus <https://github.com/Edmontosaurus>`_ in `#18670 <https://github.com/galaxyproject/galaxy/pull/18670>`_
+
+=============
+Other changes
+=============
+
+* Backport pod5 datatype by `@TomHarrop <https://github.com/TomHarrop>`_ in `#18507 <https://github.com/galaxyproject/galaxy/pull/18507>`_
+* Backport PR 18630 "Add BlobToolkit to the list of interactive tools" to release_24.1 by `@cat-bro <https://github.com/cat-bro>`_ in `#18784 <https://github.com/galaxyproject/galaxy/pull/18784>`_
 
 -------------------
 24.1.2 (2024-09-25)

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 = 24.1.3.dev0
+version = 24.1.3
 
 [options]
 include_package_data = True

packages/data/HISTORY.rst

@@ -3,11 +3,42 @@ History
 
 .. to_doc
 
------------
-24.1.3.dev0
------------
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* 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>`_
+* Improve workflow-related exception reporting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18447 <https://github.com/galaxyproject/galaxy/pull/18447>`_
+* Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18494 <https://github.com/galaxyproject/galaxy/pull/18494>`_
+* Prevent job submission if input collection element is deleted by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18517 <https://github.com/galaxyproject/galaxy/pull/18517>`_
+* Fix shared caches with extended metadata collection. by `@jmchilton <https://github.com/jmchilton>`_ in `#18520 <https://github.com/galaxyproject/galaxy/pull/18520>`_
+* Also check dataset.deleted when determining if data can be displayed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18547 <https://github.com/galaxyproject/galaxy/pull/18547>`_
+* Fix for not-null in 'column_list' object by `@hujambo-dunia <https://github.com/hujambo-dunia>`_ in `#18553 <https://github.com/galaxyproject/galaxy/pull/18553>`_
+* Fix h5ad metadata by `@nilchia <https://github.com/nilchia>`_ in `#18635 <https://github.com/galaxyproject/galaxy/pull/18635>`_
+* Don't set file size to zero by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18653 <https://github.com/galaxyproject/galaxy/pull/18653>`_
+* Make sure we set file size also for purged outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18681 <https://github.com/galaxyproject/galaxy/pull/18681>`_
+* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
+* Fix copying workflow with subworkflow step for step that you own by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18802 <https://github.com/galaxyproject/galaxy/pull/18802>`_
+* Make pylibmagic import optional by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18813 <https://github.com/galaxyproject/galaxy/pull/18813>`_
+* Ignore converted datasets in invalid input states by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18850 <https://github.com/galaxyproject/galaxy/pull/18850>`_
+* Fix discovered outputs with directory metadata and distributed object by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18855 <https://github.com/galaxyproject/galaxy/pull/18855>`_
+* Raise MessageException instead of assertions on rerun problems by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18858 <https://github.com/galaxyproject/galaxy/pull/18858>`_
+* Fix wrong final state when init_from is used by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18871 <https://github.com/galaxyproject/galaxy/pull/18871>`_
+* Fix history import when parent_hda not serialized by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18873 <https://github.com/galaxyproject/galaxy/pull/18873>`_
+* Limit max number of items in dataproviders by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18881 <https://github.com/galaxyproject/galaxy/pull/18881>`_
+* Allow cors in biom and q2view display applications by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18890 <https://github.com/galaxyproject/galaxy/pull/18890>`_
+* Disable locking when opening h5 files, add missing ``with`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18976 <https://github.com/galaxyproject/galaxy/pull/18976>`_
 
+=============
+Other changes
+=============
 
+* Backport pod5 datatype by `@TomHarrop <https://github.com/TomHarrop>`_ in `#18507 <https://github.com/galaxyproject/galaxy/pull/18507>`_
 
 -------------------
 24.1.2 (2024-09-25)

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 = 24.1.3.dev0
+version = 24.1.3
 
 [options]
 include_package_data = True

packages/files/HISTORY.rst

@@ -3,11 +3,11 @@ History
 
 .. to_doc
 
------------
-24.1.3.dev0
------------
-
+-------------------
+24.1.3 (2024-10-25)
+-------------------
 
+No recorded changes since last release
 
 -------------------
 24.1.2 (2024-09-25)

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 = 24.1.3.dev0
+version = 24.1.3
 
 [options]
 include_package_data = True

packages/job_execution/HISTORY.rst

@@ -3,11 +3,17 @@ History
 
 .. to_doc
 
------------
-24.1.3.dev0
------------
+-------------------
+24.1.3 (2024-10-25)
+-------------------
 
 
+=========
+Bug fixes
+=========
+
+* Add input extra files to `get_input_fnames` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18462 <https://github.com/galaxyproject/galaxy/pull/18462>`_
+* Retry container monitor POST if it fails (don't assume it succeeded) by `@natefoo <https://github.com/natefoo>`_ in `#18863 <https://github.com/galaxyproject/galaxy/pull/18863>`_
 
 -------------------
 24.1.2 (2024-09-25)

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 = 24.1.3.dev0
+version = 24.1.3
 
 [options]
 include_package_data = True

packages/job_metrics/HISTORY.rst

@@ -3,11 +3,11 @@ History
 
 .. to_doc
 
------------
-24.1.3.dev0
------------
-
+-------------------
+24.1.3 (2024-10-25)
+-------------------
 
+No recorded changes since last release
 
 -------------------
 24.1.2 (2024-09-25)

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 = 24.1.3.dev0
+version = 24.1.3
 
 [options]
 include_package_data = True

packages/navigation/HISTORY.rst

@@ -3,11 +3,11 @@ History
 
 .. to_doc
 
------------
-24.1.3.dev0
------------
-
+-------------------
+24.1.3 (2024-10-25)
+-------------------
 
+No recorded changes since last release
 
 -------------------
 24.1.2 (2024-09-25)

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 = 24.1.3.dev0
+version = 24.1.3
 
 [options]
 include_package_data = True

packages/objectstore/HISTORY.rst

@@ -3,11 +3,16 @@ History
 
 .. to_doc
 
------------
-24.1.3.dev0
------------
+-------------------
+24.1.3 (2024-10-25)
+-------------------
 
 
+=========
+Bug fixes
+=========
+
+* Fix shared caches with extended metadata collection. by `@jmchilton <https://github.com/jmchilton>`_ in `#18520 <https://github.com/galaxyproject/galaxy/pull/18520>`_
 
 -------------------
 24.1.2 (2024-09-25)

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 = 24.1.3.dev0
+version = 24.1.3
 
 [options]
 include_package_data = True

packages/schema/HISTORY.rst

@@ -3,11 +3,27 @@ History
 
 .. to_doc
 
------------
-24.1.3.dev0
------------
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Handle error when workflow is unowned in Invocation view by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18730 <https://github.com/galaxyproject/galaxy/pull/18730>`_
+* Fix datatype validation of newly built collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18738 <https://github.com/galaxyproject/galaxy/pull/18738>`_
+* Fix job summary for optional unset job data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18754 <https://github.com/galaxyproject/galaxy/pull/18754>`_
+* Fix ``TypeError`` from Pydantic 2.9.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18788 <https://github.com/galaxyproject/galaxy/pull/18788>`_
+* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
+* Make all fields optional for HelpForumPost by `@davelopez <https://github.com/davelopez>`_ in `#18839 <https://github.com/galaxyproject/galaxy/pull/18839>`_
 
+============
+Enhancements
+============
 
+* Include workflow invocation id in exception logs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18594 <https://github.com/galaxyproject/galaxy/pull/18594>`_
 
 -------------------
 24.1.2 (2024-09-25)

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 = 24.1.3.dev0
+version = 24.1.3
 
 [options]
 include_package_data = True