From e196a581969760419920400ba5bf646858fac162 Mon Sep 17 00:00:00 2001 From: John Davis Date: Thu, 20 Jun 2024 18:46:33 -0400 Subject: [PATCH] Create version 24.1.0 --- 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, 669 insertions(+), 109 deletions(-) diff --git a/lib/galaxy/version.py b/lib/galaxy/version.py index 319c7fefb8a0..2c7c62709afb 100644 --- a/lib/galaxy/version.py +++ b/lib/galaxy/version.py @@ -1,3 +1,3 @@ -VERSION_MAJOR = "24.2" -VERSION_MINOR = "dev0" +VERSION_MAJOR = "24.1" +VERSION_MINOR = "0" VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else "") diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst index c68d6c7dbe2f..ebc22e559824 100644 --- a/packages/app/HISTORY.rst +++ b/packages/app/HISTORY.rst @@ -3,11 +3,116 @@ History .. to_doc ---------- -24.1.dev0 ---------- +------------------- +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 `_ +============ +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 640cacc77d3d..efd86c989a69 100644 --- a/packages/app/setup.cfg +++ b/packages/app/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-app url = https://github.com/galaxyproject/galaxy -version = 23.2.dev0 +version = 24.1.0 [options] include_package_data = True @@ -85,4 +85,4 @@ console_scripts = [options.packages.find] exclude = galaxy.tools.bundled* - tests* + tests* \ No newline at end of file diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst index e87c36a52403..d52e9ca3fbb4 100644 --- a/packages/auth/HISTORY.rst +++ b/packages/auth/HISTORY.rst @@ -3,11 +3,17 @@ History .. to_doc ---------- -24.1.dev0 ---------- +------------------- +24.1.0 (2024-06-20) +------------------- + +============ +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 adad08ddb323..6c23290e7847 100644 --- a/packages/auth/setup.cfg +++ b/packages/auth/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-auth url = https://github.com/galaxyproject/galaxy -version = 23.2.dev0 +version = 24.1.0 [options] include_package_data = True @@ -39,4 +39,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/config/HISTORY.rst b/packages/config/HISTORY.rst index 746ecf383fc6..70eba23f945a 100644 --- a/packages/config/HISTORY.rst +++ b/packages/config/HISTORY.rst @@ -3,11 +3,52 @@ History .. to_doc ---------- -24.1.dev0 ---------- +------------------- +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 `_ +============ +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 b1691b58d9a5..0df6f912e9e0 100644 --- a/packages/config/setup.cfg +++ b/packages/config/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-config url = https://github.com/galaxyproject/galaxy -version = 23.2.dev0 +version = 24.1.0 [options] include_package_data = True @@ -46,4 +46,4 @@ console_scripts = [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst index 1d3a447f88ba..81b4b8b0f9b5 100644 --- a/packages/data/HISTORY.rst +++ b/packages/data/HISTORY.rst @@ -3,11 +3,72 @@ History .. to_doc ---------- -24.1.dev0 ---------- +------------------- +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 `_ +============ +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 6f1ce7204eb6..8d4a36edaec4 100644 --- a/packages/data/setup.cfg +++ b/packages/data/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-data url = https://github.com/galaxyproject/galaxy -version = 23.2.dev0 +version = 24.1.0 [options] include_package_data = True @@ -75,4 +75,4 @@ 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 2fc21b40fea9..558ec71d7ead 100644 --- a/packages/files/HISTORY.rst +++ b/packages/files/HISTORY.rst @@ -3,11 +3,50 @@ History .. to_doc ---------- -24.1.dev0 ---------- +------------------- +24.1.0 (2024-06-20) +------------------- + +========= +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 dc0599c9b7c3..5ba5a0c9f51b 100644 --- a/packages/files/setup.cfg +++ b/packages/files/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-files url = https://github.com/galaxyproject/galaxy -version = 23.2.dev0 +version = 24.1.0 [options] include_package_data = True @@ -41,4 +41,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst index 65d9d4244618..b589a147acf8 100644 --- a/packages/job_execution/HISTORY.rst +++ b/packages/job_execution/HISTORY.rst @@ -3,11 +3,30 @@ History .. to_doc ---------- -24.1.dev0 ---------- +------------------- +24.1.0 (2024-06-20) +------------------- + +========= +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 05394dca8e27..08621310f32c 100644 --- a/packages/job_execution/setup.cfg +++ b/packages/job_execution/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-job-execution url = https://github.com/galaxyproject/galaxy -version = 23.2.dev0 +version = 24.1.0 [options] include_package_data = True @@ -49,4 +49,4 @@ console_scripts = [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst index aa0c39f3599d..8378c7de785e 100644 --- a/packages/job_metrics/HISTORY.rst +++ b/packages/job_metrics/HISTORY.rst @@ -3,11 +3,17 @@ History .. to_doc ---------- -24.1.dev0 ---------- +------------------- +24.1.0 (2024-06-20) +------------------- + +============ +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 476eea3712ad..ef8166e9d420 100644 --- a/packages/job_metrics/setup.cfg +++ b/packages/job_metrics/setup.cfg @@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-job-metrics url = https://github.com/galaxyproject/galaxy -version = 23.2.dev0 +version = 24.1.0 [options] include_package_data = True @@ -39,4 +39,4 @@ python_requires = >=3.7 [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/navigation/HISTORY.rst b/packages/navigation/HISTORY.rst index 0db4ab93679c..8a6ae3b0a460 100644 --- a/packages/navigation/HISTORY.rst +++ b/packages/navigation/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc ---------- -24.1.dev0 ---------- - +------------------- +24.1.0 (2024-06-20) +------------------- +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 a2635d9e49fe..567951323bae 100644 --- a/packages/navigation/setup.cfg +++ b/packages/navigation/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-navigation url = https://github.com/galaxyproject/galaxy -version = 23.2.dev0 +version = 24.1.0 [options] include_package_data = True @@ -39,4 +39,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst index 2f6dc31f61a7..1c0cf9b1cc3b 100644 --- a/packages/objectstore/HISTORY.rst +++ b/packages/objectstore/HISTORY.rst @@ -3,11 +3,40 @@ History .. to_doc ---------- -24.1.dev0 ---------- +------------------- +24.1.0 (2024-06-20) +------------------- + +========= +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 6ba5fe551e67..c4d7b93939f1 100644 --- a/packages/objectstore/setup.cfg +++ b/packages/objectstore/setup.cfg @@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-objectstore url = https://github.com/galaxyproject/galaxy -version = 23.2.dev0 +version = 24.1.0 [options] include_package_data = True @@ -41,4 +41,4 @@ python_requires = >=3.7 [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/schema/HISTORY.rst b/packages/schema/HISTORY.rst index 16def6b775a4..732ec11cc498 100644 --- a/packages/schema/HISTORY.rst +++ b/packages/schema/HISTORY.rst @@ -3,11 +3,35 @@ History .. to_doc ---------- -24.1.dev0 ---------- +------------------- +24.1.0 (2024-06-20) +------------------- + +========= +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 1ebcb6abef60..6eeb8da4ac31 100644 --- a/packages/schema/setup.cfg +++ b/packages/schema/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-schema url = https://github.com/galaxyproject/galaxy -version = 23.2.dev0 +version = 24.1.0 [options] include_package_data = True @@ -39,4 +39,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst index 5beab1aae25b..bcf149a43ac3 100644 --- a/packages/selenium/HISTORY.rst +++ b/packages/selenium/HISTORY.rst @@ -3,11 +3,26 @@ History .. to_doc ---------- -24.1.dev0 ---------- +------------------- +24.1.0 (2024-06-20) +------------------- + +========= +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 07fab81680d9..c6a16adf34e0 100644 --- a/packages/selenium/setup.cfg +++ b/packages/selenium/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-selenium url = https://github.com/galaxyproject/galaxy -version = 23.2.dev0 +version = 24.1.0 [options] include_package_data = True @@ -47,4 +47,4 @@ console_scripts = [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/test_api/HISTORY.rst b/packages/test_api/HISTORY.rst index 792c69a9334e..042086db2b7a 100644 --- a/packages/test_api/HISTORY.rst +++ b/packages/test_api/HISTORY.rst @@ -3,11 +3,32 @@ History .. to_doc ---------- -24.1.dev0 ---------- +------------------- +24.1.0 (2024-06-20) +------------------- + +========= +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 a6754d91250f..be490357e54a 100644 --- a/packages/test_api/setup.cfg +++ b/packages/test_api/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-test-api url = https://github.com/galaxyproject/galaxy -version = 23.2.dev0 +version = 24.1.0 [options] include_package_data = True @@ -46,4 +46,4 @@ driver = [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/test_base/HISTORY.rst b/packages/test_base/HISTORY.rst index 29b159027296..097ede1ba0b2 100644 --- a/packages/test_base/HISTORY.rst +++ b/packages/test_base/HISTORY.rst @@ -3,11 +3,29 @@ History .. to_doc ---------- -24.1.dev0 ---------- +------------------- +24.1.0 (2024-06-20) +------------------- + +========= +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 f5e3b8b0c9da..9a976cb6394e 100644 --- a/packages/test_base/setup.cfg +++ b/packages/test_base/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-test-base url = https://github.com/galaxyproject/galaxy -version = 23.2.dev0 +version = 24.1.0 [options] include_package_data = True @@ -45,4 +45,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/test_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst index 35bc848859c4..8c0a69c3f975 100644 --- a/packages/test_driver/HISTORY.rst +++ b/packages/test_driver/HISTORY.rst @@ -3,11 +3,26 @@ History .. to_doc ---------- -24.1.dev0 ---------- +------------------- +24.1.0 (2024-06-20) +------------------- + +========= +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 5c3292823c1b..e3a014342d04 100644 --- a/packages/test_driver/setup.cfg +++ b/packages/test_driver/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-test-driver url = https://github.com/galaxyproject/galaxy -version = 23.2.dev0 +version = 24.1.0 [options] include_package_data = True @@ -45,4 +45,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/tool_shed/HISTORY.rst b/packages/tool_shed/HISTORY.rst index 4d37ec4ce31c..6815807cbe66 100644 --- a/packages/tool_shed/HISTORY.rst +++ b/packages/tool_shed/HISTORY.rst @@ -3,11 +3,28 @@ History .. to_doc ---------- -24.1.dev0 ---------- +------------------- +24.1.0 (2024-06-20) +------------------- + +========= +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 0181412712ea..3b9d55525171 100644 --- a/packages/tool_shed/setup.cfg +++ b/packages/tool_shed/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-tool-shed url = https://github.com/galaxyproject/galaxy -version = 23.2.dev0 +version = 24.1.0 [options] include_package_data = True @@ -64,4 +64,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst index 1192cd5b732d..98af9ffd06d9 100644 --- a/packages/tool_util/HISTORY.rst +++ b/packages/tool_util/HISTORY.rst @@ -3,11 +3,47 @@ History .. to_doc ---------- -24.1.dev0 ---------- +------------------- +24.1.0 (2024-06-20) +------------------- + +========= +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 848a609a6b2c..7ef58346fa83 100644 --- a/packages/tool_util/setup.cfg +++ b/packages/tool_util/setup.cfg @@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-tool-util url = https://github.com/galaxyproject/galaxy -version = 23.2.dev0 +version = 24.1.0 [options] include_package_data = True @@ -74,4 +74,4 @@ extended-assertions = [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/tours/HISTORY.rst b/packages/tours/HISTORY.rst index 98b94ca159cc..32ca810e2794 100644 --- a/packages/tours/HISTORY.rst +++ b/packages/tours/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc ---------- -24.1.dev0 ---------- - +------------------- +24.1.0 (2024-06-20) +------------------- +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 3197c7e1eeab..4d3480d9cadd 100644 --- a/packages/tours/setup.cfg +++ b/packages/tours/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-tours url = https://github.com/galaxyproject/galaxy -version = 23.2.dev0 +version = 24.1.0 [options] include_package_data = True @@ -44,4 +44,4 @@ console_scripts = [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/util/HISTORY.rst b/packages/util/HISTORY.rst index f181c3c71bce..e00cc9a73542 100644 --- a/packages/util/HISTORY.rst +++ b/packages/util/HISTORY.rst @@ -3,11 +3,35 @@ History .. to_doc ---------- -24.1.dev0 ---------- +------------------- +24.1.0 (2024-06-20) +------------------- + +========= +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 d0a614868fa5..e4cf4a61686f 100644 --- a/packages/util/setup.cfg +++ b/packages/util/setup.cfg @@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-util url = https://github.com/galaxyproject/galaxy -version = 23.2.dev0 +version = 24.1.0 [options] include_package_data = True @@ -59,4 +59,4 @@ config_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 364d1133a1d6..c775acca03b7 100644 --- a/packages/web_apps/HISTORY.rst +++ b/packages/web_apps/HISTORY.rst @@ -3,11 +3,74 @@ History .. to_doc ---------- -24.1.dev0 ---------- +------------------- +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 `_ +============ +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 ee9b36f2f70c..778409b0e07f 100644 --- a/packages/web_apps/setup.cfg +++ b/packages/web_apps/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-web-apps url = https://github.com/galaxyproject/galaxy -version = 23.2.dev0 +version = 24.1.0 [options] include_package_data = True @@ -72,4 +72,4 @@ python_requires = >=3.8 [options.packages.find] exclude = tests* - tool_shed.test* + tool_shed.test* \ No newline at end of file diff --git a/packages/web_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst index f3bb5f762efd..2379ef897dfe 100644 --- a/packages/web_framework/HISTORY.rst +++ b/packages/web_framework/HISTORY.rst @@ -3,11 +3,27 @@ History .. to_doc ---------- -24.1.dev0 ---------- +------------------- +24.1.0 (2024-06-20) +------------------- + +========= +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 2cdcd90c3776..60ff905f63f3 100644 --- a/packages/web_framework/setup.cfg +++ b/packages/web_framework/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-web-framework url = https://github.com/galaxyproject/galaxy -version = 23.2.dev0 +version = 24.1.0 [options] include_package_data = True @@ -48,4 +48,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* + tests* \ No newline at end of file diff --git a/packages/web_stack/HISTORY.rst b/packages/web_stack/HISTORY.rst index bcb6837658c6..f9a78ac82167 100644 --- a/packages/web_stack/HISTORY.rst +++ b/packages/web_stack/HISTORY.rst @@ -3,11 +3,16 @@ History .. to_doc ---------- -24.1.dev0 ---------- +------------------- +24.1.0 (2024-06-20) +------------------- + +============ +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 16e6d08f1c15..ff228e37f4d3 100644 --- a/packages/web_stack/setup.cfg +++ b/packages/web_stack/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-web-stack url = https://github.com/galaxyproject/galaxy -version = 23.2.dev0 +version = 24.1.0 [options] include_package_data = True @@ -40,4 +40,4 @@ python_requires = >=3.8 [options.packages.find] exclude = - tests* + tests* \ No newline at end of file