Bioblend

[Marius van den Beek](https://github.com/mvdbeek)).

* 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.

(see `.travis.yml` for details).

* Many documentation improvements (thanks to
[Helena Rasche](https://github.com/erasche)).

* Added Galaxy clients for the tool data tables, the roles, and library
folders (thanks to [Anthony Bretaudeau](https://github.com/abretaud)).

* Added method to get the standard error and standard output for the
job corresponding to a Galaxy dataset (thanks to
[Anthony Bretaudeau](https://github.com/abretaud)).

* Added ``get_state()`` method to ``JobsClient``.

* Added ``copy_from_dataset()`` method to ``LibraryClient``.

* Added ``create_repository()`` method to ``ToolShedRepositoryClient`` (thanks
to [Helena Rasche](https://github.com/erasche)).

* Fixed ``DatasetClient.download_dataset()`` for certain proxied Galaxy
deployments.

* Made ``LibraryClient._get_root_folder_id()`` method safer and faster for
Galaxy release 13.06 and later.

* Deprecate and ignore invalid ``deleted`` parameter to
``WorkflowClient.get_workflows()``.

* CloudMan: added method to fetch instance types.

* CloudMan: updated cluster options to reflect change to SLURM.

* BioBlend.objects: deprecate and ignore invalid ``deleted`` parameter
to ``ObjWorkflowClient.list()``.

* BioBlend.objects: added ``paste_content()`` method to ``History`` objects.

* BioBlend.objects: added ``copy_from_dataset()`` method and ``root_folder``
property to ``Library`` objects.

* BioBlend.objects: added ``container`` and ``deleted`` attributes to ``Folder``
objects.

* BioBlend.objects: the ``parent`` property of a ``Folder`` object is now set to
its parent folder object (thanks to John M. Eppley).

* BioBlend.objects: added ``deleted`` parameter to ``list()`` method
of libraries and histories.

* BioBlend.objects: added ``state`` and ``state_details`` attributes to
``History`` objects (thanks to [Gianmauro Cuccuru](https://github.com/gmauro)).

* BioBlend.objects: renamed ``upload_dataset()`` method to ``upload_file()``
for ``History`` objects.

* BioBlend.objects: renamed ``input_ids`` and ``output_ids`` attributes of
``Workflow`` objects to ``source_ids`` and ``sink_ids`` respectively.

* Add ``run_bioblend_tests.sh`` script (useful for Continuous Integration
testing).

* 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](https://github.com/cat-bro) and
[Matthias Bernt](https://github.com/bernt-matthias)).

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

* Added ``delete_unused_dependency_paths()`` and ``unused_dependency_paths()``
methods to ``ToolDependenciesClient`` (thanks to
[Matthias Bernt](https://github.com/bernt-matthias)).

* Added ``data_manager_mode`` parameter to ``ToolClient.run_tool()`` method
(thanks to [Marius van den Beek](https://github.com/mvdbeek)).

* Added ``user_data`` parameter to ``UserClient.update_user()`` method
(thanks to [Uwe Winter](https://github.com/uwwint)).

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

* Improvements to tests and documentation (thanks to
[kxk302](https://github.com/kxk302) and
[Simon Bray](https://github.com/simonbray)).

* 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.

* Added ``py.typed`` marker file to distributed packages (as per PEP 561) to
declare type checking support.

* Improvements to tests and documentation.

* 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.