diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst index b0d01e41d70c..47cae38a34ed 100644 --- a/packages/app/HISTORY.rst +++ b/packages/app/HISTORY.rst @@ -4,11 +4,35 @@ History .. to_doc --------- -23.2.dev0 +23.3.dev0 --------- +------------------- +23.1.2 (2023-11-29) +------------------- + + +========= +Bug fixes +========= + +* Fix unbound ``runner`` variable when there is an error in the job config by `@mvdbeek `_ in `#16906 `_ +* Fix discarded dataset ordering in Storage Dashboard by `@davelopez `_ in `#16929 `_ +* Include owner's annotation when exporting workflow by `@dannon `_ in `#16930 `_ +* Skip state filtering in ``__MERGE_COLLECTION__`` tool by `@mvdbeek `_ in `#16937 `_ +* Prevent Singular external auth users from disconnecting identity by `@ahmedhamidawan `_ in `#16961 `_ +* Prevent workflow submission with missing input values by `@mvdbeek `_ in `#17048 `_ +* Fix extra files collection if using ``store_by="id"`` and `outputs_to_working_directory` by `@mvdbeek `_ in `#17067 `_ +* Remove rollback from ``__check_jobs_at_startup`` by `@mvdbeek `_ in `#17085 `_ + +============ +Enhancements +============ + +* Improve invocation error reporting by `@mvdbeek `_ in `#16917 `_ + ------------------- 23.1.1 (2023-10-23) ------------------- @@ -158,6 +182,7 @@ Other changes Bug fixes ========= +* * Fix upload paramfile handling (for real user setups) by `@bernt-matthias `_ in `#16504 `_ * Fix extra files path handling by `@mvdbeek `_ in `#16541 `_ * Make sure job_wrapper uses a consistent metadata strategy by `@mvdbeek `_ in `#16569 `_ @@ -171,6 +196,7 @@ Bug fixes Enhancements ============ +* * Update pulsar client library to 0.15.5 by `@mvdbeek `_ in `#16701 `_ ------------------- @@ -182,6 +208,7 @@ Enhancements Bug fixes ========= +* * * Skip installing npm/yarn if available, fix conditional dependency parsing, create virtualenv via conda when conda active by `@bernt-matthias `_ in `#16403 `_ * Fix test discovery in vscode by `@mvdbeek `_ in `#16413 `_ @@ -196,6 +223,7 @@ Bug fixes Bug fixes ========= +* * * * Fix default when statement evaluation by `@mvdbeek `_ in `#16332 `_ @@ -213,12 +241,14 @@ Bug fixes * * * +* * Bump galaxy-release-util version to 0.1.2 by `@mvdbeek `_ in `#16241 `_ ============ Enhancements ============ +* * * When importing tool data bundles, use the first loc file for the matching table by `@natefoo `_ in `#16247 `_ @@ -226,6 +256,7 @@ Enhancements Other changes ============= +* * Forward port of slugify username received from oidc by `@nuwang `_ in `#16271 `_ ------------------- @@ -241,6 +272,7 @@ Bug fixes * * * +* * Fix ``Text File Busy`` errors at the source by `@mvdbeek `_ in `#16212 `_ ============ @@ -251,6 +283,7 @@ Enhancements * * * +* * Point release deps fixes and docs by `@mvdbeek `_ in `#16214 `_ * Use galaxy-release-util to upload python packages by `@mvdbeek `_ in `#16240 `_ @@ -268,6 +301,7 @@ Bug fixes * * * +* * Display DCE in job parameter component, allow rerunning with DCE input by `@mvdbeek `_ in `#15744 `_ * Fix mixed outputs_to_working_directory pulsar destinations by `@mvdbeek `_ in `#15927 `_ * Update Gravity to 1.0.3 by `@natefoo `_ in `#15939 `_ @@ -295,6 +329,7 @@ Other changes * * * +* * Startup fix when tool removed between reboot by `@mvdbeek `_ in `#16175 `_ ------------------- diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst index 3bff8a7b7b14..a5d88011d189 100644 --- a/packages/auth/HISTORY.rst +++ b/packages/auth/HISTORY.rst @@ -4,11 +4,17 @@ History .. to_doc --------- -23.2.dev0 +23.3.dev0 --------- +------------------- +23.1.2 (2023-11-29) +------------------- + +No recorded changes since last release + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/config/HISTORY.rst b/packages/config/HISTORY.rst index 9ccf708e7354..a3393b389c4e 100644 --- a/packages/config/HISTORY.rst +++ b/packages/config/HISTORY.rst @@ -4,11 +4,29 @@ History .. to_doc --------- -23.2.dev0 +23.3.dev0 --------- +------------------- +23.1.2 (2023-11-29) +------------------- + + +========= +Bug fixes +========= + +* Prevent Singular external auth users from disconnecting identity by `@ahmedhamidawan `_ in `#16961 `_ +* Set correct tool_path for packaged galaxy by `@mvdbeek `_ in `#17102 `_ + +============ +Enhancements +============ + +* Add support for larch datatypes by `@patrick-austin `_ in `#17080 `_ + ------------------- 23.1.1 (2023-10-23) ------------------- @@ -71,6 +89,7 @@ No recorded changes since last release Bug fixes ========= +* * Minor bug fix for default mail templates by `@neoformit `_ in `#16362 `_ ------------------- @@ -100,6 +119,7 @@ No recorded changes since last release Bug fixes ========= +* * * * Change default watchdog inotify_buffer log level to info by `@mvdbeek `_ in `#15967 `_ @@ -108,6 +128,7 @@ Bug fixes Enhancements ============ +* * Add ``ca_certs`` option for sentry client by `@mvdbeek `_ in `#15943 `_ ------------------- diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst index e35636ecebaa..937ee7c61875 100644 --- a/packages/data/HISTORY.rst +++ b/packages/data/HISTORY.rst @@ -4,11 +4,34 @@ History .. to_doc --------- -23.2.dev0 +23.3.dev0 --------- +------------------- +23.1.2 (2023-11-29) +------------------- + + +========= +Bug fixes +========= + +* Skip change_datatype things if we're not actually changing the extension by `@mvdbeek `_ in `#16931 `_ +* Fix copying metadata to copied job outputs by `@mvdbeek `_ in `#17007 `_ +* Update tar_to_directory dependency by `@mvdbeek `_ in `#17009 `_ +* Assert that ``DatasetCollectioElement`` has an associated object by `@mvdbeek `_ in `#17071 `_ +* Fix input dates in notifications: consider timezone offset by `@davelopez `_ in `#17088 `_ +* Allow relative URLs in broadcasts action links by `@davelopez `_ in `#17093 `_ + +============ +Enhancements +============ + +* Improve invocation error reporting by `@mvdbeek `_ in `#16917 `_ +* Add support for larch datatypes by `@patrick-austin `_ in `#17080 `_ + ------------------- 23.1.1 (2023-10-23) ------------------- @@ -106,6 +129,7 @@ Other changes Bug fixes ========= +* * Fix extra files path handling by `@mvdbeek `_ in `#16541 `_ * Don't fail invocation message without dependent_workflow_step_id by `@mvdbeek `_ in `#16628 `_ @@ -118,6 +142,7 @@ Bug fixes Bug fixes ========= +* * * Copy when_expression when copying workflow step by `@mvdbeek `_ in `#16377 `_ @@ -148,6 +173,7 @@ No recorded changes since last release Bug fixes ========= +* * * * Display DCE in job parameter component, allow rerunning with DCE input by `@mvdbeek `_ in `#15744 `_ diff --git a/packages/files/HISTORY.rst b/packages/files/HISTORY.rst index 0e421ead2f62..fb7af8327431 100644 --- a/packages/files/HISTORY.rst +++ b/packages/files/HISTORY.rst @@ -4,11 +4,22 @@ History .. to_doc --------- -23.2.dev0 +23.3.dev0 --------- +------------------- +23.1.2 (2023-11-29) +------------------- + + +========= +Bug fixes +========= + +* Implement missing upload for S3 file sources by `@davelopez `_ in `#17100 `_ + ------------------- 23.1.1 (2023-10-23) ------------------- @@ -62,6 +73,7 @@ No recorded changes since last release Bug fixes ========= +* * Fix dropbox import to support newer versions by `@nuwang `_ in `#16239 `_ ------------------- diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst index 293a0b094613..4184ca61a225 100644 --- a/packages/job_execution/HISTORY.rst +++ b/packages/job_execution/HISTORY.rst @@ -4,11 +4,24 @@ History .. to_doc --------- -23.2.dev0 +23.3.dev0 --------- +------------------- +23.1.2 (2023-11-29) +------------------- + + +========= +Bug fixes +========= + +* Fix library import from path linking files by `@davelopez `_ in `#16919 `_ +* Don't store job in JobIO instance attributes by `@mvdbeek `_ in `#16965 `_ +* Fix extra files collection if using ``store_by="id"`` and `outputs_to_working_directory` by `@mvdbeek `_ in `#17067 `_ + ------------------- 23.1.1 (2023-10-23) ------------------- @@ -46,6 +59,7 @@ Enhancements Bug fixes ========= +* * Fix extra files path handling by `@mvdbeek `_ in `#16541 `_ * Make sure job_wrapper uses a consistent metadata strategy by `@mvdbeek `_ in `#16569 `_ * Fixes for extra files handling and cached object stores by `@mvdbeek `_ in `#16595 `_ diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst index aa0f5dc62d37..f98aa82405d1 100644 --- a/packages/job_metrics/HISTORY.rst +++ b/packages/job_metrics/HISTORY.rst @@ -4,11 +4,17 @@ History .. to_doc --------- -23.2.dev0 +23.3.dev0 --------- +------------------- +23.1.2 (2023-11-29) +------------------- + +No recorded changes since last release + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/navigation/HISTORY.rst b/packages/navigation/HISTORY.rst index e327ef00676a..9fb4cd6994b4 100644 --- a/packages/navigation/HISTORY.rst +++ b/packages/navigation/HISTORY.rst @@ -4,11 +4,17 @@ History .. to_doc --------- -23.2.dev0 +23.3.dev0 --------- +------------------- +23.1.2 (2023-11-29) +------------------- + +No recorded changes since last release + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst index 1cc0ad482c91..b6522c1f5eb9 100644 --- a/packages/objectstore/HISTORY.rst +++ b/packages/objectstore/HISTORY.rst @@ -4,11 +4,17 @@ History .. to_doc --------- -23.2.dev0 +23.3.dev0 --------- +------------------- +23.1.2 (2023-11-29) +------------------- + +No recorded changes since last release + ------------------- 23.1.1 (2023-10-23) ------------------- @@ -49,6 +55,7 @@ Other changes Bug fixes ========= +* * Fix extra files path handling by `@mvdbeek `_ in `#16541 `_ * Fixes for extra files handling and cached object stores by `@mvdbeek `_ in `#16595 `_ diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst index 7034e144749d..82dc2d8b3736 100644 --- a/packages/selenium/HISTORY.rst +++ b/packages/selenium/HISTORY.rst @@ -4,11 +4,17 @@ History .. to_doc --------- -23.2.dev0 +23.3.dev0 --------- +------------------- +23.1.2 (2023-11-29) +------------------- + +No recorded changes since last release + ------------------- 23.1.1 (2023-10-23) ------------------- @@ -74,6 +80,7 @@ No recorded changes since last release Enhancements ============ +* * Port selenium setup to non-deprecated selenium options by `@mvdbeek `_ in `#16215 `_ ------------------- @@ -90,6 +97,7 @@ Enhancements * * * +* * Add support for launching workflows via Tutorial Mode by `@hexylena `_ in `#15684 `_ ------------------- diff --git a/packages/test_api/HISTORY.rst b/packages/test_api/HISTORY.rst index d92eeba74c5a..b47a562c434a 100644 --- a/packages/test_api/HISTORY.rst +++ b/packages/test_api/HISTORY.rst @@ -4,11 +4,29 @@ History .. to_doc --------- -23.2.dev0 +23.3.dev0 --------- +------------------- +23.1.2 (2023-11-29) +------------------- + + +========= +Bug fixes +========= + +* Skip state filtering in ``__MERGE_COLLECTION__`` tool by `@mvdbeek `_ in `#16937 `_ +* Fix duplicated tools in tool panel view section copying by `@jmchilton `_ in `#17036 `_ + +============ +Enhancements +============ + +* Improve invocation error reporting by `@mvdbeek `_ in `#16917 `_ + ------------------- 23.1.1 (2023-10-23) ------------------- @@ -91,6 +109,7 @@ No recorded changes since last release Bug fixes ========= +* * Display DCE in job parameter component, allow rerunning with DCE input by `@mvdbeek `_ in `#15744 `_ * Fix folder listing via file browser by `@mvdbeek `_ in `#15950 `_ * Fix case sensitive filtering by name in histories by `@davelopez `_ in `#16036 `_ @@ -101,6 +120,7 @@ Bug fixes Enhancements ============ +* * Add support for launching workflows via Tutorial Mode by `@hexylena `_ in `#15684 `_ * Allow setting auto_decompress property in staging interface by `@mvdbeek `_ in `#16014 `_ diff --git a/packages/test_base/HISTORY.rst b/packages/test_base/HISTORY.rst index d0ccb6166ef4..f07fb31de5d5 100644 --- a/packages/test_base/HISTORY.rst +++ b/packages/test_base/HISTORY.rst @@ -4,11 +4,22 @@ History .. to_doc --------- -23.2.dev0 +23.3.dev0 --------- +------------------- +23.1.2 (2023-11-29) +------------------- + + +========= +Bug fixes +========= + +* Fix duplicated tools in tool panel view section copying by `@jmchilton `_ in `#17036 `_ + ------------------- 23.1.1 (2023-10-23) ------------------- @@ -78,6 +89,7 @@ No recorded changes since last release Bug fixes ========= +* * Ensure history export contains all expected datasets by `@davelopez `_ in `#16013 `_ * Fix extended metadata file size handling by `@mvdbeek `_ in `#16109 `_ diff --git a/packages/test_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst index e6b6a3563240..715ffa12c043 100644 --- a/packages/test_driver/HISTORY.rst +++ b/packages/test_driver/HISTORY.rst @@ -4,11 +4,22 @@ History .. to_doc --------- -23.2.dev0 +23.3.dev0 --------- +------------------- +23.1.2 (2023-11-29) +------------------- + + +========= +Bug fixes +========= + +* Assert that ``DatasetCollectioElement`` has an associated object by `@mvdbeek `_ in `#17071 `_ + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst index b56109e98356..1d45bf4b1822 100644 --- a/packages/tool_util/HISTORY.rst +++ b/packages/tool_util/HISTORY.rst @@ -4,11 +4,30 @@ History .. to_doc --------- -23.2.dev0 +23.3.dev0 --------- +------------------- +23.1.2 (2023-11-29) +------------------- + + +========= +Bug fixes +========= + +* Change log level for duplicate data table entries to warning by `@mvdbeek `_ in `#16988 `_ +* Upgrade minimum conda to be compatible with latest conda-build by `@bernt-matthias `_ in `#17013 `_ +* Fix duplicated tools in tool panel view section copying by `@jmchilton `_ in `#17036 `_ + +============ +Enhancements +============ + +* Adds `biii` as supported xref reference type by `@kostrykin `_ in `#16952 `_ + ------------------- 23.1.1 (2023-10-23) ------------------- @@ -75,6 +94,7 @@ Other changes Bug fixes ========= +* * Fixes for extra files handling and cached object stores by `@mvdbeek `_ in `#16595 `_ * Fix create/install commands for conda 23.9.0 by `@nsoranzo `_ in `#16831 `_ @@ -87,6 +107,7 @@ Bug fixes Bug fixes ========= +* * * Allow duplicate labels in linter if outputs contain filters by `@bernt-matthias `_ in `#15933 `_ * Fix parsing tool metadata from bio.tools by `@kysrpex `_ in `#16449 `_ @@ -108,6 +129,7 @@ No recorded changes since last release Bug fixes ========= +* * * * xsd: add missing `sep` attribute for `has_n_columns` by `@bernt-matthias `_ in `#16262 `_ @@ -117,6 +139,7 @@ Bug fixes Enhancements ============ +* * When importing tool data bundles, use the first loc file for the matching table by `@natefoo `_ in `#16247 `_ ------------------- @@ -132,6 +155,7 @@ Bug fixes * * * +* * Don't fail CWL tool parsing when Cheetah not installed by `@mvdbeek `_ in `#16219 `_ * Allow skipping ``expect_num_outputs`` when ``expect_failure`` is set in tool test by `@bernt-matthias `_ in `#16237 `_ @@ -149,6 +173,7 @@ Bug fixes * * * +* * Fix assertion linting to not fail on byte suffixes by `@bernt-matthias `_ in `#15873 `_ * Fix ``get_test_from_anaconda()`` and ``base_image_for_targets()`` functions by `@nsoranzo `_ in `#16125 `_ * Fix test search for mulled container hashes by `@mvdbeek `_ in `#16170 `_ @@ -161,6 +186,7 @@ Enhancements * * * +* * Allow setting auto_decompress property in staging interface by `@mvdbeek `_ in `#16014 `_ ------------------- diff --git a/packages/tours/HISTORY.rst b/packages/tours/HISTORY.rst index b140d54e55d0..acb429863b2f 100644 --- a/packages/tours/HISTORY.rst +++ b/packages/tours/HISTORY.rst @@ -4,11 +4,17 @@ History .. to_doc --------- -23.2.dev0 +23.3.dev0 --------- +------------------- +23.1.2 (2023-11-29) +------------------- + +No recorded changes since last release + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/util/HISTORY.rst b/packages/util/HISTORY.rst index 1d1b02b7716c..c3b42ab3c7de 100644 --- a/packages/util/HISTORY.rst +++ b/packages/util/HISTORY.rst @@ -4,11 +4,22 @@ History .. to_doc --------- -23.2.dev0 +23.3.dev0 --------- +------------------- +23.1.2 (2023-11-29) +------------------- + + +============ +Enhancements +============ + +* Improve invocation error reporting by `@mvdbeek `_ in `#16917 `_ + ------------------- 23.1.1 (2023-10-23) ------------------- @@ -83,6 +94,7 @@ No recorded changes since last release Bug fixes ========= +* * Replace httpbin service with pytest-httpserver by `@mvdbeek `_ in `#16042 `_ ------------------- diff --git a/packages/web_apps/HISTORY.rst b/packages/web_apps/HISTORY.rst index f8bba3ddd201..a0b8cc6e7c03 100644 --- a/packages/web_apps/HISTORY.rst +++ b/packages/web_apps/HISTORY.rst @@ -4,11 +4,29 @@ History .. to_doc --------- -23.2.dev0 +23.3.dev0 --------- +------------------- +23.1.2 (2023-11-29) +------------------- + + +========= +Bug fixes +========= + +* Provide error message instead of internal server error by `@mvdbeek `_ in `#16905 `_ +* Fix input dates in notifications: consider timezone offset by `@davelopez `_ in `#17088 `_ + +============ +Enhancements +============ + +* Add HEAD route to job_files endpoint by `@mvdbeek `_ in `#17072 `_ + ------------------- 23.1.1 (2023-10-23) ------------------- @@ -95,6 +113,7 @@ Other changes Bug fixes ========= +* * Fix incorrect ASGI request host by `@davelopez `_ in `#16574 `_ * Allow the legacy DELETE dataset endpoint to accept any string for the history_id by `@assuntad23 `_ in `#16593 `_ @@ -107,6 +126,7 @@ Bug fixes Bug fixes ========= +* * * Fix active step display in workflow editor side panel by `@mvdbeek `_ in `#16364 `_ @@ -119,6 +139,7 @@ Bug fixes Bug fixes ========= +* * * * Fix folder access for anonymous user by `@mvdbeek `_ in `#16330 `_ @@ -135,12 +156,14 @@ Bug fixes * * * +* * Fix converting Enum value to str for Python 3.11 by `@nsoranzo `_ in `#16284 `_ ============ Enhancements ============ +* * When importing tool data bundles, use the first loc file for the matching table by `@natefoo `_ in `#16247 `_ ------------------- @@ -162,6 +185,7 @@ Bug fixes * * * +* * Display DCE in job parameter component, allow rerunning with DCE input by `@mvdbeek `_ in `#15744 `_ * Various fixes to path prefix handling by `@mvdbeek `_ in `#16033 `_ * Fix dataype_change not updating HDCA update_time by `@mvdbeek `_ in `#16099 `_ diff --git a/packages/web_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst index 03fd917fc884..f0168f08dc2c 100644 --- a/packages/web_framework/HISTORY.rst +++ b/packages/web_framework/HISTORY.rst @@ -4,11 +4,28 @@ History .. to_doc --------- -23.2.dev0 +23.3.dev0 --------- +------------------- +23.1.2 (2023-11-29) +------------------- + + +========= +Bug fixes +========= + +* Workaround issue in Routes by `@nsoranzo `_ in `#16981 `_ + +============ +Enhancements +============ + +* Add HEAD route to job_files endpoint by `@mvdbeek `_ in `#17072 `_ + ------------------- 23.1.1 (2023-10-23) ------------------- @@ -37,6 +54,7 @@ Enhancements Bug fixes ========= +* * Don't read request body into memory by `@mvdbeek `_ in `#16585 `_ ------------------- @@ -48,6 +66,7 @@ Bug fixes Bug fixes ========= +* * * Media player fix issue 16415 by `@bdwheele `_ in `#16443 `_ * Fix static file serving for ``robots.txt`` and ``favicon.ico`` when using per_host settings by `@mira-miracoli `_ in `#16459 `_ @@ -79,6 +98,7 @@ No recorded changes since last release Bug fixes ========= +* * * * Various fixes to path prefix handling by `@mvdbeek `_ in `#16033 `_ diff --git a/packages/web_stack/HISTORY.rst b/packages/web_stack/HISTORY.rst index 9c3e3b4f072b..b54deaa422be 100644 --- a/packages/web_stack/HISTORY.rst +++ b/packages/web_stack/HISTORY.rst @@ -4,11 +4,17 @@ History .. to_doc --------- -23.2.dev0 +23.3.dev0 --------- +------------------- +23.1.2 (2023-11-29) +------------------- + +No recorded changes since last release + ------------------- 23.1.1 (2023-10-23) ------------------- @@ -49,6 +55,7 @@ No recorded changes since last release Bug fixes ========= +* * Don't attempt to call a bool when using mem-self handler assignment. by `@natefoo `_ in `#16359 `_ -------------------