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Create version 24.1.4
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‎lib/galaxy/version.py

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VERSION_MAJOR = "24.1"
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VERSION_MINOR = "4.dev0"
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VERSION_MINOR = "4"
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VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else "")

‎packages/app/HISTORY.rst

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.. to_doc
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6-
-----------
7-
24.1.4.dev0
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-----------
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-------------------
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24.1.4 (2024-12-11)
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-------------------
9+
10+
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=========
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Bug fixes
13+
=========
14+
15+
* 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>`_
16+
* Update mercurial to non-yanked 6.7.4 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18434 <https://github.com/galaxyproject/galaxy/pull/18434>`_
17+
* Fix dropped when_expression on step upgrade by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18446 <https://github.com/galaxyproject/galaxy/pull/18446>`_
18+
* Improve workflow-related exception reporting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18447 <https://github.com/galaxyproject/galaxy/pull/18447>`_
19+
* Fix subwofklow tags serialization type by `@arash77 <https://github.com/arash77>`_ in `#18456 <https://github.com/galaxyproject/galaxy/pull/18456>`_
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* by `@laperlej <https://github.com/laperlej>`_ in `#18459 <https://github.com/galaxyproject/galaxy/pull/18459>`_
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* Add input extra files to `get_input_fnames` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18462 <https://github.com/galaxyproject/galaxy/pull/18462>`_
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* Return generic message for password reset email by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18479 <https://github.com/galaxyproject/galaxy/pull/18479>`_
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* 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>`_
24+
* Don't call job_runner.stop_job on jobs in new state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18495 <https://github.com/galaxyproject/galaxy/pull/18495>`_
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* Prevent job submission if input collection element is deleted by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18517 <https://github.com/galaxyproject/galaxy/pull/18517>`_
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* Strip unicode null from tool stdio by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18527 <https://github.com/galaxyproject/galaxy/pull/18527>`_
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* Fix map over calculation for runtime inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18535 <https://github.com/galaxyproject/galaxy/pull/18535>`_
28+
* 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>`_
29+
* 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>`_
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* Fix sqlalchemy statement in tooltagmanager reset output by `@dannon <https://github.com/dannon>`_ in `#18591 <https://github.com/galaxyproject/galaxy/pull/18591>`_
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* Set minimum weasyprint version by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18606 <https://github.com/galaxyproject/galaxy/pull/18606>`_
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* 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>`_
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* 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>`_
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* 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>`_
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* File source and object store instance api fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18685 <https://github.com/galaxyproject/galaxy/pull/18685>`_
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* Fix change datatype PJA on expression tool data outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18691 <https://github.com/galaxyproject/galaxy/pull/18691>`_
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* Fill in missing help for cross product tools. by `@jmchilton <https://github.com/jmchilton>`_ in `#18698 <https://github.com/galaxyproject/galaxy/pull/18698>`_
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* 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>`_
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* Catch and display exceptions when importing malformatted yaml workflows by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18734 <https://github.com/galaxyproject/galaxy/pull/18734>`_
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* 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>`_
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* Fix directory get or create logic by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18752 <https://github.com/galaxyproject/galaxy/pull/18752>`_
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* Fix job summary for optional unset job data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18754 <https://github.com/galaxyproject/galaxy/pull/18754>`_
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* 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>`_
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* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
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* Fix unspecified ``oidc_endpoint`` variable overwriting specified ``redirect_url`` by `@bgruening <https://github.com/bgruening>`_ in `#18818 <https://github.com/galaxyproject/galaxy/pull/18818>`_
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* 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>`_
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* Fix ``named cursor is not valid anymore`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18825 <https://github.com/galaxyproject/galaxy/pull/18825>`_
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* Tighten TRS url check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18841 <https://github.com/galaxyproject/galaxy/pull/18841>`_
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* Fix Workflow index bookmark filter by `@itisAliRH <https://github.com/itisAliRH>`_ in `#18842 <https://github.com/galaxyproject/galaxy/pull/18842>`_
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* 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>`_
51+
* 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>`_
52+
* Raise MessageException instead of assertions on rerun problems by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18858 <https://github.com/galaxyproject/galaxy/pull/18858>`_
53+
* Fix data_column ref to nested collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18875 <https://github.com/galaxyproject/galaxy/pull/18875>`_
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* Fix loading very old workflows with data inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18876 <https://github.com/galaxyproject/galaxy/pull/18876>`_
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* Access tool data table filters in workflow building mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18900 <https://github.com/galaxyproject/galaxy/pull/18900>`_
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* Fix username used in invocation report by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18932 <https://github.com/galaxyproject/galaxy/pull/18932>`_
57+
* Disable locking when opening h5 files, add missing ``with`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18976 <https://github.com/galaxyproject/galaxy/pull/18976>`_
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* Fix job search statement building by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19010 <https://github.com/galaxyproject/galaxy/pull/19010>`_
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* Put cached jobs back into queue on handler restart by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19012 <https://github.com/galaxyproject/galaxy/pull/19012>`_
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* Fix various invocation export issues by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19215 <https://github.com/galaxyproject/galaxy/pull/19215>`_
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* Create harmonized collections from correct tool outputs by `@wm75 <https://github.com/wm75>`_ in `#19222 <https://github.com/galaxyproject/galaxy/pull/19222>`_
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============
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Enhancements
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============
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* Include workflow invocation id in exception logs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18594 <https://github.com/galaxyproject/galaxy/pull/18594>`_
68+
* 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>`_
69+
* Collect job metrics also when job failed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18809 <https://github.com/galaxyproject/galaxy/pull/18809>`_
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* 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>`_
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24.1.3 (2024-10-25)
@@ -23,7 +83,7 @@ Bug fixes
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* Fix dropped when_expression on step upgrade by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18446 <https://github.com/galaxyproject/galaxy/pull/18446>`_
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* Improve workflow-related exception reporting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18447 <https://github.com/galaxyproject/galaxy/pull/18447>`_
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* Fix subwofklow tags serialization type by `@arash77 <https://github.com/arash77>`_ in `#18456 <https://github.com/galaxyproject/galaxy/pull/18456>`_
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* by `@laperlej <https://github.com/laperlej>`_ in `#18459 <https://github.com/galaxyproject/galaxy/pull/18459>`_
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* by `@laperlej <https://github.com/laperlej>`_ in `#18459 <https://github.com/galaxyproject/galaxy/pull/18459>`_
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* Add input extra files to `get_input_fnames` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18462 <https://github.com/galaxyproject/galaxy/pull/18462>`_
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* Return generic message for password reset email by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18479 <https://github.com/galaxyproject/galaxy/pull/18479>`_
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* 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>`_

‎packages/app/setup.cfg

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long_description_content_type = text/x-rst
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name = galaxy-app
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url = https://github.com/galaxyproject/galaxy
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version = 24.1.4.dev0
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version = 24.1.4
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include_package_data = True

‎packages/auth/HISTORY.rst

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-----------
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24.1.4.dev0
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-----------
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-------------------
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24.1.4 (2024-12-11)
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-------------------
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No recorded changes since last release
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24.1.3 (2024-10-25)

‎packages/auth/setup.cfg

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name = galaxy-auth
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version = 24.1.4.dev0
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version = 24.1.4
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‎packages/config/HISTORY.rst

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-----------
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24.1.4.dev0
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-------------------
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-------------------
9+
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=========
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Bug fixes
13+
=========
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* 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>`_
16+
* Strip whitespace when listifying admin users by `@jdavcs <https://github.com/jdavcs>`_ in `#18656 <https://github.com/galaxyproject/galaxy/pull/18656>`_
17+
* Remove defaults channel for conda usage by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18859 <https://github.com/galaxyproject/galaxy/pull/18859>`_
18+
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============
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Enhancements
21+
============
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* Make `default_panel_view` a `_by_host` option by `@natefoo <https://github.com/natefoo>`_ in `#18471 <https://github.com/galaxyproject/galaxy/pull/18471>`_
24+
* More datatype deprecation warnings by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18612 <https://github.com/galaxyproject/galaxy/pull/18612>`_
25+
* 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>`_
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=============
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Other changes
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=============
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* Backport pod5 datatype by `@TomHarrop <https://github.com/TomHarrop>`_ in `#18507 <https://github.com/galaxyproject/galaxy/pull/18507>`_
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* 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>`_
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24.1.3 (2024-10-25)

‎packages/config/setup.cfg

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name = galaxy-config
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‎packages/data/HISTORY.rst

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-------------------
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=========
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=========
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* 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>`_
16+
* Improve workflow-related exception reporting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18447 <https://github.com/galaxyproject/galaxy/pull/18447>`_
17+
* 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>`_
18+
* Prevent job submission if input collection element is deleted by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18517 <https://github.com/galaxyproject/galaxy/pull/18517>`_
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* Fix shared caches with extended metadata collection. by `@jmchilton <https://github.com/jmchilton>`_ in `#18520 <https://github.com/galaxyproject/galaxy/pull/18520>`_
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* 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>`_
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* 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>`_
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* Fix h5ad metadata by `@nilchia <https://github.com/nilchia>`_ in `#18635 <https://github.com/galaxyproject/galaxy/pull/18635>`_
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* Don't set file size to zero by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18653 <https://github.com/galaxyproject/galaxy/pull/18653>`_
24+
* 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>`_
25+
* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
26+
* 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>`_
27+
* Make pylibmagic import optional by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18813 <https://github.com/galaxyproject/galaxy/pull/18813>`_
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* Ignore converted datasets in invalid input states by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18850 <https://github.com/galaxyproject/galaxy/pull/18850>`_
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* Fix discovered outputs with directory metadata and distributed object by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18855 <https://github.com/galaxyproject/galaxy/pull/18855>`_
30+
* Raise MessageException instead of assertions on rerun problems by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18858 <https://github.com/galaxyproject/galaxy/pull/18858>`_
31+
* Fix wrong final state when init_from is used by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18871 <https://github.com/galaxyproject/galaxy/pull/18871>`_
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* Fix history import when parent_hda not serialized by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18873 <https://github.com/galaxyproject/galaxy/pull/18873>`_
33+
* Limit max number of items in dataproviders by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18881 <https://github.com/galaxyproject/galaxy/pull/18881>`_
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* Allow cors in biom and q2view display applications by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18890 <https://github.com/galaxyproject/galaxy/pull/18890>`_
35+
* Disable locking when opening h5 files, add missing ``with`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18976 <https://github.com/galaxyproject/galaxy/pull/18976>`_
36+
* Optimize/fix sqlite hid update statement by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19106 <https://github.com/galaxyproject/galaxy/pull/19106>`_
37+
* Prefer auto-decompressed datatype when picking conversion target by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19162 <https://github.com/galaxyproject/galaxy/pull/19162>`_
38+
* Fix various invocation export issues by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19215 <https://github.com/galaxyproject/galaxy/pull/19215>`_
39+
* Fix bad merge conflict resolution by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19297 <https://github.com/galaxyproject/galaxy/pull/19297>`_
40+
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=============
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Other changes
43+
=============
44+
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* Backport pod5 datatype by `@TomHarrop <https://github.com/TomHarrop>`_ in `#18507 <https://github.com/galaxyproject/galaxy/pull/18507>`_
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24.1.3 (2024-10-25)

‎packages/data/setup.cfg

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‎packages/files/HISTORY.rst

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=========
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* Fix production_aws_private_bucket.yml by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19155 <https://github.com/galaxyproject/galaxy/pull/19155>`_
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24.1.3 (2024-10-25)

‎packages/files/setup.cfg

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‎packages/job_execution/HISTORY.rst

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-------------------
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=========
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Bug fixes
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=========
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* Add input extra files to `get_input_fnames` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18462 <https://github.com/galaxyproject/galaxy/pull/18462>`_
16+
* 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>`_
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‎packages/job_execution/setup.cfg

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name = galaxy-job-execution
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url = https://github.com/galaxyproject/galaxy
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version = 24.1.4.dev0
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version = 24.1.4
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include_package_data = True

‎packages/job_metrics/HISTORY.rst

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24.1.3 (2024-10-25)

‎packages/job_metrics/setup.cfg

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name = galaxy-job-metrics
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url = https://github.com/galaxyproject/galaxy
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version = 24.1.4.dev0
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‎packages/navigation/HISTORY.rst

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24.1.3 (2024-10-25)

‎packages/navigation/setup.cfg

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name = galaxy-navigation
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url = https://github.com/galaxyproject/galaxy
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version = 24.1.4.dev0
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version = 24.1.4
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include_package_data = True

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