diff --git a/lib/galaxy/version.py b/lib/galaxy/version.py index d7d7f3f7f491..a4a18e6f108c 100644 --- a/lib/galaxy/version.py +++ b/lib/galaxy/version.py @@ -1,3 +1,3 @@ VERSION_MAJOR = "24.1" -VERSION_MINOR = "3.dev0" +VERSION_MINOR = "3" VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else "") diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst index 27a82fd91ccd..2cfdc0715200 100644 --- a/packages/app/HISTORY.rst +++ b/packages/app/HISTORY.rst @@ -3,11 +3,68 @@ History .. to_doc ------------ -24.1.3.dev0 ------------ +------------------- +24.1.3 (2024-10-25) +------------------- +========= +Bug fixes +========= + +* Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek `_ 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 `_ +* 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 `_ + +============ +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 `_ ------------------- 24.1.2 (2024-09-25) diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg index 80e4d38c3d85..a143935eb5f5 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 = 24.1.3.dev0 +version = 24.1.3 [options] include_package_data = True diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst index b46693de1bb3..32cdb97ae952 100644 --- a/packages/auth/HISTORY.rst +++ b/packages/auth/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc ------------ -24.1.3.dev0 ------------ - +------------------- +24.1.3 (2024-10-25) +------------------- +No recorded changes since last release ------------------- 24.1.2 (2024-09-25) diff --git a/packages/auth/setup.cfg b/packages/auth/setup.cfg index ab82a95b3be2..49da1a858e15 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 = 24.1.3.dev0 +version = 24.1.3 [options] include_package_data = True diff --git a/packages/config/HISTORY.rst b/packages/config/HISTORY.rst index e36fc636cb1f..e26373214aeb 100644 --- a/packages/config/HISTORY.rst +++ b/packages/config/HISTORY.rst @@ -3,11 +3,33 @@ History .. to_doc ------------ -24.1.3.dev0 ------------ +------------------- +24.1.3 (2024-10-25) +------------------- + + +========= +Bug fixes +========= +* Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek `_ 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 `_ ------------------- 24.1.2 (2024-09-25) diff --git a/packages/config/setup.cfg b/packages/config/setup.cfg index 68a09c9de456..8e2c029f7c74 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 = 24.1.3.dev0 +version = 24.1.3 [options] include_package_data = True diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst index 3b7ca75f5722..4f8db26820bd 100644 --- a/packages/data/HISTORY.rst +++ b/packages/data/HISTORY.rst @@ -3,11 +3,42 @@ History .. to_doc ------------ -24.1.3.dev0 ------------ +------------------- +24.1.3 (2024-10-25) +------------------- + + +========= +Bug fixes +========= + +* Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek `_ 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 `_ +============= +Other changes +============= +* Backport pod5 datatype by `@TomHarrop `_ in `#18507 `_ ------------------- 24.1.2 (2024-09-25) diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg index 809981ea6394..df8729395324 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 = 24.1.3.dev0 +version = 24.1.3 [options] include_package_data = True diff --git a/packages/files/HISTORY.rst b/packages/files/HISTORY.rst index 8777207afa0f..2977800420b0 100644 --- a/packages/files/HISTORY.rst +++ b/packages/files/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc ------------ -24.1.3.dev0 ------------ - +------------------- +24.1.3 (2024-10-25) +------------------- +No recorded changes since last release ------------------- 24.1.2 (2024-09-25) diff --git a/packages/files/setup.cfg b/packages/files/setup.cfg index 85b2493e0f5b..90e05e0c88c3 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 = 24.1.3.dev0 +version = 24.1.3 [options] include_package_data = True diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst index 3f2f246b5331..837b10a16bb5 100644 --- a/packages/job_execution/HISTORY.rst +++ b/packages/job_execution/HISTORY.rst @@ -3,11 +3,17 @@ History .. to_doc ------------ -24.1.3.dev0 ------------ +------------------- +24.1.3 (2024-10-25) +------------------- +========= +Bug fixes +========= + +* Add input extra files to `get_input_fnames` by `@mvdbeek `_ in `#18462 `_ +* Retry container monitor POST if it fails (don't assume it succeeded) by `@natefoo `_ in `#18863 `_ ------------------- 24.1.2 (2024-09-25) diff --git a/packages/job_execution/setup.cfg b/packages/job_execution/setup.cfg index 1dfa56e605e2..e879823fa0c9 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 = 24.1.3.dev0 +version = 24.1.3 [options] include_package_data = True diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst index 025d1cb59bcf..4a27a18e2f3b 100644 --- a/packages/job_metrics/HISTORY.rst +++ b/packages/job_metrics/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc ------------ -24.1.3.dev0 ------------ - +------------------- +24.1.3 (2024-10-25) +------------------- +No recorded changes since last release ------------------- 24.1.2 (2024-09-25) diff --git a/packages/job_metrics/setup.cfg b/packages/job_metrics/setup.cfg index 83ce8bebcf0e..3f025e2e7b1c 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 = 24.1.3.dev0 +version = 24.1.3 [options] include_package_data = True diff --git a/packages/navigation/HISTORY.rst b/packages/navigation/HISTORY.rst index 7c2eb4dde9ff..4b2922b16894 100644 --- a/packages/navigation/HISTORY.rst +++ b/packages/navigation/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc ------------ -24.1.3.dev0 ------------ - +------------------- +24.1.3 (2024-10-25) +------------------- +No recorded changes since last release ------------------- 24.1.2 (2024-09-25) diff --git a/packages/navigation/setup.cfg b/packages/navigation/setup.cfg index 63851150c254..6ca1cb9ceb1e 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 = 24.1.3.dev0 +version = 24.1.3 [options] include_package_data = True diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst index bbf9af4264fa..2d03908fe63e 100644 --- a/packages/objectstore/HISTORY.rst +++ b/packages/objectstore/HISTORY.rst @@ -3,11 +3,16 @@ History .. to_doc ------------ -24.1.3.dev0 ------------ +------------------- +24.1.3 (2024-10-25) +------------------- +========= +Bug fixes +========= + +* Fix shared caches with extended metadata collection. by `@jmchilton `_ in `#18520 `_ ------------------- 24.1.2 (2024-09-25) diff --git a/packages/objectstore/setup.cfg b/packages/objectstore/setup.cfg index 986fd23622e0..7b2639dc5265 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 = 24.1.3.dev0 +version = 24.1.3 [options] include_package_data = True diff --git a/packages/schema/HISTORY.rst b/packages/schema/HISTORY.rst index eab78124ea70..7d14c9f4cc5d 100644 --- a/packages/schema/HISTORY.rst +++ b/packages/schema/HISTORY.rst @@ -3,11 +3,27 @@ History .. to_doc ------------ -24.1.3.dev0 ------------ +------------------- +24.1.3 (2024-10-25) +------------------- + + +========= +Bug fixes +========= + +* Handle error when workflow is unowned in Invocation view by `@ahmedhamidawan `_ 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 `_ +============ +Enhancements +============ +* Include workflow invocation id in exception logs by `@mvdbeek `_ in `#18594 `_ ------------------- 24.1.2 (2024-09-25) diff --git a/packages/schema/setup.cfg b/packages/schema/setup.cfg index d8d9801ffcd5..e9e5c544f52f 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 = 24.1.3.dev0 +version = 24.1.3 [options] include_package_data = True diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst index 514f1cd8b30d..214afe898a1b 100644 --- a/packages/selenium/HISTORY.rst +++ b/packages/selenium/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc ------------ -24.1.3.dev0 ------------ - +------------------- +24.1.3 (2024-10-25) +------------------- +No recorded changes since last release ------------------- 24.1.2 (2024-09-25) diff --git a/packages/selenium/setup.cfg b/packages/selenium/setup.cfg index 6e6e3028e5a0..453814c9eedf 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 = 24.1.3.dev0 +version = 24.1.3 [options] include_package_data = True diff --git a/packages/test_api/HISTORY.rst b/packages/test_api/HISTORY.rst index 9c111a54405c..b01c74d6e4cf 100644 --- a/packages/test_api/HISTORY.rst +++ b/packages/test_api/HISTORY.rst @@ -3,11 +3,30 @@ History .. to_doc ------------ -24.1.3.dev0 ------------ +------------------- +24.1.3 (2024-10-25) +------------------- + +========= +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 `_ ------------------- 24.1.2 (2024-09-25) diff --git a/packages/test_api/setup.cfg b/packages/test_api/setup.cfg index e12a23480d30..1be4124469ce 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 = 24.1.3.dev0 +version = 24.1.3 [options] include_package_data = True diff --git a/packages/test_base/HISTORY.rst b/packages/test_base/HISTORY.rst index 8ff6be4ce45b..853474357755 100644 --- a/packages/test_base/HISTORY.rst +++ b/packages/test_base/HISTORY.rst @@ -3,11 +3,20 @@ History .. to_doc ------------ -24.1.3.dev0 ------------ +------------------- +24.1.3 (2024-10-25) +------------------- + +========= +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 `_ ------------------- 24.1.2 (2024-09-25) diff --git a/packages/test_base/setup.cfg b/packages/test_base/setup.cfg index 10bf9226dfce..a64852e825f9 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 = 24.1.3.dev0 +version = 24.1.3 [options] include_package_data = True diff --git a/packages/test_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst index 3c7b1543b69a..3e9e63eefc27 100644 --- a/packages/test_driver/HISTORY.rst +++ b/packages/test_driver/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc ------------ -24.1.3.dev0 ------------ - +------------------- +24.1.3 (2024-10-25) +------------------- +No recorded changes since last release ------------------- 24.1.2 (2024-09-25) diff --git a/packages/test_driver/setup.cfg b/packages/test_driver/setup.cfg index 7b17e7629764..c23e40a31f93 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 = 24.1.3.dev0 +version = 24.1.3 [options] include_package_data = True diff --git a/packages/tool_shed/HISTORY.rst b/packages/tool_shed/HISTORY.rst index 4bbe31d51aa5..5cfb5ec4e92f 100644 --- a/packages/tool_shed/HISTORY.rst +++ b/packages/tool_shed/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc ------------ -24.1.3.dev0 ------------ - +------------------- +24.1.3 (2024-10-25) +------------------- +No recorded changes since last release ------------------- 24.1.2 (2024-09-25) diff --git a/packages/tool_shed/setup.cfg b/packages/tool_shed/setup.cfg index 7a0edb5c9b86..ef77987c564b 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 = 24.1.3.dev0 +version = 24.1.3 [options] include_package_data = True diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst index d82cb227c96a..29ff0190f927 100644 --- a/packages/tool_util/HISTORY.rst +++ b/packages/tool_util/HISTORY.rst @@ -3,11 +3,28 @@ History .. to_doc ------------ -24.1.3.dev0 ------------ +------------------- +24.1.3 (2024-10-25) +------------------- + + +========= +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 `_ +============ +Enhancements +============ + +* Make `default_panel_view` a `_by_host` option by `@natefoo `_ in `#18471 `_ ------------------- 24.1.2 (2024-09-25) diff --git a/packages/tool_util/setup.cfg b/packages/tool_util/setup.cfg index 321d9bbfb8e5..ad32aeabb0e4 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 = 24.1.3.dev0 +version = 24.1.3 [options] include_package_data = True diff --git a/packages/tours/HISTORY.rst b/packages/tours/HISTORY.rst index 7a53137118c6..321a1b5fc521 100644 --- a/packages/tours/HISTORY.rst +++ b/packages/tours/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc ------------ -24.1.3.dev0 ------------ - +------------------- +24.1.3 (2024-10-25) +------------------- +No recorded changes since last release ------------------- 24.1.2 (2024-09-25) diff --git a/packages/tours/setup.cfg b/packages/tours/setup.cfg index a3dc6338c312..9e7884748c7b 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 = 24.1.3.dev0 +version = 24.1.3 [options] include_package_data = True diff --git a/packages/util/HISTORY.rst b/packages/util/HISTORY.rst index befaeb6789f5..dd5e4e77963a 100644 --- a/packages/util/HISTORY.rst +++ b/packages/util/HISTORY.rst @@ -3,11 +3,23 @@ History .. to_doc ------------ -24.1.3.dev0 ------------ +------------------- +24.1.3 (2024-10-25) +------------------- + + +========= +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 `_ ------------------- 24.1.2 (2024-09-25) diff --git a/packages/util/setup.cfg b/packages/util/setup.cfg index fdef15f66594..97d4122f78d7 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 = 24.1.3.dev0 +version = 24.1.3 [options] include_package_data = True diff --git a/packages/web_apps/HISTORY.rst b/packages/web_apps/HISTORY.rst index 4444fe0f88e6..a8521a887965 100644 --- a/packages/web_apps/HISTORY.rst +++ b/packages/web_apps/HISTORY.rst @@ -3,11 +3,46 @@ History .. to_doc ------------ -24.1.3.dev0 ------------ +------------------- +24.1.3 (2024-10-25) +------------------- + + +========= +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 `_ +============ +Enhancements +============ + +* Make `default_panel_view` a `_by_host` option by `@natefoo `_ in `#18471 `_ + +============= +Other changes +============= +* Fix check dataset check by `@mvdbeek `_ in `#18856 `_ ------------------- 24.1.2 (2024-09-25) diff --git a/packages/web_apps/setup.cfg b/packages/web_apps/setup.cfg index e1b5a1b3df03..9772c0a0d9d7 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 = 24.1.3.dev0 +version = 24.1.3 [options] include_package_data = True diff --git a/packages/web_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst index a0bd6b14bb14..d280b6551f60 100644 --- a/packages/web_framework/HISTORY.rst +++ b/packages/web_framework/HISTORY.rst @@ -3,11 +3,18 @@ History .. to_doc ------------ -24.1.3.dev0 ------------ +------------------- +24.1.3 (2024-10-25) +------------------- +========= +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 `_ ------------------- 24.1.2 (2024-09-25) diff --git a/packages/web_framework/setup.cfg b/packages/web_framework/setup.cfg index 818b3bef6076..dcc1d586e5b0 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 = 24.1.3.dev0 +version = 24.1.3 [options] include_package_data = True diff --git a/packages/web_stack/HISTORY.rst b/packages/web_stack/HISTORY.rst index e7ebb3235a0a..3f8e8989d6cd 100644 --- a/packages/web_stack/HISTORY.rst +++ b/packages/web_stack/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc ------------ -24.1.3.dev0 ------------ - +------------------- +24.1.3 (2024-10-25) +------------------- +No recorded changes since last release ------------------- 24.1.2 (2024-09-25) diff --git a/packages/web_stack/setup.cfg b/packages/web_stack/setup.cfg index dd04dc39fe43..552e33bfa664 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 = 24.1.3.dev0 +version = 24.1.3 [options] include_package_data = True