Bioblend

* 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](https://github.com/Paprikant)).

* Added ``require_exact_tool_versions`` parameter to
``WorkflowClient.invoke_workflow()`` method (thanks to
[cat-bro](https://github.com/cat-bro)).

* Added ``name`` and ``owner`` parameters to
``ToolShedRepositoryClient.get_repositories()``.

* Remove 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](https://github.com/innovate-invent)).

* 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](https://github.com/cat-bro),
[Fabio Cumbo](https://github.com/cumbof),
[Jayadev Joshi](https://github.com/jaidevjoshi83),
[thepineapplepirate](https://github.com/thepineapplepirate)).

* Improvements to tests and documentation.

* Added support for Galaxy release 22.05.

* Added tus support to ``ToolClient.upload_file()`` (thanks to
[Nate Coraor](https://github.com/natefoo)).

* Formatted Python code with black and isort.

* Improvements to type annotations, tests and documentation.

* 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](https://github.com/cat-bro)).

* Added ``get_extra_files()`` method to ``HistoryClient``.

* Added ``build()`` and ``reload()`` methods to ``ToolClient`` (thanks to
[Jayadev Joshi](https://github.com/jaidevjoshi83) and
[cat-bro](https://github.com/cat-bro) respectively).

* Added ``get_repositories()`` method to ``ToolShedCategoryClient`` (thanks to
[cat-bro](https://github.com/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](https://github.com/galaxyproject/bioblend/issues/398) when
instantiating ``GalaxyInstance`` with ``email`` and ``password`` (reported by
[Peter Briggs](https://github.com/pjbriggs)).

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

* Code cleanups (thanks to [Martmists](https://github.com/Martmists-GH)).

* Improvements to type annotations, tests and documentation.

* 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](https://github.com/rikeshi)).

* Pass the API key for all requests as the ``x-api-key`` header instead of as a
parameter (thanks to [rikeshi](https://github.com/rikeshi)).

* Try prepending "https://" and "http://" if the scheme is missing in the
``url`` argument passed to ``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](https://github.com/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](https://github.com/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](https://github.com/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](https://github.com/Mcgregor381) and
[rikeshi](https://github.com/rikeshi)).

* Added ``get_citations()`` and ``uninstall_dependencies()`` methods to
``ToolClient`` (thanks to [rikeshi](https://github.com/rikeshi)).

* Added ``extract_workflow_from_history()``, ``refactor_workflow()`` and
``show_versions()`` methods to ``WorkflowClient`` (thanks to
[rikeshi](https://github.com/rikeshi)).

* Added several parameters to ``DatasetClient.get_datasets()`` method (thanks to
[rikeshi](https://github.com/rikeshi)).

* Added several parameters to ``InvocationClient.get_invocations()`` method
(thanks to [Nolan Woods](https://github.com/innovate-invent) and
[rikeshi](https://github.com/rikeshi)).

* Added several parameters to ``JobsClient.get_jobs()`` method (thanks to
[rikeshi](https://github.com/rikeshi)).

* Added ``parameters_normalized`` parameter to
``WorkflowClient.invoke_workflow()`` method (thanks to
[rikeshi](https://github.com/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](https://github.com/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](https://github.com/innovate-invent)).

* BioBlend.objects: Deprecated ``run()`` method of ``Workflow``.

* Added ``use_ssl``, ``verify`` and ``authuser`` parameters to
``CloudManInstance.__init__()`` (thanks to
[Nathan Edwards](https://github.com/edwardsnj)).

* Improvements to type annotations, tests and documentation (thanks to
[rikeshi](https://github.com/rikeshi)).

* 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](https://github.com/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 ``Workflow`` 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](https://github.com/OlegZharkov)).

* Improvements to tests and documentation (thanks to
[Gianmauro Cuccuru](https://github.com/gmauro)).

* 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](https://github.com/simonbray)).

* Added ``get_datasets()`` method to ``DatasetClient`` (thanks to
[Simon Bray](https://github.com/simonbray)).

* Added ``import_history()`` method to ``HistoryClient`` (thanks to
[David Christiany](https://github.com/davidchristiany) and
[Marius van den Beek](https://github.com/mvdbeek)).

* Added ``copy_dataset()`` method to ``HistoryClient`` (thanks to
[Simon Bray](https://github.com/simonbray)).

* Added ``get_metrics()`` method to ``JobsClient`` (thanks to
[Andreas Skorczyk](https://github.com/AndreasSko)).

* Added ``report_error()`` method to ``JobsClient`` (thanks to
[Peter Selten](https://github.com/selten)).

* Added ``get_dataset_permissions()`` and ``set_dataset_permissions()`` methods
to ``LibraryClient`` (thanks to
[Frederic Sapet](https://github.com/FredericBGA)).

* Added ``update_user()`` method to ``UserClient`` (thanks to
[Anthony Bretaudeau](https://github.com/abretaud)).

* 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](https://github.com/abretaud)).

* 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](https://github.com/abretaud)).

* 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](https://github.com/mvdbeek)).

* 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](https://github.com/innovate-invent)).

* Fixed ``HistoryClient.export_history(..., wait=False, maxwait=None)``
(reported by [David Christiany](https://github.com/davidchristiany)).

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