diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst index 8441a9d276ac..da771a434711 100644 --- a/packages/app/HISTORY.rst +++ b/packages/app/HISTORY.rst @@ -8,6 +8,131 @@ History --------- + +------------------- +23.2.1 (2024-02-21) +------------------- + + +========= +Bug fixes +========= + +* pin fs.dropboxfs to >=1 by `@bernt-matthias `_ in `#16451 `_ +* Remove unnecessary check: item cannot be None by `@jdavcs `_ in `#16550 `_ +* Fix: serialize `tool_shed_urls` directly from the API by `@davelopez `_ in `#16561 `_ +* Fix dependency update GitHub workflow by `@nsoranzo `_ in `#16639 `_ +* Ensure Job belongs to current SA session by `@jdavcs `_ in `#16647 `_ +* Account for shared usage between TS and galaxy apps by `@jdavcs `_ in `#16746 `_ +* move the email and username redacting from the role loop by `@martenson `_ in `#16805 `_ +* Fix shed unit test by `@mvdbeek `_ in `#16811 `_ +* chore: fix typos by `@afuetterer `_ in `#16851 `_ +* Fix bug in SQLAlchemy statement by `@jdavcs `_ in `#16881 `_ +* Ruff and flake8 fixes by `@nsoranzo `_ in `#16884 `_ +* Update help in relabel_from_file.xml by `@lldelisle `_ in `#16891 `_ +* Fix subtle bug in listify function + simplify list munging by `@jdavcs `_ in `#16904 `_ +* prep for updated h5py and typos by `@mr-c `_ in `#16963 `_ +* Enhancement to Tool Form page, Repeating form fields implement parameter instructions by `@hujambo-dunia `_ in `#17018 `_ +* Expose file_name property in DatasetFilenameWrapper by `@jdavcs `_ in `#17107 `_ +* Fix ``to_cwl`` for nested collections by `@mvdbeek `_ in `#17276 `_ +* Rollback invalidated transaction by `@jdavcs `_ in `#17280 `_ +* Install newer celery on python 3.8+ by `@mvdbeek `_ in `#17309 `_ +* Backport Rollback invalidated transaction: catch them earlier by `@mvdbeek `_ in `#17315 `_ +* Discard sqlalchemy session after task completion by `@mvdbeek `_ in `#17317 `_ +* Scope session for job runner monitor loop by `@mvdbeek `_ in `#17319 `_ +* Fix History contents `genome_build` filter postgresql bug by `@ahmedhamidawan `_ in `#17384 `_ +* Update python-multipart to 0.0.7 by `@nsoranzo `_ in `#17429 `_ +* Build param dict before creating entrypoint by `@mvdbeek `_ in `#17440 `_ +* Fix bug: true >> True by `@jdavcs `_ in `#17446 `_ +* Set metadata states on dataset association, not dataset by `@mvdbeek `_ in `#17474 `_ +* Remove two print statements by `@bernt-matthias `_ in `#17480 `_ +* Provide working routes.url_for every ASGI request by `@mvdbeek `_ in `#17497 `_ + +============ +Enhancements +============ + +* Implement default locations for data and collection parameters. by `@jmchilton `_ in `#14955 `_ +* Enable job resubmissions in k8s runner by `@pcm32 `_ in `#15238 `_ +* Add parameter name to validation errors by `@bernt-matthias `_ in `#15440 `_ +* Tool Shed 2.0 by `@jmchilton `_ in `#15639 `_ +* Add ability to assert metadata properties on input dataset parameters by `@bernt-matthias `_ in `#15825 `_ +* Limit number of celery task executions per second per user by `@claudiofr `_ in `#16232 `_ +* Delete non-terminal jobs and subworkflow invocations when cancelling invocation by `@mvdbeek `_ in `#16252 `_ +* Towards SQLAlchemy 2.0 (upgrades to SA Core usage) by `@jdavcs `_ in `#16264 `_ +* Update Python dependencies by `@galaxybot `_ in `#16305 `_ +* Add carbon emissions admin configuration options by `@Renni771 `_ in `#16307 `_ +* Migrate a part of the users API to Fast API by `@heisner-tillman `_ in `#16341 `_ +* Update Python dependencies by `@galaxybot `_ in `#16360 `_ +* Add Invenio RDM repository integration by `@davelopez `_ in `#16381 `_ +* Update Python dependencies by `@galaxybot `_ in `#16389 `_ +* Update Python dependencies by `@galaxybot `_ in `#16409 `_ +* Refactor FilesDialog + Remote Files API schema improvements by `@davelopez `_ in `#16420 `_ +* Towards SQLAlchemy 2.0 (upgrades to SA ORM usage in /test) by `@jdavcs `_ in `#16431 `_ +* SQLAlchemy 2.0 upgrades to ORM usage in /lib by `@jdavcs `_ in `#16434 `_ +* Update Python dependencies by `@galaxybot `_ in `#16436 `_ +* Update Python dependencies by `@galaxybot `_ in `#16485 `_ +* Rename MetadataEqualsValidator by `@bernt-matthias `_ in `#16489 `_ +* Add support for CILogon deployments in different regions than the US by `@uwwint `_ in `#16490 `_ +* Refactor/OIDC custos by `@uwwint `_ in `#16497 `_ +* Update Python dependencies by `@galaxybot `_ in `#16521 `_ +* Move database access code out of ``galaxy.util`` by `@jdavcs `_ in `#16526 `_ +* Tweak tool memory use and optimize shared memory when using preload by `@mvdbeek `_ in `#16536 `_ +* Update Python dependencies by `@galaxybot `_ in `#16577 `_ +* Vueify Tool Form Data Selector by `@guerler `_ in `#16578 `_ +* Workflow Comments 💬 by `@ElectronicBlueberry `_ in `#16612 `_ +* Switch out conditional requirement parser by `@mvdbeek `_ in `#16636 `_ +* Add scroll pagination and username filter to `HistoryPublishedList` by `@ahmedhamidawan `_ in `#16642 `_ +* Bump samtools converters by `@bernt-matthias `_ in `#16668 `_ +* Galaxy Markdown - add workflow image and license to Galaxy markdown. by `@jmchilton `_ in `#16672 `_ +* Implement instance URLs in Galaxy markdown. by `@jmchilton `_ in `#16675 `_ +* Change Sentry error reporting plug-in by `@kysrpex `_ in `#16686 `_ +* Use fs.onedatarestfs for Onedata files source plugin implementation by `@lopiola `_ in `#16690 `_ +* Enhance task monitor composable by `@davelopez `_ in `#16695 `_ +* Misc. edits/refactorings to session handling by `@jdavcs `_ in `#16712 `_ +* SQLAlchemy 2.0 upgrades (part 2) by `@jdavcs `_ in `#16724 `_ +* Update Python dependencies by `@galaxybot `_ in `#16735 `_ +* Convert ISO to UTC for Date/Time in workflow reports by `@assuntad23 `_ in `#16758 `_ +* Replace ELIXIR AAI button with Life Science login by `@sebastian-schaaf `_ in `#16762 `_ +* Update Python dependencies by `@galaxybot `_ in `#16770 `_ +* Migrate a part of the jobs API to Fast API by `@heisner-tillman `_ in `#16778 `_ +* Add EGI Check-in as OIDC authentication option by `@enolfc `_ in `#16782 `_ +* Replace file_name property with get_file_name function by `@SergeyYakubov `_ in `#16783 `_ +* Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including Podman job_conf by `@sveinugu `_ in `#16795 `_ +* Galaxy help forum integration by `@ElectronicBlueberry `_ in `#16798 `_ +* Update Python dependencies by `@galaxybot `_ in `#16807 `_ +* Another batch of SA2.0 edits in TS2.0 (part 3) by `@jdavcs `_ in `#16833 `_ +* Remove remaining legacy backbone form input elements by `@guerler `_ in `#16834 `_ +* SQLAlchemy 2.0 upgrades (part 4) by `@jdavcs `_ in `#16852 `_ +* Update Python dependencies by `@galaxybot `_ in `#16853 `_ +* Drop unused HistoryContentManager code and related tests by `@jdavcs `_ in `#16882 `_ +* Vueify Visualizations Grid by `@guerler `_ in `#16892 `_ +* Update Python dependencies by `@galaxybot `_ in `#16896 `_ +* Enable some flake8-logging-format rules in ruff by `@nsoranzo `_ in `#16915 `_ +* Remove "Create Workflow" form and allow workflow creation in editor by `@ahmedhamidawan `_ in `#16938 `_ +* Update Python dependencies by `@galaxybot `_ in `#16939 `_ +* Add helper to get dataset or collection via ``src`` and ``id`` by `@mr-c `_ in `#16953 `_ +* Allow non-optional integer/float params without value attribute by `@nsoranzo `_ in `#16966 `_ +* Update Python dependencies by `@galaxybot `_ in `#16978 `_ +* Fix invocation report to target correct workflow version. by `@jmchilton `_ in `#17008 `_ +* Update Python dependencies by `@galaxybot `_ in `#17011 `_ +* Upgrade job manager's index_query method to SA2.0 by `@jdavcs `_ in `#17020 `_ +* optimize object store cache operations by `@SergeyYakubov `_ in `#17025 `_ +* Require name for workflows on save, set default to Unnamed Workflow by `@ahmedhamidawan `_ in `#17038 `_ +* Update Python dependencies by `@galaxybot `_ in `#17050 `_ +* Migrate groups API to fastAPI by `@arash77 `_ in `#17051 `_ +* Migrate ItemTags API to FastAPI by `@arash77 `_ in `#17064 `_ +* Update Python dependencies by `@galaxybot `_ in `#17084 `_ +* Use python-isal for fast zip deflate compression in rocrate export by `@mvdbeek `_ in `#17342 `_ + +============= +Other changes +============= + +* Merge 23.1 into dev by `@mvdbeek `_ in `#16534 `_ +* Revert "[23.1] Enable job resubmissions in k8s runner" by `@nuwang `_ in `#17323 `_ +* Fix succces typo by `@mvdbeek `_ in `#17481 `_ + ------------------- 23.1.4 (2024-01-04) ------------------- diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst index d34767538af7..f31d9eb93e77 100644 --- a/packages/auth/HISTORY.rst +++ b/packages/auth/HISTORY.rst @@ -8,6 +8,13 @@ History --------- + +------------------- +23.2.1 (2024-02-21) +------------------- + +No recorded changes since last release + ------------------- 23.1.4 (2024-01-04) ------------------- diff --git a/packages/config/HISTORY.rst b/packages/config/HISTORY.rst index 7de666556510..88f3999dd738 100644 --- a/packages/config/HISTORY.rst +++ b/packages/config/HISTORY.rst @@ -8,6 +8,57 @@ History --------- + +------------------- +23.2.1 (2024-02-21) +------------------- + + +========= +Bug fixes +========= + +* pin fs.dropboxfs to >=1 by `@bernt-matthias `_ in `#16451 `_ +* MINERVA display application: enable cors, add for tabular by `@hexylena `_ in `#16737 `_ +* chore: fix typos by `@afuetterer `_ in `#16851 `_ +* Add back 1.1.0 version of Filtering1 tool by `@mvdbeek `_ in `#16883 `_ +* Set webdav file source to use temp files by default by `@davelopez `_ in `#17388 `_ + +============ +Enhancements +============ + +* Update cellxgene interactive tool to 1.1.1 by `@pcm32 `_ in `#15313 `_ +* Tool Shed 2.0 by `@jmchilton `_ in `#15639 `_ +* Limit number of celery task executions per second per user by `@claudiofr `_ in `#16232 `_ +* Add carbon emissions admin configuration options by `@Renni771 `_ in `#16307 `_ +* Add Invenio RDM repository integration by `@davelopez `_ in `#16381 `_ +* Add new datatype: STL by `@TanguyGen `_ in `#16478 `_ +* add new tabular file formats cns,cnr and cnn to datatypes_conf.xml.sample file as they are neaded for cnvkit galaxy tools by `@khaled196 `_ in `#16503 `_ +* Tweak tool memory use and optimize shared memory when using preload by `@mvdbeek `_ in `#16536 `_ +* Implement datatype upload warnings by `@jmchilton `_ in `#16564 `_ +* Support new genome browser chain file format by `@claudiofr `_ in `#16576 `_ +* Update Python dependencies by `@galaxybot `_ in `#16577 `_ +* Implement instance URLs in Galaxy markdown. by `@jmchilton `_ in `#16675 `_ +* Use fs.onedatarestfs for Onedata files source plugin implementation by `@lopiola `_ in `#16690 `_ +* Update datatypes_conf.xml.sample with docx type by `@yvanlebras `_ in `#16713 `_ +* Replace ELIXIR AAI button with Life Science login by `@sebastian-schaaf `_ in `#16762 `_ +* Add EGI Check-in as OIDC authentication option by `@enolfc `_ in `#16782 `_ +* Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including Podman job_conf by `@sveinugu `_ in `#16795 `_ +* Galaxy help forum integration by `@ElectronicBlueberry `_ in `#16798 `_ +* Remove record access handling for Invenio RDM plugin by `@davelopez `_ in `#16900 `_ +* optimize object store cache operations by `@SergeyYakubov `_ in `#17025 `_ +* Support configuring job metrics inline, update documentation by `@natefoo `_ in `#17178 `_ +* Add binary datatypes for intermediate output of fastk tools by `@astrovsky01 `_ in `#17265 `_ +* Add magres datatype by `@martenson `_ in `#17499 `_ + +============= +Other changes +============= + +* Merge 23.1 into dev by `@mvdbeek `_ in `#16534 `_ +* Remove xml remnant in sample yml job conf by `@bernt-matthias `_ in `#16609 `_ + ------------------- 23.1.4 (2024-01-04) ------------------- diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst index fb62bc58b6c7..cd266a6800ec 100644 --- a/packages/data/HISTORY.rst +++ b/packages/data/HISTORY.rst @@ -8,6 +8,77 @@ History --------- + +------------------- +23.2.1 (2024-02-21) +------------------- + + +========= +Bug fixes +========= + +* Rename to_dict to populate in FormDefintion to fix bug by `@jdavcs `_ in `#16553 `_ +* MINERVA display application: enable cors, add for tabular by `@hexylena `_ in `#16737 `_ +* Use AlignedSegment.to_string by `@mvdbeek `_ in `#16803 `_ +* Ruff and flake8 fixes by `@nsoranzo `_ in `#16884 `_ +* prep for updated h5py and typos by `@mr-c `_ in `#16963 `_ +* Fix cardinality violation error: subquery returns multiple results by `@jdavcs `_ in `#17224 `_ +* Fix Display Application link generation by `@mvdbeek `_ in `#17227 `_ +* Display application fixes and tests by `@mvdbeek `_ in `#17233 `_ +* Rollback invalidated transaction by `@jdavcs `_ in `#17280 `_ +* Set metadata states on dataset association, not dataset by `@mvdbeek `_ in `#17474 `_ +* Provide working routes.url_for every ASGI request by `@mvdbeek `_ in `#17497 `_ + +============ +Enhancements +============ + +* Implement default locations for data and collection parameters. by `@jmchilton `_ in `#14955 `_ +* Display beginning of non-text files as text instead of triggering a download by `@SergeyYakubov `_ in `#15447 `_ +* Tool Shed 2.0 by `@jmchilton `_ in `#15639 `_ +* Limit number of celery task executions per second per user by `@claudiofr `_ in `#16232 `_ +* Delete non-terminal jobs and subworkflow invocations when cancelling invocation by `@mvdbeek `_ in `#16252 `_ +* Towards SQLAlchemy 2.0 (upgrades to SA Core usage) by `@jdavcs `_ in `#16264 `_ +* Update Python dependencies by `@galaxybot `_ in `#16409 `_ +* Towards SQLAlchemy 2.0 (upgrades to SA ORM usage in /test) by `@jdavcs `_ in `#16431 `_ +* SQLAlchemy 2.0 upgrades to ORM usage in /lib by `@jdavcs `_ in `#16434 `_ +* Update Python dependencies by `@galaxybot `_ in `#16436 `_ +* Implement datatype upload warnings by `@jmchilton `_ in `#16564 `_ +* Support new genome browser chain file format by `@claudiofr `_ in `#16576 `_ +* Workflow Comments 💬 by `@ElectronicBlueberry `_ in `#16612 `_ +* Bump samtools converters by `@bernt-matthias `_ in `#16668 `_ +* Misc. edits/refactorings to session handling by `@jdavcs `_ in `#16712 `_ +* SQLAlchemy 2.0 upgrades (part 2) by `@jdavcs `_ in `#16724 `_ +* Migrate `collection elements` store to Pinia by `@davelopez `_ in `#16725 `_ +* Reset autocommit to False by `@jdavcs `_ in `#16745 `_ +* Drop legacy server-side search by `@jdavcs `_ in `#16755 `_ +* Optimize iteration in DatasetInstance model + SA2.0 fix by `@jdavcs `_ in `#16776 `_ +* Migrate a part of the jobs API to Fast API by `@heisner-tillman `_ in `#16778 `_ +* Replace file_name property with get_file_name function by `@SergeyYakubov `_ in `#16783 `_ +* Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including Podman job_conf by `@sveinugu `_ in `#16795 `_ +* Allow partial matches in workflow name tag search and search all tags for unquoted query by `@ahmedhamidawan `_ in `#16860 `_ +* Vueify Visualizations Grid by `@guerler `_ in `#16892 `_ +* Standardize to W3C naming for color. by `@dannon `_ in `#16949 `_ +* Move and re-use persist_extra_files by `@mvdbeek `_ in `#16955 `_ +* Fix invocation report to target correct workflow version. by `@jmchilton `_ in `#17008 `_ +* optimize object store cache operations by `@SergeyYakubov `_ in `#17025 `_ +* Use python-isal for fast zip deflate compression in rocrate export by `@mvdbeek `_ in `#17342 `_ +* Add magres datatype by `@martenson `_ in `#17499 `_ + +============= +Other changes +============= + +* Merge 23.1 into dev by `@mvdbeek `_ in `#16534 `_ +* Merge release_23.1 into dev by `@mvdbeek `_ in `#16768 `_ +* Create db head merge revision. by `@dannon `_ in `#16838 `_ +* merge release_23.1 into dev by `@martenson `_ in `#16933 `_ +* Minor clarification/typo fix in datatypes.data by `@dannon `_ in `#16993 `_ +* Fix `.file_name` access in merge forward by `@mvdbeek `_ in `#17097 `_ +* Backport model store fixes by `@mvdbeek `_ in `#17439 `_ +* Fix succces typo by `@mvdbeek `_ in `#17481 `_ + ------------------- 23.1.4 (2024-01-04) ------------------- diff --git a/packages/files/HISTORY.rst b/packages/files/HISTORY.rst index 92cfb088f68e..76ae16eb1c73 100644 --- a/packages/files/HISTORY.rst +++ b/packages/files/HISTORY.rst @@ -8,6 +8,31 @@ History --------- + +------------------- +23.2.1 (2024-02-21) +------------------- + + +========= +Bug fixes +========= + +* pin fs.dropboxfs to >=1 by `@bernt-matthias `_ in `#16451 `_ +* Write to a temp filename in posix file source plugin by `@natefoo `_ in `#17350 `_ +* Set webdav file source to use temp files by default by `@davelopez `_ in `#17388 `_ +* More defensive access of extra props in filesources by `@nuwang `_ in `#17445 `_ + +============ +Enhancements +============ + +* Add Invenio RDM repository integration by `@davelopez `_ in `#16381 `_ +* Refactor FilesDialog + Remote Files API schema improvements by `@davelopez `_ in `#16420 `_ +* Use fs.onedatarestfs for Onedata files source plugin implementation by `@lopiola `_ in `#16690 `_ +* Remove record access handling for Invenio RDM plugin by `@davelopez `_ in `#16900 `_ +* Enhance Invenio RDM integration by `@davelopez `_ in `#16964 `_ + ------------------- 23.1.4 (2024-01-04) ------------------- diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst index e153373a4889..f06fe643a273 100644 --- a/packages/job_execution/HISTORY.rst +++ b/packages/job_execution/HISTORY.rst @@ -8,6 +8,21 @@ History --------- + +------------------- +23.2.1 (2024-02-21) +------------------- + + +============ +Enhancements +============ + +* Replace file_name property with get_file_name function by `@SergeyYakubov `_ in `#16783 `_ +* Enable some flake8-logging-format rules in ruff by `@nsoranzo `_ in `#16915 `_ +* Move and re-use persist_extra_files by `@mvdbeek `_ in `#16955 `_ +* optimize object store cache operations by `@SergeyYakubov `_ in `#17025 `_ + ------------------- 23.1.4 (2024-01-04) ------------------- diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst index e44fe3049ab9..77a01312a7d2 100644 --- a/packages/job_metrics/HISTORY.rst +++ b/packages/job_metrics/HISTORY.rst @@ -8,6 +8,24 @@ History --------- + +------------------- +23.2.1 (2024-02-21) +------------------- + + +========= +Bug fixes +========= + +* Add support for Cgroupsv2 by `@natefoo `_ in `#17169 `_ + +============ +Enhancements +============ + +* Support configuring job metrics inline, update documentation by `@natefoo `_ in `#17178 `_ + ------------------- 23.1.4 (2024-01-04) ------------------- diff --git a/packages/navigation/HISTORY.rst b/packages/navigation/HISTORY.rst index 6ce702dca0cf..ec2f2037b3b2 100644 --- a/packages/navigation/HISTORY.rst +++ b/packages/navigation/HISTORY.rst @@ -8,6 +8,13 @@ History --------- + +------------------- +23.2.1 (2024-02-21) +------------------- + +No recorded changes since last release + ------------------- 23.1.4 (2024-01-04) ------------------- diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst index d036a4451c51..7cf4cc52e3a0 100644 --- a/packages/objectstore/HISTORY.rst +++ b/packages/objectstore/HISTORY.rst @@ -8,6 +8,25 @@ History --------- + +------------------- +23.2.1 (2024-02-21) +------------------- + + +============ +Enhancements +============ + +* Move and re-use persist_extra_files by `@mvdbeek `_ in `#16955 `_ +* optimize object store cache operations by `@SergeyYakubov `_ in `#17025 `_ + +============= +Other changes +============= + +* Merge 23.1 into dev by `@mvdbeek `_ in `#16534 `_ + ------------------- 23.1.4 (2024-01-04) ------------------- diff --git a/packages/schema/HISTORY.rst b/packages/schema/HISTORY.rst index a23b80b80131..57e805c129cb 100644 --- a/packages/schema/HISTORY.rst +++ b/packages/schema/HISTORY.rst @@ -4,7 +4,13 @@ History .. to_doc --------- -23.2.dev0 +24.0.dev0 --------- -* First release. + + +------------------- +23.2.1 (2024-02-21) +------------------- + +First release diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst index d8a77c091d9e..452e421c32e8 100644 --- a/packages/selenium/HISTORY.rst +++ b/packages/selenium/HISTORY.rst @@ -8,6 +8,25 @@ History --------- + +------------------- +23.2.1 (2024-02-21) +------------------- + + +============ +Enhancements +============ + +* Vueify Data Uploader by `@guerler `_ in `#16472 `_ +* Create reusable `FilterMenu` with advanced options by `@ahmedhamidawan `_ in `#16522 `_ +* Implement datatype upload warnings by `@jmchilton `_ in `#16564 `_ +* Update Python dependencies by `@galaxybot `_ in `#16577 `_ +* Vueify Tool Form Data Selector by `@guerler `_ in `#16578 `_ +* Workflow Comments 💬 by `@ElectronicBlueberry `_ in `#16612 `_ +* Workflow Embed by `@ElectronicBlueberry `_ in `#16657 `_ +* Remove "Create Workflow" form and allow workflow creation in editor by `@ahmedhamidawan `_ in `#16938 `_ + ------------------- 23.1.4 (2024-01-04) ------------------- diff --git a/packages/test_api/HISTORY.rst b/packages/test_api/HISTORY.rst index 13160613feb4..d6caa01d1841 100644 --- a/packages/test_api/HISTORY.rst +++ b/packages/test_api/HISTORY.rst @@ -8,6 +8,44 @@ History --------- + +------------------- +23.2.1 (2024-02-21) +------------------- + + +========= +Bug fixes +========= + +* Fix: serialize `tool_shed_urls` directly from the API by `@davelopez `_ in `#16561 `_ +* Restore ToolsApi and create new api route for new panel structure by `@ahmedhamidawan `_ in `#16872 `_ +* Ruff and flake8 fixes by `@nsoranzo `_ in `#16884 `_ +* Make payload optional again for create tag API by `@nsoranzo `_ in `#17144 `_ +* Only check access permissions in `/api/{history_dataset_collection_id}/contents/{dataset_collection_id}` by `@mvdbeek `_ in `#17459 `_ + +============ +Enhancements +============ + +* Implement default locations for data and collection parameters. by `@jmchilton `_ in `#14955 `_ +* Delete non-terminal jobs and subworkflow invocations when cancelling invocation by `@mvdbeek `_ in `#16252 `_ +* Migrate a part of the users API to Fast API by `@heisner-tillman `_ in `#16341 `_ +* Refactor Tool Panel views structures and combine ToolBox and ToolBoxWorkflow into one component by `@ahmedhamidawan `_ in `#16739 `_ +* Don't copy collection elements in ``test_dataset_collection_hide_originals`` by `@nsoranzo `_ in `#16747 `_ +* Drop legacy server-side search by `@jdavcs `_ in `#16755 `_ +* Migrate a part of the jobs API to Fast API by `@heisner-tillman `_ in `#16778 `_ +* Vueify Visualizations Grid by `@guerler `_ in `#16892 `_ +* Change `api/tool_panel` to `api/tool_panels/...` by `@ahmedhamidawan `_ in `#16928 `_ +* Require name for workflows on save, set default to Unnamed Workflow by `@ahmedhamidawan `_ in `#17038 `_ +* Migrate ItemTags API to FastAPI by `@arash77 `_ in `#17064 `_ + +============= +Other changes +============= + +* Merge 23.1 into dev by `@mvdbeek `_ in `#16534 `_ + ------------------- 23.1.4 (2024-01-04) ------------------- diff --git a/packages/test_base/HISTORY.rst b/packages/test_base/HISTORY.rst index beb7c49f68c6..ed1e6f6a19a5 100644 --- a/packages/test_base/HISTORY.rst +++ b/packages/test_base/HISTORY.rst @@ -8,6 +8,28 @@ History --------- + +------------------- +23.2.1 (2024-02-21) +------------------- + + +========= +Bug fixes +========= + +* Restore ToolsApi and create new api route for new panel structure by `@ahmedhamidawan `_ in `#16872 `_ + +============ +Enhancements +============ + +* Implement default locations for data and collection parameters. by `@jmchilton `_ in `#14955 `_ +* Delete non-terminal jobs and subworkflow invocations when cancelling invocation by `@mvdbeek `_ in `#16252 `_ +* Augment pgcleanup to allow periodically deleting old datasets. by `@jmchilton `_ in `#16340 `_ +* Refactor Tool Panel views structures and combine ToolBox and ToolBoxWorkflow into one component by `@ahmedhamidawan `_ in `#16739 `_ +* Change `api/tool_panel` to `api/tool_panels/...` by `@ahmedhamidawan `_ in `#16928 `_ + ------------------- 23.1.4 (2024-01-04) ------------------- diff --git a/packages/test_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst index 6af909c4c5fd..8065b4b64e8b 100644 --- a/packages/test_driver/HISTORY.rst +++ b/packages/test_driver/HISTORY.rst @@ -8,6 +8,25 @@ History --------- + +------------------- +23.2.1 (2024-02-21) +------------------- + + +========= +Bug fixes +========= + +* Tool Shed 2.0 fixes by `@nsoranzo `_ in `#16825 `_ + +============ +Enhancements +============ + +* Limit number of celery task executions per second per user by `@claudiofr `_ in `#16232 `_ +* Tweak tool memory use and optimize shared memory when using preload by `@mvdbeek `_ in `#16536 `_ + ------------------- 23.1.4 (2024-01-04) ------------------- diff --git a/packages/tool_shed/HISTORY.rst b/packages/tool_shed/HISTORY.rst index a23b80b80131..57e805c129cb 100644 --- a/packages/tool_shed/HISTORY.rst +++ b/packages/tool_shed/HISTORY.rst @@ -4,7 +4,13 @@ History .. to_doc --------- -23.2.dev0 +24.0.dev0 --------- -* First release. + + +------------------- +23.2.1 (2024-02-21) +------------------- + +First release diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst index a97ccaa5ba05..a84ffd9e5d71 100644 --- a/packages/tool_util/HISTORY.rst +++ b/packages/tool_util/HISTORY.rst @@ -8,6 +8,51 @@ History --------- + +------------------- +23.2.1 (2024-02-21) +------------------- + + +========= +Bug fixes +========= + +* Never consider `_galaxy_` conda env as unused by `@bernt-matthias `_ in `#16460 `_ +* chore: fix typos by `@afuetterer `_ in `#16851 `_ +* Ruff and flake8 fixes by `@nsoranzo `_ in `#16884 `_ +* Quote singularity env parameters by `@bernt-matthias `_ in `#17055 `_ +* Remove duplicates when copying sections for tool panel view by `@bernt-matthias `_ in `#17117 `_ +* Display application fixes and tests by `@mvdbeek `_ in `#17233 `_ + +============ +Enhancements +============ + +* Implement default locations for data and collection parameters. by `@jmchilton `_ in `#14955 `_ +* Add framework test for profile behavior of `format="input"` by `@bernt-matthias `_ in `#15482 `_ +* Tool Shed 2.0 by `@jmchilton `_ in `#15639 `_ +* Add ability to assert metadata properties on input dataset parameters by `@bernt-matthias `_ in `#15825 `_ +* Migrate a part of the users API to Fast API by `@heisner-tillman `_ in `#16341 `_ +* Update Python dependencies by `@galaxybot `_ in `#16436 `_ +* Tweak tool memory use and optimize shared memory when using preload by `@mvdbeek `_ in `#16536 `_ +* Document that required text parameters need a validator by `@bernt-matthias `_ in `#16538 `_ +* Include `regex` when linting validators by `@davelopez `_ in `#16684 `_ +* Refactor Tool Panel views structures and combine ToolBox and ToolBoxWorkflow into one component by `@ahmedhamidawan `_ in `#16739 `_ +* Replace file_name property with get_file_name function by `@SergeyYakubov `_ in `#16783 `_ +* Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including Podman job_conf by `@sveinugu `_ in `#16795 `_ +* Remove remaining legacy backbone form input elements by `@guerler `_ in `#16834 `_ +* Change `api/tool_panel` to `api/tool_panels/...` by `@ahmedhamidawan `_ in `#16928 `_ +* optimize object store cache operations by `@SergeyYakubov `_ in `#17025 `_ +* Enhance xsd schema and allow simpler assertion lists by `@mvdbeek `_ in `#17134 `_ + +============= +Other changes +============= + +* Merge 23.1 into dev by `@mvdbeek `_ in `#16534 `_ +* Explicitly document default of multiple by `@bernt-matthias `_ in `#16625 `_ + ------------------- 23.1.4 (2024-01-04) ------------------- diff --git a/packages/tours/HISTORY.rst b/packages/tours/HISTORY.rst index 3bc82b6c4f18..02c67c32e28c 100644 --- a/packages/tours/HISTORY.rst +++ b/packages/tours/HISTORY.rst @@ -8,6 +8,13 @@ History --------- + +------------------- +23.2.1 (2024-02-21) +------------------- + +No recorded changes since last release + ------------------- 23.1.4 (2024-01-04) ------------------- diff --git a/packages/util/HISTORY.rst b/packages/util/HISTORY.rst index 0be43a48e4ed..a4c49979fa9a 100644 --- a/packages/util/HISTORY.rst +++ b/packages/util/HISTORY.rst @@ -8,6 +8,35 @@ History --------- + +------------------- +23.2.1 (2024-02-21) +------------------- + + +========= +Bug fixes +========= + +* Ruff and flake8 fixes by `@nsoranzo `_ in `#16884 `_ + +============ +Enhancements +============ + +* Tool Shed 2.0 by `@jmchilton `_ in `#15639 `_ +* Move database access code out of ``galaxy.util`` by `@jdavcs `_ in `#16526 `_ +* Tweak tool memory use and optimize shared memory when using preload by `@mvdbeek `_ in `#16536 `_ +* Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including Podman job_conf by `@sveinugu `_ in `#16795 `_ +* Allow partial matches in workflow name tag search and search all tags for unquoted query by `@ahmedhamidawan `_ in `#16860 `_ +* Use python-isal for fast zip deflate compression in rocrate export by `@mvdbeek `_ in `#17342 `_ + +============= +Other changes +============= + +* Merge 23.1 into dev by `@mvdbeek `_ in `#16534 `_ + ------------------- 23.1.4 (2024-01-04) ------------------- diff --git a/packages/web_apps/HISTORY.rst b/packages/web_apps/HISTORY.rst index a4302f2eae08..22b94ba98888 100644 --- a/packages/web_apps/HISTORY.rst +++ b/packages/web_apps/HISTORY.rst @@ -8,6 +8,80 @@ History --------- + +------------------- +23.2.1 (2024-02-21) +------------------- + + +========= +Bug fixes +========= + +* Rename to_dict to populate in FormDefintion to fix bug by `@jdavcs `_ in `#16553 `_ +* Fix: serialize `tool_shed_urls` directly from the API by `@davelopez `_ in `#16561 `_ +* chore: fix typos by `@afuetterer `_ in `#16851 `_ +* Restore ToolsApi and create new api route for new panel structure by `@ahmedhamidawan `_ in `#16872 `_ +* Ruff and flake8 fixes by `@nsoranzo `_ in `#16884 `_ +* Make payload optional again for create tag API by `@nsoranzo `_ in `#17144 `_ +* Fix Display Application link generation by `@mvdbeek `_ in `#17227 `_ +* Display application fixes and tests by `@mvdbeek `_ in `#17233 `_ +* Respect ``upstream_gzip`` setting when streaming dataset collection archive by `@mvdbeek `_ in `#17400 `_ +* Fix history bulk operations menu conditions by `@davelopez `_ in `#17433 `_ +* Only check access permissions in `/api/{history_dataset_collection_id}/contents/{dataset_collection_id}` by `@mvdbeek `_ in `#17459 `_ +* Set metadata states on dataset association, not dataset by `@mvdbeek `_ in `#17474 `_ +* Provide working routes.url_for every ASGI request by `@mvdbeek `_ in `#17497 `_ + +============ +Enhancements +============ + +* Tool Shed 2.0 by `@jmchilton `_ in `#15639 `_ +* Limit number of celery task executions per second per user by `@claudiofr `_ in `#16232 `_ +* Delete non-terminal jobs and subworkflow invocations when cancelling invocation by `@mvdbeek `_ in `#16252 `_ +* Towards SQLAlchemy 2.0 (upgrades to SA Core usage) by `@jdavcs `_ in `#16264 `_ +* Notifications admin panel by `@itisAliRH `_ in `#16278 `_ +* Migrate cloud API to Fast API by `@heisner-tillman `_ in `#16296 `_ +* Drop (admin only) userskeys controller by `@dannon `_ in `#16318 `_ +* Migrate a part of the users API to Fast API by `@heisner-tillman `_ in `#16341 `_ +* Add Invenio RDM repository integration by `@davelopez `_ in `#16381 `_ +* Refactor FilesDialog + Remote Files API schema improvements by `@davelopez `_ in `#16420 `_ +* SQLAlchemy 2.0 upgrades to ORM usage in /lib by `@jdavcs `_ in `#16434 `_ +* Update Python dependencies by `@galaxybot `_ in `#16436 `_ +* Published Workflow Sharing Page Overhaul by `@ElectronicBlueberry `_ in `#16510 `_ +* Tweak tool memory use and optimize shared memory when using preload by `@mvdbeek `_ in `#16536 `_ +* Update Python dependencies by `@galaxybot `_ in `#16577 `_ +* Workflow Comments 💬 by `@ElectronicBlueberry `_ in `#16612 `_ +* Galaxy Markdown - add workflow image and license to Galaxy markdown. by `@jmchilton `_ in `#16672 `_ +* Implement instance URLs in Galaxy markdown. by `@jmchilton `_ in `#16675 `_ +* Enhance task monitor composable by `@davelopez `_ in `#16695 `_ +* SQLAlchemy 2.0 upgrades (part 2) by `@jdavcs `_ in `#16724 `_ +* Migrate `collection elements` store to Pinia by `@davelopez `_ in `#16725 `_ +* Refactor Tool Panel views structures and combine ToolBox and ToolBoxWorkflow into one component by `@ahmedhamidawan `_ in `#16739 `_ +* Don't copy collection elements in ``test_dataset_collection_hide_originals`` by `@nsoranzo `_ in `#16747 `_ +* Drop legacy server-side search by `@jdavcs `_ in `#16755 `_ +* Migrate a part of the jobs API to Fast API by `@heisner-tillman `_ in `#16778 `_ +* Replace file_name property with get_file_name function by `@SergeyYakubov `_ in `#16783 `_ +* Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including Podman job_conf by `@sveinugu `_ in `#16795 `_ +* Galaxy help forum integration by `@ElectronicBlueberry `_ in `#16798 `_ +* SQLAlchemy 2.0 upgrades (part 4) by `@jdavcs `_ in `#16852 `_ +* Vueify Visualizations Grid by `@guerler `_ in `#16892 `_ +* Change `api/tool_panel` to `api/tool_panels/...` by `@ahmedhamidawan `_ in `#16928 `_ +* Remove "Create Workflow" form and allow workflow creation in editor by `@ahmedhamidawan `_ in `#16938 `_ +* Update API tool_panels route conditions by `@dannon `_ in `#16991 `_ +* Fix invocation report to target correct workflow version. by `@jmchilton `_ in `#17008 `_ +* Upgrade job manager's index_query method to SA2.0 by `@jdavcs `_ in `#17020 `_ +* Require name for workflows on save, set default to Unnamed Workflow by `@ahmedhamidawan `_ in `#17038 `_ +* Migrate groups API to fastAPI by `@arash77 `_ in `#17051 `_ +* Migrate ItemTags API to FastAPI by `@arash77 `_ in `#17064 `_ + +============= +Other changes +============= + +* Merge 23.1 into dev by `@mvdbeek `_ in `#16534 `_ +* Fix succces typo by `@mvdbeek `_ in `#17481 `_ + ------------------- 23.1.4 (2024-01-04) ------------------- diff --git a/packages/web_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst index ef338c1005da..c332d31be278 100644 --- a/packages/web_framework/HISTORY.rst +++ b/packages/web_framework/HISTORY.rst @@ -8,6 +8,25 @@ History --------- + +------------------- +23.2.1 (2024-02-21) +------------------- + + +========= +Bug fixes +========= + +* Ruff and flake8 fixes by `@nsoranzo `_ in `#16884 `_ +* Provide working routes.url_for every ASGI request by `@mvdbeek `_ in `#17497 `_ + +============ +Enhancements +============ + +* Drop (admin only) userskeys controller by `@dannon `_ in `#16318 `_ + ------------------- 23.1.4 (2024-01-04) ------------------- diff --git a/packages/web_stack/HISTORY.rst b/packages/web_stack/HISTORY.rst index 5b912ab6d100..2af705d8507c 100644 --- a/packages/web_stack/HISTORY.rst +++ b/packages/web_stack/HISTORY.rst @@ -8,6 +8,18 @@ History --------- + +------------------- +23.2.1 (2024-02-21) +------------------- + + +============ +Enhancements +============ + +* Tweak tool memory use and optimize shared memory when using preload by `@mvdbeek `_ in `#16536 `_ + ------------------- 23.1.4 (2024-01-04) -------------------