From e77b17df064fcddfc983c081bdd7b1027ece3e9f Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Mon, 23 Oct 2023 21:35:24 +0200 Subject: [PATCH 1/2] Create version 23.1.1 --- lib/galaxy/version.py | 2 +- packages/app/HISTORY.rst | 148 ++++++++++++++++++++++++++++- packages/app/setup.cfg | 4 +- packages/auth/HISTORY.rst | 11 ++- packages/auth/setup.cfg | 2 +- packages/config/HISTORY.rst | 48 +++++++++- packages/config/setup.cfg | 2 +- packages/data/HISTORY.rst | 90 +++++++++++++++++- packages/data/setup.cfg | 4 +- packages/files/HISTORY.rst | 20 +++- packages/files/setup.cfg | 4 +- packages/job_execution/HISTORY.rst | 28 +++++- packages/job_execution/setup.cfg | 2 +- packages/job_metrics/HISTORY.rst | 8 +- packages/job_metrics/setup.cfg | 2 +- packages/navigation/HISTORY.rst | 11 ++- packages/navigation/setup.cfg | 2 +- packages/objectstore/HISTORY.rst | 31 +++++- packages/objectstore/setup.cfg | 2 +- packages/selenium/HISTORY.rst | 33 ++++++- packages/selenium/setup.cfg | 2 +- packages/test_api/HISTORY.rst | 43 ++++++++- packages/test_api/setup.cfg | 2 +- packages/test_base/HISTORY.rst | 30 +++++- packages/test_base/setup.cfg | 2 +- packages/test_driver/HISTORY.rst | 28 +++++- packages/test_driver/setup.cfg | 2 +- packages/tool_util/HISTORY.rst | 62 +++++++++++- packages/tool_util/setup.cfg | 4 +- packages/tours/HISTORY.rst | 8 +- packages/tours/setup.cfg | 4 +- packages/util/HISTORY.rst | 35 ++++++- packages/util/setup.cfg | 4 +- packages/web_apps/HISTORY.rst | 81 +++++++++++++++- packages/web_apps/setup.cfg | 4 +- packages/web_framework/HISTORY.rst | 21 +++- packages/web_framework/setup.cfg | 4 +- packages/web_stack/HISTORY.rst | 25 ++++- packages/web_stack/setup.cfg | 2 +- 39 files changed, 730 insertions(+), 87 deletions(-) diff --git a/lib/galaxy/version.py b/lib/galaxy/version.py index 8305d90f715f..55ee632c85c1 100644 --- a/lib/galaxy/version.py +++ b/lib/galaxy/version.py @@ -1,3 +1,3 @@ VERSION_MAJOR = "23.1" -VERSION_MINOR = "1.dev0" +VERSION_MINOR = "1" VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else "") diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst index 65f4cc0e6c44..ea05fc1e9ecd 100644 --- a/packages/app/HISTORY.rst +++ b/packages/app/HISTORY.rst @@ -3,11 +3,145 @@ History .. to_doc ------------ -23.1.1.dev0 ------------ +------------------- +23.1.1 (2023-10-23) +------------------- + + +========= +Bug fixes +========= + +* read job_conf directly from `config_dir` instead of computing it again from `config_file` by `@bernt-matthias `_ in `#15596 `_ +* Fix some drs handling issues by `@nuwang `_ in `#15777 `_ +* Fix filesource file url support by `@nuwang `_ in `#15794 `_ +* Fix revision scripts, run migrations in CI, add repair option, improve migrations utils by `@jdavcs `_ in `#15811 `_ +* Change confusing pulsar logs message by `@kysrpex `_ in `#16038 `_ +* Fix and test startup with Python 3.11 on macOS by `@nsoranzo `_ in `#16082 `_ +* Fix : Ignore error messages for admin created accounts by `@jvanbraekel `_ in `#16132 `_ +* Ensure session is request-scoped for legacy endpoints by `@jdavcs `_ in `#16207 `_ +* Fix "database is locked" error (occurring in the context of workflow testing under SQLite) by `@jdavcs `_ in `#16208 `_ +* Fix ordering of data libraries from API by `@martenson `_ in `#16300 `_ +* qualify querying for an api-key by `@martenson `_ in `#16320 `_ +* Fix tags ownership by `@davelopez `_ in `#16339 `_ +* Job cache fixes for DCEs by `@mvdbeek `_ in `#16384 `_ +* Fix histories count by `@davelopez `_ in `#16400 `_ +* Fix select statement syntax for SQLAlchemy 2.0 by `@jdavcs `_ in `#16421 `_ +* Fix up unit tests for local use by `@mvdbeek `_ in `#16483 `_ +* Run through tmp_dir_creation_statement only once by `@mvdbeek `_ in `#16529 `_ +* Fix double-encoding notification content by `@mvdbeek `_ in `#16530 `_ +* Limit tool document cache to tool configs with explicit cache path by `@mvdbeek `_ in `#16537 `_ +* Fix `multiple` remote test data by `@davelopez `_ in `#16542 `_ +* Ignore errors with user-set job resources by `@mvdbeek `_ in `#16579 `_ +* Fix replacement parameters for subworkflows. by `@jmchilton `_ in `#16592 `_ +* make sure that TMP, TEMP, and TMPDIR are set by `@bernt-matthias `_ in `#16594 `_ +* Bump minimum tpv version to 2.3.2 by `@mvdbeek `_ in `#16597 `_ +* Backport tool mem fixes by `@mvdbeek `_ in `#16601 `_ +* Reload toolbox after forking when using `--preload` by `@mvdbeek `_ in `#16620 `_ +* Account for expires/expires_in when refreshing token by `@mvdbeek `_ in `#16621 `_ +* Fixes for conditional subworkflow steps by `@mvdbeek `_ in `#16632 `_ +* Fix nested conditional workflow steps by `@mvdbeek `_ in `#16641 `_ +* Ensure Job belongs to current SA session by `@mvdbeek `_ in `#16655 `_ +* Fix expression evaluation for nested state by `@mvdbeek `_ in `#16656 `_ +* Make sort_collection tool require terminal datasets by `@mvdbeek `_ in `#16661 `_ +* Push to object store even if ``set_meta`` fails by `@mvdbeek `_ in `#16667 `_ +* Fix metadata setting in extended metadata + outputs_to_working_directory mode by `@mvdbeek `_ in `#16678 `_ +* Fix regex validation for global inline flags by `@mvdbeek `_ in `#16683 `_ +* Fix closed transaction error on galaxy startup/check jobs by `@jdavcs `_ in `#16687 `_ +* Add missing join condition in job search by `@mvdbeek `_ in `#16710 `_ +* Fix job search query by `@mvdbeek `_ in `#16714 `_ +* Copy the collection contents by default when copying a collection by `@mvdbeek `_ in `#16717 `_ +* Fix collection id encoding by `@davelopez `_ in `#16718 `_ +* Workaround for XML nodes of job resource parameters losing their children by `@kysrpex `_ in `#16728 `_ +* move the email and username redacting from the role loop by `@martenson `_ in `#16820 `_ +* Fix parameter display in job info page for tools with sections by `@mvdbeek `_ in `#16821 `_ +* Fix workflow preview display if tool state does not contain all parameter values by `@mvdbeek `_ in `#16829 `_ +* Fix up local tool version handling by `@mvdbeek `_ in `#16836 `_ +* Fix and prevent persisting null file_size by `@mvdbeek `_ in `#16855 `_ +* Allow referring to steps by label only in markdown editor by `@mvdbeek `_ in `#16861 `_ +* Fix safe update version handling in run form by `@mvdbeek `_ in `#16865 `_ +* Remove more flushes in database operation tools by `@mvdbeek `_ in `#16875 `_ +* Fix tag ownership check by `@mvdbeek `_ in `#16877 `_ + +============ +Enhancements +============ +* Empower Users to Select Storage Destination by `@jmchilton `_ in `#14073 `_ +* External Login Flow: Redirect users if account already exists by `@ahmedhamidawan `_ in `#15019 `_ +* Add slack error reporting plugin by `@hexylena `_ in `#15025 `_ +* Various Tool Shed Cleanup by `@jmchilton `_ in `#15247 `_ +* Add Storage Management API by `@davelopez `_ in `#15295 `_ +* OIDC tokens by `@SergeyYakubov `_ in `#15300 `_ +* Expose additional beaker caching backends by `@claudiofr `_ in `#15349 `_ +* Add support for visualizing HDF5 datasets. by `@jarrah42 `_ in `#15394 `_ +* Towards SQLAlchemy 2.0: drop session autocommit setting by `@jdavcs `_ in `#15421 `_ +* Update Python dependencies by `@galaxybot `_ in `#15435 `_ +* Fix for new style conda packages by `@bernt-matthias `_ in `#15446 `_ +* Move database access code out of tool_util by `@jdavcs `_ in `#15467 `_ +* Protection against problematic boolean parameters. by `@jmchilton `_ in `#15493 `_ +* Use connection instead of session for ItemGrabber by `@jdavcs `_ in `#15496 `_ +* Unify url handling with filesources by `@nuwang `_ in `#15497 `_ +* Move TS to Alembic by `@jdavcs `_ in `#15509 `_ +* Explore tool remote test data by `@davelopez `_ in `#15510 `_ +* Handle "email_from" config option consistently, as per schema description by `@jdavcs `_ in `#15557 `_ +* Update Python dependencies by `@galaxybot `_ in `#15564 `_ +* Drop workflow exports to myexperiment.org by `@dannon `_ in `#15576 `_ +* Update database_heartbeat for SA 2.0 compatibility by `@jdavcs `_ in `#15611 `_ +* Add suggested Training material to Tool Form by `@ElectronicBlueberry `_ in `#15628 `_ +* Wrap check_jobs_at_startup operation in a transaction (SA 2.0 compatibility) by `@jdavcs `_ in `#15643 `_ +* Add Galaxy Notification System by `@davelopez `_ in `#15663 `_ +* Unpin Beaker requirement by `@nsoranzo `_ in `#15665 `_ +* Add transactional state to JobHandlerStopQueue by `@jdavcs `_ in `#15671 `_ +* Verify that activation and reset emails are properly generated by `@guerler `_ in `#15681 `_ +* Add transactional state to workflow scheduling manager by `@jdavcs `_ in `#15683 `_ +* Remove DELETED_NEW job state from code base by `@jdavcs `_ in `#15690 `_ +* Fix/Enhance recalculate disk usage API endpoint by `@davelopez `_ in `#15739 `_ +* Add API test and refactor code for related:hid history filter by `@ahmedhamidawan `_ in `#15786 `_ +* Migrate to MyST-Parser for Markdown docs by `@nsoranzo `_ in `#15844 `_ +* Drop use_legacy_history from config by `@dannon `_ in `#15861 `_ +* Drop database views by `@jdavcs `_ in `#15876 `_ +* Update Python dependencies by `@galaxybot `_ in `#15890 `_ +* Allow pending inputs in some collection operation tools by `@mvdbeek `_ in `#15892 `_ +* Updated doc and tests for attribute value filter by `@tuncK `_ in `#15929 `_ +* Update Python dependencies by `@galaxybot `_ in `#15942 `_ +* Record input datasets and collections at full parameter path by `@mvdbeek `_ in `#15978 `_ +* Export tool citations configurable message by `@minh-biocommons `_ in `#15998 `_ +* Add History Archival feature by `@davelopez `_ in `#16003 `_ +* Code cleanups from ruff and pyupgrade by `@nsoranzo `_ in `#16035 `_ +* Add missing fields to HistorySummary schema model by `@davelopez `_ in `#16041 `_ +* Vendorise ``packaging.versions.LegacyVersion`` by `@nsoranzo `_ in `#16058 `_ +* Add Repository owner field to ToolSearch by `@ahmedhamidawan `_ in `#16061 `_ +* Add count support for listing filters by `@davelopez `_ in `#16075 `_ +* Update Python dependencies by `@galaxybot `_ in `#16086 `_ +* Improved Cache Monitoring for Object Stores by `@jmchilton `_ in `#16110 `_ +* Integrate accessibility testing into Selenium testing by `@jmchilton `_ in `#16122 `_ +* Update Python dependencies by `@galaxybot `_ in `#16123 `_ +* Improve histories and datasets immutability checks by `@davelopez `_ in `#16143 `_ +* Update Python dependencies by `@galaxybot `_ in `#16153 `_ +* Migrate display applications API to Fast API by `@heisner-tillman `_ in `#16156 `_ +* adjust grid sharing indicators by `@martenson `_ in `#16163 `_ +* Update Python dependencies by `@galaxybot `_ in `#16182 `_ +* Drop workarounds for old ro-crate-py and docutils versions by `@mvdbeek `_ in `#16198 `_ +* Remove various fallback behaviors by `@mvdbeek `_ in `#16199 `_ +* bring grids for (published) pages on par with workflows by `@martenson `_ in `#16209 `_ +* Update Python dependencies by `@galaxybot `_ in `#16227 `_ +* Update Python dependencies by `@galaxybot `_ in `#16267 `_ +* Fix tool remote test data by `@davelopez `_ in `#16311 `_ +* Hide conditionally skipped output by `@mvdbeek `_ in `#16356 `_ +* Fix Storage Dashboard missing archived histories by `@davelopez `_ in `#16473 `_ +* Bump bx-python to 0.10.0 by `@mvdbeek `_ in `#16484 `_ +* Drop expunge_all() call in WebTransactionRequest by `@mvdbeek `_ in `#16606 `_ +============= +Other changes +============= + +* Follow up on object store selection PR. by `@jmchilton `_ in `#15654 `_ +* merge release_23.0 into dev by `@martenson `_ in `#15830 `_ +* Move axe-selenium-python to dev dependencies by `@nsoranzo `_ in `#16162 `_ +* Bump msal version by `@mvdbeek `_ in `#16285 `_ +* Fix error_reports linting by `@mvdbeek `_ in `#16465 `_ ------------------- 23.0.6 (2023-10-23) @@ -42,6 +176,7 @@ 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 `_ * Fixes for (gitlab) error reporting by `@bernt-matthias `_ in `#16424 `_ @@ -55,6 +190,7 @@ Bug fixes Bug fixes ========= +* * * Fix default when statement evaluation by `@mvdbeek `_ in `#16332 `_ * Redact private role name and description when purging user by `@mvdbeek `_ in `#16349 `_ @@ -68,6 +204,7 @@ Bug fixes Bug fixes ========= +* * * * Bump galaxy-release-util version to 0.1.2 by `@mvdbeek `_ in `#16241 `_ @@ -76,6 +213,7 @@ Bug fixes Enhancements ============ +* * When importing tool data bundles, use the first loc file for the matching table by `@natefoo `_ in `#16247 `_ ============= @@ -96,6 +234,7 @@ Bug fixes * * * +* * Fix ``Text File Busy`` errors at the source by `@mvdbeek `_ in `#16212 `_ ============ @@ -105,6 +244,7 @@ Enhancements * * * +* * Point release deps fixes and docs by `@mvdbeek `_ in `#16214 `_ * Use galaxy-release-util to upload python packages by `@mvdbeek `_ in `#16240 `_ @@ -121,6 +261,7 @@ 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 `_ @@ -147,6 +288,7 @@ Other changes * * * +* * Startup fix when tool removed between reboot by `@mvdbeek `_ in `#16175 `_ ------------------- diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg index daaa99ffbb3f..4696724ce902 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 = 23.1.dev0 +version = 23.1.1 [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 98b94ee2ca7a..ca03f489a5e9 100644 --- a/packages/auth/HISTORY.rst +++ b/packages/auth/HISTORY.rst @@ -3,11 +3,16 @@ History .. to_doc ------------ -23.1.1.dev0 ------------ +------------------- +23.1.1 (2023-10-23) +------------------- + +============ +Enhancements +============ +* Update Python dependencies by `@galaxybot `_ in `#15435 `_ ------------------- 23.0.6 (2023-10-23) diff --git a/packages/auth/setup.cfg b/packages/auth/setup.cfg index cca3a9b7ad7c..db3cffca6ee7 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 = 23.1.dev0 +version = 23.1.1 [options] include_package_data = True diff --git a/packages/config/HISTORY.rst b/packages/config/HISTORY.rst index 62af2924f905..bc7d346c8f30 100644 --- a/packages/config/HISTORY.rst +++ b/packages/config/HISTORY.rst @@ -3,11 +3,52 @@ History .. to_doc ------------ -23.1.1.dev0 ------------ +------------------- +23.1.1 (2023-10-23) +------------------- + + +========= +Bug fixes +========= + +* Fix some drs handling issues by `@nuwang `_ in `#15777 `_ +* Improve container resolver documentation by `@mvdbeek `_ in `#16280 `_ +* Limit tool document cache to tool configs with explicit cache path by `@mvdbeek `_ in `#16537 `_ +* Backport tool mem fixes by `@mvdbeek `_ in `#16601 `_ +* Fix allowlist deserialization in file sources by `@mvdbeek `_ in `#16729 `_ +============ +Enhancements +============ +* External Login Flow: Redirect users if account already exists by `@ahmedhamidawan `_ in `#15019 `_ +* Add slack error reporting plugin by `@hexylena `_ in `#15025 `_ +* Documents use of k8s_extra_job_envs in job_conf sample advanced by `@pcm32 `_ in `#15110 `_ +* Expose additional beaker caching backends by `@claudiofr `_ in `#15349 `_ +* Unify url handling with filesources by `@nuwang `_ in `#15497 `_ +* Handle "email_from" config option consistently, as per schema description by `@jdavcs `_ in `#15557 `_ +* Drop workflow exports to myexperiment.org by `@dannon `_ in `#15576 `_ +* Container resolvers: add docs, typing and tests by `@bernt-matthias `_ in `#15614 `_ +* Add suggested Training material to Tool Form by `@ElectronicBlueberry `_ in `#15628 `_ +* Deprecate tools/evolution by `@bernt-matthias `_ in `#15656 `_ +* Add Galaxy Notification System by `@davelopez `_ in `#15663 `_ +* More object store documentation. by `@jmchilton `_ in `#15707 `_ +* Drop use_legacy_history from config by `@dannon `_ in `#15861 `_ +* FITS data format by `@volodymyrss `_ in `#15905 `_ +* Export tool citations configurable message by `@minh-biocommons `_ in `#15998 `_ +* Rename object stores in config. by `@jmchilton `_ in `#16029 `_ +* Add hdf4 datatype by `@TheoMathurin `_ in `#16105 `_ +* Improved Cache Monitoring for Object Stores by `@jmchilton `_ in `#16110 `_ +* Refactor caching object stores ahead of adding task-based store. by `@jmchilton `_ in `#16144 `_ +* Add zipped mongodb and genenotebook datatypes by `@abretaud `_ in `#16173 `_ +* Add Visium datatype for squidpy and spatialomics tools by `@astrovsky01 `_ in `#16255 `_ + +============= +Other changes +============= + +* Implement some initial object store selection end-to-end tests. by `@jmchilton `_ in `#15785 `_ ------------------- 23.0.6 (2023-10-23) @@ -53,6 +94,7 @@ No recorded changes since last release Bug fixes ========= +* * * Change default watchdog inotify_buffer log level to info by `@mvdbeek `_ in `#15967 `_ diff --git a/packages/config/setup.cfg b/packages/config/setup.cfg index 16d2815d2a2e..19f27d18d1db 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 = 23.1.dev0 +version = 23.1.1 [options] include_package_data = True diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst index 679bc14b9bd5..7ef01c4529e6 100644 --- a/packages/data/HISTORY.rst +++ b/packages/data/HISTORY.rst @@ -3,11 +3,93 @@ History .. to_doc ------------ -23.1.1.dev0 ------------ +------------------- +23.1.1 (2023-10-23) +------------------- +========= +Bug fixes +========= + +* Fix bad auto-merge of dev. by `@jmchilton `_ in `#15386 `_ +* Merge conflicting db migration branches into one by `@jdavcs `_ in `#15771 `_ +* Enable ``strict_equality`` mypy option by `@nsoranzo `_ in `#15808 `_ +* Fix revision scripts, run migrations in CI, add repair option, improve migrations utils by `@jdavcs `_ in `#15811 `_ +* Fix anonymous user uploads when vault is configured by `@tchaussepiedifb `_ in `#15858 `_ +* Fix nullable deleted column in API Keys table by `@davelopez `_ in `#15956 `_ +* Attempt to fix mypy check by `@davelopez `_ in `#16103 `_ +* Ensure session is request-scoped for legacy endpoints by `@jdavcs `_ in `#16207 `_ +* Reset autocommit to True (temporarily) by `@jdavcs `_ in `#16283 `_ +* Update 23.1 release tags for migration scripts by `@jdavcs `_ in `#16294 `_ +* Fix form builder value handling by `@guerler `_ in `#16304 `_ +* Fix tags ownership by `@davelopez `_ in `#16339 `_ +* Fix disk usage recalculation for distributed object stores by `@mvdbeek `_ in `#16380 `_ +* Job cache fixes for DCEs by `@mvdbeek `_ in `#16384 `_ +* Fix histories count by `@davelopez `_ in `#16400 `_ +* Fix double-encoding notification content by `@mvdbeek `_ in `#16530 `_ +* Optimize getting current user session by `@mvdbeek `_ in `#16604 `_ +* Fixes for conditional subworkflow steps by `@mvdbeek `_ in `#16632 `_ +* Copy the collection contents by default when copying a collection by `@mvdbeek `_ in `#16717 `_ +* Fix allowlist deserialization in file sources by `@mvdbeek `_ in `#16729 `_ +* Fix workflow output display without label by `@mvdbeek `_ in `#16749 `_ +* Fix and prevent persisting null file_size by `@mvdbeek `_ in `#16855 `_ +* Fix workflow import losing tool_version by `@mvdbeek `_ in `#16869 `_ +* Remove more flushes in database operation tools by `@mvdbeek `_ in `#16875 `_ +* Fix join condition for nested collection query by `@mvdbeek `_ in `#16880 `_ + +============ +Enhancements +============ + +* Empower Users to Select Storage Destination by `@jmchilton `_ in `#14073 `_ +* Add Storage Dashboard visualizations for histories by `@davelopez `_ in `#14820 `_ +* Towards decoupling datatypes and model by `@jdavcs `_ in `#15186 `_ +* Add Storage Management API by `@davelopez `_ in `#15295 `_ +* OIDC tokens by `@SergeyYakubov `_ in `#15300 `_ +* Expose additional beaker caching backends by `@claudiofr `_ in `#15349 `_ +* Follow up to #15186 by `@jdavcs `_ in `#15388 `_ +* Add support for visualizing HDF5 datasets. by `@jarrah42 `_ in `#15394 `_ +* Towards SQLAlchemy 2.0: drop session autocommit setting by `@jdavcs `_ in `#15421 `_ +* Update Python dependencies by `@galaxybot `_ in `#15435 `_ +* Unify url handling with filesources by `@nuwang `_ in `#15497 `_ +* Move TS to Alembic by `@jdavcs `_ in `#15509 `_ +* Update Python dependencies by `@galaxybot `_ in `#15564 `_ +* Update database_heartbeat for SA 2.0 compatibility by `@jdavcs `_ in `#15611 `_ +* Update supports_skip_locked, supports_returning for SA 2.0 compatibility by `@jdavcs `_ in `#15633 `_ +* Add Galaxy Notification System by `@davelopez `_ in `#15663 `_ +* Drop model mapping unit tests by `@jdavcs `_ in `#15669 `_ +* Add transactional state to workflow scheduling manager by `@jdavcs `_ in `#15683 `_ +* Remove DELETED_NEW job state from code base by `@jdavcs `_ in `#15690 `_ +* Fix/Enhance recalculate disk usage API endpoint by `@davelopez `_ in `#15739 `_ +* Drop database views by `@jdavcs `_ in `#15876 `_ +* Update Python dependencies by `@galaxybot `_ in `#15890 `_ +* FITS data format by `@volodymyrss `_ in `#15905 `_ +* Improve display chunk generation for BAMs by `@wm75 `_ in `#15972 `_ +* Add History Archival feature by `@davelopez `_ in `#16003 `_ +* Add alter_column migration utility by `@jdavcs `_ in `#16009 `_ +* Code cleanups from ruff and pyupgrade by `@nsoranzo `_ in `#16035 `_ +* Add missing fields to HistorySummary schema model by `@davelopez `_ in `#16041 `_ +* Dataset chunking tests (and small fixes) by `@jmchilton `_ in `#16069 `_ +* Add create_foreign_key migration utility by `@jdavcs `_ in `#16077 `_ +* Refactor models enums to eliminate schema dependency on model layer. by `@jmchilton `_ in `#16080 `_ +* Use automated naming convention to generate indexes and constraints in database by `@jdavcs `_ in `#16089 `_ +* Add zipped mongodb and genenotebook datatypes by `@abretaud `_ in `#16173 `_ +* Drop workarounds for old ro-crate-py and docutils versions by `@mvdbeek `_ in `#16198 `_ +* bring grids for (published) pages on par with workflows by `@martenson `_ in `#16209 `_ +* Add Visium datatype for squidpy and spatialomics tools by `@astrovsky01 `_ in `#16255 `_ +* Filter deleted keys from api_keys relationship by `@dannon `_ in `#16321 `_ +* Increase `CustosAuthnzToken.external_user_id` column size by `@davelopez `_ in `#16818 `_ + +============= +Other changes +============= + +* Follow up on object store selection PR. by `@jmchilton `_ in `#15654 `_ +* Fix Enums in API docs by `@davelopez `_ in `#15740 `_ +* merge release_23.0 into dev by `@martenson `_ in `#15830 `_ +* Fix linting of FITS datatype code by `@mvdbeek `_ in `#16169 `_ +* backport of pysam tostring by `@martenson `_ in `#16822 `_ ------------------- 23.0.6 (2023-10-23) @@ -30,6 +112,7 @@ Bug fixes Bug fixes ========= +* * Copy when_expression when copying workflow step by `@mvdbeek `_ in `#16377 `_ ------------------- @@ -59,6 +142,7 @@ 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 `_ diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg index a0e4228e33f8..02e99512f7c6 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 = 23.1.dev0 +version = 23.1.1 [options] include_package_data = True @@ -70,4 +70,4 @@ 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 0ea8a36a4dd8..853a29b5b2a4 100644 --- a/packages/files/HISTORY.rst +++ b/packages/files/HISTORY.rst @@ -3,11 +3,25 @@ History .. to_doc ------------ -23.1.1.dev0 ------------ +------------------- +23.1.1 (2023-10-23) +------------------- + + +========= +Bug fixes +========= + +* Fix some drs handling issues by `@nuwang `_ in `#15777 `_ +* Fix filesource file url support by `@nuwang `_ in `#15794 `_ +* Fix unittest mocks to support us checking geturl() by `@dannon `_ in `#16726 `_ +* Fix allowlist deserialization in file sources by `@mvdbeek `_ in `#16729 `_ +============ +Enhancements +============ +* Unify url handling with filesources by `@nuwang `_ in `#15497 `_ ------------------- 23.0.6 (2023-10-23) diff --git a/packages/files/setup.cfg b/packages/files/setup.cfg index 9f89c257b476..df0ce6d04da5 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 = 23.1.dev0 +version = 23.1.1 [options] include_package_data = True @@ -40,4 +40,4 @@ python_requires = >=3.7 [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 1f5d1f27002c..982ed66fdbc9 100644 --- a/packages/job_execution/HISTORY.rst +++ b/packages/job_execution/HISTORY.rst @@ -3,11 +3,33 @@ History .. to_doc ------------ -23.1.1.dev0 ------------ +------------------- +23.1.1 (2023-10-23) +------------------- + +========= +Bug fixes +========= +* Fix tags ownership by `@davelopez `_ in `#16339 `_ +* Push to object store even if ``set_meta`` fails by `@mvdbeek `_ in `#16667 `_ +* Fix metadata setting in extended metadata + outputs_to_working_directory mode by `@mvdbeek `_ in `#16678 `_ +* Fix ItemOwnerShipException in tag removal by `@mvdbeek `_ in `#16773 `_ +* Fix and prevent persisting null file_size by `@mvdbeek `_ in `#16855 `_ + +============ +Enhancements +============ + +* Empower Users to Select Storage Destination by `@jmchilton `_ in `#14073 `_ +* Towards SQLAlchemy 2.0: drop session autocommit setting by `@jdavcs `_ in `#15421 `_ +* Unify url handling with filesources by `@nuwang `_ in `#15497 `_ +* Handle "email_from" config option consistently, as per schema description by `@jdavcs `_ in `#15557 `_ +* Record input datasets and collections at full parameter path by `@mvdbeek `_ in `#15978 `_ +* Code cleanups from ruff and pyupgrade by `@nsoranzo `_ in `#16035 `_ +* Improved Cache Monitoring for Object Stores by `@jmchilton `_ in `#16110 `_ +* Remove various fallback behaviors by `@mvdbeek `_ in `#16199 `_ ------------------- 23.0.6 (2023-10-23) diff --git a/packages/job_execution/setup.cfg b/packages/job_execution/setup.cfg index ea1943235b8a..206c84309a87 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 = 23.1.dev0 +version = 23.1.1 [options] include_package_data = True diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst index 464d80a31e52..79419abffd68 100644 --- a/packages/job_metrics/HISTORY.rst +++ b/packages/job_metrics/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc ------------ -23.1.1.dev0 ------------ - +------------------- +23.1.1 (2023-10-23) +------------------- +No recorded changes since last release ------------------- 23.0.6 (2023-10-23) diff --git a/packages/job_metrics/setup.cfg b/packages/job_metrics/setup.cfg index d9576a25c86d..1ccb6607e12d 100644 --- a/packages/job_metrics/setup.cfg +++ b/packages/job_metrics/setup.cfg @@ -27,7 +27,7 @@ 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 = 23.1.dev0 +version = 23.1.1 [options] include_package_data = True diff --git a/packages/navigation/HISTORY.rst b/packages/navigation/HISTORY.rst index 4e8f720f2bf3..d9445a75a242 100644 --- a/packages/navigation/HISTORY.rst +++ b/packages/navigation/HISTORY.rst @@ -3,11 +3,16 @@ History .. to_doc ------------ -23.1.1.dev0 ------------ +------------------- +23.1.1 (2023-10-23) +------------------- + +============ +Enhancements +============ +* Initial end-to-end tests for separate quota sources per object store by `@jmchilton `_ in `#15800 `_ ------------------- 23.0.6 (2023-10-23) diff --git a/packages/navigation/setup.cfg b/packages/navigation/setup.cfg index 3b16102ad68c..f886aa2f0c1f 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 = 23.1.dev0 +version = 23.1.1 [options] include_package_data = True diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst index 0e324f7a81b9..1be61711f26b 100644 --- a/packages/objectstore/HISTORY.rst +++ b/packages/objectstore/HISTORY.rst @@ -3,11 +3,36 @@ History .. to_doc ------------ -23.1.1.dev0 ------------ +------------------- +23.1.1 (2023-10-23) +------------------- + + +========= +Bug fixes +========= + +* Enable ``strict_equality`` mypy option by `@nsoranzo `_ in `#15808 `_ + +============ +Enhancements +============ + +* Empower Users to Select Storage Destination by `@jmchilton `_ in `#14073 `_ +* Update Python dependencies by `@galaxybot `_ in `#15435 `_ +* Refactor badge parsing/serialization/typing for reuse. by `@jmchilton `_ in `#15987 `_ +* Rename object stores in config. by `@jmchilton `_ in `#16029 `_ +* Code cleanups from ruff and pyupgrade by `@nsoranzo `_ in `#16035 `_ +* De-duplicate code around object store caches. by `@jmchilton `_ in `#16108 `_ +* Improved Cache Monitoring for Object Stores by `@jmchilton `_ in `#16110 `_ +* De-duplication and improvements to the in-process object store cache monitor by `@jmchilton `_ in `#16111 `_ +* Refactor caching object stores ahead of adding task-based store. by `@jmchilton `_ in `#16144 `_ +============= +Other changes +============= +* Follow up on object store selection PR. by `@jmchilton `_ in `#15654 `_ ------------------- 23.0.6 (2023-10-23) diff --git a/packages/objectstore/setup.cfg b/packages/objectstore/setup.cfg index e283840cb5d5..0362b1883053 100644 --- a/packages/objectstore/setup.cfg +++ b/packages/objectstore/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-objectstore url = https://github.com/galaxyproject/galaxy -version = 23.1.dev0 +version = 23.1.1 [options] include_package_data = True diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst index 348299577f68..876fe39289f7 100644 --- a/packages/selenium/HISTORY.rst +++ b/packages/selenium/HISTORY.rst @@ -3,11 +3,37 @@ History .. to_doc ------------ -23.1.1.dev0 ------------ +------------------- +23.1.1 (2023-10-23) +------------------- + +========= +Bug fixes +========= +* Improve robustness of collection upload tests. by `@jmchilton `_ in `#16093 `_ +* Accessibility fixes for workflows, login, and registration. by `@jmchilton `_ in `#16146 `_ +* Login/Register fixes by `@dannon `_ in `#16652 `_ + +============ +Enhancements +============ + +* Upgraded to new multiselect Tags component for Workflows, DatasetList, Attributes by `@hujambo-dunia `_ in `#15225 `_ +* Add basic selenium test for shared histories by `@davelopez `_ in `#15538 `_ +* Initial end-to-end tests for separate quota sources per object store by `@jmchilton `_ in `#15800 `_ +* Vueify Select field by `@guerler `_ in `#16010 `_ +* implement admin jobs filtering by `@martenson `_ in `#16020 `_ +* Selenium test for displaying workflows with problems in pages. by `@jmchilton `_ in `#16085 `_ +* Integrate accessibility testing into Selenium testing by `@jmchilton `_ in `#16122 `_ +* bring grids for (published) pages on par with workflows by `@martenson `_ in `#16209 `_ +* Small test decorator improvements. by `@jmchilton `_ in `#16220 `_ +* Initial e2e test for history storage. by `@jmchilton `_ in `#16221 `_ +* Selenium test for page history links. by `@jmchilton `_ in `#16222 `_ +* E2E Tests for Edit Dataset Attributes Page by `@jmchilton `_ in `#16224 `_ +* Selenium type fixes and annotations. by `@jmchilton `_ in `#16242 `_ +* e2e test for workflow license selector by `@jmchilton `_ in `#16243 `_ ------------------- 23.0.6 (2023-10-23) @@ -57,6 +83,7 @@ Enhancements * * * +* * Add support for launching workflows via Tutorial Mode by `@hexylena `_ in `#15684 `_ ------------------- diff --git a/packages/selenium/setup.cfg b/packages/selenium/setup.cfg index a95b3a449dfa..7f80d64d9131 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 = 23.1.dev0 +version = 23.1.1 [options] include_package_data = True diff --git a/packages/test_api/HISTORY.rst b/packages/test_api/HISTORY.rst index fb84e6c7ceea..f300a1212050 100644 --- a/packages/test_api/HISTORY.rst +++ b/packages/test_api/HISTORY.rst @@ -3,11 +3,48 @@ History .. to_doc ------------ -23.1.1.dev0 ------------ +------------------- +23.1.1 (2023-10-23) +------------------- + +========= +Bug fixes +========= + +* Ensure session is request-scoped for legacy endpoints by `@jdavcs `_ in `#16207 `_ +* allow anon access for api/datasets/get_content_as_text by `@martenson `_ in `#16226 `_ +* qualify querying for an api-key by `@martenson `_ in `#16320 `_ +* Fix tags ownership by `@davelopez `_ in `#16339 `_ +* Job cache fixes for DCEs by `@mvdbeek `_ in `#16384 `_ +* Fix histories count by `@davelopez `_ in `#16400 `_ +* Fix replacement parameters for subworkflows. by `@jmchilton `_ in `#16592 `_ +* Fixes for conditional subworkflow steps by `@mvdbeek `_ in `#16632 `_ +* Fix nested conditional workflow steps by `@mvdbeek `_ in `#16641 `_ +* Fix expression evaluation for nested state by `@mvdbeek `_ in `#16656 `_ +* Push to object store even if ``set_meta`` fails by `@mvdbeek `_ in `#16667 `_ +* Copy the collection contents by default when copying a collection by `@mvdbeek `_ in `#16717 `_ +* Fix allowlist deserialization in file sources by `@mvdbeek `_ in `#16729 `_ +* Fix workflow import losing tool_version by `@mvdbeek `_ in `#16869 `_ +* Fix tag ownership check by `@mvdbeek `_ in `#16877 `_ +* Fix delete collection + elements by `@davelopez `_ in `#16879 `_ + +============ +Enhancements +============ +* Empower Users to Select Storage Destination by `@jmchilton `_ in `#14073 `_ +* Outline Deployment Tests by `@jmchilton `_ in `#15420 `_ +* Unify url handling with filesources by `@nuwang `_ in `#15497 `_ +* Update Python dependencies by `@galaxybot `_ in `#15564 `_ +* Add API test and refactor code for related:hid history filter by `@ahmedhamidawan `_ in `#15786 `_ +* Allow pending inputs in some collection operation tools by `@mvdbeek `_ in `#15892 `_ +* Record input datasets and collections at full parameter path by `@mvdbeek `_ in `#15978 `_ +* Add History Archival feature by `@davelopez `_ in `#16003 `_ +* Dataset chunking tests (and small fixes) by `@jmchilton `_ in `#16069 `_ +* Improve histories and datasets immutability checks by `@davelopez `_ in `#16143 `_ +* Migrate display applications API to Fast API by `@heisner-tillman `_ in `#16156 `_ +* bring grids for (published) pages on par with workflows by `@martenson `_ in `#16209 `_ ------------------- 23.0.6 (2023-10-23) diff --git a/packages/test_api/setup.cfg b/packages/test_api/setup.cfg index 2a09121053d3..178b2aa731fd 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 = 23.1.dev0 +version = 23.1.1 [options] include_package_data = True diff --git a/packages/test_base/HISTORY.rst b/packages/test_base/HISTORY.rst index 779fbd8e4520..473df9383e98 100644 --- a/packages/test_base/HISTORY.rst +++ b/packages/test_base/HISTORY.rst @@ -3,11 +3,35 @@ History .. to_doc ------------ -23.1.1.dev0 ------------ +------------------- +23.1.1 (2023-10-23) +------------------- + + +========= +Bug fixes +========= + +* Ensure session is request-scoped for legacy endpoints by `@jdavcs `_ in `#16207 `_ + +============ +Enhancements +============ + +* Empower Users to Select Storage Destination by `@jmchilton `_ in `#14073 `_ +* Outline Deployment Tests by `@jmchilton `_ in `#15420 `_ +* Update Python dependencies by `@galaxybot `_ in `#15890 `_ +* Add History Archival feature by `@davelopez `_ in `#16003 `_ +* Dataset chunking tests (and small fixes) by `@jmchilton `_ in `#16069 `_ +* Improve histories and datasets immutability checks by `@davelopez `_ in `#16143 `_ +* bring grids for (published) pages on par with workflows by `@martenson `_ in `#16209 `_ +* Small test decorator improvements. by `@jmchilton `_ in `#16220 `_ +============= +Other changes +============= +* Tweaks to new object store and quota APIs by `@jmchilton `_ in `#15709 `_ ------------------- 23.0.6 (2023-10-23) diff --git a/packages/test_base/setup.cfg b/packages/test_base/setup.cfg index a1eec0ef392e..af1f0062518b 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 = 23.1.dev0 +version = 23.1.1 [options] include_package_data = True diff --git a/packages/test_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst index 98b94ee2ca7a..65883a3bf597 100644 --- a/packages/test_driver/HISTORY.rst +++ b/packages/test_driver/HISTORY.rst @@ -3,11 +3,33 @@ History .. to_doc ------------ -23.1.1.dev0 ------------ +------------------- +23.1.1 (2023-10-23) +------------------- + + +========= +Bug fixes +========= + +* Backport tool mem fixes by `@mvdbeek `_ in `#16601 `_ +* Fix allowlist deserialization in file sources by `@mvdbeek `_ in `#16729 `_ + +============ +Enhancements +============ + +* Towards SQLAlchemy 2.0: drop session autocommit setting by `@jdavcs `_ in `#15421 `_ +* Explore tool remote test data by `@davelopez `_ in `#15510 `_ +* Refactor integration tests to create utility for setting up a database vault. by `@jmchilton `_ in `#16027 `_ +* Merge ``Target`` class with ``CondaTarget`` by `@nsoranzo `_ in `#16181 `_ +* Fix tool remote test data by `@davelopez `_ in `#16311 `_ +============= +Other changes +============= +* Implement some initial object store selection end-to-end tests. by `@jmchilton `_ in `#15785 `_ ------------------- 23.0.6 (2023-10-23) diff --git a/packages/test_driver/setup.cfg b/packages/test_driver/setup.cfg index 699fd1706699..9d0d3c28838c 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 = 23.1.dev0 +version = 23.1.1 [options] include_package_data = True diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst index 07fe672acf88..d561c4e065c3 100644 --- a/packages/tool_util/HISTORY.rst +++ b/packages/tool_util/HISTORY.rst @@ -3,11 +3,62 @@ History .. to_doc ------------ -23.1.1.dev0 ------------ +------------------- +23.1.1 (2023-10-23) +------------------- + + +========= +Bug fixes +========= + +* Fixes for two framework test tools by `@bernt-matthias `_ in `#15483 `_ +* add missing f for f-string by `@bernt-matthias `_ in `#15584 `_ +* Fix call to `docker_cached_container_description` by `@bernt-matthias `_ in `#15598 `_ +* Fix log message by `@bernt-matthias `_ in `#15838 `_ +* add required_files to the tag list for linting by `@bernt-matthias `_ in `#16129 `_ +* Handle appending to a results file that does not exists. by `@ksuderman `_ in `#16233 `_ +* Improve container resolver documentation by `@mvdbeek `_ in `#16280 `_ +* Add missing singularity_no_mount prop parsing by `@mvdbeek `_ in `#16367 `_ +* Restore resolution of Conda environments generated from non-lowercase package names by `@nsoranzo `_ in `#16474 `_ +* Fix up unit tests for local use by `@mvdbeek `_ in `#16483 `_ +* Fix `multiple` remote test data by `@davelopez `_ in `#16542 `_ +* Don't use ``docker run`` --user flag on OSX by `@mvdbeek `_ in `#16573 `_ +* Backport tool mem fixes by `@mvdbeek `_ in `#16601 `_ +* xsd: allow name attribute of test collections by `@bernt-matthias `_ in `#16663 `_ +* Fix short ids in tool panel views. by `@jmchilton `_ in `#16800 `_ +* Fix tool panel views for versionless tool ids by `@mvdbeek `_ in `#16809 `_ +============ +Enhancements +============ +* Decompress history data for testing assertions by `@bernt-matthias `_ in `#15085 `_ +* OIDC tokens by `@SergeyYakubov `_ in `#15300 `_ +* Fix for new style conda packages by `@bernt-matthias `_ in `#15446 `_ +* Move database access code out of tool_util by `@jdavcs `_ in `#15467 `_ +* Protection against problematic boolean parameters. by `@jmchilton `_ in `#15493 `_ +* Implement initial tool/wf test assertions module for JSON data. by `@jmchilton `_ in `#15494 `_ +* Explore tool remote test data by `@davelopez `_ in `#15510 `_ +* xsd: add multiple to the list of attributes for all parameter types deriving from select by `@bernt-matthias `_ in `#15534 `_ +* Update Python dependencies by `@galaxybot `_ in `#15564 `_ +* Container resolvers: add docs, typing and tests by `@bernt-matthias `_ in `#15614 `_ +* Migrate to MyST-Parser for Markdown docs by `@nsoranzo `_ in `#15844 `_ +* Enable per-destination ``container_resolver_config_file`` by `@bernt-matthias `_ in `#15884 `_ +* Updated doc and tests for attribute value filter by `@tuncK `_ in `#15929 `_ +* Make container builders use mamba by `@bernt-matthias `_ in `#15953 `_ +* Code cleanups from ruff and pyupgrade by `@nsoranzo `_ in `#16035 `_ +* Vendorise ``packaging.versions.LegacyVersion`` by `@nsoranzo `_ in `#16058 `_ +* Merge ``Target`` class with ``CondaTarget`` by `@nsoranzo `_ in `#16181 `_ +* Small test decorator improvements. by `@jmchilton `_ in `#16220 `_ +* tool_util: switch to mambaforge on non-32bit; add arm64 support by `@mr-c `_ in `#16223 `_ +* Fix tool remote test data by `@davelopez `_ in `#16311 `_ + +============= +Other changes +============= + +* Restore tmp mounting by `@mvdbeek `_ in `#16533 `_ ------------------- 23.0.6 (2023-10-23) @@ -30,6 +81,7 @@ 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 `_ * Linter: fix regex for profile version by `@bernt-matthias `_ in `#16480 `_ @@ -50,6 +102,7 @@ No recorded changes since last release Bug fixes ========= +* * * xsd: add missing `sep` attribute for `has_n_columns` by `@bernt-matthias `_ in `#16262 `_ * Missing init prevents models.py being bundled into tool_util by `@nuwang `_ in `#16308 `_ @@ -72,6 +125,7 @@ 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 `_ @@ -88,6 +142,7 @@ 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 `_ @@ -99,6 +154,7 @@ Enhancements * * * +* * Allow setting auto_decompress property in staging interface by `@mvdbeek `_ in `#16014 `_ ------------------- diff --git a/packages/tool_util/setup.cfg b/packages/tool_util/setup.cfg index 817bd9080842..ceec9dd1d85a 100644 --- a/packages/tool_util/setup.cfg +++ b/packages/tool_util/setup.cfg @@ -27,7 +27,7 @@ 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 = 23.1.dev0 +version = 23.1.1 [options] include_package_data = True @@ -68,4 +68,4 @@ edam = [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 4e8f720f2bf3..430964b8c49d 100644 --- a/packages/tours/HISTORY.rst +++ b/packages/tours/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc ------------ -23.1.1.dev0 ------------ - +------------------- +23.1.1 (2023-10-23) +------------------- +No recorded changes since last release ------------------- 23.0.6 (2023-10-23) diff --git a/packages/tours/setup.cfg b/packages/tours/setup.cfg index 1186d0ad6ccf..c6799468f862 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 = 23.1.dev0 +version = 23.1.1 [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 06157073e447..8215d9e51d7c 100644 --- a/packages/util/HISTORY.rst +++ b/packages/util/HISTORY.rst @@ -3,11 +3,40 @@ History .. to_doc ------------ -23.1.1.dev0 ------------ +------------------- +23.1.1 (2023-10-23) +------------------- + +========= +Bug fixes +========= +* Fix bad auto-merge of dev. by `@jmchilton `_ in `#15386 `_ +* Fix some drs handling issues by `@nuwang `_ in `#15777 `_ +* Enable ``strict_equality`` mypy option by `@nsoranzo `_ in `#15808 `_ +* Ensure session is request-scoped for legacy endpoints by `@jdavcs `_ in `#16207 `_ +* Fix form builder value handling by `@guerler `_ in `#16304 `_ +* Backport tool mem fixes by `@mvdbeek `_ in `#16601 `_ +* Workaround for XML nodes of job resource parameters losing their children by `@kysrpex `_ in `#16728 `_ +* Fix allowlist deserialization in file sources by `@mvdbeek `_ in `#16729 `_ +* Exclude on_opened and on_closed from watcher events by `@mvdbeek `_ in `#16850 `_ + +============ +Enhancements +============ + +* Various Tool Shed Cleanup by `@jmchilton `_ in `#15247 `_ +* Protection against problematic boolean parameters. by `@jmchilton `_ in `#15493 `_ +* Unify url handling with filesources by `@nuwang `_ in `#15497 `_ +* Explore tool remote test data by `@davelopez `_ in `#15510 `_ +* Drop database views by `@jdavcs `_ in `#15876 `_ +* Update Python dependencies by `@galaxybot `_ in `#15890 `_ +* Record input datasets and collections at full parameter path by `@mvdbeek `_ in `#15978 `_ +* Code cleanups from ruff and pyupgrade by `@nsoranzo `_ in `#16035 `_ +* Vendorise ``packaging.versions.LegacyVersion`` by `@nsoranzo `_ in `#16058 `_ +* Improve histories and datasets immutability checks by `@davelopez `_ in `#16143 `_ +* Merge ``Target`` class with ``CondaTarget`` by `@nsoranzo `_ in `#16181 `_ ------------------- 23.0.6 (2023-10-23) diff --git a/packages/util/setup.cfg b/packages/util/setup.cfg index 03afa41b853b..02e977b9f612 100644 --- a/packages/util/setup.cfg +++ b/packages/util/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-util url = https://github.com/galaxyproject/galaxy -version = 23.1.dev0 +version = 23.1.1 [options] include_package_data = True @@ -55,4 +55,4 @@ 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 cbdc9a8098d4..482d5197d6e8 100644 --- a/packages/web_apps/HISTORY.rst +++ b/packages/web_apps/HISTORY.rst @@ -3,11 +3,82 @@ History .. to_doc ------------ -23.1.1.dev0 ------------ +------------------- +23.1.1 (2023-10-23) +------------------- +========= +Bug fixes +========= + +* Create ToolSuccess route and refactor component by `@ahmedhamidawan `_ in `#15484 `_ +* fix premature return in user API by `@martenson `_ in `#15781 `_ +* Ensure session is request-scoped for legacy endpoints by `@jdavcs `_ in `#16207 `_ +* allow anon access for api/datasets/get_content_as_text by `@martenson `_ in `#16226 `_ +* Fix form builder value handling by `@guerler `_ in `#16304 `_ +* Fix tags ownership by `@davelopez `_ in `#16339 `_ +* Fix histories count by `@davelopez `_ in `#16400 `_ +* Make datatype edit default value a string instead of list of strings by `@mvdbeek `_ in `#16591 `_ +* Backport tool mem fixes by `@mvdbeek `_ in `#16601 `_ +* Optimize getting current user session by `@mvdbeek `_ in `#16604 `_ +* Drop RecursiveMiddleware by `@mvdbeek `_ in `#16605 `_ +* List extra files only for terminal datasets by `@mvdbeek `_ in `#16705 `_ +* Copy the collection contents by default when copying a collection by `@mvdbeek `_ in `#16717 `_ +* Fix up local tool version handling by `@mvdbeek `_ in `#16836 `_ +* Fix delete collection + elements by `@davelopez `_ in `#16879 `_ + +============ +Enhancements +============ + +* Empower Users to Select Storage Destination by `@jmchilton `_ in `#14073 `_ +* Add Storage Dashboard visualizations for histories by `@davelopez `_ in `#14820 `_ +* External Login Flow: Redirect users if account already exists by `@ahmedhamidawan `_ in `#15019 `_ +* Various Tool Shed Cleanup by `@jmchilton `_ in `#15247 `_ +* Add Storage Management API by `@davelopez `_ in `#15295 `_ +* OIDC tokens by `@SergeyYakubov `_ in `#15300 `_ +* Add support for visualizing HDF5 datasets. by `@jarrah42 `_ in `#15394 `_ +* Towards SQLAlchemy 2.0: drop session autocommit setting by `@jdavcs `_ in `#15421 `_ +* Update Python dependencies by `@galaxybot `_ in `#15435 `_ +* Unify url handling with filesources by `@nuwang `_ in `#15497 `_ +* Explore tool remote test data by `@davelopez `_ in `#15510 `_ +* Update Python dependencies by `@galaxybot `_ in `#15564 `_ +* Drop workflow exports to myexperiment.org by `@dannon `_ in `#15576 `_ +* Add Galaxy Notification System by `@davelopez `_ in `#15663 `_ +* Mention OpenAPI docs in Galaxy API Documentation by `@bernt-matthias `_ in `#15713 `_ +* Fix/Enhance recalculate disk usage API endpoint by `@davelopez `_ in `#15739 `_ +* Update Python dependencies by `@galaxybot `_ in `#15890 `_ +* Add History Archival feature by `@davelopez `_ in `#16003 `_ +* Code cleanups from ruff and pyupgrade by `@nsoranzo `_ in `#16035 `_ +* Dataset chunking tests (and small fixes) by `@jmchilton `_ in `#16069 `_ +* Paginate History Store by `@ahmedhamidawan `_ in `#16084 `_ +* Allow HEAD request for requesting metadata files by `@martenson `_ in `#16113 `_ +* Add option to see invocations related to a history by `@martenson `_ in `#16136 `_ +* Improve histories and datasets immutability checks by `@davelopez `_ in `#16143 `_ +* Migrate display applications API to Fast API by `@heisner-tillman `_ in `#16156 `_ +* adjust grid sharing indicators by `@martenson `_ in `#16163 `_ +* Remove various fallback behaviors by `@mvdbeek `_ in `#16199 `_ +* bring grids for (published) pages on par with workflows by `@martenson `_ in `#16209 `_ +* Small test decorator improvements. by `@jmchilton `_ in `#16220 `_ +* Don't error on missing parameters or unused parameters in UI controllers by `@mvdbeek `_ in `#16246 `_ +* Update Python dependencies by `@galaxybot `_ in `#16267 `_ +* Fix Storage Dashboard missing archived histories by `@davelopez `_ in `#16473 `_ +* Add missing archived filter in saved histories by `@davelopez `_ in `#16475 `_ +* Drop expunge_all() call in WebTransactionRequest by `@mvdbeek `_ in `#16606 `_ + +============= +Other changes +============= + +* Follow up on object store selection PR. by `@jmchilton `_ in `#15654 `_ +* Tweaks to new object store and quota APIs by `@jmchilton `_ in `#15709 `_ +* Fix Enums in API docs by `@davelopez `_ in `#15740 `_ +* Quota source labelling bug fixes and improvements by `@jmchilton `_ in `#15795 `_ +* merge release_23.0 into dev by `@martenson `_ in `#15830 `_ +* merge release_23.0 into dev by `@martenson `_ in `#15854 `_ +* Merge 23.0 into dev by `@nsoranzo `_ in `#15902 `_ +* Fix recalculate_quota throug kombu message by `@mvdbeek `_ in `#16299 `_ ------------------- 23.0.6 (2023-10-23) @@ -30,6 +101,7 @@ Bug fixes Bug fixes ========= +* * Fix active step display in workflow editor side panel by `@mvdbeek `_ in `#16364 `_ ------------------- @@ -41,6 +113,7 @@ Bug fixes Bug fixes ========= +* * * Fix folder access for anonymous user by `@mvdbeek `_ in `#16330 `_ @@ -53,6 +126,7 @@ Bug fixes Bug fixes ========= +* * * * Fix converting Enum value to str for Python 3.11 by `@nsoranzo `_ in `#16284 `_ @@ -81,6 +155,7 @@ 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_apps/setup.cfg b/packages/web_apps/setup.cfg index f2468f577aba..916964380629 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 = 23.1.dev0 +version = 23.1.1 [options] include_package_data = True @@ -74,4 +74,4 @@ python_requires = >=3.7 [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 02dcaa428e4e..7a086468bd45 100644 --- a/packages/web_framework/HISTORY.rst +++ b/packages/web_framework/HISTORY.rst @@ -3,11 +3,24 @@ History .. to_doc ------------ -23.1.1.dev0 ------------ +------------------- +23.1.1 (2023-10-23) +------------------- + + +========= +Bug fixes +========= + +* Fix some drs handling issues by `@nuwang `_ in `#15777 `_ +* Ensure session is request-scoped for legacy endpoints by `@jdavcs `_ in `#16207 `_ +============ +Enhancements +============ +* Update Python dependencies by `@galaxybot `_ in `#15435 `_ +* Don't error on missing parameters or unused parameters in UI controllers by `@mvdbeek `_ in `#16246 `_ ------------------- 23.0.6 (2023-10-23) @@ -29,6 +42,7 @@ 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 `_ @@ -59,6 +73,7 @@ No recorded changes since last release Bug fixes ========= +* * * Various fixes to path prefix handling by `@mvdbeek `_ in `#16033 `_ diff --git a/packages/web_framework/setup.cfg b/packages/web_framework/setup.cfg index 6919f2c9b07c..d3b990925e61 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 = 23.1.dev0 +version = 23.1.1 [options] include_package_data = True @@ -49,4 +49,4 @@ python_requires = >=3.7 [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 8e7d5f02ce7e..12f10290b335 100644 --- a/packages/web_stack/HISTORY.rst +++ b/packages/web_stack/HISTORY.rst @@ -3,11 +3,30 @@ History .. to_doc ------------ -23.1.1.dev0 ------------ +------------------- +23.1.1 (2023-10-23) +------------------- + + +========= +Bug fixes +========= + +* Backport tool mem fixes by `@mvdbeek `_ in `#16601 `_ +* Reload toolbox after forking when using `--preload` by `@mvdbeek `_ in `#16620 `_ + +============ +Enhancements +============ + +* Towards SQLAlchemy 2.0: drop session autocommit setting by `@jdavcs `_ in `#15421 `_ +* Update supports_skip_locked, supports_returning for SA 2.0 compatibility by `@jdavcs `_ in `#15633 `_ +============= +Other changes +============= +* Make serving address more visible in console by `@davelopez `_ in `#15468 `_ ------------------- 23.0.6 (2023-10-23) diff --git a/packages/web_stack/setup.cfg b/packages/web_stack/setup.cfg index 54b91dfad20c..604cb8f2d484 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 = 23.1.dev0 +version = 23.1.1 [options] include_package_data = True From 3dd88a4357168764dd0126988218f5f2c7a4e3d1 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Mon, 23 Oct 2023 21:35:28 +0200 Subject: [PATCH 2/2] Start work on 23.1.2.dev0 --- lib/galaxy/version.py | 2 +- packages/app/HISTORY.rst | 6 ++++++ packages/app/setup.cfg | 2 +- packages/auth/HISTORY.rst | 6 ++++++ packages/auth/setup.cfg | 2 +- packages/config/HISTORY.rst | 6 ++++++ packages/config/setup.cfg | 2 +- packages/data/HISTORY.rst | 6 ++++++ packages/data/setup.cfg | 2 +- packages/files/HISTORY.rst | 6 ++++++ packages/files/setup.cfg | 2 +- packages/job_execution/HISTORY.rst | 6 ++++++ packages/job_execution/setup.cfg | 2 +- packages/job_metrics/HISTORY.rst | 6 ++++++ packages/job_metrics/setup.cfg | 2 +- packages/navigation/HISTORY.rst | 6 ++++++ packages/navigation/setup.cfg | 2 +- packages/objectstore/HISTORY.rst | 6 ++++++ packages/objectstore/setup.cfg | 2 +- packages/selenium/HISTORY.rst | 6 ++++++ packages/selenium/setup.cfg | 2 +- packages/test_api/HISTORY.rst | 6 ++++++ packages/test_api/setup.cfg | 2 +- packages/test_base/HISTORY.rst | 6 ++++++ packages/test_base/setup.cfg | 2 +- packages/test_driver/HISTORY.rst | 6 ++++++ packages/test_driver/setup.cfg | 2 +- packages/tool_util/HISTORY.rst | 6 ++++++ packages/tool_util/setup.cfg | 2 +- packages/tours/HISTORY.rst | 6 ++++++ packages/tours/setup.cfg | 2 +- packages/util/HISTORY.rst | 6 ++++++ packages/util/setup.cfg | 2 +- packages/web_apps/HISTORY.rst | 6 ++++++ packages/web_apps/setup.cfg | 2 +- packages/web_framework/HISTORY.rst | 6 ++++++ packages/web_framework/setup.cfg | 2 +- packages/web_stack/HISTORY.rst | 6 ++++++ packages/web_stack/setup.cfg | 2 +- 39 files changed, 134 insertions(+), 20 deletions(-) diff --git a/lib/galaxy/version.py b/lib/galaxy/version.py index 55ee632c85c1..30d127053a80 100644 --- a/lib/galaxy/version.py +++ b/lib/galaxy/version.py @@ -1,3 +1,3 @@ VERSION_MAJOR = "23.1" -VERSION_MINOR = "1" +VERSION_MINOR = "2.dev0" VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else "") diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst index ea05fc1e9ecd..884e67179db5 100644 --- a/packages/app/HISTORY.rst +++ b/packages/app/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +23.1.2.dev0 +----------- + + + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg index 4696724ce902..ac03c7255745 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 = 23.1.1 +version = 23.1.2.dev0 [options] include_package_data = True diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst index ca03f489a5e9..7dedbbe78f6d 100644 --- a/packages/auth/HISTORY.rst +++ b/packages/auth/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +23.1.2.dev0 +----------- + + + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/auth/setup.cfg b/packages/auth/setup.cfg index db3cffca6ee7..1b0782e84fd8 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 = 23.1.1 +version = 23.1.2.dev0 [options] include_package_data = True diff --git a/packages/config/HISTORY.rst b/packages/config/HISTORY.rst index bc7d346c8f30..34d8415905f7 100644 --- a/packages/config/HISTORY.rst +++ b/packages/config/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +23.1.2.dev0 +----------- + + + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/config/setup.cfg b/packages/config/setup.cfg index 19f27d18d1db..37b797bf64d5 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 = 23.1.1 +version = 23.1.2.dev0 [options] include_package_data = True diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst index 7ef01c4529e6..8cbcdb031097 100644 --- a/packages/data/HISTORY.rst +++ b/packages/data/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +23.1.2.dev0 +----------- + + + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg index 02e99512f7c6..cc33ece598bd 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 = 23.1.1 +version = 23.1.2.dev0 [options] include_package_data = True diff --git a/packages/files/HISTORY.rst b/packages/files/HISTORY.rst index 853a29b5b2a4..89b63ebe659d 100644 --- a/packages/files/HISTORY.rst +++ b/packages/files/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +23.1.2.dev0 +----------- + + + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/files/setup.cfg b/packages/files/setup.cfg index df0ce6d04da5..0e58071e685e 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 = 23.1.1 +version = 23.1.2.dev0 [options] include_package_data = True diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst index 982ed66fdbc9..bd61e86efdc8 100644 --- a/packages/job_execution/HISTORY.rst +++ b/packages/job_execution/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +23.1.2.dev0 +----------- + + + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/job_execution/setup.cfg b/packages/job_execution/setup.cfg index 206c84309a87..09a3f2cd3f3c 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 = 23.1.1 +version = 23.1.2.dev0 [options] include_package_data = True diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst index 79419abffd68..52ab679e3715 100644 --- a/packages/job_metrics/HISTORY.rst +++ b/packages/job_metrics/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +23.1.2.dev0 +----------- + + + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/job_metrics/setup.cfg b/packages/job_metrics/setup.cfg index 1ccb6607e12d..32ffb58abee4 100644 --- a/packages/job_metrics/setup.cfg +++ b/packages/job_metrics/setup.cfg @@ -27,7 +27,7 @@ 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 = 23.1.1 +version = 23.1.2.dev0 [options] include_package_data = True diff --git a/packages/navigation/HISTORY.rst b/packages/navigation/HISTORY.rst index d9445a75a242..16b41cf9e8d6 100644 --- a/packages/navigation/HISTORY.rst +++ b/packages/navigation/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +23.1.2.dev0 +----------- + + + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/navigation/setup.cfg b/packages/navigation/setup.cfg index f886aa2f0c1f..afb7c1e03764 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 = 23.1.1 +version = 23.1.2.dev0 [options] include_package_data = True diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst index 1be61711f26b..b6a52fff6867 100644 --- a/packages/objectstore/HISTORY.rst +++ b/packages/objectstore/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +23.1.2.dev0 +----------- + + + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/objectstore/setup.cfg b/packages/objectstore/setup.cfg index 0362b1883053..f384a64227e4 100644 --- a/packages/objectstore/setup.cfg +++ b/packages/objectstore/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-objectstore url = https://github.com/galaxyproject/galaxy -version = 23.1.1 +version = 23.1.2.dev0 [options] include_package_data = True diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst index 876fe39289f7..8222c874ea74 100644 --- a/packages/selenium/HISTORY.rst +++ b/packages/selenium/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +23.1.2.dev0 +----------- + + + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/selenium/setup.cfg b/packages/selenium/setup.cfg index 7f80d64d9131..29ca2b0066a7 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 = 23.1.1 +version = 23.1.2.dev0 [options] include_package_data = True diff --git a/packages/test_api/HISTORY.rst b/packages/test_api/HISTORY.rst index f300a1212050..b37778474ca7 100644 --- a/packages/test_api/HISTORY.rst +++ b/packages/test_api/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +23.1.2.dev0 +----------- + + + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/test_api/setup.cfg b/packages/test_api/setup.cfg index 178b2aa731fd..863186f7b917 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 = 23.1.1 +version = 23.1.2.dev0 [options] include_package_data = True diff --git a/packages/test_base/HISTORY.rst b/packages/test_base/HISTORY.rst index 473df9383e98..f36cad4911c5 100644 --- a/packages/test_base/HISTORY.rst +++ b/packages/test_base/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +23.1.2.dev0 +----------- + + + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/test_base/setup.cfg b/packages/test_base/setup.cfg index af1f0062518b..68e121205796 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 = 23.1.1 +version = 23.1.2.dev0 [options] include_package_data = True diff --git a/packages/test_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst index 65883a3bf597..3d3f5a0fcca9 100644 --- a/packages/test_driver/HISTORY.rst +++ b/packages/test_driver/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +23.1.2.dev0 +----------- + + + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/test_driver/setup.cfg b/packages/test_driver/setup.cfg index 9d0d3c28838c..36080a2415a1 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 = 23.1.1 +version = 23.1.2.dev0 [options] include_package_data = True diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst index d561c4e065c3..05b3d5dcf95a 100644 --- a/packages/tool_util/HISTORY.rst +++ b/packages/tool_util/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +23.1.2.dev0 +----------- + + + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/tool_util/setup.cfg b/packages/tool_util/setup.cfg index ceec9dd1d85a..2b87df9f750b 100644 --- a/packages/tool_util/setup.cfg +++ b/packages/tool_util/setup.cfg @@ -27,7 +27,7 @@ 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 = 23.1.1 +version = 23.1.2.dev0 [options] include_package_data = True diff --git a/packages/tours/HISTORY.rst b/packages/tours/HISTORY.rst index 430964b8c49d..e9042eb8d46a 100644 --- a/packages/tours/HISTORY.rst +++ b/packages/tours/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +23.1.2.dev0 +----------- + + + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/tours/setup.cfg b/packages/tours/setup.cfg index c6799468f862..696f43bc4732 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 = 23.1.1 +version = 23.1.2.dev0 [options] include_package_data = True diff --git a/packages/util/HISTORY.rst b/packages/util/HISTORY.rst index 8215d9e51d7c..d2b4b4e5ab02 100644 --- a/packages/util/HISTORY.rst +++ b/packages/util/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +23.1.2.dev0 +----------- + + + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/util/setup.cfg b/packages/util/setup.cfg index 02e977b9f612..e966f4f6cd08 100644 --- a/packages/util/setup.cfg +++ b/packages/util/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-util url = https://github.com/galaxyproject/galaxy -version = 23.1.1 +version = 23.1.2.dev0 [options] include_package_data = True diff --git a/packages/web_apps/HISTORY.rst b/packages/web_apps/HISTORY.rst index 482d5197d6e8..bf17b141b62c 100644 --- a/packages/web_apps/HISTORY.rst +++ b/packages/web_apps/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +23.1.2.dev0 +----------- + + + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/web_apps/setup.cfg b/packages/web_apps/setup.cfg index 916964380629..3ce0bf1087e4 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 = 23.1.1 +version = 23.1.2.dev0 [options] include_package_data = True diff --git a/packages/web_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst index 7a086468bd45..8db60e7d122d 100644 --- a/packages/web_framework/HISTORY.rst +++ b/packages/web_framework/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +23.1.2.dev0 +----------- + + + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/web_framework/setup.cfg b/packages/web_framework/setup.cfg index d3b990925e61..c652c12246ec 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 = 23.1.1 +version = 23.1.2.dev0 [options] include_package_data = True diff --git a/packages/web_stack/HISTORY.rst b/packages/web_stack/HISTORY.rst index 12f10290b335..8c6779d229b7 100644 --- a/packages/web_stack/HISTORY.rst +++ b/packages/web_stack/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +23.1.2.dev0 +----------- + + + ------------------- 23.1.1 (2023-10-23) ------------------- diff --git a/packages/web_stack/setup.cfg b/packages/web_stack/setup.cfg index 604cb8f2d484..778d684f3687 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 = 23.1.1 +version = 23.1.2.dev0 [options] include_package_data = True