v1.8.0

What's Changed

• Dropped support for Python 3.9. Added support for Galaxy release 26.0.
• Added copy_history() method to HistoryClient (thanks to Peter van Heusden ).
• Added get_tool_source() method to ToolClient (thanks to Anup Kumar).
• Added preferred_object_store_id parameter to HistoryClient.update_history().
• Improvements to documentation, tests and type annotation.

New Contributors

• @pvanheus made their first contribution in #528
• @anuprulez made their first contribution in #529

Full Changelog: v1.7.0...v1.8.0

v1.7.0

Deprecations

• This is the last release to support end-of-life Python 3.9.

What's Changed

• Added support for Python 3.14. Added support for Galaxy release 25.1.

• Added get_invocation_request() method to InvocationClient (thanks to Martin Čech).

• Added get_tool_tests() method to ToolClient (thanks to JunhaoQiu).

• Added job_id parameter to InvocationClient.get_invocations().

• Added resource_params and use_cached_job parameters to InvocationClient.rerun_invocation() (thanks to Martin Čech).

• Added parameters, instance, resource_params, preferred_object_store_id, preferred_intermediate_object_store_id and preferred_outputs_object_store_id parameters to WorkflowClient.invoke_workflow() (thanks to Martin Čech).

• Refactored implementation of InvocationClient.rerun_invocation() to use InvocationClient.get_invocation_request() on Galaxy release 24.2 and later. Also fixed reuse of parameter inputs from the original invocation on Galaxy release 24.1 and earlier. (thanks to Martin Čech).

• Migrated from setup.cfg to pyproject.toml .

• Improvements to documentation and tests.

New Contributors

• @qchiujunhao made their first contribution in #522

Full Changelog: v1.6.0...v1.7.0

v1.6.0

What's Changed

• Added support for Galaxy release 25.0.
• Added support for API auth with access token (thanks to Nuwan Goonasekera).
• Added decode_id() and encode_id() methods to ConfigClient (thanks to Simon Bray).
• Added get_invocation_archive() method to InvocationClient (thanks to Patrik Smeds).
• Added instance and legacy parameters to WorkflowClient.show_workflow() (thanks to Patrik Smeds).
• Improvements to documentation, tests and type annotation (thanks to Dannon and Matthias Bernt).

New Contributors

• @Smeds made their first contribution in #505
• @ahmedhamidawan made their first contribution in #507

Full Changelog: v1.5.0...v1.6.0

v1.5.0

What's Changed

• Dropped support for Python 3.8. Added support for Galaxy release 24.2.
• Added limit, offset and include_deleted parameters to FoldersClient.show_folder() (thanks to Matthias Bernt).
• Added offset parameter to InvocationClient.get_invocations() and BioBlend.objects ObjInvocationClient.list() methods.
• Added quota_source_label parameter to QuotaClient.create_quota() (thanks to Matthias Bernt).
• Added style parameter to WorkflowClient.export_workflow_dict() method to allow exporting in gxformat2 format (thanks to Marius van den Beek).
• Improvements to type annotations and documentation.

New Contributors

• @jdavcs made their first contribution in #495

Full Changelog: v1.4.0...v1.5.0

v1.4.0

What's Changed

• Added support for Python 3.13. Added support for Galaxy release 24.1.

• Added user_agent parameter to the __init__() method of the GalaxyClient, GalaxyInstance and ToolShedInstance classes (thanks to Daniel Blankenberg).

• Added version and use_cached_job parameters to WorkflowClient.invoke_workflow() method (reported by Bérénice Batut).

• Changed the default values for the operation and default parameters of the QuotaClient.update_quota() method (thanks to Matthias Bernt).

• Improvements to tests and documentation (thanks to Matthias Bernt).

New Contributors

• @blankenberg made their first contribution in #318

Full Changelog: v1.3.0...v1.4.0

v1.3.0

What's Changed

• Dropped support for Python 3.7. Added support for Python 3.12. Added support for Galaxy releases 23.2 and 24.0.

• Added copy_elements parameter to HistoryClient.create_dataset_collection() and BioBlend.objects History.create_dataset_collection() methods.

• Added wait parameter to HistoryClient.delete_dataset() and BioBlend.objects HistoryDatasetAssociation.delete() methods.

• Added create_time_min, create_time_max, update_time_min, update_time_max, view, keys, limit and offset parameters to HistoryClient.get_histories() (thanks to cat-bro).

• Added create_time_min, create_time_max, update_time_min and update_time_max parameters to HistoryClient.get_published_histories() (thanks to cat-bro).

• Added keys parameter to HistoryClient.show_history() (thanks to cat-bro).

• Dropped broken deleted parameter of DatasetClient.show_dataset().

• Parameters after password in the __init__() method of the GalaxyClient, GalaxyInstance and ToolShedInstance classes are now keyword-only.

• Classes defined in bioblend.galaxy.objects.wrappers are no more re-exported by bioblend.galaxy.objects.

• DatasetTimeoutException and DatasetCollectionTimeoutException are now aliases for TimeoutException instead of subclasses.

• Added support for the new "cancelling" invocation state.

• Fixed InvocationClient.get_invocation_biocompute_object() method on upcoming Galaxy 24.1 .

• Improvements to linting and tests (thanks to Matthias Bernt).

Full Changelog: v1.2.0...v1.3.0

v1.2.0

• Dropped support for Galaxy releases 17.09-19.01. Added support for Galaxy release 23.1.

• Added a new container_resolution attribute to GalaxyInstance objects, which is an instance of the new ContainerResolutionClient. This new module can be used to list container resolvers, and to resolve (and install) tool requirements against specified container resolvers (thanks to cat-bro and Matthias Bernt).

• Added reload_toolbox() method to ConfigClient (thanks to Anthony Bretaudeau).

• Added delete_unused_dependency_paths() and unused_dependency_paths() methods to ToolDependenciesClient (thanks to Matthias Bernt).

• Added data_manager_mode parameter to ToolClient.run_tool() method (thanks to Marius van den Beek).

• Added user_data parameter to UserClient.update_user() method (thanks to Uwe Winter).

• Fixed bug in DatasetClient.download_dataset() and BioBlend.objects HistoryDatasetAssociation.get_stream() where the wrong download URL was generated if the Galaxy instance is served at a subdirectory (reported by Anil Thanki).

• Improvements to tests and documentation (thanks to kxk302 and Simon Bray).

v1.1.1

• Same as BioBlend v1.1.0, briefly released with wrong version number 1.0.1 on GitHub, PyPI and Bioconda.
• Added support for Python 3.11. Added support for Galaxy release 23.0.
• Using the deprecated folder_id parameter of the LibraryClient.get_folders() method now raises a ValueError exception.
• Using the deprecated library_id parameter of the LibraryClient.get_libraries() method now raises a ValueError exception.
• Using the deprecated tool_id parameter of the ToolClient.get_tools() method now raises a ValueError exception.
• Using the deprecated workflow_id parameter of the WorkflowClient.get_workflows() method now raises a ValueError exception.
• Modified delete_workflow() method of WorkflowClient to return None instead of a string.
• Add py.typed marker file to distributed packages (as per PEP 561) to declare type checking support.
• Improvements to tests and documentation.

v1.0.0

• Dropped support for deprecated CloudMan, see https://galaxyproject.org/blog/2021-10-sunsetting-cloudlaunch/

• Added dependency on typing-extensions package, removed dependencies on boto and pyyaml.

• Deprecated max_get_retries(), set_max_get_retries(), get_retry_delay() and set_get_retry_delay() methods of Client.

• Moved max_get_attempts and get_retry_delay properties from GalaxyInstance to GalaxyClient, so they are also available in ToolshedInstance.

• Added get_or_create_user_apikey() method to UserClient.

• Added all parameter to HistoryClient.get_histories() method (thanks to Paprikant).

• Added require_exact_tool_versions parameter to WorkflowClient.invoke_workflow() method (thanks to cat-bro).

• Added name and owner parameters to
  ToolShedRepositoryClient.get_repositories().

• Removed unused methods from bioblend.config.Config. If needed, use the methods inherited from configparser.ConfigParser instead.

• Allowed any 2XX HTTP response status code in Client._delete() to correctly support history purging via Celery (thanks to Nolan Woods).

• Fixed bug in FormsClient.create_form() where the form_xml_text argument was not passed correctly to the Galaxy API.

• Fixed bug in HistoryClient.show_dataset_provenance() where the follow argument was not passed to the Galaxy API.

• BioBlend.objects: Added delete() abstract method to DatasetContainer class.

• Added Code of Conduct for the project.

• Finished the full type annotation of the library (thanks to cat-bro, Fabio Cumbo, Jayadev Joshi, thepineapplepirate).

• Improvements to tests and documentation.

v0.18.0

• Added support for Galaxy release 22.05.

• Added tus support to ToolClient.upload_file() (thanks to Nate Coraor).

• Format Python code with black and isort.

• Improvements to type annotations, tests and documentation.