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).

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

* Added ``version`` and ``use_cached_job`` parameters to
``WorkflowClient.invoke_workflow()`` method (reported by
[Bérénice Batut](https://github.com/bebatut)).

* Changed the default values for the ``operation`` and ``default`` parameters of
the ``QuotaClient.update_quota()`` method (thanks to
[Matthias Bernt](https://github.com/bernt-matthias)).

* Improvements to tests and documentation (thanks to
[Matthias Bernt](https://github.com/bernt-matthias)).

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

* Added ``keys`` parameter to ``HistoryClient.show_history()`` (thanks to
[cat-bro](https://github.com/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](https://github.com/bernt-matthias)).

* 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.