diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst index ea152aca9bc8..f9be5d0c2c44 100644 --- a/packages/app/HISTORY.rst +++ b/packages/app/HISTORY.rst @@ -9,6 +9,69 @@ History +------------------- +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/auth/HISTORY.rst b/packages/auth/HISTORY.rst index 5d9a1f321ef1..0b1fe1f96777 100644 --- a/packages/auth/HISTORY.rst +++ b/packages/auth/HISTORY.rst @@ -9,6 +9,12 @@ History +------------------- +24.1.3 (2024-10-25) +------------------- + +No recorded changes since last release + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/config/HISTORY.rst b/packages/config/HISTORY.rst index 0d24cbb05150..f0830913c6ba 100644 --- a/packages/config/HISTORY.rst +++ b/packages/config/HISTORY.rst @@ -9,6 +9,34 @@ History +------------------- +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/data/HISTORY.rst b/packages/data/HISTORY.rst index f3b5913f9da8..8675381f8ed3 100644 --- a/packages/data/HISTORY.rst +++ b/packages/data/HISTORY.rst @@ -9,6 +9,43 @@ History +------------------- +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/files/HISTORY.rst b/packages/files/HISTORY.rst index 8bc4ff5427ab..43ce2b0b9aed 100644 --- a/packages/files/HISTORY.rst +++ b/packages/files/HISTORY.rst @@ -9,6 +9,12 @@ History +------------------- +24.1.3 (2024-10-25) +------------------- + +No recorded changes since last release + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst index 2153ce10970b..8c8b3e582df9 100644 --- a/packages/job_execution/HISTORY.rst +++ b/packages/job_execution/HISTORY.rst @@ -9,6 +9,18 @@ History +------------------- +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_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst index d6a048415a20..ba1f72267756 100644 --- a/packages/job_metrics/HISTORY.rst +++ b/packages/job_metrics/HISTORY.rst @@ -9,6 +9,12 @@ History +------------------- +24.1.3 (2024-10-25) +------------------- + +No recorded changes since last release + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/navigation/HISTORY.rst b/packages/navigation/HISTORY.rst index 65a78836ad82..9335c5e711c3 100644 --- a/packages/navigation/HISTORY.rst +++ b/packages/navigation/HISTORY.rst @@ -9,6 +9,12 @@ History +------------------- +24.1.3 (2024-10-25) +------------------- + +No recorded changes since last release + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst index 7a28dbaa4557..3dd302f33af3 100644 --- a/packages/objectstore/HISTORY.rst +++ b/packages/objectstore/HISTORY.rst @@ -9,6 +9,17 @@ History +------------------- +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/schema/HISTORY.rst b/packages/schema/HISTORY.rst index 3bf84da813cc..3d3f7906b03e 100644 --- a/packages/schema/HISTORY.rst +++ b/packages/schema/HISTORY.rst @@ -9,6 +9,28 @@ History +------------------- +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/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst index d1b195a7f953..4ffefd1ed665 100644 --- a/packages/selenium/HISTORY.rst +++ b/packages/selenium/HISTORY.rst @@ -9,6 +9,12 @@ History +------------------- +24.1.3 (2024-10-25) +------------------- + +No recorded changes since last release + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/test_api/HISTORY.rst b/packages/test_api/HISTORY.rst index 75536b62bb90..bf234028ba4a 100644 --- a/packages/test_api/HISTORY.rst +++ b/packages/test_api/HISTORY.rst @@ -9,6 +9,31 @@ History +------------------- +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_base/HISTORY.rst b/packages/test_base/HISTORY.rst index e2fbc283b025..b1fe44d62527 100644 --- a/packages/test_base/HISTORY.rst +++ b/packages/test_base/HISTORY.rst @@ -9,6 +9,21 @@ History +------------------- +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_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst index b568c88d14e3..9bf0b3bb9a6a 100644 --- a/packages/test_driver/HISTORY.rst +++ b/packages/test_driver/HISTORY.rst @@ -9,6 +9,12 @@ History +------------------- +24.1.3 (2024-10-25) +------------------- + +No recorded changes since last release + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/tool_shed/HISTORY.rst b/packages/tool_shed/HISTORY.rst index 19ef42776f91..2aa871d38110 100644 --- a/packages/tool_shed/HISTORY.rst +++ b/packages/tool_shed/HISTORY.rst @@ -9,6 +9,12 @@ History +------------------- +24.1.3 (2024-10-25) +------------------- + +No recorded changes since last release + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst index 8210bdf311bc..2029f248f474 100644 --- a/packages/tool_util/HISTORY.rst +++ b/packages/tool_util/HISTORY.rst @@ -9,6 +9,29 @@ History +------------------- +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/tours/HISTORY.rst b/packages/tours/HISTORY.rst index 5841b78a1b2a..299f49d226cb 100644 --- a/packages/tours/HISTORY.rst +++ b/packages/tours/HISTORY.rst @@ -9,6 +9,12 @@ History +------------------- +24.1.3 (2024-10-25) +------------------- + +No recorded changes since last release + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/util/HISTORY.rst b/packages/util/HISTORY.rst index 99e03538b67a..b10181d09d18 100644 --- a/packages/util/HISTORY.rst +++ b/packages/util/HISTORY.rst @@ -9,6 +9,24 @@ History +------------------- +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/web_apps/HISTORY.rst b/packages/web_apps/HISTORY.rst index d60e3b0910f7..5bd9bbd99b5e 100644 --- a/packages/web_apps/HISTORY.rst +++ b/packages/web_apps/HISTORY.rst @@ -9,6 +9,47 @@ History +------------------- +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_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst index 4aeb57285e9d..e292950eda69 100644 --- a/packages/web_framework/HISTORY.rst +++ b/packages/web_framework/HISTORY.rst @@ -9,6 +9,19 @@ History +------------------- +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_stack/HISTORY.rst b/packages/web_stack/HISTORY.rst index ddde231f1d27..6f38d7c99476 100644 --- a/packages/web_stack/HISTORY.rst +++ b/packages/web_stack/HISTORY.rst @@ -9,6 +9,12 @@ History +------------------- +24.1.3 (2024-10-25) +------------------- + +No recorded changes since last release + ------------------- 24.1.2 (2024-09-25) -------------------