From db7395b42378fe8aec00a5d25e452e033bc19164 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Wed, 11 Dec 2024 10:47:48 +0100 Subject: [PATCH] Create version 24.1.4 --- lib/galaxy/version.py | 2 +- packages/app/HISTORY.rst | 68 ++++++++++++++++++++++++++++-- packages/app/setup.cfg | 2 +- packages/auth/HISTORY.rst | 8 ++-- packages/auth/setup.cfg | 2 +- packages/config/HISTORY.rst | 28 ++++++++++-- packages/config/setup.cfg | 2 +- packages/data/HISTORY.rst | 41 ++++++++++++++++-- packages/data/setup.cfg | 4 +- packages/files/HISTORY.rst | 11 +++-- packages/files/setup.cfg | 2 +- packages/job_execution/HISTORY.rst | 12 ++++-- packages/job_execution/setup.cfg | 2 +- packages/job_metrics/HISTORY.rst | 8 ++-- packages/job_metrics/setup.cfg | 2 +- packages/navigation/HISTORY.rst | 8 ++-- packages/navigation/setup.cfg | 2 +- packages/objectstore/HISTORY.rst | 11 +++-- packages/objectstore/setup.cfg | 2 +- packages/schema/HISTORY.rst | 23 ++++++++-- packages/schema/setup.cfg | 2 +- packages/selenium/HISTORY.rst | 11 +++-- packages/selenium/setup.cfg | 2 +- packages/test_api/HISTORY.rst | 25 +++++++++-- packages/test_api/setup.cfg | 2 +- packages/test_base/HISTORY.rst | 15 +++++-- packages/test_base/setup.cfg | 2 +- packages/test_driver/HISTORY.rst | 8 ++-- packages/test_driver/setup.cfg | 2 +- packages/tool_shed/HISTORY.rst | 8 ++-- packages/tool_shed/setup.cfg | 2 +- packages/tool_util/HISTORY.rst | 25 +++++++++-- packages/tool_util/setup.cfg | 2 +- packages/tours/HISTORY.rst | 8 ++-- packages/tours/setup.cfg | 2 +- packages/util/HISTORY.rst | 18 ++++++-- packages/util/setup.cfg | 2 +- packages/web_apps/HISTORY.rst | 42 ++++++++++++++++-- packages/web_apps/setup.cfg | 2 +- packages/web_framework/HISTORY.rst | 13 ++++-- packages/web_framework/setup.cfg | 2 +- packages/web_stack/HISTORY.rst | 8 ++-- packages/web_stack/setup.cfg | 2 +- 43 files changed, 351 insertions(+), 94 deletions(-) diff --git a/lib/galaxy/version.py b/lib/galaxy/version.py index 740e8c55109..a5268a98f85 100644 --- a/lib/galaxy/version.py +++ b/lib/galaxy/version.py @@ -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 "") diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst index 375aa8d9a32..ffcbc878078 100644 --- a/packages/app/HISTORY.rst +++ b/packages/app/HISTORY.rst @@ -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 `_ in `#18428 `_ +* Update mercurial to non-yanked 6.7.4 by `@nsoranzo `_ in `#18434 `_ +* Fix dropped when_expression on step upgrade by `@mvdbeek `_ in `#18446 `_ +* Improve workflow-related exception reporting by `@mvdbeek `_ in `#18447 `_ +* Fix subwofklow tags serialization type by `@arash77 `_ in `#18456 `_ +* by `@laperlej `_ in `#18459 `_ +* Add input extra files to `get_input_fnames` by `@mvdbeek `_ in `#18462 `_ +* Return generic message for password reset email by `@ahmedhamidawan `_ in `#18479 `_ +* Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek `_ in `#18494 `_ +* Don't call job_runner.stop_job on jobs in new state by `@mvdbeek `_ in `#18495 `_ +* Prevent job submission if input collection element is deleted by `@mvdbeek `_ in `#18517 `_ +* Strip unicode null from tool stdio by `@mvdbeek `_ in `#18527 `_ +* Fix map over calculation for runtime inputs by `@mvdbeek `_ in `#18535 `_ +* Fix for not-null in 'column_list' object by `@hujambo-dunia `_ in `#18553 `_ +* Also fail ``ensure_dataset_on_disk`` if dataset is in new state by `@mvdbeek `_ in `#18559 `_ +* Fix sqlalchemy statement in tooltagmanager reset output by `@dannon `_ in `#18591 `_ +* Set minimum weasyprint version by `@mvdbeek `_ in `#18606 `_ +* Improve relabel identifiers message when number of columns is not 2 by `@mvdbeek `_ in `#18634 `_ +* Fix extract workflow from history when implicit collection has no jobs by `@mvdbeek `_ in `#18661 `_ +* Make sure we set file size also for purged outputs by `@mvdbeek `_ in `#18681 `_ +* File source and object store instance api fixes by `@mvdbeek `_ in `#18685 `_ +* Fix change datatype PJA on expression tool data outputs by `@mvdbeek `_ in `#18691 `_ +* Fill in missing help for cross product tools. by `@jmchilton `_ in `#18698 `_ +* Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by `@mvdbeek `_ in `#18731 `_ +* Catch and display exceptions when importing malformatted yaml workflows by `@mvdbeek `_ in `#18734 `_ +* Fix infinitely delayed workflow scheduling if skipped step creates HDCA by `@mvdbeek `_ in `#18751 `_ +* Fix directory get or create logic by `@mvdbeek `_ in `#18752 `_ +* Fix job summary for optional unset job data inputs by `@mvdbeek `_ in `#18754 `_ +* Allow to change only the description of a quota by `@bernt-matthias `_ in `#18775 `_ +* Fix wrong extension on pick data output by `@mvdbeek `_ in `#18798 `_ +* Fix unspecified ``oidc_endpoint`` variable overwriting specified ``redirect_url`` by `@bgruening `_ in `#18818 `_ +* Fix wrong celery_app config on job and workflow handlers by `@mvdbeek `_ in `#18819 `_ +* Fix ``named cursor is not valid anymore`` by `@mvdbeek `_ in `#18825 `_ +* Tighten TRS url check by `@mvdbeek `_ in `#18841 `_ +* Fix Workflow index bookmark filter by `@itisAliRH `_ in `#18842 `_ +* Skip metric collection if job working directory doesn't exist by `@mvdbeek `_ in `#18845 `_ +* Extend on disk checks to running, queued and error states by `@mvdbeek `_ in `#18846 `_ +* Raise MessageException instead of assertions on rerun problems by `@mvdbeek `_ in `#18858 `_ +* Fix data_column ref to nested collection by `@mvdbeek `_ in `#18875 `_ +* Fix loading very old workflows with data inputs by `@mvdbeek `_ in `#18876 `_ +* Access tool data table filters in workflow building mode by `@mvdbeek `_ in `#18900 `_ +* Fix username used in invocation report by `@mvdbeek `_ in `#18932 `_ +* Disable locking when opening h5 files, add missing ``with`` by `@mvdbeek `_ in `#18976 `_ +* Fix job search statement building by `@mvdbeek `_ in `#19010 `_ +* Put cached jobs back into queue on handler restart by `@mvdbeek `_ in `#19012 `_ +* Fix various invocation export issues by `@mvdbeek `_ in `#19215 `_ +* Create harmonized collections from correct tool outputs by `@wm75 `_ in `#19222 `_ + +============ +Enhancements +============ + +* Include workflow invocation id in exception logs by `@mvdbeek `_ in `#18594 `_ +* Implemented the generic OIDC backend from python-social-auth into Gal… by `@Edmontosaurus `_ in `#18670 `_ +* Collect job metrics also when job failed by `@mvdbeek `_ in `#18809 `_ +* prevent "missing refresh_token" errors by supporting also with Keycloak backend by `@ljocha `_ in `#18826 `_ ------------------- 24.1.3 (2024-10-25) @@ -23,7 +83,7 @@ Bug fixes * Fix dropped when_expression on step upgrade by `@mvdbeek `_ in `#18446 `_ * Improve workflow-related exception reporting by `@mvdbeek `_ in `#18447 `_ * Fix subwofklow tags serialization type by `@arash77 `_ in `#18456 `_ -* by `@laperlej `_ in `#18459 `_ +* by `@laperlej `_ in `#18459 `_ * Add input extra files to `get_input_fnames` by `@mvdbeek `_ in `#18462 `_ * Return generic message for password reset email by `@ahmedhamidawan `_ in `#18479 `_ * Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek `_ in `#18494 `_ diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg index dc0d88dd41a..d723bfe5115 100644 --- 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 = 24.1.4.dev0 +version = 24.1.4 [options] include_package_data = True diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst index 46756807673..47c167e1096 100644 --- a/packages/auth/HISTORY.rst +++ b/packages/auth/HISTORY.rst @@ -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) diff --git a/packages/auth/setup.cfg b/packages/auth/setup.cfg index eb248d1816b..da6a4ad77cf 100644 --- 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 = 24.1.4.dev0 +version = 24.1.4 [options] include_package_data = True diff --git a/packages/config/HISTORY.rst b/packages/config/HISTORY.rst index 8efec14afea..41fd061d0cb 100644 --- a/packages/config/HISTORY.rst +++ b/packages/config/HISTORY.rst @@ -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 `_ in `#18428 `_ +* Strip whitespace when listifying admin users by `@jdavcs `_ in `#18656 `_ +* Remove defaults channel for conda usage by `@bernt-matthias `_ in `#18859 `_ + +============ +Enhancements +============ + +* Make `default_panel_view` a `_by_host` option by `@natefoo `_ in `#18471 `_ +* More datatype deprecation warnings by `@mvdbeek `_ in `#18612 `_ +* Implemented the generic OIDC backend from python-social-auth into Gal… by `@Edmontosaurus `_ in `#18670 `_ + +============= +Other changes +============= + +* Backport pod5 datatype by `@TomHarrop `_ in `#18507 `_ +* Backport PR 18630 "Add BlobToolkit to the list of interactive tools" to release_24.1 by `@cat-bro `_ in `#18784 `_ ------------------- 24.1.3 (2024-10-25) diff --git a/packages/config/setup.cfg b/packages/config/setup.cfg index 2dc4e93d62d..e9751e6b5f1 100644 --- 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 = 24.1.4.dev0 +version = 24.1.4 [options] include_package_data = True diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst index e5cfcbeed5d..c690e8b89ea 100644 --- a/packages/data/HISTORY.rst +++ b/packages/data/HISTORY.rst @@ -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 `_ in `#18428 `_ +* Improve workflow-related exception reporting by `@mvdbeek `_ in `#18447 `_ +* Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek `_ in `#18494 `_ +* Prevent job submission if input collection element is deleted by `@mvdbeek `_ in `#18517 `_ +* Fix shared caches with extended metadata collection. by `@jmchilton `_ in `#18520 `_ +* Also check dataset.deleted when determining if data can be displayed by `@mvdbeek `_ in `#18547 `_ +* Fix for not-null in 'column_list' object by `@hujambo-dunia `_ in `#18553 `_ +* Fix h5ad metadata by `@nilchia `_ in `#18635 `_ +* Don't set file size to zero by `@mvdbeek `_ in `#18653 `_ +* Make sure we set file size also for purged outputs by `@mvdbeek `_ in `#18681 `_ +* Fix wrong extension on pick data output by `@mvdbeek `_ in `#18798 `_ +* Fix copying workflow with subworkflow step for step that you own by `@mvdbeek `_ in `#18802 `_ +* Make pylibmagic import optional by `@mvdbeek `_ in `#18813 `_ +* Ignore converted datasets in invalid input states by `@mvdbeek `_ in `#18850 `_ +* Fix discovered outputs with directory metadata and distributed object by `@mvdbeek `_ in `#18855 `_ +* Raise MessageException instead of assertions on rerun problems by `@mvdbeek `_ in `#18858 `_ +* Fix wrong final state when init_from is used by `@mvdbeek `_ in `#18871 `_ +* Fix history import when parent_hda not serialized by `@mvdbeek `_ in `#18873 `_ +* Limit max number of items in dataproviders by `@mvdbeek `_ in `#18881 `_ +* Allow cors in biom and q2view display applications by `@mvdbeek `_ in `#18890 `_ +* Disable locking when opening h5 files, add missing ``with`` by `@mvdbeek `_ in `#18976 `_ +* Optimize/fix sqlite hid update statement by `@mvdbeek `_ in `#19106 `_ +* Prefer auto-decompressed datatype when picking conversion target by `@mvdbeek `_ in `#19162 `_ +* Fix various invocation export issues by `@mvdbeek `_ in `#19215 `_ +* Fix bad merge conflict resolution by `@nsoranzo `_ in `#19297 `_ + +============= +Other changes +============= + +* Backport pod5 datatype by `@TomHarrop `_ in `#18507 `_ ------------------- 24.1.3 (2024-10-25) diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg index e8d437ad8fb..7307f46e392 100644 --- 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 = 24.1.4.dev0 +version = 24.1.4 [options] include_package_data = True @@ -75,4 +75,4 @@ console_scripts = [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/files/HISTORY.rst b/packages/files/HISTORY.rst index 87b49e4b087..ac81f81f3c3 100644 --- a/packages/files/HISTORY.rst +++ b/packages/files/HISTORY.rst @@ -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 `_ in `#19155 `_ ------------------- 24.1.3 (2024-10-25) diff --git a/packages/files/setup.cfg b/packages/files/setup.cfg index 2df0e171f98..d2b7d3e1ce8 100644 --- 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 = 24.1.4.dev0 +version = 24.1.4 [options] include_package_data = True diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst index 5eb53e4e1fa..51f89887e58 100644 --- a/packages/job_execution/HISTORY.rst +++ b/packages/job_execution/HISTORY.rst @@ -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 `_ in `#18462 `_ +* Retry container monitor POST if it fails (don't assume it succeeded) by `@natefoo `_ in `#18863 `_ ------------------- 24.1.3 (2024-10-25) diff --git a/packages/job_execution/setup.cfg b/packages/job_execution/setup.cfg index 6a643765efc..d2b8d0fa18a 100644 --- 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 = 24.1.4.dev0 +version = 24.1.4 [options] include_package_data = True diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst index 580c4de9b2c..8c2c8fbd3b3 100644 --- a/packages/job_metrics/HISTORY.rst +++ b/packages/job_metrics/HISTORY.rst @@ -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) diff --git a/packages/job_metrics/setup.cfg b/packages/job_metrics/setup.cfg index d439275d9d9..e051ba96b43 100644 --- 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 = 24.1.4.dev0 +version = 24.1.4 [options] include_package_data = True diff --git a/packages/navigation/HISTORY.rst b/packages/navigation/HISTORY.rst index 929a673f626..e977aa60a40 100644 --- a/packages/navigation/HISTORY.rst +++ b/packages/navigation/HISTORY.rst @@ -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) diff --git a/packages/navigation/setup.cfg b/packages/navigation/setup.cfg index e693f6c2a02..ce3d7731334 100644 --- 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 = 24.1.4.dev0 +version = 24.1.4 [options] include_package_data = True diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst index c990081333a..d7eb0602e49 100644 --- a/packages/objectstore/HISTORY.rst +++ b/packages/objectstore/HISTORY.rst @@ -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 `_ in `#18520 `_ ------------------- 24.1.3 (2024-10-25) diff --git a/packages/objectstore/setup.cfg b/packages/objectstore/setup.cfg index 39767e69099..5789981489a 100644 --- 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 = 24.1.4.dev0 +version = 24.1.4 [options] include_package_data = True diff --git a/packages/schema/HISTORY.rst b/packages/schema/HISTORY.rst index eb2810a260a..d465442b7ad 100644 --- a/packages/schema/HISTORY.rst +++ b/packages/schema/HISTORY.rst @@ -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 `_ in `#18730 `_ +* Fix datatype validation of newly built collection by `@mvdbeek `_ in `#18738 `_ +* Fix job summary for optional unset job data inputs by `@mvdbeek `_ in `#18754 `_ +* Fix ``TypeError`` from Pydantic 2.9.0 by `@nsoranzo `_ in `#18788 `_ +* Fix wrong extension on pick data output by `@mvdbeek `_ in `#18798 `_ +* Make all fields optional for HelpForumPost by `@davelopez `_ in `#18839 `_ +* Remove the default `Incoming` suffix in `GenericModel` class by `@davelopez `_ in `#19174 `_ + +============ +Enhancements +============ + +* Include workflow invocation id in exception logs by `@mvdbeek `_ in `#18594 `_ ------------------- 24.1.3 (2024-10-25) diff --git a/packages/schema/setup.cfg b/packages/schema/setup.cfg index 9be5db3aa17..f43a5044138 100644 --- 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 = 24.1.4.dev0 +version = 24.1.4 [options] include_package_data = True diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst index ab2d98bc714..09beb5764b6 100644 --- a/packages/selenium/HISTORY.rst +++ b/packages/selenium/HISTORY.rst @@ -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 `_ in `#19083 `_ ------------------- 24.1.3 (2024-10-25) diff --git a/packages/selenium/setup.cfg b/packages/selenium/setup.cfg index 7a3605e6f7d..2e40c2ea81f 100644 --- 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 = 24.1.4.dev0 +version = 24.1.4 [options] include_package_data = True diff --git a/packages/test_api/HISTORY.rst b/packages/test_api/HISTORY.rst index 8e637e4de77..e9fbd18b6f7 100644 --- a/packages/test_api/HISTORY.rst +++ b/packages/test_api/HISTORY.rst @@ -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 `_ in `#18456 `_ +* Prevent job submission if input collection element is deleted by `@mvdbeek `_ in `#18517 `_ +* Fix view parameter type in Job index API by `@davelopez `_ in `#18521 `_ +* Fix map over calculation for runtime inputs by `@mvdbeek `_ in `#18535 `_ +* Fix Archive header encoding by `@arash77 `_ in `#18583 `_ +* Don't set file size to zero by `@mvdbeek `_ in `#18653 `_ +* Fix extract workflow from history when implicit collection has no jobs by `@mvdbeek `_ in `#18661 `_ +* Fix change datatype PJA on expression tool data outputs by `@mvdbeek `_ in `#18691 `_ +* Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by `@mvdbeek `_ in `#18731 `_ +* Catch and display exceptions when importing malformatted yaml workflows by `@mvdbeek `_ in `#18734 `_ +* Fix infinitely delayed workflow scheduling if skipped step creates HDCA by `@mvdbeek `_ in `#18751 `_ +* Fix copying workflow with subworkflow step for step that you own by `@mvdbeek `_ in `#18802 `_ +* Raise MessageException instead of assertions on rerun problems by `@mvdbeek `_ in `#18858 `_ +* Fix data_column ref to nested collection by `@mvdbeek `_ in `#18875 `_ +* Access tool data table filters in workflow building mode by `@mvdbeek `_ in `#18900 `_ ------------------- 24.1.3 (2024-10-25) diff --git a/packages/test_api/setup.cfg b/packages/test_api/setup.cfg index db106db0ec1..24648c86235 100644 --- a/packages/test_api/setup.cfg +++ b/packages/test_api/setup.cfg @@ -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 diff --git a/packages/test_base/HISTORY.rst b/packages/test_base/HISTORY.rst index a1c6f403f30..c148366cc90 100644 --- a/packages/test_base/HISTORY.rst +++ b/packages/test_base/HISTORY.rst @@ -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 `_ in `#18456 `_ +* Fix infinitely delayed workflow scheduling if skipped step creates HDCA by `@mvdbeek `_ in `#18751 `_ +* Fix wrong extension on pick data output by `@mvdbeek `_ in `#18798 `_ +* Fix data_column ref to nested collection by `@mvdbeek `_ in `#18875 `_ +* Access tool data table filters in workflow building mode by `@mvdbeek `_ in `#18900 `_ ------------------- 24.1.3 (2024-10-25) diff --git a/packages/test_base/setup.cfg b/packages/test_base/setup.cfg index fafecda1778..3a33f6b61a2 100644 --- a/packages/test_base/setup.cfg +++ b/packages/test_base/setup.cfg @@ -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 diff --git a/packages/test_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst index 748d54ae2b2..d3a7928618f 100644 --- a/packages/test_driver/HISTORY.rst +++ b/packages/test_driver/HISTORY.rst @@ -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) diff --git a/packages/test_driver/setup.cfg b/packages/test_driver/setup.cfg index 88114f539ba..b0d583101fb 100644 --- a/packages/test_driver/setup.cfg +++ b/packages/test_driver/setup.cfg @@ -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 diff --git a/packages/tool_shed/HISTORY.rst b/packages/tool_shed/HISTORY.rst index 45265b23a40..9316dc2b7b7 100644 --- a/packages/tool_shed/HISTORY.rst +++ b/packages/tool_shed/HISTORY.rst @@ -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) diff --git a/packages/tool_shed/setup.cfg b/packages/tool_shed/setup.cfg index a9b0ab22166..7566e32446f 100644 --- a/packages/tool_shed/setup.cfg +++ b/packages/tool_shed/setup.cfg @@ -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 diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst index 40e993c6369..5dda63d564e 100644 --- a/packages/tool_util/HISTORY.rst +++ b/packages/tool_util/HISTORY.rst @@ -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 `_ in `#18510 `_ +* xsd: allow `change_format` and `actions` also in statically defined collection elements, and break recursion by `@bernt-matthias `_ in `#18605 `_ +* Remove defaults channel for conda usage by `@bernt-matthias `_ in `#18859 `_ +* Don't check availability of shellescape by `@nsoranzo `_ in `#18954 `_ +* Backport 2 CI fixes by `@nsoranzo `_ in `#18973 `_ +* Disable locking when opening h5 files, add missing ``with`` by `@mvdbeek `_ in `#18976 `_ +* Fix extra call to test_data_path that requires an admin key by `@jmchilton `_ in `#19011 `_ +* flip default value for use_mamba to false by `@bgruening `_ in `#19295 `_ +* Linter: allow dynamic option definition by from_url by `@bernt-matthias `_ in `#19300 `_ + +============ +Enhancements +============ + +* Make `default_panel_view` a `_by_host` option by `@natefoo `_ in `#18471 `_ ------------------- 24.1.3 (2024-10-25) diff --git a/packages/tool_util/setup.cfg b/packages/tool_util/setup.cfg index b359c259b2b..d530d408c93 100644 --- a/packages/tool_util/setup.cfg +++ b/packages/tool_util/setup.cfg @@ -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 diff --git a/packages/tours/HISTORY.rst b/packages/tours/HISTORY.rst index 4013128ac26..30cbb115430 100644 --- a/packages/tours/HISTORY.rst +++ b/packages/tours/HISTORY.rst @@ -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) diff --git a/packages/tours/setup.cfg b/packages/tours/setup.cfg index 2cd4132a18c..f765ceb86c8 100644 --- a/packages/tours/setup.cfg +++ b/packages/tours/setup.cfg @@ -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 diff --git a/packages/util/HISTORY.rst b/packages/util/HISTORY.rst index aaba18ec97f..4ec9ec4b7e5 100644 --- a/packages/util/HISTORY.rst +++ b/packages/util/HISTORY.rst @@ -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 `_ in `#18583 `_ +* File source and object store instance api fixes by `@mvdbeek `_ in `#18685 `_ + +============ +Enhancements +============ + +* Use smtplib send_message to support utf-8 chars in to and from by `@mvdbeek `_ in `#18805 `_ ------------------- 24.1.3 (2024-10-25) diff --git a/packages/util/setup.cfg b/packages/util/setup.cfg index 38a50c30939..b62f4a4ddc8 100644 --- a/packages/util/setup.cfg +++ b/packages/util/setup.cfg @@ -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 diff --git a/packages/web_apps/HISTORY.rst b/packages/web_apps/HISTORY.rst index c533962cc5c..e8682f81da8 100644 --- a/packages/web_apps/HISTORY.rst +++ b/packages/web_apps/HISTORY.rst @@ -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 `_ in `#18479 `_ +* Fix view parameter type in Job index API by `@davelopez `_ in `#18521 `_ +* Check if dataset has any data before running provider checks by `@mvdbeek `_ in `#18526 `_ +* Raise appropriate exception if ldda not found by `@mvdbeek `_ in `#18569 `_ +* Close install model session when request ends by `@mvdbeek `_ in `#18629 `_ +* Fix resume_paused_jobs if no session provided by `@mvdbeek `_ in `#18640 `_ +* Fix extract workflow from history when implicit collection has no jobs by `@mvdbeek `_ in `#18661 `_ +* Return error when following a link to a non-ready display application by `@mvdbeek `_ in `#18672 `_ +* Only load authnz routes when oidc enabled by `@mvdbeek `_ in `#18683 `_ +* File source and object store instance api fixes by `@mvdbeek `_ in `#18685 `_ +* Fix sorting users in admin by last login by `@jdavcs `_ in `#18694 `_ +* Fix resume paused jobs response handling by `@dannon `_ in `#18733 `_ +* Fix wrong extension on pick data output by `@mvdbeek `_ in `#18798 `_ +* Tighten TRS url check by `@mvdbeek `_ in `#18841 `_ +* Fix Workflow index bookmark filter by `@itisAliRH `_ in `#18842 `_ +* Extend on disk checks to running, queued and error states by `@mvdbeek `_ in `#18846 `_ +* Limit max number of items in dataproviders by `@mvdbeek `_ in `#18881 `_ +* Access tool data table filters in workflow building mode by `@mvdbeek `_ in `#18900 `_ +* Don't use ``async def`` where not appropriate by `@mvdbeek `_ in `#18944 `_ +* Fix very slow workflow editor loading by `@mvdbeek `_ in `#19068 `_ + +============ +Enhancements +============ + +* Make `default_panel_view` a `_by_host` option by `@natefoo `_ in `#18471 `_ + +============= +Other changes +============= + +* Fix check dataset check by `@mvdbeek `_ in `#18856 `_ ------------------- 24.1.3 (2024-10-25) diff --git a/packages/web_apps/setup.cfg b/packages/web_apps/setup.cfg index 18260c932b0..f2426503b9f 100644 --- a/packages/web_apps/setup.cfg +++ b/packages/web_apps/setup.cfg @@ -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 diff --git a/packages/web_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst index 63b02e282c9..e84f2ca26e7 100644 --- a/packages/web_framework/HISTORY.rst +++ b/packages/web_framework/HISTORY.rst @@ -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 `_ in `#18494 `_ +* Apply statsd arg sanitization to all pages by `@mvdbeek `_ in `#18509 `_ +* Close install model session when request ends by `@mvdbeek `_ in `#18629 `_ ------------------- 24.1.3 (2024-10-25) diff --git a/packages/web_framework/setup.cfg b/packages/web_framework/setup.cfg index 0b5e4b03783..c6aa7f4f8f7 100644 --- a/packages/web_framework/setup.cfg +++ b/packages/web_framework/setup.cfg @@ -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 diff --git a/packages/web_stack/HISTORY.rst b/packages/web_stack/HISTORY.rst index ddd95820fa4..0fec6408b79 100644 --- a/packages/web_stack/HISTORY.rst +++ b/packages/web_stack/HISTORY.rst @@ -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) diff --git a/packages/web_stack/setup.cfg b/packages/web_stack/setup.cfg index dd1cac358fe..bf13d33f716 100644 --- a/packages/web_stack/setup.cfg +++ b/packages/web_stack/setup.cfg @@ -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