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Recent Releases of bioblend

bioblend - 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 https://github.com/galaxyproject/bioblend/pull/495

Full Changelog: https://github.com/galaxyproject/bioblend/compare/v1.4.0...v1.5.0

- Python
Published by bernt-matthias 12 months ago

bioblend - 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 https://github.com/galaxyproject/bioblend/pull/318

Full Changelog: https://github.com/galaxyproject/bioblend/compare/v1.3.0...v1.4.0

- Python
Published by nsoranzo over 1 year ago

bioblend - 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: https://github.com/galaxyproject/bioblend/compare/v1.2.0...v1.3.0

- Python
Published by nsoranzo almost 2 years ago

bioblend - 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).

- Python
Published by nsoranzo over 2 years ago

bioblend - 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.

- Python
Published by nsoranzo about 3 years ago

bioblend - 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.

- Python
Published by nsoranzo over 3 years ago

bioblend - 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.

- Python
Published by nsoranzo over 3 years ago

bioblend - v0.17.0

  • Dropped support for Python 3.6. Added support for Python 3.10. Added support for Galaxy releases 21.09 and 22.01.

  • Removed deprecated run_workflow() method of WorkflowClient.

  • Using the deprecated history_id parameter of the HistoryClient.get_histories() method now raises a ValueError exception.

  • Made tool_inputs_update parameter of JobsClient.rerun_job() more flexible.

  • Added whoami() method to ConfigClient (thanks to cat-bro).

  • Added get_extra_files() method to HistoryClient.

  • Added build() and reload() methods to ToolClient (thanks to Jayadev Joshi and cat-bro respectively).

  • Added get_repositories() method to ToolShedCategoryClient (thanks to cat-bro).

  • Added update_repository_metadata() method to ToolShedRepositoryClient.

  • Added order_by parameter to JobsClient.get_jobs() method.

  • BioBlend.objects: Removed deprecated run() method of Workflow.

  • BioBlend.objects: Fail if multiple libraries/histories/workflows match when deleting by name, instead of deleting them all.

  • BioBlend.objects: in HistoryDatasetAssociation.get_stream(), wait for the dataset to be ready.

  • BioBlend.objects: in Workflow.invoke(), check that the workflow is mapped and runnable before invoking, allow the inputs parameter to be an instance of a Dataset subclass, and allow the history parameter to be the name of a new history.

  • BioBlend.objects: Added new datasets and dataset_collections attributes to GalaxyInstance objects, which are instances of the new ObjDatasetClient and ObjDatasetCollectionClient respectively.

  • BioBlend.objects: Added refresh(), get_outputs() and get_output_collections() methods to InvocationStep.

  • Fixed error when instantiating GalaxyInstance with email and password (reported by Peter Briggs).

  • Fixed parameter validation errors for POST requests with attached files on upcoming Galaxy 22.05.

  • Code cleanups (thanks to Martmists).

  • Improvements to type annotations, tests and documentation.

- Python
Published by nsoranzo almost 4 years ago

bioblend - v0.16.0

  • Added support for Galaxy release 21.05.

  • Replaced the job_info parameter with separate tool_id, inputs and state parameters in JobsClient.search_jobs() (thanks to rikeshi).

  • Pass the API key for all requests as the x-api-key header instead of as a parameter (thanks to rikeshi).

  • Try prepending https:// and http:// if the scheme is missing in the url parameter of GalaxyClient, i.e. when initialising a Galaxy or ToolShed instance.

  • Added a new dataset_collections attribute to GalaxyInstance objects, which is an instance of the new DatasetCollectionClient. This new module can be used to get details of a dataset collection, wait until elements of a dataset collection are in a terminal state, and download a history dataset collection as an archive (thanks to rikeshi).

  • Added a new tool_dependencies attribute to GalaxyInstance objects, which is an instance of the new ToolDependenciesClient. This new module can be used to summarize requirements across toolbox (thanks to cat-bro).

  • Added publish_dataset() update_permissions() and wait_for_dataset() methods to DatasetClient.

  • Added get_invocation_biocompute_object(), get_invocation_report_pdf(), get_invocation_step_jobs_summary(), rerun_invocation() and wait_for_invocation() methods to InvocationClient (thanks to rikeshi).

  • Added cancel_job(), get_common_problems(), get_destination_params(), get_inputs(), get_outputs(), resume_job(), show_job_lock(), update_job_lock() and wait_for_job() methods to JobsClient (thanks to Andrew Mcgregor and rikeshi).

  • Added get_citations() and uninstall_dependencies() methods to ToolClient (thanks to rikeshi).

  • Added extract_workflow_from_history(), refactor_workflow() and show_versions() methods to WorkflowClient (thanks to rikeshi).

  • Added several parameters to DatasetClient.get_datasets() method (thanks to rikeshi).

  • Added several parameters to InvocationClient.get_invocations() method (thanks to Nolan Woods and rikeshi).

  • Added several parameters to JobsClient.get_jobs() method (thanks to rikeshi).

  • Added parameters_normalized parameter to WorkflowClient.invoke_workflow() method (thanks to rikeshi).

  • Deprecated folder_id parameter of LibraryClient.get_folders() method.

  • Deprecated library_id parameter of LibraryClient.get_libraries() method.

  • Deprecated tool_id parameter of ToolClient.get_tools() method.

  • Deprecated workflow_id parameter of WorkflowClient.get_workflows() method.

  • BioBlend.objects: Removed deprecated container_id property of Dataset and Folder objects.

  • BioBlend.objects: Removed Preview abstract class.

  • BioBlend.objects: Added invoke() method to Workflow. Added ObjInvocationClient, and Invocation and InvocationPreview wrappers (thanks to rikeshi).

  • BioBlend.objects: Added latest_workflow_uuid property to Workflow objects. Added deleted, latest_workflow_uuid, number_of_steps, owner and show_in_tool_panel properties to WorkflowPreview (thanks to Nolan Woods).

  • BioBlend.objects: Deprecated run() method of Workflow.

  • Added use_ssl, verify and authuser parameters to CloudManInstance.__init__() (thanks to Nathan Edwards).

  • Improvements to type annotations, tests and documentation (thanks to rikeshi).

- Python
Published by nsoranzo over 4 years ago

bioblend - v0.15.0

  • Dropped support for Python 3.5. Added support for Python 3.9. Added support for Galaxy releases 20.09 and 21.01.

  • Changed the return value of RolesClient.create_role() method from a 1-element list containing a dict to a dict.

  • Removed deprecated download_dataset() and get_current_history methods of HistoryClient.

  • Removed deprecated export_workflow_json() and import_workflow_json methods of WorkflowClient.

  • Added copy_content(), get_published_histories() and open_history() methods to HistoryClient.

  • Added rerun_job() method to JobsClient.

  • Added requirements() method to ToolClient (thanks to cat-bro).

  • Added published and slug parameters to HistoryClient.get_histories().

  • Added require_state_ok parameter to DatasetClient.download_dataset().

  • Added input_format parameter to ToolClient.run_tool().

  • Deprecated history_id parameter of HistoryClient.get_histories() method.

  • BioBlend.objects: Added owner property to all objects. Added annotation, published and purged properties to HistoryPreview objects.

  • Fixed issue where specifying the Galaxy URL with "http://" instead of "https://" when creating a GalaxyInstance made the subsequent non-GET requests to silently fail.

  • Moved the Continuous Integration (CI) from TravisCI to GitHub workflows (thanks to Oleg Zharkov).

  • Improvements to tests and documentation (thanks to Gianmauro Cuccuru).

- Python
Published by nsoranzo about 5 years ago

bioblend - v0.14.0

  • Dropped support for Python 2.7. Dropped support for Galaxy releases 14.10-17.05. Added support for Python 3.8. Added support for Galaxy releases 19.09, 20.01 and 20.05.

  • Added a new invocations attribute to GalaxyInstance objects, which is an instance of the new InvocationClient class. This new module can be used to get all workflow invocations, show or cancel an invocation, show or pause an invocation step, get a summary or a report for an invocation (thanks to Simon Bray).

  • Added get_datasets() method to DatasetClient (thanks to Simon Bray).

  • Added import_history() method to HistoryClient (thanks to David Christiany and Marius van den Beek).

  • Added copy_dataset() method to HistoryClient (thanks to Simon Bray).

  • Added get_metrics() method to JobsClient (thanks to Andreas Skorczyk).

  • Added report_error() method to JobsClient (thanks to Peter Selten).

  • Added get_dataset_permissions() and set_dataset_permissions() methods to LibraryClient (thanks to Frederic Sapet).

  • Added update_user() method to UserClient (thanks to Anthony Bretaudeau).

  • Added update_workflow() method to WorkflowClient.

  • Added tags parameter to upload_file_from_url(), upload_file_contents(), upload_file_from_local_path(), upload_file_from_server() and upload_from_galaxy_filesystem() methods of LibraryClient (thanks to Anthony Bretaudeau).

  • Changed the default for the tag_using_filenames parameter of upload_file_from_server() and upload_from_galaxy_filesystem() methods of LibraryClient from True to False (thanks to Anthony Bretaudeau).

  • Added version parameter to show_workflow() and export_workflow_dict() methods of WorkflowClient.

  • Added inputs_by option to invoke_workflow() method of WorkflowClient (thanks to Marius van den Beek).

  • Removed deprecated show_stderr() and show_stdout methods of DatasetClient.

  • BioBlend.objects: Allowed workflow steps of type parameter_input and subworkflow. Added parameter_input_ids property to Workflow objects (reported by Nolan Woods).

  • Fixed HistoryClient.export_history(..., wait=False, maxwait=None) (reported by David Christiany).

  • Moved internal _make_url() method from GalaxyClient to Client class.

- Python
Published by nsoranzo over 5 years ago

bioblend -

  • Dropped support for Python 3.4. Added support for Galaxy releases 19.01 and 19.05.

  • Updated requests-toolbelt requirement to >=0.5.1 to prevent failing of uploads to Galaxy (reported by m93).

  • Added toolshed attribute to GalaxyInstance and made toolShed an alias to it (reported by Miriam Payá).

  • Added uninstall_repository_revision() method to ToolShedClient (thanks to Helena Rasche, reported by Alexander Lenail).

  • Added maxwait parameter to HistoryClient.export_history() and History.export() methods.

  • Fixed handling of type parameter in HistoryClient.show_history() (thanks to Marius van den Beek).

  • Fixed handling of deleted parameter in LibraryClient.get_libraries() (thanks to Luke Sargent, reported by Katie).

  • Fixed LibraryClient.wait_for_dataset() when maxwait or interval parameters are of type float.

  • Unify JSON-encoding of non-file parameters of POST requests inside GalaxyClient.make_post_request().

  • Improvements to tests and documentation (thanks to Helena Rasche, selten and Pablo Moreno).

- Python
Published by nsoranzo over 6 years ago

bioblend - v0.12.0

  • Added supported for Python 3.7. Added support for Galaxy releases 18.05 and 18.09.

  • Added update_library_dataset() method to LibraryClient (thanks to Anthony Bretaudeau).

  • Added preserve_dirs and tag_using_filenames parameters to upload_file_from_server() and upload_from_galaxy_filesystem() methods of LibraryClient (thanks to Anthony Bretaudeau).

  • Removed deprecated wait_for_completion parameter of DatasetClient.download_dataset() method.

  • BioBlend.objects: added genome_build and misc_info attributes to Dataset objects. Moved deleted attribute from Dataset to HistoryDatasetAssociation and LibraryDatasetDatasetAssociation objects. Moved purged attribute from Dataset to HistoryDatasetAssociation objects.

  • BioBlend.objects: added update() method to LibraryDataset (thanks to Anthony Bretaudeau).

  • Run tests with pytest instead of nose.

- Python
Published by nsoranzo about 7 years ago

bioblend - v0.11.0

  • Dropped supported for Python 3.3. Added support for Galaxy release 18.01.

  • Always wait for terminal state when downloading a dataset.

  • Deprecated wait_for_completion parameter of DatasetClient.download_dataset() method.

  • Fixed downloading of datasets receiving a HTTP 500 status code (thanks to Eric Rasche).

  • Added wait_for_dataset() method to LibraryClient.

  • Added verify parameter to GalaxyInstance.__init__() method (thanks to Devon Ryan).

  • Improvements to tests and documentation.

- Python
Published by nsoranzo almost 8 years ago

bioblend - v0.10.0

  • Dropped support for Python 2.6. Added support for Galaxy release 17.09.

  • Added contents parameter to FoldersClient.show_folder() method (thanks to Eric Rasche).

  • Exposed the verify attribute of GalaxyInstance and ToolShedInstance objects as __init__() parameter.

  • Added create_role() method to RolesClient (thanks to Ashok Varadharajan).

  • Added timeout parameter to GalaxyClient.__init__() method.

  • Added publish parameter to import_workflow_dict() and import_workflow_from_local_path() methods of WorkflowClient (thanks to Marco Enrico Piras).

  • BioBlend.objects: added publish parameter to ObjWorkflowClient.import_new() method (thanks to Marco Enrico Piras).

  • Do not check for mismatching content size when streaming a dataset to file (reported by Jorrit Boekel).

  • Fixed delete requests when Galaxy uses external authentication (thanks to Eric Rasche).

  • Fixed retrieval of the API key when a GalaxyClient object is initialised with email and password on Python 3 (thanks to Marius van den Beek).

  • Documentation improvements.

- Python
Published by nsoranzo over 8 years ago

bioblend - v0.9.0

  • Dropped support for Galaxy releases 14.02, 14.04, 14.06 and 14.08. Added support for Python 3.5 and 3.6, and Galaxy releases 16.07, 16.10, 17.01 and 17.05.

  • Deprecated import_workflow_json() and export_workflow_json() methods of WorkflowClient in favor of import_workflow_dict() and export_workflow_dict() (reported by @manabuishii)

  • Deprecated show_stderr() and show_stdout() methods of DatasetClient in favour of JobsClient.show_job() with full_details=True.

  • Added install_dependencies() method to ToolClient (thanks to Marius van den Beek).

  • Added reload_data_table() method to ToolDataClient (thanks to Marius van den Beek).

  • Added create_folder(), update_folder(), get_permissions(), set_permissions() methods to FoldersClient (thanks to Eric Rasche).

  • Added get_version() method to ConfigClient (thanks to Eric Rasche).

  • Added get_user_apikey() method to UserClient (thanks to Eric Rasche).

  • Added create_quota(), update_quota(), delete_quota() and undelete_quota() methods to QuotaClient (thanks to Eric Rasche).

  • Added purge parameter to HistoryClient.delete_dataset() method.

  • Added f_email, f_name, and f_any parameters to UserClient.get_users() method (thanks to Eric Rasche).

  • Updated WorkflowClient.import_shared_workflow() method to use the newer Galaxy API request (thanks to @DamCorreia).

  • Fixed HistoryClient.update_history() and History.update() methods when name parameter is not specified

  • Added warning if content size differs from content-length header in DatasetClient.download_dataset()

  • BioBlend.objects: added purge parameter to HistoryDatasetAssociation.delete() method.

  • BioBlend.objects: added purged attribute to Dataset objects.

  • BioBlend.objects: added published attribute to History objects.

  • Code refactoring, added tests and documentation improvements.

- Python
Published by nsoranzo over 8 years ago

bioblend - release-0.8.0

  • Removed deprecated method create_user() of UserClient.
  • Deprecated HistoryClient.download_dataset() in favor of DatasetClient.download_dataset().
  • Modified update_dataset(), update_dataset_collection() and update_history() methods of HistoryClient to return the details instead of the status code.
  • Modified update_dataset(), update_dataset_collection() and update_history() methods of HistoryClient to return the details instead of the status code.
  • Modified GalaxyClient.make_put_request() to return the decoded response content.
  • Added install_resolver_dependencies parameter to ToolShedClient.install_repository_revision(), applicable for Galaxy release_16.07 and later (thanks to Marius van den Beek).
  • Improve DatasetClient.download_dataset() by downloading the dataset in chunks when saving to file (thanks to Jorrit Boekel).
  • Added bioblend.toolshed.categories.ToolShedCategoryClient; renamed bioblend.toolshed.repositories.ToolShedClient class to bioblend.toolshed.repositories.ToolShedRepositoryClient; renamed bioblend.toolshed.tools.ToolShedClient class to bioblend.toolshed.tools.ToolShedToolClient.
  • Added delete_user() method to UserClient.
  • BioBlend.objects: added update() method to HistoryDatasetAssociation.
  • BioBlend.objects: added annotation and genome_build attributes to HistoryDatasetAssociation objects.
  • BioBlend.objects: added update() method to HistoryDatasetAssociation.
  • BioBlend.objects: added ability to create and delete dataset collections (thanks to Alex MacLean).
  • BioBlend.objects: added dataset collections to the outputs of Workflow.run().
  • Added ability to launch Galaxy CloudMan instances into AWS VPC.
  • A number of testing tweaks, documentation improvements and minor fixes.

- Python
Published by afgane over 9 years ago