diff --git a/lib/galaxy/version.py b/lib/galaxy/version.py index f40bd4b82832..c85466cf1beb 100644 --- a/lib/galaxy/version.py +++ b/lib/galaxy/version.py @@ -1,3 +1,3 @@ VERSION_MAJOR = "24.0" -VERSION_MINOR = "0.dev0" +VERSION_MINOR = "0" VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else "") diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst index da771a434711..271a6ed903f3 100644 --- a/packages/app/HISTORY.rst +++ b/packages/app/HISTORY.rst @@ -3,11 +3,105 @@ History .. to_doc ---------- -24.0.dev0 ---------- +------------------- +24.0.0 (2024-04-02) +------------------- + + +========= +Bug fixes +========= + +* Reload built-in converters on toolbox reload by `@bernt-matthias `_ in `#17209 `_ +* Optional Reply-to SMTP header in tool error reports by `@neoformit `_ in `#17243 `_ +* Package tests fixes by `@nsoranzo `_ in `#17301 `_ +* Follow-up on #17274 and #17262 by `@nsoranzo `_ in `#17302 `_ +* Rollback invalidated transaction: catch them earlier by `@jdavcs `_ in `#17312 `_ +* Fixes for flake8-bugbear 24.1.17 by `@nsoranzo `_ in `#17340 `_ +* Fix data_source and data_source_async bugs by `@wm75 `_ in `#17422 `_ +* More efficient change_state queries, maybe fix deadlock by `@mvdbeek `_ in `#17632 `_ +* Don't index tasks without task_uuid by `@mvdbeek `_ in `#17646 `_ +* Separate `ConnectedValue` from `RuntimeValue` by `@mvdbeek `_ in `#17678 `_ +* Fix step type serialization for StoredWorkflowDetailed models by `@mvdbeek `_ in `#17716 `_ +* Fix usage of DISTINCT by `@jdavcs `_ in `#17759 `_ +* Also set extension and metadata on copies of job outputs when finishing job by `@mvdbeek `_ in `#17777 `_ +* Use ``hg clone --stream`` to clone repos by `@mvdbeek `_ in `#17786 `_ +* Defer job attributes that are usually not needed by `@mvdbeek `_ in `#17795 `_ +* Fix change_datatype PJA for dynamic collections by `@mvdbeek `_ in `#17803 `_ +* Fix archived histories mixing with active in histories list by `@davelopez `_ in `#17856 `_ +* Normalize extensions when loading tool by `@mvdbeek `_ in `#17868 `_ +* Ignore user data table errors for now by `@mvdbeek `_ in `#17880 `_ +============ +Enhancements +============ + +* Add harmonize collections tool (or whatever other name) by `@lldelisle `_ in `#16662 `_ +* Add support for Python 3.12 by `@tuncK `_ in `#16796 `_ +* SQLAlchemy 2.0 upgrades (part 5) by `@jdavcs `_ in `#16932 `_ +* Python 3.8 as minimum by `@mr-c `_ in `#16954 `_ +* Support for OIDC API Auth and OIDC integration tests by `@nuwang `_ in `#16977 `_ +* Toward declarative help for Galaxy markdown directives. by `@jmchilton `_ in `#16979 `_ +* Extend regex groups in stdio regex matches by `@bernt-matthias `_ in `#17016 `_ +* Vueify Admin User Grid by `@guerler `_ in `#17030 `_ +* Remove web framework dependency from tools by `@davelopez `_ in `#17058 `_ +* Add select parameter with options from remote resources by `@mvdbeek `_ in `#17087 `_ +* Expose more tool information / navigability in UI. by `@jmchilton `_ in `#17105 `_ +* Vueify Admin Roles Grid by `@guerler `_ in `#17118 `_ +* SA2.0 updates: handling "object is being merged into a Session along the backref cascade path" by `@jdavcs `_ in `#17122 `_ +* Update Python dependencies by `@galaxybot `_ in `#17123 `_ +* Vueify Admin Groups Grid by `@guerler `_ in `#17126 `_ +* Towards SQLAlchemy 2.0: fix last cases of RemovedIn20Warning by `@jdavcs `_ in `#17132 `_ +* Vueify Admin Forms and Quota grids by `@guerler `_ in `#17141 `_ +* Update Python dependencies by `@galaxybot `_ in `#17157 `_ +* Update Python dependencies by `@galaxybot `_ in `#17201 `_ +* Vendorize fastapi-utls.cbv by `@jdavcs `_ in `#17205 `_ +* Fix usage of graphene-sqlalchemy, bump to 3.0.0rc1 by `@jdavcs `_ in `#17216 `_ +* Vueifiy History Grids by `@guerler `_ in `#17219 `_ +* Update Python dependencies by `@galaxybot `_ in `#17230 `_ +* Update Python dependencies by `@galaxybot `_ in `#17235 `_ +* Allow job files to consume TUS uploads by `@jmchilton `_ in `#17242 `_ +* Update Python dependencies by `@galaxybot `_ in `#17247 `_ +* Migrate models to pydantic 2 by `@mvdbeek `_ in `#17262 `_ +* Consider Null inputs by `@bernt-matthias `_ in `#17271 `_ +* Add OIDC backend configuration schema and validation by `@uwwint `_ in `#17274 `_ +* Adds delete, purge and undelete batch operations to History Grid by `@guerler `_ in `#17282 `_ +* Add ``__KEEP_SUCCESS_DATASETS__`` by `@lldelisle `_ in `#17294 `_ +* Improve ModelManager type hints by `@mvdbeek `_ in `#17299 `_ +* API endpoint that allows "changing" the objectstore for "safe" scenarios. by `@jmchilton `_ in `#17329 `_ +* Update Python dependencies by `@galaxybot `_ in `#17333 `_ +* Add element_identifier and ext to inputs config file export by `@bernt-matthias `_ in `#17357 `_ +* Remove unused statements in job search function by `@mvdbeek `_ in `#17361 `_ +* Enable ``warn_unreachable`` mypy option by `@mvdbeek `_ in `#17365 `_ +* Fix type annotation of code using XML etree by `@nsoranzo `_ in `#17367 `_ +* More specific type annotation for ``BaseJobExec.parse_status()`` by `@nsoranzo `_ in `#17381 `_ +* Cancel all active jobs when the user is deleted by `@davelopez `_ in `#17390 `_ +* Update to black 2024 stable style by `@nsoranzo `_ in `#17391 `_ +* Purge `groups` and `roles` from DB (for real) by `@davelopez `_ in `#17411 `_ +* Update Python dependencies by `@galaxybot `_ in `#17420 `_ +* Allow using tool data bundles as inputs to reference data select parameters by `@mvdbeek `_ in `#17435 `_ +* Adds published histories to grid list by `@guerler `_ in `#17449 `_ +* Allow filtering history datasets by object store ID and quota source. by `@jmchilton `_ in `#17460 `_ +* `data_column` parameter: use `column_names` metadata if present by `@bernt-matthias `_ in `#17478 `_ +* Update Python dependencies by `@galaxybot `_ in `#17486 `_ +* Consolidate resource grids into tab views by `@guerler `_ in `#17487 `_ +* Update k8s docker python to 3.12 by `@nuwang `_ in `#17494 `_ +* add encode ID API endpoint by `@mira-miracoli `_ in `#17510 `_ +* Fixing data_source tools and incrementing tool profile by `@wm75 `_ in `#17515 `_ +* Update Python dependencies by `@galaxybot `_ in `#17541 `_ +* Add `image_diff` comparison method for test output verification using images by `@kostrykin `_ in `#17556 `_ +* Filter out subworkflow invocations by `@mvdbeek `_ in `#17558 `_ +* Update Python dependencies by `@galaxybot `_ in `#17580 `_ +* Restore histories API behavior for `keys` query parameter by `@davelopez `_ in `#17779 `_ +* Fix datasets API custom keys encoding by `@davelopez `_ in `#17793 `_ +* Improved error messages for runtime sharing problems. by `@jmchilton `_ in `#17794 `_ +* Allow admin to sharpen language about selected object stores. by `@jmchilton `_ in `#17806 `_ + +============= +Other changes +============= +* consistently compare profile versions by `@bernt-matthias `_ in `#16492 `_ ------------------- 23.2.1 (2024-02-21) @@ -87,7 +181,7 @@ Enhancements * 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 `_ +* 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 `_ diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg index 4360d7181811..45569a14a3b2 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 = 23.2.dev0 +version = 24.0.0 [options] include_package_data = True @@ -85,4 +85,4 @@ console_scripts = [options.packages.find] exclude = galaxy.tools.bundled* - tests* + tests* \ No newline at end of file diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst index f31d9eb93e77..8c6db48ddbf6 100644 --- a/packages/auth/HISTORY.rst +++ b/packages/auth/HISTORY.rst @@ -3,11 +3,23 @@ History .. to_doc ---------- -24.0.dev0 ---------- +------------------- +24.0.0 (2024-04-02) +------------------- + + +========= +Bug fixes +========= +* LDAP3 fix for attributes returned as strings by `@bernt-matthias `_ in `#17305 `_ + +============ +Enhancements +============ +* Python 3.8 as minimum by `@mr-c `_ in `#16954 `_ +* Update to black 2024 stable style by `@nsoranzo `_ in `#17391 `_ ------------------- 23.2.1 (2024-02-21) diff --git a/packages/auth/setup.cfg b/packages/auth/setup.cfg index adad08ddb323..15a6ed1d5b49 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 = 23.2.dev0 +version = 24.0.0 [options] include_package_data = True @@ -39,4 +39,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/config/HISTORY.rst b/packages/config/HISTORY.rst index 88f3999dd738..c65fed112db3 100644 --- a/packages/config/HISTORY.rst +++ b/packages/config/HISTORY.rst @@ -3,11 +3,38 @@ History .. to_doc ---------- -24.0.dev0 ---------- +------------------- +24.0.0 (2024-04-02) +------------------- + +========= +Bug fixes +========= + +* Follow-up on #17274 and #17262 by `@nsoranzo `_ in `#17302 `_ +* Fix minor oidc_backends_config comment bug by `@ahmedhamidawan `_ in `#17385 `_ + +============ +Enhancements +============ +* Add harmonize collections tool (or whatever other name) by `@lldelisle `_ in `#16662 `_ +* Python 3.8 as minimum by `@mr-c `_ in `#16954 `_ +* Support for OIDC API Auth and OIDC integration tests by `@nuwang `_ in `#16977 `_ +* Add support for (fast5.tar).xz binary compressed files by `@tuncK `_ in `#17106 `_ +* Add a3m datatype by `@astrovsky01 `_ in `#17217 `_ +* Convert sample object store configuration to YAML and support configuring inline by `@natefoo `_ in `#17222 `_ +* Allow job files to consume TUS uploads by `@jmchilton `_ in `#17242 `_ +* Add OIDC backend configuration schema and validation by `@uwwint `_ in `#17274 `_ +* Update to black 2024 stable style by `@nsoranzo `_ in `#17391 `_ +* Allow using tool data bundles as inputs to reference data select parameters by `@mvdbeek `_ in `#17435 `_ +* Use short link for TPV shared database by `@nuwang `_ in `#17467 `_ +* Feature SBOL datatypes by `@guillaume-gricourt `_ in `#17482 `_ +* Add documentation on how to use vault keys in file sources by `@bernt-matthias `_ in `#17498 `_ +* add npy datatype by `@astrovsky01 `_ in `#17517 `_ +* Enhance Avivator display app to support regular Tiffs by `@davelopez `_ in `#17554 `_ +* Allow admin to sharpen language about selected object stores. by `@jmchilton `_ in `#17806 `_ ------------------- 23.2.1 (2024-02-21) @@ -40,7 +67,7 @@ Enhancements * 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 `_ +* 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 `_ diff --git a/packages/config/setup.cfg b/packages/config/setup.cfg index b1691b58d9a5..e4e605549716 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 = 23.2.dev0 +version = 24.0.0 [options] include_package_data = True @@ -46,4 +46,4 @@ console_scripts = [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst index cd266a6800ec..054db496d2d2 100644 --- a/packages/data/HISTORY.rst +++ b/packages/data/HISTORY.rst @@ -3,11 +3,75 @@ History .. to_doc ---------- -24.0.dev0 ---------- +------------------- +24.0.0 (2024-04-02) +------------------- + +========= +Bug fixes +========= + +* Fix for converter tests by `@bernt-matthias `_ in `#17188 `_ +* correct dbkey for minerva display app by `@hexylena `_ in `#17196 `_ +* Fix invocation serialization if no state was set by `@mvdbeek `_ in `#17278 `_ +* Fix quotas ID encoding by `@davelopez `_ in `#17335 `_ +* Fix model store exports that include implicit conversions. by `@jmchilton `_ in `#17346 `_ +* Fix bug: create new PSAAssociation if not in database by `@jdavcs `_ in `#17516 `_ +* Fix social_core methods by `@jdavcs `_ in `#17530 `_ +* Fix ancient bug: incorrect usage of func.coalesce in User model by `@jdavcs `_ in `#17577 `_ +* Account for newlines in CIF Datatype sniffer by `@patrick-austin `_ in `#17582 `_ +* Anticipate PendingRollbackError in ``check_database_connection`` by `@mvdbeek `_ in `#17598 `_ +* Add basic model import attribute validation by `@mvdbeek `_ in `#17628 `_ +* More efficient change_state queries, maybe fix deadlock by `@mvdbeek `_ in `#17632 `_ +* Npz sniffing: do not read the whole file by `@bernt-matthias `_ in `#17672 `_ +* Assert that at least one file in npz zipfile ends with .npy by `@mvdbeek `_ in `#17679 `_ +* Workflow Comment Indexing by `@ElectronicBlueberry `_ in `#17700 `_ +* Fix source history update_time being updated when importing a public history by `@jmchilton `_ in `#17728 `_ +* Also set extension and metadata on copies of job outputs when finishing job by `@mvdbeek `_ in `#17777 `_ +* Defer job attributes that are usually not needed by `@mvdbeek `_ in `#17795 `_ +* Fix change_datatype PJA for dynamic collections by `@mvdbeek `_ in `#17803 `_ +* Simplify nested collection joins by `@mvdbeek `_ in `#17817 `_ +* Fix very slow user data table query by `@mvdbeek `_ in `#17830 `_ +* Update db revision 24.0 release tags by `@jdavcs `_ in `#17834 `_ +* Minor refactor of query building logic for readability by `@jdavcs `_ in `#17835 `_ +* Fix user login when duplicate UserRoleAssociation exists by `@mvdbeek `_ in `#17854 `_ + +============ +Enhancements +============ +* Make columns types an empty list for empty tabular data by `@bernt-matthias `_ in `#13918 `_ +* port invocation API to fastapi by `@martenson `_ in `#16707 `_ +* SQLAlchemy 2.0 upgrades (part 5) by `@jdavcs `_ in `#16932 `_ +* Python 3.8 as minimum by `@mr-c `_ in `#16954 `_ +* Expose more tool information / navigability in UI. by `@jmchilton `_ in `#17105 `_ +* Add support for (fast5.tar).xz binary compressed files by `@tuncK `_ in `#17106 `_ +* SA2.0 updates: handling "object is being merged into a Session along the backref cascade path" by `@jdavcs `_ in `#17122 `_ +* Towards SQLAlchemy 2.0: fix last cases of RemovedIn20Warning by `@jdavcs `_ in `#17132 `_ +* Create pydantic model for the return of show operation - get: `/api/jobs/{job_id}` by `@heisner-tillman `_ in `#17153 `_ +* Much simpler default dataset permissions for typical users. by `@jmchilton `_ in `#17166 `_ +* Add future=True flag to SA engine by `@jdavcs `_ in `#17174 `_ +* Add future=True flag to SA session by `@jdavcs `_ in `#17179 `_ +* Vueifiy History Grids by `@guerler `_ in `#17219 `_ +* Convert sample object store configuration to YAML and support configuring inline by `@natefoo `_ in `#17222 `_ +* Migrate models to pydantic 2 by `@mvdbeek `_ in `#17262 `_ +* API endpoint that allows "changing" the objectstore for "safe" scenarios. by `@jmchilton `_ in `#17329 `_ +* Enable ``warn_unreachable`` mypy option by `@mvdbeek `_ in `#17365 `_ +* Fix type annotation of code using XML etree by `@nsoranzo `_ in `#17367 `_ +* Add explicit cache_ok attribute to JSONType subclass by `@mvdbeek `_ in `#17376 `_ +* More specific type annotation for ``BaseJobExec.parse_status()`` by `@nsoranzo `_ in `#17381 `_ +* Update to black 2024 stable style by `@nsoranzo `_ in `#17391 `_ +* Allow using tool data bundles as inputs to reference data select parameters by `@mvdbeek `_ in `#17435 `_ +* UI for "relocating" a dataset to a new object store (when safe) by `@jmchilton `_ in `#17437 `_ +* Allow filtering history datasets by object store ID and quota source. by `@jmchilton `_ in `#17460 `_ +* Faster FASTA and FASTQ metadata setting by `@bernt-matthias `_ in `#17462 `_ +* Feature SBOL datatypes by `@guillaume-gricourt `_ in `#17482 `_ +* Display workflow invocation counts. by `@jmchilton `_ in `#17488 `_ +* add npy datatype by `@astrovsky01 `_ in `#17517 `_ +* Enhance Avivator display app to support regular Tiffs by `@davelopez `_ in `#17554 `_ +* Update Python dependencies by `@galaxybot `_ in `#17580 `_ +* Add migrations revision identifier for 24.0 by `@jdavcs `_ in `#17589 `_ ------------------- 23.2.1 (2024-02-21) diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg index 157324e102a8..41caf684196e 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 = 23.2.dev0 +version = 24.0.0 [options] include_package_data = True @@ -73,4 +73,4 @@ console_scripts = [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/files/HISTORY.rst b/packages/files/HISTORY.rst index 76ae16eb1c73..d4c85c2fc67e 100644 --- a/packages/files/HISTORY.rst +++ b/packages/files/HISTORY.rst @@ -3,11 +3,20 @@ History .. to_doc ---------- -24.0.dev0 ---------- +------------------- +24.0.0 (2024-04-02) +------------------- + +============ +Enhancements +============ +* Add support for Python 3.12 by `@tuncK `_ in `#16796 `_ +* Python 3.8 as minimum by `@mr-c `_ in `#16954 `_ +* Update Python dependencies by `@galaxybot `_ in `#17235 `_ +* fix s3fs templating by `@bgruening `_ in `#17311 `_ +* Update to black 2024 stable style by `@nsoranzo `_ in `#17391 `_ ------------------- 23.2.1 (2024-02-21) @@ -29,7 +38,7 @@ 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 `_ +* 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 `_ diff --git a/packages/files/setup.cfg b/packages/files/setup.cfg index f294659aa77f..705312e9d43b 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 = 23.2.dev0 +version = 24.0.0 [options] include_package_data = True @@ -41,4 +41,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst index f06fe643a273..763a1cf5a312 100644 --- a/packages/job_execution/HISTORY.rst +++ b/packages/job_execution/HISTORY.rst @@ -3,11 +3,25 @@ History .. to_doc ---------- -24.0.dev0 ---------- +------------------- +24.0.0 (2024-04-02) +------------------- + +========= +Bug fixes +========= + +* Fixes for output discovery by `@bernt-matthias `_ in `#17266 `_ +* Fix change_datatype PJA for dynamic collections by `@mvdbeek `_ in `#17803 `_ + +============ +Enhancements +============ +* Python 3.8 as minimum by `@mr-c `_ in `#16954 `_ +* Extend regex groups in stdio regex matches by `@bernt-matthias `_ in `#17016 `_ +* Update to black 2024 stable style by `@nsoranzo `_ in `#17391 `_ ------------------- 23.2.1 (2024-02-21) diff --git a/packages/job_execution/setup.cfg b/packages/job_execution/setup.cfg index 40c3be56f524..4ffe5031c8d9 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 = 23.2.dev0 +version = 24.0.0 [options] include_package_data = True @@ -49,4 +49,4 @@ console_scripts = [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst index 77a01312a7d2..2247f0d6919e 100644 --- a/packages/job_metrics/HISTORY.rst +++ b/packages/job_metrics/HISTORY.rst @@ -3,11 +3,22 @@ History .. to_doc ---------- -24.0.dev0 ---------- +------------------- +24.0.0 (2024-04-02) +------------------- + +========= +Bug fixes +========= + +* Stringify cgroups metrics formatted value return by `@dannon `_ in `#17520 `_ + +============ +Enhancements +============ +* Update to black 2024 stable style by `@nsoranzo `_ in `#17391 `_ ------------------- 23.2.1 (2024-02-21) diff --git a/packages/job_metrics/setup.cfg b/packages/job_metrics/setup.cfg index 476eea3712ad..8c694402ddea 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 = 23.2.dev0 +version = 24.0.0 [options] include_package_data = True @@ -39,4 +39,4 @@ python_requires = >=3.7 [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/navigation/HISTORY.rst b/packages/navigation/HISTORY.rst index ec2f2037b3b2..3b188ef09618 100644 --- a/packages/navigation/HISTORY.rst +++ b/packages/navigation/HISTORY.rst @@ -3,11 +3,16 @@ History .. to_doc ---------- -24.0.dev0 ---------- +------------------- +24.0.0 (2024-04-02) +------------------- + +============ +Enhancements +============ +* Python 3.8 as minimum by `@mr-c `_ in `#16954 `_ ------------------- 23.2.1 (2024-02-21) diff --git a/packages/navigation/setup.cfg b/packages/navigation/setup.cfg index a2635d9e49fe..4eaf1a9b75c1 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 = 23.2.dev0 +version = 24.0.0 [options] include_package_data = True @@ -39,4 +39,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst index 7cf4cc52e3a0..8da0c0502cfc 100644 --- a/packages/objectstore/HISTORY.rst +++ b/packages/objectstore/HISTORY.rst @@ -3,11 +3,21 @@ History .. to_doc ---------- -24.0.dev0 ---------- +------------------- +24.0.0 (2024-04-02) +------------------- + +============ +Enhancements +============ +* Convert sample object store configuration to YAML and support configuring inline by `@natefoo `_ in `#17222 `_ +* Migrate models to pydantic 2 by `@mvdbeek `_ in `#17262 `_ +* API endpoint that allows "changing" the objectstore for "safe" scenarios. by `@jmchilton `_ in `#17329 `_ +* Update to black 2024 stable style by `@nsoranzo `_ in `#17391 `_ +* Allow filtering history datasets by object store ID and quota source. by `@jmchilton `_ in `#17460 `_ +* Improved error messages for runtime sharing problems. by `@jmchilton `_ in `#17794 `_ ------------------- 23.2.1 (2024-02-21) diff --git a/packages/objectstore/setup.cfg b/packages/objectstore/setup.cfg index 496b60c2ce75..a24271f4fcd9 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 = 23.2.dev0 +version = 24.0.0 [options] include_package_data = True @@ -41,4 +41,4 @@ python_requires = >=3.7 [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/schema/HISTORY.rst b/packages/schema/HISTORY.rst index 57e805c129cb..3b3722960056 100644 --- a/packages/schema/HISTORY.rst +++ b/packages/schema/HISTORY.rst @@ -3,11 +3,45 @@ History .. to_doc ---------- -24.0.dev0 ---------- +------------------- +24.0.0 (2024-04-02) +------------------- + + +========= +Bug fixes +========= + +* Fix Workflow Comment Model for Pydantic 2 by `@ElectronicBlueberry `_ in `#17296 `_ +* Add basic model import attribute validation by `@mvdbeek `_ in `#17628 `_ +* Make latest_workflow_uuid optional by `@mvdbeek `_ in `#17629 `_ +* Fix workflow person validation by `@dannon `_ in `#17636 `_ +* Make WorkflowInput label, value and uuid optional by `@mvdbeek `_ in `#17638 `_ +* Fix step type serialization for StoredWorkflowDetailed models by `@mvdbeek `_ in `#17716 `_ +* Fix input parameter step type by `@mvdbeek `_ in `#17767 `_ +* Fix optional types in Help Forum API by `@davelopez `_ in `#17832 `_ +* Fix archived histories mixing with active in histories list by `@davelopez `_ in `#17856 `_ +============ +Enhancements +============ +* port invocation API to fastapi by `@martenson `_ in `#16707 `_ +* Python 3.8 as minimum by `@mr-c `_ in `#16954 `_ +* Toward declarative help for Galaxy markdown directives. by `@jmchilton `_ in `#16979 `_ +* Create pydantic model for the return of show operation - get: `/api/jobs/{job_id}` by `@heisner-tillman `_ in `#17153 `_ +* Vueifiy History Grids by `@guerler `_ in `#17219 `_ +* Refactor two of the missing invocation routes to FastAPI by `@heisner-tillman `_ in `#17237 `_ +* Migrate models to pydantic 2 by `@mvdbeek `_ in `#17262 `_ +* Combines legacy qv-pattern and advanced filter pattern in history index endpoint by `@guerler `_ in `#17368 `_ +* Update to black 2024 stable style by `@nsoranzo `_ in `#17391 `_ +* Allow using tool data bundles as inputs to reference data select parameters by `@mvdbeek `_ in `#17435 `_ +* Refactor Workflow API routes - Part 1 by `@heisner-tillman `_ in `#17463 `_ +* Consolidate resource grids into tab views by `@guerler `_ in `#17487 `_ +* Display workflow invocation counts. by `@jmchilton `_ in `#17488 `_ +* Filter out subworkflow invocations by `@mvdbeek `_ in `#17558 `_ +* Restore histories API behavior for `keys` query parameter by `@davelopez `_ in `#17779 `_ +* Fix datasets API custom keys encoding by `@davelopez `_ in `#17793 `_ ------------------- 23.2.1 (2024-02-21) diff --git a/packages/schema/setup.cfg b/packages/schema/setup.cfg index dce6efc479ef..3a7cc7409e08 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 = 23.2.dev0 +version = 24.0.0 [options] include_package_data = True @@ -39,4 +39,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst index 452e421c32e8..7277f9e02689 100644 --- a/packages/selenium/HISTORY.rst +++ b/packages/selenium/HISTORY.rst @@ -3,11 +3,31 @@ History .. to_doc ---------- -24.0.dev0 ---------- +------------------- +24.0.0 (2024-04-02) +------------------- + +========= +Bug fixes +========= + +* Update tour testing selector usage. by `@jmchilton `_ in `#14005 `_ +* Fix history filters taking up space in `GridList` by `@ahmedhamidawan `_ in `#17652 `_ + +============ +Enhancements +============ +* New Workflow List and Card View by `@itisAliRH `_ in `#16607 `_ +* Python 3.8 as minimum by `@mr-c `_ in `#16954 `_ +* Vueifiy History Grids by `@guerler `_ in `#17219 `_ +* Adds delete, purge and undelete batch operations to History Grid by `@guerler `_ in `#17282 `_ +* Custom Multiselect by `@ElectronicBlueberry `_ in `#17331 `_ +* Enable ``warn_unreachable`` mypy option by `@mvdbeek `_ in `#17365 `_ +* Update to black 2024 stable style by `@nsoranzo `_ in `#17391 `_ +* Adds published histories to grid list by `@guerler `_ in `#17449 `_ +* Consolidate resource grids into tab views by `@guerler `_ in `#17487 `_ ------------------- 23.2.1 (2024-02-21) diff --git a/packages/selenium/setup.cfg b/packages/selenium/setup.cfg index 07fab81680d9..e0ab2af2d75a 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 = 23.2.dev0 +version = 24.0.0 [options] include_package_data = True @@ -47,4 +47,4 @@ console_scripts = [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/test_api/HISTORY.rst b/packages/test_api/HISTORY.rst index d6caa01d1841..685a3663c719 100644 --- a/packages/test_api/HISTORY.rst +++ b/packages/test_api/HISTORY.rst @@ -3,11 +3,48 @@ History .. to_doc ---------- -24.0.dev0 ---------- +------------------- +24.0.0 (2024-04-02) +------------------- + +========= +Bug fixes +========= + +* Only check access permissions in ``/api/{history_dataset_collection_id}/contents/{dataset_collection_id}`` by `@ahmedhamidawan `_ in `#17444 `_ +* Fix ``test_index_advanced_filter`` API test re-running by `@nsoranzo `_ in `#17547 `_ +* Limit new anon histories by `@mvdbeek `_ in `#17657 `_ +* Fix step type serialization for StoredWorkflowDetailed models by `@mvdbeek `_ in `#17716 `_ +* Fix histories API index_query serialization by `@davelopez `_ in `#17726 `_ +* Fix source history update_time being updated when importing a public history by `@jmchilton `_ in `#17728 `_ +* Also set extension and metadata on copies of job outputs when finishing job by `@mvdbeek `_ in `#17777 `_ +* Fix change_datatype PJA for dynamic collections by `@mvdbeek `_ in `#17803 `_ +* Fix archived histories mixing with active in histories list by `@davelopez `_ in `#17856 `_ + +============ +Enhancements +============ +* Python 3.8 as minimum by `@mr-c `_ in `#16954 `_ +* Toward declarative help for Galaxy markdown directives. by `@jmchilton `_ in `#16979 `_ +* Extend regex groups in stdio regex matches by `@bernt-matthias `_ in `#17016 `_ +* Create pydantic model for the return of show operation - get: `/api/jobs/{job_id}` by `@heisner-tillman `_ in `#17153 `_ +* Don't require admin user to list ``/api/tool_data`` by `@jozh2008 `_ in `#17161 `_ +* Vueifiy History Grids by `@guerler `_ in `#17219 `_ +* Reuse test instance during non-integration tests by `@mvdbeek `_ in `#17234 `_ +* Migrate models to pydantic 2 by `@mvdbeek `_ in `#17262 `_ +* Add ``__KEEP_SUCCESS_DATASETS__`` by `@lldelisle `_ in `#17294 `_ +* Enable ``warn_unreachable`` mypy option by `@mvdbeek `_ in `#17365 `_ +* Combines legacy qv-pattern and advanced filter pattern in history index endpoint by `@guerler `_ in `#17368 `_ +* Cancel all active jobs when the user is deleted by `@davelopez `_ in `#17390 `_ +* Update to black 2024 stable style by `@nsoranzo `_ in `#17391 `_ +* Purge `groups` and `roles` from DB (for real) by `@davelopez `_ in `#17411 `_ +* Refactor Workflow API routes - Part 1 by `@heisner-tillman `_ in `#17463 `_ +* Consolidate resource grids into tab views by `@guerler `_ in `#17487 `_ +* Filter out subworkflow invocations by `@mvdbeek `_ in `#17558 `_ +* Restore histories API behavior for `keys` query parameter by `@davelopez `_ in `#17779 `_ +* Fix datasets API custom keys encoding by `@davelopez `_ in `#17793 `_ ------------------- 23.2.1 (2024-02-21) diff --git a/packages/test_api/setup.cfg b/packages/test_api/setup.cfg index a6754d91250f..7ca5b459fb7d 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 = 23.2.dev0 +version = 24.0.0 [options] include_package_data = True @@ -46,4 +46,4 @@ driver = [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/test_base/HISTORY.rst b/packages/test_base/HISTORY.rst index ed1e6f6a19a5..cd028fc129a5 100644 --- a/packages/test_base/HISTORY.rst +++ b/packages/test_base/HISTORY.rst @@ -3,11 +3,24 @@ History .. to_doc ---------- -24.0.dev0 ---------- +------------------- +24.0.0 (2024-04-02) +------------------- + +============ +Enhancements +============ +* port invocation API to fastapi by `@martenson `_ in `#16707 `_ +* Python 3.8 as minimum by `@mr-c `_ in `#16954 `_ +* Support for OIDC API Auth and OIDC integration tests by `@nuwang `_ in `#16977 `_ +* Reuse test instance during non-integration tests by `@mvdbeek `_ in `#17234 `_ +* API endpoint that allows "changing" the objectstore for "safe" scenarios. by `@jmchilton `_ in `#17329 `_ +* Update to black 2024 stable style by `@nsoranzo `_ in `#17391 `_ +* Allow filtering history datasets by object store ID and quota source. by `@jmchilton `_ in `#17460 `_ +* Refactor Workflow API routes - Part 1 by `@heisner-tillman `_ in `#17463 `_ +* Filter out subworkflow invocations by `@mvdbeek `_ in `#17558 `_ ------------------- 23.2.1 (2024-02-21) diff --git a/packages/test_base/setup.cfg b/packages/test_base/setup.cfg index f5e3b8b0c9da..22973d786e2c 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 = 23.2.dev0 +version = 24.0.0 [options] include_package_data = True @@ -45,4 +45,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/test_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst index 8065b4b64e8b..b55808590888 100644 --- a/packages/test_driver/HISTORY.rst +++ b/packages/test_driver/HISTORY.rst @@ -3,11 +3,18 @@ History .. to_doc ---------- -24.0.dev0 ---------- +------------------- +24.0.0 (2024-04-02) +------------------- + +============ +Enhancements +============ +* Python 3.8 as minimum by `@mr-c `_ in `#16954 `_ +* Update to black 2024 stable style by `@nsoranzo `_ in `#17391 `_ +* Type annotation and refactoring of tests by `@nsoranzo `_ in `#17484 `_ ------------------- 23.2.1 (2024-02-21) diff --git a/packages/test_driver/setup.cfg b/packages/test_driver/setup.cfg index 6f4efce2cfab..22706e300e2c 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 = 23.2.dev0 +version = 24.0.0 [options] include_package_data = True @@ -47,4 +47,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/tool_shed/HISTORY.rst b/packages/tool_shed/HISTORY.rst index 57e805c129cb..2d1af0e339da 100644 --- a/packages/tool_shed/HISTORY.rst +++ b/packages/tool_shed/HISTORY.rst @@ -3,11 +3,22 @@ History .. to_doc ---------- -24.0.dev0 ---------- +------------------- +24.0.0 (2024-04-02) +------------------- + + +========= +Bug fixes +========= + +* Reload built-in converters on toolbox reload by `@bernt-matthias `_ in `#17209 `_ +============ +Enhancements +============ +* Enable ``warn_unreachable`` mypy option by `@mvdbeek `_ in `#17365 `_ ------------------- 23.2.1 (2024-02-21) diff --git a/packages/tool_shed/setup.cfg b/packages/tool_shed/setup.cfg index 4e78a7c84c29..8fd469fe35ea 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 = 23.2.dev0 +version = 24.0.0 [options] include_package_data = True @@ -39,4 +39,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst index a84ffd9e5d71..7a2b0eba6c65 100644 --- a/packages/tool_util/HISTORY.rst +++ b/packages/tool_util/HISTORY.rst @@ -3,11 +3,55 @@ History .. to_doc ---------- -24.0.dev0 ---------- +------------------- +24.0.0 (2024-04-02) +------------------- + + +========= +Bug fixes +========= + +* xsd: reorder choices for permissive boolean by `@bernt-matthias `_ in `#17187 `_ +* Allow for upper case container tags by `@bernt-matthias `_ in `#17254 `_ +* Fixes for flake8-bugbear 24.1.17 by `@nsoranzo `_ in `#17340 `_ +* Escape pipe character in tool XSD docs by `@neoformit `_ in `#17359 `_ +* XSD schema doc building: quote pipe characters in attribute tables by `@bernt-matthias `_ in `#17364 `_ +* Fix IUC best practices links, mention data_source_async in XSD by `@wm75 `_ in `#17409 `_ +* Fix data_source and data_source_async bugs by `@wm75 `_ in `#17422 `_ +* Add tool XML schema documention for outputs - collection - data by `@bernt-matthias `_ in `#17465 `_ +* has_size assertion: implement size (as synonym for value) by `@bernt-matthias `_ in `#17490 `_ +* Yaml nested assertions: fix parsing by `@bernt-matthias `_ in `#17641 `_ +============ +Enhancements +============ + +* build_mulled: also use namespace for building singularity images by `@bernt-matthias `_ in `#15657 `_ +* Python 3.8 as minimum by `@mr-c `_ in `#16954 `_ +* Extend regex groups in stdio regex matches by `@bernt-matthias `_ in `#17016 `_ +* Split linters in separate classes by `@bernt-matthias `_ in `#17081 `_ +* Add select parameter with options from remote resources by `@mvdbeek `_ in `#17087 `_ +* Replace discouraged Mambaforge with Miniforge3 by `@nsoranzo `_ in `#17177 `_ +* Clarify the meaning of lexical sorting of discovered datasets by `@bernt-matthias `_ in `#17190 `_ +* Migrate models to pydantic 2 by `@mvdbeek `_ in `#17262 `_ +* Add element_identifier and ext to inputs config file export by `@bernt-matthias `_ in `#17357 `_ +* Enable ``warn_unreachable`` mypy option by `@mvdbeek `_ in `#17365 `_ +* Fix type annotation of code using XML etree by `@nsoranzo `_ in `#17367 `_ +* Update to black 2024 stable style by `@nsoranzo `_ in `#17391 `_ +* Some additional typing for test interactor stuff. by `@jmchilton `_ in `#17398 `_ +* Allow using tool data bundles as inputs to reference data select parameters by `@mvdbeek `_ in `#17435 `_ +* `data_column` parameter: use `column_names` metadata if present by `@bernt-matthias `_ in `#17478 `_ +* Fixing data_source tools and incrementing tool profile by `@wm75 `_ in `#17515 `_ +* Add `image_diff` comparison method for test output verification using images by `@kostrykin `_ in `#17556 `_ +* add shm_size based on ShmSize by `@richard-burhans `_ in `#17565 `_ +* Record missing outputs as test errors by `@bernt-matthias `_ in `#17874 `_ + +============= +Other changes +============= +* consistently compare profile versions by `@bernt-matthias `_ in `#16492 `_ ------------------- 23.2.1 (2024-02-21) diff --git a/packages/tool_util/setup.cfg b/packages/tool_util/setup.cfg index 5d6b9b9a378d..a72c04b58a59 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 = 23.2.dev0 +version = 24.0.0 [options] include_package_data = True @@ -73,4 +73,4 @@ extended-assertions = [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/tours/HISTORY.rst b/packages/tours/HISTORY.rst index 02c67c32e28c..2018e6710790 100644 --- a/packages/tours/HISTORY.rst +++ b/packages/tours/HISTORY.rst @@ -3,11 +3,17 @@ History .. to_doc ---------- -24.0.dev0 ---------- +------------------- +24.0.0 (2024-04-02) +------------------- + +============ +Enhancements +============ +* Migrate models to pydantic 2 by `@mvdbeek `_ in `#17262 `_ +* Update to black 2024 stable style by `@nsoranzo `_ in `#17391 `_ ------------------- 23.2.1 (2024-02-21) diff --git a/packages/tours/setup.cfg b/packages/tours/setup.cfg index 1e14d2215a75..e5c775192b79 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 = 23.2.dev0 +version = 24.0.0 [options] include_package_data = True @@ -44,4 +44,4 @@ console_scripts = [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/util/HISTORY.rst b/packages/util/HISTORY.rst index a4c49979fa9a..a2d47eeab81d 100644 --- a/packages/util/HISTORY.rst +++ b/packages/util/HISTORY.rst @@ -3,11 +3,33 @@ History .. to_doc ---------- -24.0.dev0 ---------- +------------------- +24.0.0 (2024-04-02) +------------------- + +========= +Bug fixes +========= + +* Optional Reply-to SMTP header in tool error reports by `@neoformit `_ in `#17243 `_ +* Follow-up on #17274 and #17262 by `@nsoranzo `_ in `#17302 `_ +* Fixes for flake8-bugbear 24.1.17 by `@nsoranzo `_ in `#17340 `_ + +============ +Enhancements +============ +* Add support for Python 3.12 by `@tuncK `_ in `#16796 `_ +* Python 3.8 as minimum by `@mr-c `_ in `#16954 `_ +* Remove web framework dependency from tools by `@davelopez `_ in `#17058 `_ +* Add support for (fast5.tar).xz binary compressed files by `@tuncK `_ in `#17106 `_ +* Reuse test instance during non-integration tests by `@mvdbeek `_ in `#17234 `_ +* Add OIDC backend configuration schema and validation by `@uwwint `_ in `#17274 `_ +* Enable ``warn_unreachable`` mypy option by `@mvdbeek `_ in `#17365 `_ +* Fix type annotation of code using XML etree by `@nsoranzo `_ in `#17367 `_ +* Update to black 2024 stable style by `@nsoranzo `_ in `#17391 `_ +* Add `image_diff` comparison method for test output verification using images by `@kostrykin `_ in `#17556 `_ ------------------- 23.2.1 (2024-02-21) diff --git a/packages/util/setup.cfg b/packages/util/setup.cfg index 70add5d8311c..9156b2cfcb9e 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 = 23.2.dev0 +version = 24.0.0 [options] include_package_data = True @@ -56,4 +56,4 @@ template = [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/web_apps/HISTORY.rst b/packages/web_apps/HISTORY.rst index 22b94ba98888..1d4ca683af94 100644 --- a/packages/web_apps/HISTORY.rst +++ b/packages/web_apps/HISTORY.rst @@ -3,11 +3,84 @@ History .. to_doc ---------- -24.0.dev0 ---------- +------------------- +24.0.0 (2024-04-02) +------------------- + +========= +Bug fixes +========= + +* tus wants a json response from v2.0.0 by `@mira-miracoli `_ in `#17246 `_ +* Fix quotas ID encoding by `@davelopez `_ in `#17335 `_ +* Fixes for flake8-bugbear 24.1.17 by `@nsoranzo `_ in `#17340 `_ +* Fix data_source and data_source_async bugs by `@wm75 `_ in `#17422 `_ +* Only check access permissions in ``/api/{history_dataset_collection_id}/contents/{dataset_collection_id}`` by `@ahmedhamidawan `_ in `#17444 `_ +* Associate default history with session when creating a new session by `@mvdbeek `_ in `#17557 `_ +* Fix tool shed webapp by `@mvdbeek `_ in `#17597 `_ +* Don't call ``get_or_create_default_history()`` twice for invalidated sessions by `@nsoranzo `_ in `#17613 `_ +* Fix tool panel workflow and favorites button bugs by `@ahmedhamidawan `_ in `#17634 `_ +* Fix DataResult type by `@mvdbeek `_ in `#17639 `_ +* Prevent 500 for anon /api/invocations by `@mvdbeek `_ in `#17640 `_ +* Don't fail for anon /api/users request by `@mvdbeek `_ in `#17645 `_ +* Limit new anon histories by `@mvdbeek `_ in `#17657 `_ +* Fix histories API index_query serialization by `@davelopez `_ in `#17726 `_ +* Handle missing indexer for a dataset by `@ahmedhamidawan `_ in `#17736 `_ +* Don't require history to calculate anon disk usage by `@mvdbeek `_ in `#17765 `_ +* Fix anon user values again by `@mvdbeek `_ in `#17772 `_ +* Fix new default history creation when in remote or single user mode by `@dannon `_ in `#17796 `_ +* Return published histories first in display_by_username_and_slug by `@mvdbeek `_ in `#17808 `_ +* Fix archived histories mixing with active in histories list by `@davelopez `_ in `#17856 `_ + +============ +Enhancements +============ +* New Workflow List and Card View by `@itisAliRH `_ in `#16607 `_ +* port invocation API to fastapi by `@martenson `_ in `#16707 `_ +* Python 3.8 as minimum by `@mr-c `_ in `#16954 `_ +* Support for OIDC API Auth and OIDC integration tests by `@nuwang `_ in `#16977 `_ +* Toward declarative help for Galaxy markdown directives. by `@jmchilton `_ in `#16979 `_ +* Vueify Admin User Grid by `@guerler `_ in `#17030 `_ +* Remove web framework dependency from tools by `@davelopez `_ in `#17058 `_ +* Vueify Admin Roles Grid by `@guerler `_ in `#17118 `_ +* SA2.0 updates: handling "object is being merged into a Session along the backref cascade path" by `@jdavcs `_ in `#17122 `_ +* Vueify Admin Groups Grid by `@guerler `_ in `#17126 `_ +* Towards SQLAlchemy 2.0: fix last cases of RemovedIn20Warning by `@jdavcs `_ in `#17132 `_ +* Vueify Admin Forms and Quota grids by `@guerler `_ in `#17141 `_ +* Migrate dataset extra files store to Pinia by `@davelopez `_ in `#17145 `_ +* Create pydantic model for the return of show operation - get: `/api/jobs/{job_id}` by `@heisner-tillman `_ in `#17153 `_ +* Remove legacy tool versions list from admin panel by `@guerler `_ in `#17155 `_ +* Don't require admin user to list ``/api/tool_data`` by `@jozh2008 `_ in `#17161 `_ +* Drop fastapi-utils.InferringRouter in favor of fastapi.APIRouter by `@jdavcs `_ in `#17184 `_ +* Vendorize fastapi-utls.cbv by `@jdavcs `_ in `#17205 `_ +* Vueifiy History Grids by `@guerler `_ in `#17219 `_ +* Update Python dependencies by `@galaxybot `_ in `#17235 `_ +* Refactor two of the missing invocation routes to FastAPI by `@heisner-tillman `_ in `#17237 `_ +* Allow job files to consume TUS uploads by `@jmchilton `_ in `#17242 `_ +* Migrate models to pydantic 2 by `@mvdbeek `_ in `#17262 `_ +* Adds delete, purge and undelete batch operations to History Grid by `@guerler `_ in `#17282 `_ +* Fix any type for tool_data_file_path by `@mvdbeek `_ in `#17293 `_ +* API endpoint that allows "changing" the objectstore for "safe" scenarios. by `@jmchilton `_ in `#17329 `_ +* Update Python dependencies by `@galaxybot `_ in `#17333 `_ +* Combines legacy qv-pattern and advanced filter pattern in history index endpoint by `@guerler `_ in `#17368 `_ +* Update to black 2024 stable style by `@nsoranzo `_ in `#17391 `_ +* Replaces Trackster Grids with Data Dialog, Removes Phyloviz, Circster and Sweepster by `@guerler `_ in `#17415 `_ +* Removes outdated Grid controller and backbone modules by `@guerler `_ in `#17434 `_ +* Allow using tool data bundles as inputs to reference data select parameters by `@mvdbeek `_ in `#17435 `_ +* Modernize bits and pieces of storage display by `@jmchilton `_ in `#17436 `_ +* UI for "relocating" a dataset to a new object store (when safe) by `@jmchilton `_ in `#17437 `_ +* Refactor Workflow API routes - Part 1 by `@heisner-tillman `_ in `#17463 `_ +* Consolidate resource grids into tab views by `@guerler `_ in `#17487 `_ +* Display workflow invocation counts. by `@jmchilton `_ in `#17488 `_ +* Removes legacy history xml makos by `@guerler `_ in `#17505 `_ +* add encode ID API endpoint by `@mira-miracoli `_ in `#17510 `_ +* Fixing data_source tools and incrementing tool profile by `@wm75 `_ in `#17515 `_ +* Filter out subworkflow invocations by `@mvdbeek `_ in `#17558 `_ +* Links to individual invocations. by `@jmchilton `_ in `#17566 `_ +* Restore histories API behavior for `keys` query parameter by `@davelopez `_ in `#17779 `_ +* Fix datasets API custom keys encoding by `@davelopez `_ in `#17793 `_ ------------------- 23.2.1 (2024-02-21) diff --git a/packages/web_apps/setup.cfg b/packages/web_apps/setup.cfg index 20ac5878220b..bc05f3bc471f 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 = 23.2.dev0 +version = 24.0.0 [options] include_package_data = True @@ -74,4 +74,4 @@ python_requires = >=3.8 [options.packages.find] exclude = tests* - tool_shed.test* + tool_shed.test* \ No newline at end of file diff --git a/packages/web_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst index c332d31be278..94af53c636f6 100644 --- a/packages/web_framework/HISTORY.rst +++ b/packages/web_framework/HISTORY.rst @@ -3,11 +3,22 @@ History .. to_doc ---------- -24.0.dev0 ---------- +------------------- +24.0.0 (2024-04-02) +------------------- + +============ +Enhancements +============ +* Python 3.8 as minimum by `@mr-c `_ in `#16954 `_ +* Vueify Admin User Grid by `@guerler `_ in `#17030 `_ +* Remove web framework dependency from tools by `@davelopez `_ in `#17058 `_ +* Vueify Admin Groups Grid by `@guerler `_ in `#17126 `_ +* Migrate models to pydantic 2 by `@mvdbeek `_ in `#17262 `_ +* Update to black 2024 stable style by `@nsoranzo `_ in `#17391 `_ +* Removes outdated Grid controller and backbone modules by `@guerler `_ in `#17434 `_ ------------------- 23.2.1 (2024-02-21) diff --git a/packages/web_framework/setup.cfg b/packages/web_framework/setup.cfg index e04d3f101f32..42ac3eb61ad9 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 = 23.2.dev0 +version = 24.0.0 [options] include_package_data = True @@ -48,4 +48,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/web_stack/HISTORY.rst b/packages/web_stack/HISTORY.rst index 2af705d8507c..341968e7158b 100644 --- a/packages/web_stack/HISTORY.rst +++ b/packages/web_stack/HISTORY.rst @@ -3,11 +3,16 @@ History .. to_doc ---------- -24.0.dev0 ---------- +------------------- +24.0.0 (2024-04-02) +------------------- + +============ +Enhancements +============ +* Update to black 2024 stable style by `@nsoranzo `_ in `#17391 `_ ------------------- 23.2.1 (2024-02-21) diff --git a/packages/web_stack/setup.cfg b/packages/web_stack/setup.cfg index f7bc6adc5d54..242a7eb0da6d 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 = 23.2.dev0 +version = 24.0.0 [options] include_package_data = True @@ -40,4 +40,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* + tests* \ No newline at end of file