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Create version 24.1.4

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Matthias Bernt
2024-12-11 10:47:48 +01:00
parent 58496b913e
commit db7395b423
43 changed files with 351 additions and 94 deletions
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lib/galaxy/version.py
+1 -1
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@@ -1,3 +1,3 @@
VERSION_MAJOR = "24.1"
VERSION_MINOR = "4.dev0"
VERSION_MINOR = "4"
VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else "")
packages/app/HISTORY.rst
+64 -4
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@@ -3,11 +3,71 @@ History
.. to_doc
-----------
24.1.4.dev0
-----------
-------------------
24.1.4 (2024-12-11)
-------------------
=========
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>`_
* 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>`_
* 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>`_
* Fix various invocation export issues by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19215 <https://github.com/galaxyproject/galaxy/pull/19215>`_
* Create harmonized collections from correct tool outputs by `@wm75 <https://github.com/wm75>`_ in `#19222 <https://github.com/galaxyproject/galaxy/pull/19222>`_
============
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>`_
-------------------
24.1.3 (2024-10-25)
@@ -23,7 +83,7 @@ Bug fixes
* 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>`_
* 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>`_
packages/app/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-app
url = https://github.com/galaxyproject/galaxy
version = 24.1.4.dev0
version = 24.1.4
[options]
include_package_data = True
packages/auth/HISTORY.rst
+4 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
24.1.4.dev0
-----------
-------------------
24.1.4 (2024-12-11)
-------------------
No recorded changes since last release
-------------------
24.1.3 (2024-10-25)
packages/auth/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-auth
url = https://github.com/galaxyproject/galaxy
version = 24.1.4.dev0
version = 24.1.4
[options]
include_package_data = True
packages/config/HISTORY.rst
+25 -3
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@@ -3,11 +3,33 @@ History
.. to_doc
-----------
24.1.4.dev0
-----------
-------------------
24.1.4 (2024-12-11)
-------------------
=========
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>`_
-------------------
24.1.3 (2024-10-25)
packages/config/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-config
url = https://github.com/galaxyproject/galaxy
version = 24.1.4.dev0
version = 24.1.4
[options]
include_package_data = True
packages/data/HISTORY.rst
+38 -3
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@@ -3,11 +3,46 @@ History
.. to_doc
-----------
24.1.4.dev0
-----------
-------------------
24.1.4 (2024-12-11)
-------------------
=========
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>`_
* Optimize/fix sqlite hid update statement by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19106 <https://github.com/galaxyproject/galaxy/pull/19106>`_
* Prefer auto-decompressed datatype when picking conversion target by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19162 <https://github.com/galaxyproject/galaxy/pull/19162>`_
* Fix various invocation export issues by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19215 <https://github.com/galaxyproject/galaxy/pull/19215>`_
* Fix bad merge conflict resolution by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19297 <https://github.com/galaxyproject/galaxy/pull/19297>`_
=============
Other changes
=============
* Backport pod5 datatype by `@TomHarrop <https://github.com/TomHarrop>`_ in `#18507 <https://github.com/galaxyproject/galaxy/pull/18507>`_
-------------------
24.1.3 (2024-10-25)
packages/data/setup.cfg
+2 -2
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-data
url = https://github.com/galaxyproject/galaxy
version = 24.1.4.dev0
version = 24.1.4
[options]
include_package_data = True
@@ -75,4 +75,4 @@ console_scripts =
[options.packages.find]
exclude =
tests*
tests*
packages/files/HISTORY.rst
+8 -3
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@@ -3,11 +3,16 @@ History
.. to_doc
-----------
24.1.4.dev0
-----------
-------------------
24.1.4 (2024-12-11)
-------------------
=========
Bug fixes
=========
* Fix production_aws_private_bucket.yml by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19155 <https://github.com/galaxyproject/galaxy/pull/19155>`_
-------------------
24.1.3 (2024-10-25)
packages/files/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-files
url = https://github.com/galaxyproject/galaxy
version = 24.1.4.dev0
version = 24.1.4
[options]
include_package_data = True
packages/job_execution/HISTORY.rst
+9 -3
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@@ -3,11 +3,17 @@ History
.. to_doc
-----------
24.1.4.dev0
-----------
-------------------
24.1.4 (2024-12-11)
-------------------
=========
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>`_
-------------------
24.1.3 (2024-10-25)
packages/job_execution/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-job-execution
url = https://github.com/galaxyproject/galaxy
version = 24.1.4.dev0
version = 24.1.4
[options]
include_package_data = True
packages/job_metrics/HISTORY.rst
+4 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
24.1.4.dev0
-----------
-------------------
24.1.4 (2024-12-11)
-------------------
No recorded changes since last release
-------------------
24.1.3 (2024-10-25)
packages/job_metrics/setup.cfg
+1 -1
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@@ -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 = 24.1.4.dev0
version = 24.1.4
[options]
include_package_data = True
packages/navigation/HISTORY.rst
+4 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
24.1.4.dev0
-----------
-------------------
24.1.4 (2024-12-11)
-------------------
No recorded changes since last release
-------------------
24.1.3 (2024-10-25)
packages/navigation/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-navigation
url = https://github.com/galaxyproject/galaxy
version = 24.1.4.dev0
version = 24.1.4
[options]
include_package_data = True
packages/objectstore/HISTORY.rst
+8 -3
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@@ -3,11 +3,16 @@ History
.. to_doc
-----------
24.1.4.dev0
-----------
-------------------
24.1.4 (2024-12-11)
-------------------
=========
Bug fixes
=========
* Fix shared caches with extended metadata collection. by `@jmchilton <https://github.com/jmchilton>`_ in `#18520 <https://github.com/galaxyproject/galaxy/pull/18520>`_
-------------------
24.1.3 (2024-10-25)
packages/objectstore/setup.cfg
+1 -1
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@@ -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 = 24.1.4.dev0
version = 24.1.4
[options]
include_package_data = True
packages/schema/HISTORY.rst
+20 -3
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@@ -3,11 +3,28 @@ History
.. to_doc
-----------
24.1.4.dev0
-----------
-------------------
24.1.4 (2024-12-11)
-------------------
=========
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>`_
* Remove the default `Incoming` suffix in `GenericModel` class by `@davelopez <https://github.com/davelopez>`_ in `#19174 <https://github.com/galaxyproject/galaxy/pull/19174>`_
============
Enhancements
============
* Include workflow invocation id in exception logs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18594 <https://github.com/galaxyproject/galaxy/pull/18594>`_
-------------------
24.1.3 (2024-10-25)
packages/schema/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-schema
url = https://github.com/galaxyproject/galaxy
version = 24.1.4.dev0
version = 24.1.4
[options]
include_package_data = True
packages/selenium/HISTORY.rst
+8 -3
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@@ -3,11 +3,16 @@ History
.. to_doc
-----------
24.1.4.dev0
-----------
-------------------
24.1.4 (2024-12-11)
-------------------
=========
Bug fixes
=========
* Persist uploaded data between Regular and Collection upload tabs by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#19083 <https://github.com/galaxyproject/galaxy/pull/19083>`_
-------------------
24.1.3 (2024-10-25)
packages/selenium/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-selenium
url = https://github.com/galaxyproject/galaxy
version = 24.1.4.dev0
version = 24.1.4
[options]
include_package_data = True
packages/test_api/HISTORY.rst
+22 -3
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@@ -3,11 +3,30 @@ History
.. to_doc
-----------
24.1.4.dev0
-----------
-------------------
24.1.4 (2024-12-11)
-------------------
=========
Bug fixes
=========
* Fix subwofklow tags serialization type by `@arash77 <https://github.com/arash77>`_ in `#18456 <https://github.com/galaxyproject/galaxy/pull/18456>`_
* 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 view parameter type in Job index API by `@davelopez <https://github.com/davelopez>`_ in `#18521 <https://github.com/galaxyproject/galaxy/pull/18521>`_
* Fix map over calculation for runtime inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18535 <https://github.com/galaxyproject/galaxy/pull/18535>`_
* Fix Archive header encoding by `@arash77 <https://github.com/arash77>`_ in `#18583 <https://github.com/galaxyproject/galaxy/pull/18583>`_
* Don't set file size to zero by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18653 <https://github.com/galaxyproject/galaxy/pull/18653>`_
* 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>`_
* Fix change datatype PJA on expression tool data outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18691 <https://github.com/galaxyproject/galaxy/pull/18691>`_
* 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 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>`_
* 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>`_
* Access tool data table filters in workflow building mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18900 <https://github.com/galaxyproject/galaxy/pull/18900>`_
-------------------
24.1.3 (2024-10-25)
packages/test_api/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-test-api
url = https://github.com/galaxyproject/galaxy
version = 24.1.4.dev0
version = 24.1.4
[options]
include_package_data = True
packages/test_base/HISTORY.rst
+12 -3
View File
@@ -3,11 +3,20 @@ History
.. to_doc
-----------
24.1.4.dev0
-----------
-------------------
24.1.4 (2024-12-11)
-------------------
=========
Bug fixes
=========
* Fix subwofklow tags serialization type by `@arash77 <https://github.com/arash77>`_ in `#18456 <https://github.com/galaxyproject/galaxy/pull/18456>`_
* 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 wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
* Fix data_column ref to nested collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18875 <https://github.com/galaxyproject/galaxy/pull/18875>`_
* Access tool data table filters in workflow building mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18900 <https://github.com/galaxyproject/galaxy/pull/18900>`_
-------------------
24.1.3 (2024-10-25)
packages/test_base/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-test-base
url = https://github.com/galaxyproject/galaxy
version = 24.1.4.dev0
version = 24.1.4
[options]
include_package_data = True
packages/test_driver/HISTORY.rst
+4 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
24.1.4.dev0
-----------
-------------------
24.1.4 (2024-12-11)
-------------------
No recorded changes since last release
-------------------
24.1.3 (2024-10-25)
packages/test_driver/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-test-driver
url = https://github.com/galaxyproject/galaxy
version = 24.1.4.dev0
version = 24.1.4
[options]
include_package_data = True
packages/tool_shed/HISTORY.rst
+4 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
24.1.4.dev0
-----------
-------------------
24.1.4 (2024-12-11)
-------------------
No recorded changes since last release
-------------------
24.1.3 (2024-10-25)
packages/tool_shed/setup.cfg
+1 -1
View File
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-tool-shed
url = https://github.com/galaxyproject/galaxy
version = 24.1.4.dev0
version = 24.1.4
[options]
include_package_data = True
packages/tool_util/HISTORY.rst
+22 -3
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@@ -3,11 +3,30 @@ History
.. to_doc
-----------
24.1.4.dev0
-----------
-------------------
24.1.4 (2024-12-11)
-------------------
=========
Bug fixes
=========
* Handle all requests error in ``ApiBiotoolsMetadataSource._raw_get_metadata`` by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18510 <https://github.com/galaxyproject/galaxy/pull/18510>`_
* xsd: allow `change_format` and `actions` also in statically defined collection elements, and break recursion by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18605 <https://github.com/galaxyproject/galaxy/pull/18605>`_
* Remove defaults channel for conda usage by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18859 <https://github.com/galaxyproject/galaxy/pull/18859>`_
* Don't check availability of shellescape by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18954 <https://github.com/galaxyproject/galaxy/pull/18954>`_
* Backport 2 CI fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18973 <https://github.com/galaxyproject/galaxy/pull/18973>`_
* 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 extra call to test_data_path that requires an admin key by `@jmchilton <https://github.com/jmchilton>`_ in `#19011 <https://github.com/galaxyproject/galaxy/pull/19011>`_
* flip default value for use_mamba to false by `@bgruening <https://github.com/bgruening>`_ in `#19295 <https://github.com/galaxyproject/galaxy/pull/19295>`_
* Linter: allow dynamic option definition by from_url by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19300 <https://github.com/galaxyproject/galaxy/pull/19300>`_
============
Enhancements
============
* Make `default_panel_view` a `_by_host` option by `@natefoo <https://github.com/natefoo>`_ in `#18471 <https://github.com/galaxyproject/galaxy/pull/18471>`_
-------------------
24.1.3 (2024-10-25)
packages/tool_util/setup.cfg
+1 -1
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@@ -28,7 +28,7 @@ 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 = 24.1.4.dev0
version = 24.1.4
[options]
include_package_data = True
packages/tours/HISTORY.rst
+4 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
24.1.4.dev0
-----------
-------------------
24.1.4 (2024-12-11)
-------------------
No recorded changes since last release
-------------------
24.1.3 (2024-10-25)
packages/tours/setup.cfg
+1 -1
View File
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-tours
url = https://github.com/galaxyproject/galaxy
version = 24.1.4.dev0
version = 24.1.4
[options]
include_package_data = True
packages/util/HISTORY.rst
+15 -3
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@@ -3,11 +3,23 @@ History
.. to_doc
-----------
24.1.4.dev0
-----------
-------------------
24.1.4 (2024-12-11)
-------------------
=========
Bug fixes
=========
* Fix Archive header encoding by `@arash77 <https://github.com/arash77>`_ in `#18583 <https://github.com/galaxyproject/galaxy/pull/18583>`_
* File source and object store instance api fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18685 <https://github.com/galaxyproject/galaxy/pull/18685>`_
============
Enhancements
============
* Use smtplib send_message to support utf-8 chars in to and from by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18805 <https://github.com/galaxyproject/galaxy/pull/18805>`_
-------------------
24.1.3 (2024-10-25)
packages/util/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-util
url = https://github.com/galaxyproject/galaxy
version = 24.1.4.dev0
version = 24.1.4
[options]
include_package_data = True
packages/web_apps/HISTORY.rst
+39 -3
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@@ -3,11 +3,47 @@ History
.. to_doc
-----------
24.1.4.dev0
-----------
-------------------
24.1.4 (2024-12-11)
-------------------
=========
Bug fixes
=========
* Return generic message for password reset email by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18479 <https://github.com/galaxyproject/galaxy/pull/18479>`_
* Fix view parameter type in Job index API by `@davelopez <https://github.com/davelopez>`_ in `#18521 <https://github.com/galaxyproject/galaxy/pull/18521>`_
* Check if dataset has any data before running provider checks by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18526 <https://github.com/galaxyproject/galaxy/pull/18526>`_
* Raise appropriate exception if ldda not found by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18569 <https://github.com/galaxyproject/galaxy/pull/18569>`_
* Close install model session when request ends by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18629 <https://github.com/galaxyproject/galaxy/pull/18629>`_
* Fix resume_paused_jobs if no session provided by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18640 <https://github.com/galaxyproject/galaxy/pull/18640>`_
* 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>`_
* Return error when following a link to a non-ready display application by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18672 <https://github.com/galaxyproject/galaxy/pull/18672>`_
* Only load authnz routes when oidc enabled by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18683 <https://github.com/galaxyproject/galaxy/pull/18683>`_
* File source and object store instance api fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18685 <https://github.com/galaxyproject/galaxy/pull/18685>`_
* Fix sorting users in admin by last login by `@jdavcs <https://github.com/jdavcs>`_ in `#18694 <https://github.com/galaxyproject/galaxy/pull/18694>`_
* Fix resume paused jobs response handling by `@dannon <https://github.com/dannon>`_ in `#18733 <https://github.com/galaxyproject/galaxy/pull/18733>`_
* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
* 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>`_
* 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>`_
* Limit max number of items in dataproviders by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18881 <https://github.com/galaxyproject/galaxy/pull/18881>`_
* Access tool data table filters in workflow building mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18900 <https://github.com/galaxyproject/galaxy/pull/18900>`_
* Don't use ``async def`` where not appropriate by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18944 <https://github.com/galaxyproject/galaxy/pull/18944>`_
* Fix very slow workflow editor loading by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19068 <https://github.com/galaxyproject/galaxy/pull/19068>`_
============
Enhancements
============
* Make `default_panel_view` a `_by_host` option by `@natefoo <https://github.com/natefoo>`_ in `#18471 <https://github.com/galaxyproject/galaxy/pull/18471>`_
=============
Other changes
=============
* Fix check dataset check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18856 <https://github.com/galaxyproject/galaxy/pull/18856>`_
-------------------
24.1.3 (2024-10-25)
packages/web_apps/setup.cfg
+1 -1
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@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-web-apps
url = https://github.com/galaxyproject/galaxy
version = 24.1.4.dev0
version = 24.1.4
[options]
include_package_data = True
packages/web_framework/HISTORY.rst
+10 -3
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@@ -3,11 +3,18 @@ History
.. to_doc
-----------
24.1.4.dev0
-----------
-------------------
24.1.4 (2024-12-11)
-------------------
=========
Bug fixes
=========
* 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>`_
* Apply statsd arg sanitization to all pages by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18509 <https://github.com/galaxyproject/galaxy/pull/18509>`_
* Close install model session when request ends by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18629 <https://github.com/galaxyproject/galaxy/pull/18629>`_
-------------------
24.1.3 (2024-10-25)
packages/web_framework/setup.cfg
+1 -1
View File
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-web-framework
url = https://github.com/galaxyproject/galaxy
version = 24.1.4.dev0
version = 24.1.4
[options]
include_package_data = True
packages/web_stack/HISTORY.rst
+4 -4
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@@ -3,11 +3,11 @@ History
.. to_doc
-----------
24.1.4.dev0
-----------
-------------------
24.1.4 (2024-12-11)
-------------------
No recorded changes since last release
-------------------
24.1.3 (2024-10-25)
packages/web_stack/setup.cfg
+1 -1
View File
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
long_description_content_type = text/x-rst
name = galaxy-web-stack
url = https://github.com/galaxyproject/galaxy
version = 24.1.4.dev0
version = 24.1.4
[options]
include_package_data = True