From f552bbf436c7fce0058a1819481bee3c128ca9c4 Mon Sep 17 00:00:00 2001 From: John Davis Date: Thu, 20 Jun 2024 20:20:48 -0400 Subject: [PATCH] Revert "Create version 24.1.0" This reverts commit e196a581969760419920400ba5bf646858fac162. --- lib/galaxy/version.py | 4 +- packages/app/HISTORY.rst | 111 +---------------------------- packages/app/setup.cfg | 4 +- packages/auth/HISTORY.rst | 12 +--- packages/auth/setup.cfg | 4 +- packages/config/HISTORY.rst | 47 +----------- packages/config/setup.cfg | 4 +- packages/data/HISTORY.rst | 67 +---------------- packages/data/setup.cfg | 4 +- packages/files/HISTORY.rst | 45 +----------- packages/files/setup.cfg | 4 +- packages/job_execution/HISTORY.rst | 25 +------ packages/job_execution/setup.cfg | 4 +- packages/job_metrics/HISTORY.rst | 12 +--- packages/job_metrics/setup.cfg | 4 +- packages/navigation/HISTORY.rst | 8 +-- packages/navigation/setup.cfg | 4 +- packages/objectstore/HISTORY.rst | 35 +-------- packages/objectstore/setup.cfg | 4 +- packages/schema/HISTORY.rst | 30 +------- packages/schema/setup.cfg | 4 +- packages/selenium/HISTORY.rst | 21 +----- packages/selenium/setup.cfg | 4 +- packages/test_api/HISTORY.rst | 27 +------ packages/test_api/setup.cfg | 4 +- packages/test_base/HISTORY.rst | 24 +------ packages/test_base/setup.cfg | 4 +- packages/test_driver/HISTORY.rst | 21 +----- packages/test_driver/setup.cfg | 4 +- packages/tool_shed/HISTORY.rst | 23 +----- packages/tool_shed/setup.cfg | 4 +- packages/tool_util/HISTORY.rst | 42 +---------- packages/tool_util/setup.cfg | 4 +- packages/tours/HISTORY.rst | 8 +-- packages/tours/setup.cfg | 4 +- packages/util/HISTORY.rst | 30 +------- packages/util/setup.cfg | 4 +- packages/web_apps/HISTORY.rst | 69 +----------------- packages/web_apps/setup.cfg | 4 +- packages/web_framework/HISTORY.rst | 22 +----- packages/web_framework/setup.cfg | 4 +- packages/web_stack/HISTORY.rst | 11 +-- packages/web_stack/setup.cfg | 4 +- 43 files changed, 109 insertions(+), 669 deletions(-) diff --git a/lib/galaxy/version.py b/lib/galaxy/version.py index 2c7c62709afb..319c7fefb8a0 100644 --- a/lib/galaxy/version.py +++ b/lib/galaxy/version.py @@ -1,3 +1,3 @@ -VERSION_MAJOR = "24.1" -VERSION_MINOR = "0" +VERSION_MAJOR = "24.2" +VERSION_MINOR = "dev0" VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else "") diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst index ebc22e559824..c68d6c7dbe2f 100644 --- a/packages/app/HISTORY.rst +++ b/packages/app/HISTORY.rst @@ -3,116 +3,11 @@ History .. to_doc -------------------- -24.1.0 (2024-06-20) -------------------- - - -========= -Bug fixes -========= - -* Unpin social-auth-core dependency by `@nsoranzo `_ in `#17607 `_ -* Dynamic tool fixes by `@dcore94 `_ in `#18085 `_ -* Raise exception if collection elements missing during download by `@jdavcs `_ in `#18094 `_ -* Allow purge query param, deprecate purge body param by `@mvdbeek `_ in `#18105 `_ -* Fix for unexpected OIDC XML validation error by `@Edmontosaurus `_ in `#18106 `_ -* Don't log exception if cancelled slurm job doesn't have stderr file by `@mvdbeek `_ in `#18121 `_ -* Downgrade missing output file in working directory to warning for failed jobs by `@mvdbeek `_ in `#18123 `_ -* Fix data default values not getting added to history by `@mvdbeek `_ in `#18132 `_ -* Drop redundant error message by `@mvdbeek `_ in `#18156 `_ -* Emit warning when user-cancelled job already complete by `@mvdbeek `_ in `#18178 `_ -* Avoid object store path lookup when constructing JobState object by `@mvdbeek `_ in `#18190 `_ -* Drop "Send to cloud" tool and associated cloudauthz code by `@jdavcs `_ in `#18196 `_ -* Revert some requests import changes by `@nsoranzo `_ in `#18199 `_ -* Add string cast for dbkey / genome_build by `@mvdbeek `_ in `#18207 `_ -* Check dataset state when attempting to acces dataset contents by `@mvdbeek `_ in `#18214 `_ -* Don't set dataset peek for errored jobs by `@mvdbeek `_ in `#18231 `_ -* Small bug fixes for user data plugins by `@jmchilton `_ in `#18246 `_ -* Raise exception when extracting dataset from collection without datasets by `@mvdbeek `_ in `#18249 `_ -* Skip tests if toolshed, dx.doi not responding by `@mvdbeek `_ in `#18250 `_ -* Fix handler: access to result row items changed in SA2.0 by `@jdavcs `_ in `#18274 `_ -* Don't attempt to download purged datasets by `@mvdbeek `_ in `#18278 `_ -* Check various preconditions in FeatureLocationIndexDataProvider by `@davelopez `_ in `#18283 `_ -* Fix various packages' issues by `@nsoranzo `_ in `#18301 `_ -* Adapt Tool prediction API to Transformer-based deep learning architecture by `@anuprulez `_ in `#18305 `_ -* Don't serialize display application links for deleted datasets by `@mvdbeek `_ in `#18307 `_ -* Downgrade doi fetch error to debug by `@mvdbeek `_ in `#18330 `_ -* Fix authentication error for anonymous users querying jobs by `@davelopez `_ in `#18333 `_ -* Fix seek in slurm memory check by `@mvdbeek `_ in `#18338 `_ -* Do not copy purged outputs to object store by `@mvdbeek `_ in `#18342 `_ -* Kill pulsar job if job stopped on galaxy side by `@mvdbeek `_ in `#18348 `_ -* Allow DCE as outer input to to_cwl by `@mvdbeek `_ in `#18349 `_ -* Fix anonymous user job retrieval logic by `@davelopez `_ in `#18358 `_ -* Fix update group API payload model by `@davelopez `_ in `#18374 `_ -* Fix empty usernames in database + bug in username generation by `@jdavcs `_ in `#18379 `_ -* Fix user's private role can be missing by `@davelopez `_ in `#18381 `_ -* Fix null inputs in database operation tools by `@mvdbeek `_ in `#18385 `_ -* Assign default ``data`` extension on discovered collection output by `@mvdbeek `_ in `#18389 `_ -* Fix ``get_accessible_job`` if called without session by `@mvdbeek `_ in `#18400 `_ -* Fix invocation step_job_summary for new collections by `@mvdbeek `_ in `#18402 `_ -* Really allow in-range validator for txt by `@bernt-matthias `_ in `#18411 `_ -* Fix collection map over status for dragged collections by `@mvdbeek `_ in `#18416 `_ -* Add TypedDict for JobsSummary by `@mvdbeek `_ in `#18418 `_ -* Serialize purged flag for datasets in collections by `@davelopez `_ in `#18420 `_ -* Pin pydantic to >=2.7.4 by `@nsoranzo `_ in `#18423 `_ +--------- +24.1.dev0 +--------- -============ -Enhancements -============ - -* Only include tool stdout/stderr in HDA info by `@natefoo `_ in `#16730 `_ -* Adding object store plugin for Rucio by `@SergeyYakubov `_ in `#17156 `_ -* Enable all-vs-all collection analysis patterns. by `@jmchilton `_ in `#17366 `_ -* Add onedata objectstore by `@bwalkowi `_ in `#17540 `_ -* Type annotation improvements by `@nsoranzo `_ in `#17601 `_ -* Type annotation and CWL-related improvements by `@nsoranzo `_ in `#17630 `_ -* Update Python dependencies by `@galaxybot `_ in `#17653 `_ -* Code cleanups from ruff and pyupgrade by `@nsoranzo `_ in `#17654 `_ -* Update Python dependencies by `@galaxybot `_ in `#17764 `_ -* SQLAlchemy 2.0 by `@jdavcs `_ in `#17778 `_ -* Update Python dependencies by `@galaxybot `_ in `#17819 `_ -* Update Python dependencies by `@galaxybot `_ in `#17870 `_ -* Add `email` notifications channel by `@davelopez `_ in `#17914 `_ -* Model edits and bug fixes by `@jdavcs `_ in `#17922 `_ -* Update Python dependencies by `@galaxybot `_ in `#17923 `_ -* Model typing and SA2.0 follow-up by `@jdavcs `_ in `#17958 `_ -* Error reporting unit tests by `@jmchilton `_ in `#17968 `_ -* Make urgent notifications mandatory by `@davelopez `_ in `#17975 `_ -* Update Python dependencies by `@galaxybot `_ in `#17982 `_ -* Enable ``warn_unused_ignores`` mypy option by `@nsoranzo `_ in `#17991 `_ -* Add galaxy to user agent by `@mvdbeek `_ in `#18003 `_ -* Add Zenodo integration by `@davelopez `_ in `#18022 `_ -* Update Python dependencies by `@galaxybot `_ in `#18035 `_ -* Add stronger type annotations in file sources + refactoring by `@davelopez `_ in `#18050 `_ -* Add pagination support to Files Source plugins by `@davelopez `_ in `#18059 `_ -* Update Python dependencies by `@galaxybot `_ in `#18063 `_ -* Enable flake8-implicit-str-concat ruff rules by `@nsoranzo `_ in `#18067 `_ -* Ensure history `update_time` is set when exporting by `@davelopez `_ in `#18086 `_ -* Overhaul Azure storage infrastructure. by `@jmchilton `_ in `#18087 `_ -* Update Python dependencies by `@galaxybot `_ in `#18095 `_ -* Update Python dependencies by `@galaxybot `_ in `#18125 `_ -* Revises handling of warnings in the workflow run form by `@guerler `_ in `#18126 `_ -* Empower users to bring their own storage and file sources by `@jmchilton `_ in `#18127 `_ -* Update s3fs dependency. by `@jmchilton `_ in `#18135 `_ -* More unit testing for object store stuff. by `@jmchilton `_ in `#18136 `_ -* Harden User Object Store and File Source Creation by `@jmchilton `_ in `#18172 `_ -* Fix boto3-stubs typecheck dependency by `@nsoranzo `_ in `#18173 `_ -* Update Python dependencies by `@galaxybot `_ in `#18226 `_ -* More structured indexing for user data objects. by `@jmchilton `_ in `#18291 `_ -* More data access tests, some refactoring and cleanup by `@jdavcs `_ in `#18312 `_ -* Onedada object store and files source stability fixes by `@bwalkowi `_ in `#18372 `_ -* Allow running and editing workflows for specific versions by `@ahmedhamidawan `_ in `#18378 `_ - -============= -Other changes -============= -* Chore: remove repetitive words by `@tianzedavid `_ in `#18076 `_ -* Fix #18316 (anonymous file sources) by `@jmchilton `_ in `#18352 `_ -* Merge 24.0 into 24.1 by `@jdavcs `_ in `#18353 `_ -* Merge 24.0 into 24.1 by `@jdavcs `_ in `#18365 `_ -* Minor linting cleanup by `@mvdbeek `_ in `#18421 `_ ------------------- 24.0.2 (2024-05-07) diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg index efd86c989a69..640cacc77d3d 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 = 24.1.0 +version = 23.2.dev0 [options] include_package_data = True @@ -85,4 +85,4 @@ console_scripts = [options.packages.find] exclude = galaxy.tools.bundled* - tests* \ No newline at end of file + tests* diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst index d52e9ca3fbb4..e87c36a52403 100644 --- a/packages/auth/HISTORY.rst +++ b/packages/auth/HISTORY.rst @@ -3,17 +3,11 @@ History .. to_doc -------------------- -24.1.0 (2024-06-20) -------------------- - +--------- +24.1.dev0 +--------- -============ -Enhancements -============ -* Code cleanups from ruff and pyupgrade by `@nsoranzo `_ in `#17654 `_ -* Update Python dependencies by `@galaxybot `_ in `#18063 `_ ------------------- 24.0.2 (2024-05-07) diff --git a/packages/auth/setup.cfg b/packages/auth/setup.cfg index 6c23290e7847..adad08ddb323 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 = 24.1.0 +version = 23.2.dev0 [options] include_package_data = True @@ -39,4 +39,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/config/HISTORY.rst b/packages/config/HISTORY.rst index 70eba23f945a..746ecf383fc6 100644 --- a/packages/config/HISTORY.rst +++ b/packages/config/HISTORY.rst @@ -3,52 +3,11 @@ History .. to_doc -------------------- -24.1.0 (2024-06-20) -------------------- - - -========= -Bug fixes -========= - -* Replace sample Celery result_backend in config by `@davelopez `_ in `#17949 `_ -* Fix for unexpected OIDC XML validation error by `@Edmontosaurus `_ in `#18106 `_ -* Backport OIDC schema fix by `@mvdbeek `_ in `#18111 `_ -* Minor fix to enable external hgweb process by `@mvdbeek `_ in `#18256 `_ -* Fix various packages' issues by `@nsoranzo `_ in `#18301 `_ -* Rebuild Galaxy config by `@bgruening `_ in `#18325 `_ -* Fix loading error for built in tool `sift` by `@bernt-matthias `_ in `#18357 `_ +--------- +24.1.dev0 +--------- -============ -Enhancements -============ - -* Enable all-vs-all collection analysis patterns. by `@jmchilton `_ in `#17366 `_ -* Add onedata objectstore by `@bwalkowi `_ in `#17540 `_ -* Add colabfold tar file datatype by `@astrovsky01 `_ in `#17567 `_ -* Update Python dependencies by `@galaxybot `_ in `#17653 `_ -* SQLAlchemy 2.0 by `@jdavcs `_ in `#17778 `_ -* Add `email` notifications channel by `@davelopez `_ in `#17914 `_ -* Update config docs about Celery by `@davelopez `_ in `#17918 `_ -* Make urgent notifications mandatory by `@davelopez `_ in `#17975 `_ -* Enable ``warn_unused_ignores`` mypy option by `@nsoranzo `_ in `#17991 `_ -* Add Zenodo integration by `@davelopez `_ in `#18022 `_ -* Add support for additional media types by `@arash77 `_ in `#18054 `_ -* Update Python dependencies by `@galaxybot `_ in `#18063 `_ -* Add Net datatype by `@martenson `_ in `#18080 `_ -* Empower users to bring their own storage and file sources by `@jmchilton `_ in `#18127 `_ -* More unit testing for object store stuff. by `@jmchilton `_ in `#18136 `_ -* Tighten axt sniffer by `@martenson `_ in `#18204 `_ -* More structured indexing for user data objects. by `@jmchilton `_ in `#18291 `_ -* Onedada object store and files source stability fixes by `@bwalkowi `_ in `#18372 `_ - -============= -Other changes -============= -* Chore: remove repetitive words by `@tianzedavid `_ in `#18076 `_ -* Fix the link to the carbon config by `@bgruening `_ in `#18314 `_ ------------------- 24.0.2 (2024-05-07) diff --git a/packages/config/setup.cfg b/packages/config/setup.cfg index 0df6f912e9e0..b1691b58d9a5 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 = 24.1.0 +version = 23.2.dev0 [options] include_package_data = True @@ -46,4 +46,4 @@ console_scripts = [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst index 81b4b8b0f9b5..1d3a447f88ba 100644 --- a/packages/data/HISTORY.rst +++ b/packages/data/HISTORY.rst @@ -3,72 +3,11 @@ History .. to_doc -------------------- -24.1.0 (2024-06-20) -------------------- - - -========= -Bug fixes -========= - -* Fix syntax for SA2.0 by `@jdavcs `_ in `#17663 `_ -* Downgrade count lines error to warning by `@mvdbeek `_ in `#18175 `_ -* Drop "Send to cloud" tool and associated cloudauthz code by `@jdavcs `_ in `#18196 `_ -* Don't set dataset peek for errored jobs by `@mvdbeek `_ in `#18231 `_ -* Transparently open compressed files in DatasetDataProvider by `@mvdbeek `_ in `#18248 `_ -* Raise exception when extracting dataset from collection without datasets by `@mvdbeek `_ in `#18249 `_ -* Set page importable to false when serializing by `@mvdbeek `_ in `#18263 `_ -* Fix first_dataset_element type hint by `@mvdbeek `_ in `#18284 `_ -* Do not copy purged outputs to object store by `@mvdbeek `_ in `#18342 `_ -* Fix empty usernames in database + bug in username generation by `@jdavcs `_ in `#18379 `_ -* Fix user's private role can be missing by `@davelopez `_ in `#18381 `_ -* Assign default ``data`` extension on discovered collection output by `@mvdbeek `_ in `#18389 `_ -* Fix `input_step_parameters` missing values that don't have a label by `@ahmedhamidawan `_ in `#18405 `_ +--------- +24.1.dev0 +--------- -============ -Enhancements -============ - -* Enable all-vs-all collection analysis patterns. by `@jmchilton `_ in `#17366 `_ -* Visualizing workflow runs with an invocation graph view by `@ahmedhamidawan `_ in `#17413 `_ -* Better display of estimated line numbers and add number of columns for tabular by `@bernt-matthias `_ in `#17492 `_ -* Enable storage management by object store by `@jmchilton `_ in `#17500 `_ -* Set minimal metadata also for empty bed datasets by `@wm75 `_ in `#17586 `_ -* Type annotation improvements by `@nsoranzo `_ in `#17601 `_ -* Type annotation and CWL-related improvements by `@nsoranzo `_ in `#17630 `_ -* Update Python dependencies by `@galaxybot `_ in `#17653 `_ -* Code cleanups from ruff and pyupgrade by `@nsoranzo `_ in `#17654 `_ -* SQLAlchemy 2.0 by `@jdavcs `_ in `#17778 `_ -* Outline use of type_annotation_map to fix mypy issues by `@jmchilton `_ in `#17902 `_ -* Add `email` notifications channel by `@davelopez `_ in `#17914 `_ -* Model edits and bug fixes by `@jdavcs `_ in `#17922 `_ -* Model typing and SA2.0 follow-up by `@jdavcs `_ in `#17958 `_ -* Enable ``warn_unused_ignores`` mypy option by `@nsoranzo `_ in `#17991 `_ -* Add galaxy to user agent by `@mvdbeek `_ in `#18003 `_ -* Refactor galaxy.files plugin loading + config handling. by `@jmchilton `_ in `#18049 `_ -* Add stronger type annotations in file sources + refactoring by `@davelopez `_ in `#18050 `_ -* Add support for additional media types by `@arash77 `_ in `#18054 `_ -* Update Python dependencies by `@galaxybot `_ in `#18063 `_ -* Enable flake8-implicit-str-concat ruff rules by `@nsoranzo `_ in `#18067 `_ -* Script for deleting userless histories from database + testing + drop unused model testing code by `@jdavcs `_ in `#18079 `_ -* Add Net datatype by `@martenson `_ in `#18080 `_ -* Empower users to bring their own storage and file sources by `@jmchilton `_ in `#18127 `_ -* Harden User Object Store and File Source Creation by `@jmchilton `_ in `#18172 `_ -* Update db revision 24.1 release tags by `@jdavcs `_ in `#18183 `_ -* Tighten axt sniffer by `@martenson `_ in `#18204 `_ -* Update Python dependencies by `@galaxybot `_ in `#18226 `_ -* More structured indexing for user data objects. by `@jmchilton `_ in `#18291 `_ -* More data access tests, some refactoring and cleanup by `@jdavcs `_ in `#18312 `_ -* Prepare for NumPy 2.0 by `@nsoranzo `_ in `#18422 `_ - -============= -Other changes -============= -* Chore: remove repetitive words by `@tianzedavid `_ in `#18076 `_ -* Fix import broken with forward merge by `@mvdbeek `_ in `#18152 `_ -* Merge 24.1 by `@jdavcs `_ in `#18386 `_ ------------------- 24.0.2 (2024-05-07) diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg index 8d4a36edaec4..6f1ce7204eb6 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 = 24.1.0 +version = 23.2.dev0 [options] include_package_data = True @@ -75,4 +75,4 @@ console_scripts = [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/files/HISTORY.rst b/packages/files/HISTORY.rst index 558ec71d7ead..2fc21b40fea9 100644 --- a/packages/files/HISTORY.rst +++ b/packages/files/HISTORY.rst @@ -3,50 +3,11 @@ History .. to_doc -------------------- -24.1.0 (2024-06-20) -------------------- - +--------- +24.1.dev0 +--------- -========= -Bug fixes -========= - -* Fix listing possibly untitled records in Invenio Plugin by `@davelopez `_ in `#18130 `_ -* Raise ``RequestParameterInvalidException`` when url is invalid by `@mvdbeek `_ in `#18155 `_ -* Fix error message when accessing restricted Zenodo records by `@davelopez `_ in `#18169 `_ -* Fix file source search query with empty string value by `@davelopez `_ in `#18191 `_ -* Raise ``RequestParameterInvalidException`` if url can't be verified by `@mvdbeek `_ in `#18230 `_ -* Small bug fixes for user data plugins by `@jmchilton `_ in `#18246 `_ -* Fix Invenio credentials handling by `@davelopez `_ in `#18255 `_ -* Fix check for anonymous by `@jdavcs `_ in `#18364 `_ - -============ -Enhancements -============ -* Add onedata objectstore by `@bwalkowi `_ in `#17540 `_ -* Update Python dependencies by `@galaxybot `_ in `#17653 `_ -* Code cleanups from ruff and pyupgrade by `@nsoranzo `_ in `#17654 `_ -* Enable ``warn_unused_ignores`` mypy option by `@nsoranzo `_ in `#17991 `_ -* Add galaxy to user agent by `@mvdbeek `_ in `#18003 `_ -* Add Zenodo integration by `@davelopez `_ in `#18022 `_ -* More typing in galaxy.files. by `@jmchilton `_ in `#18037 `_ -* Refactor galaxy.files plugin loading + config handling. by `@jmchilton `_ in `#18049 `_ -* Add stronger type annotations in file sources + refactoring by `@davelopez `_ in `#18050 `_ -* Add pagination support to Files Source plugins by `@davelopez `_ in `#18059 `_ -* Update Python dependencies by `@galaxybot `_ in `#18063 `_ -* Overhaul Azure storage infrastructure. by `@jmchilton `_ in `#18087 `_ -* Empower users to bring their own storage and file sources by `@jmchilton `_ in `#18127 `_ -* Display DOIs in Archived Histories by `@davelopez `_ in `#18134 `_ -* Update s3fs dependency. by `@jmchilton `_ in `#18135 `_ -* Onedada object store and files source stability fixes by `@bwalkowi `_ in `#18372 `_ - -============= -Other changes -============= - -* Fix #18316 (anonymous file sources) by `@jmchilton `_ in `#18352 `_ ------------------- 24.0.2 (2024-05-07) diff --git a/packages/files/setup.cfg b/packages/files/setup.cfg index 5ba5a0c9f51b..dc0599c9b7c3 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 = 24.1.0 +version = 23.2.dev0 [options] include_package_data = True @@ -41,4 +41,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst index b589a147acf8..65d9d4244618 100644 --- a/packages/job_execution/HISTORY.rst +++ b/packages/job_execution/HISTORY.rst @@ -3,30 +3,11 @@ History .. to_doc -------------------- -24.1.0 (2024-06-20) -------------------- - +--------- +24.1.dev0 +--------- -========= -Bug fixes -========= - -* Include traceback when logging email PJA exception by `@mvdbeek `_ in `#18122 `_ -* Don't commit in ``DeleteIntermediatesAction`` by `@mvdbeek `_ in `#18131 `_ -* Don't fail metadata if we only have an extra output files dir by `@mvdbeek `_ in `#18179 `_ -* Don't set dataset peek for errored jobs by `@mvdbeek `_ in `#18231 `_ -* Do not copy purged outputs to object store by `@mvdbeek `_ in `#18342 `_ - -============ -Enhancements -============ -* Enable ``warn_unused_ignores`` mypy option by `@nsoranzo `_ in `#17991 `_ -* Add galaxy to user agent by `@mvdbeek `_ in `#18003 `_ -* Refactor galaxy.files plugin loading + config handling. by `@jmchilton `_ in `#18049 `_ -* Add stronger type annotations in file sources + refactoring by `@davelopez `_ in `#18050 `_ -* Update Python dependencies by `@galaxybot `_ in `#18063 `_ ------------------- 24.0.2 (2024-05-07) diff --git a/packages/job_execution/setup.cfg b/packages/job_execution/setup.cfg index 08621310f32c..05394dca8e27 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 = 24.1.0 +version = 23.2.dev0 [options] include_package_data = True @@ -49,4 +49,4 @@ console_scripts = [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst index 8378c7de785e..aa0c39f3599d 100644 --- a/packages/job_metrics/HISTORY.rst +++ b/packages/job_metrics/HISTORY.rst @@ -3,17 +3,11 @@ History .. to_doc -------------------- -24.1.0 (2024-06-20) -------------------- - +--------- +24.1.dev0 +--------- -============ -Enhancements -============ -* Type annotation improvements by `@nsoranzo `_ in `#17601 `_ -* Update Python dependencies by `@galaxybot `_ in `#17653 `_ ------------------- 24.0.2 (2024-05-07) diff --git a/packages/job_metrics/setup.cfg b/packages/job_metrics/setup.cfg index ef8166e9d420..476eea3712ad 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 = 24.1.0 +version = 23.2.dev0 [options] include_package_data = True @@ -39,4 +39,4 @@ python_requires = >=3.7 [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/navigation/HISTORY.rst b/packages/navigation/HISTORY.rst index 8a6ae3b0a460..0db4ab93679c 100644 --- a/packages/navigation/HISTORY.rst +++ b/packages/navigation/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc -------------------- -24.1.0 (2024-06-20) -------------------- +--------- +24.1.dev0 +--------- + -No recorded changes since last release ------------------- 24.0.2 (2024-05-07) diff --git a/packages/navigation/setup.cfg b/packages/navigation/setup.cfg index 567951323bae..a2635d9e49fe 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 = 24.1.0 +version = 23.2.dev0 [options] include_package_data = True @@ -39,4 +39,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst index 1c0cf9b1cc3b..2f6dc31f61a7 100644 --- a/packages/objectstore/HISTORY.rst +++ b/packages/objectstore/HISTORY.rst @@ -3,40 +3,11 @@ History .. to_doc -------------------- -24.1.0 (2024-06-20) -------------------- - +--------- +24.1.dev0 +--------- -========= -Bug fixes -========= - -* Fix odd object store exception by `@jmchilton `_ in `#17810 `_ -* Fix AWS object store for us-east-2 by `@jmchilton `_ in `#18100 `_ -* Fairly critical fix for #18087 by `@jmchilton `_ in `#18110 `_ -* Include stack when reporting delete error by `@mvdbeek `_ in `#18208 `_ -* Only log error if deleting directory really failed by `@mvdbeek `_ in `#18236 `_ -* Do not copy purged outputs to object store by `@mvdbeek `_ in `#18342 `_ - -============ -Enhancements -============ -* Adding object store plugin for Rucio by `@SergeyYakubov `_ in `#17156 `_ -* Add onedata objectstore by `@bwalkowi `_ in `#17540 `_ -* Update Python dependencies by `@galaxybot `_ in `#17653 `_ -* Code cleanups from ruff and pyupgrade by `@nsoranzo `_ in `#17654 `_ -* Enable ``warn_unused_ignores`` mypy option by `@nsoranzo `_ in `#17991 `_ -* Update Python dependencies by `@galaxybot `_ in `#18063 `_ -* Enable flake8-implicit-str-concat ruff rules by `@nsoranzo `_ in `#18067 `_ -* Overhaul Azure storage infrastructure. by `@jmchilton `_ in `#18087 `_ -* Empower users to bring their own storage and file sources by `@jmchilton `_ in `#18127 `_ -* More unit testing for object store stuff. by `@jmchilton `_ in `#18136 `_ -* Harden User Object Store and File Source Creation by `@jmchilton `_ in `#18172 `_ -* De-duplication of onedata objectstore code. by `@jmchilton `_ in `#18174 `_ -* More structured indexing for user data objects. by `@jmchilton `_ in `#18291 `_ -* Onedada object store and files source stability fixes by `@bwalkowi `_ in `#18372 `_ ------------------- 24.0.2 (2024-05-07) diff --git a/packages/objectstore/setup.cfg b/packages/objectstore/setup.cfg index c4d7b93939f1..6ba5fe551e67 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 = 24.1.0 +version = 23.2.dev0 [options] include_package_data = True @@ -41,4 +41,4 @@ python_requires = >=3.7 [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/schema/HISTORY.rst b/packages/schema/HISTORY.rst index 732ec11cc498..16def6b775a4 100644 --- a/packages/schema/HISTORY.rst +++ b/packages/schema/HISTORY.rst @@ -3,35 +3,11 @@ History .. to_doc -------------------- -24.1.0 (2024-06-20) -------------------- - +--------- +24.1.dev0 +--------- -========= -Bug fixes -========= - -* do not expand datasets that are known to be inaccessible by `@martenson `_ in `#17818 `_ -* Allow purge query param, deprecate purge body param by `@mvdbeek `_ in `#18105 `_ -* Fix deprecated `deprecated` argument by `@mvdbeek `_ in `#18119 `_ -* Drop "Send to cloud" tool and associated cloudauthz code by `@jdavcs `_ in `#18196 `_ -* Fix users API serialization when listing users by `@davelopez `_ in `#18329 `_ -* Fix update group API payload model by `@davelopez `_ in `#18374 `_ -* Serialize purged flag for datasets in collections by `@davelopez `_ in `#18420 `_ - -============ -Enhancements -============ -* Visualizing workflow runs with an invocation graph view by `@ahmedhamidawan `_ in `#17413 `_ -* Add `email` notifications channel by `@davelopez `_ in `#17914 `_ -* Enable ``warn_unused_ignores`` mypy option by `@nsoranzo `_ in `#17991 `_ -* Add pagination support to Files Source plugins by `@davelopez `_ in `#18059 `_ -* Enable flake8-implicit-str-concat ruff rules by `@nsoranzo `_ in `#18067 `_ -* Empower users to bring their own storage and file sources by `@jmchilton `_ in `#18127 `_ -* Display DOIs in Archived Histories by `@davelopez `_ in `#18134 `_ -* Allow running and editing workflows for specific versions by `@ahmedhamidawan `_ in `#18378 `_ ------------------- 24.0.2 (2024-05-07) diff --git a/packages/schema/setup.cfg b/packages/schema/setup.cfg index 6eeb8da4ac31..1ebcb6abef60 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 = 24.1.0 +version = 23.2.dev0 [options] include_package_data = True @@ -39,4 +39,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst index bcf149a43ac3..5beab1aae25b 100644 --- a/packages/selenium/HISTORY.rst +++ b/packages/selenium/HISTORY.rst @@ -3,26 +3,11 @@ History .. to_doc -------------------- -24.1.0 (2024-06-20) -------------------- - +--------- +24.1.dev0 +--------- -========= -Bug fixes -========= - -* Fix (I think) a transiently failing selenium error. by `@jmchilton `_ in `#18065 `_ - -============ -Enhancements -============ -* Add admin activity to activity bar by `@guerler `_ in `#17877 `_ -* Add galaxy to user agent by `@mvdbeek `_ in `#18003 `_ -* Consolidate Visualization container, avoid using default iframe by `@guerler `_ in `#18016 `_ -* Update Python dependencies by `@galaxybot `_ in `#18063 `_ -* Empower users to bring their own storage and file sources by `@jmchilton `_ in `#18127 `_ ------------------- 24.0.2 (2024-05-07) diff --git a/packages/selenium/setup.cfg b/packages/selenium/setup.cfg index c6a16adf34e0..07fab81680d9 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 = 24.1.0 +version = 23.2.dev0 [options] include_package_data = True @@ -47,4 +47,4 @@ console_scripts = [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/test_api/HISTORY.rst b/packages/test_api/HISTORY.rst index 042086db2b7a..792c69a9334e 100644 --- a/packages/test_api/HISTORY.rst +++ b/packages/test_api/HISTORY.rst @@ -3,32 +3,11 @@ History .. to_doc -------------------- -24.1.0 (2024-06-20) -------------------- - +--------- +24.1.dev0 +--------- -========= -Bug fixes -========= - -* Allow purge query param, deprecate purge body param by `@mvdbeek `_ in `#18105 `_ -* Prevent anonymous and inactive users from running workflows by `@ahmedhamidawan `_ in `#18192 `_ -* Revert some requests import changes by `@nsoranzo `_ in `#18199 `_ -* Check dataset state when attempting to acces dataset contents by `@mvdbeek `_ in `#18214 `_ -* Fix update group API payload model by `@davelopez `_ in `#18374 `_ - -============ -Enhancements -============ -* Remove deprecated BCO export endpoint by `@martenson `_ in `#16645 `_ -* Enable all-vs-all collection analysis patterns. by `@jmchilton `_ in `#17366 `_ -* Code cleanups from ruff and pyupgrade by `@nsoranzo `_ in `#17654 `_ -* Enable ``warn_unused_ignores`` mypy option by `@nsoranzo `_ in `#17991 `_ -* Add galaxy to user agent by `@mvdbeek `_ in `#18003 `_ -* Refactor galaxy.files plugin loading + config handling. by `@jmchilton `_ in `#18049 `_ -* Update Python dependencies by `@galaxybot `_ in `#18063 `_ ------------------- 24.0.2 (2024-05-07) diff --git a/packages/test_api/setup.cfg b/packages/test_api/setup.cfg index be490357e54a..a6754d91250f 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 = 24.1.0 +version = 23.2.dev0 [options] include_package_data = True @@ -46,4 +46,4 @@ driver = [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/test_base/HISTORY.rst b/packages/test_base/HISTORY.rst index 097ede1ba0b2..29b159027296 100644 --- a/packages/test_base/HISTORY.rst +++ b/packages/test_base/HISTORY.rst @@ -3,29 +3,11 @@ History .. to_doc -------------------- -24.1.0 (2024-06-20) -------------------- - +--------- +24.1.dev0 +--------- -========= -Bug fixes -========= - -* Fix submitted value in workflow run form if data is constrained by tag filter by `@mvdbeek `_ in `#18193 `_ -* Revert some requests import changes by `@nsoranzo `_ in `#18199 `_ - -============ -Enhancements -============ -* Remove deprecated BCO export endpoint by `@martenson `_ in `#16645 `_ -* Enable all-vs-all collection analysis patterns. by `@jmchilton `_ in `#17366 `_ -* Code cleanups from ruff and pyupgrade by `@nsoranzo `_ in `#17654 `_ -* Error reporting unit tests by `@jmchilton `_ in `#17968 `_ -* Add galaxy to user agent by `@mvdbeek `_ in `#18003 `_ -* Empower users to bring their own storage and file sources by `@jmchilton `_ in `#18127 `_ -* More structured indexing for user data objects. by `@jmchilton `_ in `#18291 `_ ------------------- 24.0.2 (2024-05-07) diff --git a/packages/test_base/setup.cfg b/packages/test_base/setup.cfg index 9a976cb6394e..f5e3b8b0c9da 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 = 24.1.0 +version = 23.2.dev0 [options] include_package_data = True @@ -45,4 +45,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/test_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst index 8c0a69c3f975..35bc848859c4 100644 --- a/packages/test_driver/HISTORY.rst +++ b/packages/test_driver/HISTORY.rst @@ -3,26 +3,11 @@ History .. to_doc -------------------- -24.1.0 (2024-06-20) -------------------- - +--------- +24.1.dev0 +--------- -========= -Bug fixes -========= - -* Skip tests if toolshed, dx.doi not responding by `@mvdbeek `_ in `#18250 `_ -* Move tool shed specific driver function to tool_shed.test by `@mvdbeek `_ in `#18296 `_ - -============ -Enhancements -============ -* Adding object store plugin for Rucio by `@SergeyYakubov `_ in `#17156 `_ -* Code cleanups from ruff and pyupgrade by `@nsoranzo `_ in `#17654 `_ -* Overhaul Azure storage infrastructure. by `@jmchilton `_ in `#18087 `_ -* Empower users to bring their own storage and file sources by `@jmchilton `_ in `#18127 `_ ------------------- 24.0.2 (2024-05-07) diff --git a/packages/test_driver/setup.cfg b/packages/test_driver/setup.cfg index e3a014342d04..5c3292823c1b 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 = 24.1.0 +version = 23.2.dev0 [options] include_package_data = True @@ -45,4 +45,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/tool_shed/HISTORY.rst b/packages/tool_shed/HISTORY.rst index 6815807cbe66..4d37ec4ce31c 100644 --- a/packages/tool_shed/HISTORY.rst +++ b/packages/tool_shed/HISTORY.rst @@ -3,28 +3,11 @@ History .. to_doc -------------------- -24.1.0 (2024-06-20) -------------------- - +--------- +24.1.dev0 +--------- -========= -Bug fixes -========= - -* Revert some requests import changes by `@nsoranzo `_ in `#18199 `_ -* Add ``hgweb_repo_prefix`` attribute to ``TestToolShedConfig`` by `@nsoranzo `_ in `#18268 `_ -* Fix various packages' issues by `@nsoranzo `_ in `#18301 `_ -* Fix tool_shed package unit tests by `@mvdbeek `_ in `#18327 `_ -* Fix one more tool shed unit test by `@mvdbeek `_ in `#18328 `_ - -============ -Enhancements -============ -* Enable ``warn_unused_ignores`` mypy option by `@nsoranzo `_ in `#17991 `_ -* Add galaxy to user agent by `@mvdbeek `_ in `#18003 `_ -* Update Python dependencies by `@galaxybot `_ in `#18063 `_ ------------------- 24.0.2 (2024-05-07) diff --git a/packages/tool_shed/setup.cfg b/packages/tool_shed/setup.cfg index 3b9d55525171..0181412712ea 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 = 24.1.0 +version = 23.2.dev0 [options] include_package_data = True @@ -64,4 +64,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst index 98af9ffd06d9..1192cd5b732d 100644 --- a/packages/tool_util/HISTORY.rst +++ b/packages/tool_util/HISTORY.rst @@ -3,47 +3,11 @@ History .. to_doc -------------------- -24.1.0 (2024-06-20) -------------------- - +--------- +24.1.dev0 +--------- -========= -Bug fixes -========= - -* Fix bug in galaxy.xsd by `@kostrykin `_ in `#17752 `_ -* Fix bug in `assert_has_image_n_labels` by `@kostrykin `_ in `#17754 `_ -* Allow purge query param, deprecate purge body param by `@mvdbeek `_ in `#18105 `_ -* Remove linter for unstripped text content for tool xml leaves by `@bernt-matthias `_ in `#18252 `_ -* Make sure that all Linter subclasses are imported for listing them by `@bernt-matthias `_ in `#18339 `_ -* Assign default ``data`` extension on discovered collection output by `@mvdbeek `_ in `#18389 `_ -* Allow in_range validator for selects by `@bernt-matthias `_ in `#18403 `_ - -============ -Enhancements -============ -* Add test and doc showing how dynamic selects are used by `@bernt-matthias `_ in `#16885 `_ -* Add content assertion XML tags for test output verification using images by `@kostrykin `_ in `#17581 `_ -* Set minimal metadata also for empty bed datasets by `@wm75 `_ in `#17586 `_ -* Automatically bind `galaxy_data_manager_data_path` in containers by `@bernt-matthias `_ in `#17596 `_ -* Type annotation improvements by `@nsoranzo `_ in `#17601 `_ -* Type annotation and CWL-related improvements by `@nsoranzo `_ in `#17630 `_ -* Update Python dependencies by `@galaxybot `_ in `#17653 `_ -* Code cleanups from ruff and pyupgrade by `@nsoranzo `_ in `#17654 `_ -* Tool linter: check for valid bio.tools entries by `@bernt-matthias `_ in `#17655 `_ -* Tool linter: check for leaf nodes with unstripped text content by `@bernt-matthias `_ in `#17656 `_ -* Issue #17631: Make it possible to use custom invfile.lua if needed by `@martin-g `_ in `#17693 `_ -* SQLAlchemy 2.0 by `@jdavcs `_ in `#17778 `_ -* Add support for floating point TIFF files in verification of image-based tool outputs by `@kostrykin `_ in `#17797 `_ -* Add tool linting for valid EDAM terms by `@bernt-matthias `_ in `#17839 `_ -* Add `pin_labels` attribute for `image_diff` comparison method by `@kostrykin `_ in `#17866 `_ -* Enable ``warn_unused_ignores`` mypy option by `@nsoranzo `_ in `#17991 `_ -* Add galaxy to user agent by `@mvdbeek `_ in `#18003 `_ -* Document syntax for accessing nested parameters in `change_format` - `when` tags by `@bernt-matthias `_ in `#18018 `_ -* Update Python dependencies by `@galaxybot `_ in `#18063 `_ -* Enable flake8-implicit-str-concat ruff rules by `@nsoranzo `_ in `#18067 `_ ------------------- 24.0.2 (2024-05-07) diff --git a/packages/tool_util/setup.cfg b/packages/tool_util/setup.cfg index 7ef58346fa83..848a609a6b2c 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 = 24.1.0 +version = 23.2.dev0 [options] include_package_data = True @@ -74,4 +74,4 @@ extended-assertions = [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/tours/HISTORY.rst b/packages/tours/HISTORY.rst index 32ca810e2794..98b94ca159cc 100644 --- a/packages/tours/HISTORY.rst +++ b/packages/tours/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc -------------------- -24.1.0 (2024-06-20) -------------------- +--------- +24.1.dev0 +--------- + -No recorded changes since last release ------------------- 24.0.2 (2024-05-07) diff --git a/packages/tours/setup.cfg b/packages/tours/setup.cfg index 4d3480d9cadd..3197c7e1eeab 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 = 24.1.0 +version = 23.2.dev0 [options] include_package_data = True @@ -44,4 +44,4 @@ console_scripts = [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/util/HISTORY.rst b/packages/util/HISTORY.rst index e00cc9a73542..f181c3c71bce 100644 --- a/packages/util/HISTORY.rst +++ b/packages/util/HISTORY.rst @@ -3,35 +3,11 @@ History .. to_doc -------------------- -24.1.0 (2024-06-20) -------------------- - +--------- +24.1.dev0 +--------- -========= -Bug fixes -========= - -* Fix bug in image_util.py by `@kostrykin `_ in `#17749 `_ -* Revert some requests import changes by `@nsoranzo `_ in `#18199 `_ -* Use config_section to distinguish between galaxy and ts or other apps by `@jdavcs `_ in `#18215 `_ - -============ -Enhancements -============ -* Better display of estimated line numbers and add number of columns for tabular by `@bernt-matthias `_ in `#17492 `_ -* Update Python dependencies by `@galaxybot `_ in `#17653 `_ -* Code cleanups from ruff and pyupgrade by `@nsoranzo `_ in `#17654 `_ -* SQLAlchemy 2.0 by `@jdavcs `_ in `#17778 `_ -* Error reporting unit tests by `@jmchilton `_ in `#17968 `_ -* Enable ``warn_unused_ignores`` mypy option by `@nsoranzo `_ in `#17991 `_ -* Add galaxy to user agent by `@mvdbeek `_ in `#18003 `_ -* Update Python dependencies by `@galaxybot `_ in `#18063 `_ -* Enable flake8-implicit-str-concat ruff rules by `@nsoranzo `_ in `#18067 `_ -* Overhaul Azure storage infrastructure. by `@jmchilton `_ in `#18087 `_ -* Empower users to bring their own storage and file sources by `@jmchilton `_ in `#18127 `_ -* Harden User Object Store and File Source Creation by `@jmchilton `_ in `#18172 `_ ------------------- 24.0.2 (2024-05-07) diff --git a/packages/util/setup.cfg b/packages/util/setup.cfg index e4cf4a61686f..d0a614868fa5 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 = 24.1.0 +version = 23.2.dev0 [options] include_package_data = True @@ -59,4 +59,4 @@ config_template = [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/web_apps/HISTORY.rst b/packages/web_apps/HISTORY.rst index c775acca03b7..364d1133a1d6 100644 --- a/packages/web_apps/HISTORY.rst +++ b/packages/web_apps/HISTORY.rst @@ -3,74 +3,11 @@ History .. to_doc -------------------- -24.1.0 (2024-06-20) -------------------- - - -========= -Bug fixes -========= - -* do not expand datasets that are known to be inaccessible by `@martenson `_ in `#17818 `_ -* Fix permissions for temporary upload file for API uploads by `@bernt-matthias `_ in `#17850 `_ -* Dynamic tool fixes by `@dcore94 `_ in `#18085 `_ -* Raise exception if collection elements missing during download by `@jdavcs `_ in `#18094 `_ -* Allow purge query param, deprecate purge body param by `@mvdbeek `_ in `#18105 `_ -* Prevent anonymous and inactive users from running workflows by `@ahmedhamidawan `_ in `#18192 `_ -* Drop "Send to cloud" tool and associated cloudauthz code by `@jdavcs `_ in `#18196 `_ -* Revert some requests import changes by `@nsoranzo `_ in `#18199 `_ -* Fix `make all histories private` with immutable histories by `@davelopez `_ in `#18200 `_ -* Fix pca 3d rendering of tabular files and visualization error handling in general by `@mvdbeek `_ in `#18211 `_ -* Check dataset state when attempting to acces dataset contents by `@mvdbeek `_ in `#18214 `_ -* Restrict job_files access to jobs that are not terminal by `@mvdbeek `_ in `#18217 `_ -* Raise appropriate exception if accessing deleted input file by `@mvdbeek `_ in `#18223 `_ -* Fix element serialization for collections that aren't populated yet by `@mvdbeek `_ in `#18235 `_ -* Small bug fixes for user data plugins by `@jmchilton `_ in `#18246 `_ -* Fix various packages' issues by `@nsoranzo `_ in `#18301 `_ -* Skip new history creation if user is anonymous and login is required by `@mvdbeek `_ in `#18319 `_ -* Fix users API serialization when listing users by `@davelopez `_ in `#18329 `_ -* Fix authentication error for anonymous users querying jobs by `@davelopez `_ in `#18333 `_ -* Do not copy purged outputs to object store by `@mvdbeek `_ in `#18342 `_ -* Fix anonymous user job retrieval logic by `@davelopez `_ in `#18358 `_ -* Fix update group API payload model by `@davelopez `_ in `#18374 `_ -* Drop unnecessary escaping for workflow name and annotation by `@mvdbeek `_ in `#18376 `_ +--------- +24.1.dev0 +--------- -============ -Enhancements -============ - -* Remove deprecated BCO export endpoint by `@martenson `_ in `#16645 `_ -* Implement a page object accessibility dialog by `@jmchilton `_ in `#17225 `_ -* Enable storage management by object store by `@jmchilton `_ in `#17500 `_ -* Type annotation and CWL-related improvements by `@nsoranzo `_ in `#17630 `_ -* Update Python dependencies by `@galaxybot `_ in `#17653 `_ -* Code cleanups from ruff and pyupgrade by `@nsoranzo `_ in `#17654 `_ -* SQLAlchemy 2.0 by `@jdavcs `_ in `#17778 `_ -* Add `email` notifications channel by `@davelopez `_ in `#17914 `_ -* Model typing and SA2.0 follow-up by `@jdavcs `_ in `#17958 `_ -* Drop unused workflow controller methods by `@mvdbeek `_ in `#17974 `_ -* Enable ``warn_unused_ignores`` mypy option by `@nsoranzo `_ in `#17991 `_ -* Add galaxy to user agent by `@mvdbeek `_ in `#18003 `_ -* Consolidate Visualization container, avoid using default iframe by `@guerler `_ in `#18016 `_ -* Add pagination support to Files Source plugins by `@davelopez `_ in `#18059 `_ -* Update Python dependencies by `@galaxybot `_ in `#18063 `_ -* Enable flake8-implicit-str-concat ruff rules by `@nsoranzo `_ in `#18067 `_ -* Change `InvocationsList` into a grid using `GridList` by `@ahmedhamidawan `_ in `#18088 `_ -* Empower users to bring their own storage and file sources by `@jmchilton `_ in `#18127 `_ -* Harden User Object Store and File Source Creation by `@jmchilton `_ in `#18172 `_ -* Update Python dependencies by `@galaxybot `_ in `#18226 `_ -* Drop restriction to switch to immutable histories by `@davelopez `_ in `#18234 `_ -* More structured indexing for user data objects. by `@jmchilton `_ in `#18291 `_ -* More data access tests, some refactoring and cleanup by `@jdavcs `_ in `#18312 `_ -* Allow running and editing workflows for specific versions by `@ahmedhamidawan `_ in `#18378 `_ - -============= -Other changes -============= -* Decrease log level for expected visualization errors by `@mvdbeek `_ in `#18229 `_ -* Fix typing issue in reused variable by `@davelopez `_ in `#18344 `_ ------------------- 24.0.2 (2024-05-07) diff --git a/packages/web_apps/setup.cfg b/packages/web_apps/setup.cfg index 778409b0e07f..ee9b36f2f70c 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 = 24.1.0 +version = 23.2.dev0 [options] include_package_data = True @@ -72,4 +72,4 @@ python_requires = >=3.8 [options.packages.find] exclude = tests* - tool_shed.test* \ No newline at end of file + tool_shed.test* diff --git a/packages/web_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst index 2379ef897dfe..f3bb5f762efd 100644 --- a/packages/web_framework/HISTORY.rst +++ b/packages/web_framework/HISTORY.rst @@ -3,27 +3,11 @@ History .. to_doc -------------------- -24.1.0 (2024-06-20) -------------------- - +--------- +24.1.dev0 +--------- -========= -Bug fixes -========= - -* Reset content-length for unhandled exceptions by `@mvdbeek `_ in `#18233 `_ -* More fixes for running the TS with external hgweb by `@mvdbeek `_ in `#18279 `_ - -============ -Enhancements -============ -* Update Python dependencies by `@galaxybot `_ in `#17653 `_ -* Code cleanups from ruff and pyupgrade by `@nsoranzo `_ in `#17654 `_ -* SQLAlchemy 2.0 by `@jdavcs `_ in `#17778 `_ -* Add galaxy to user agent by `@mvdbeek `_ in `#18003 `_ -* Update Python dependencies by `@galaxybot `_ in `#18063 `_ ------------------- 24.0.2 (2024-05-07) diff --git a/packages/web_framework/setup.cfg b/packages/web_framework/setup.cfg index 60ff905f63f3..2cdcd90c3776 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 = 24.1.0 +version = 23.2.dev0 [options] include_package_data = True @@ -48,4 +48,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* \ No newline at end of file + tests* diff --git a/packages/web_stack/HISTORY.rst b/packages/web_stack/HISTORY.rst index f9a78ac82167..bcb6837658c6 100644 --- a/packages/web_stack/HISTORY.rst +++ b/packages/web_stack/HISTORY.rst @@ -3,16 +3,11 @@ History .. to_doc -------------------- -24.1.0 (2024-06-20) -------------------- - +--------- +24.1.dev0 +--------- -============ -Enhancements -============ -* Update Python dependencies by `@galaxybot `_ in `#17653 `_ ------------------- 24.0.2 (2024-05-07) diff --git a/packages/web_stack/setup.cfg b/packages/web_stack/setup.cfg index ff228e37f4d3..16e6d08f1c15 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 = 24.1.0 +version = 23.2.dev0 [options] include_package_data = True @@ -40,4 +40,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* \ No newline at end of file + tests*