Release 0.16.0

Also: docs fixes.

CHANGELOG.md

@@ -1,10 +1,18 @@
-### BioBlend v - unreleased
+### BioBlend v0.16.0 - 2021-06-13
 
 * 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``
+  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
@@ -16,24 +24,73 @@
   can be used to summarize requirements across toolbox (thanks to
   [cat-bro](https://github.com/cat-bro)).
 
-* Added ``publish_dataset()`` and ``update_permissions()`` methods to
-  ``DatasetClient``.
+* 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()`` methods to ``InvocationClient`` (thanks
-  to [rikeshi](https://github.com/rikeshi)).
+  ``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 tests and documentation (thanks to
+* Improvements to type annotations, tests and documentation (thanks to
   [rikeshi](https://github.com/rikeshi)).
 
 ### BioBlend v0.15.0 - 2021-02-10

bioblend/__init__.py

@@ -7,7 +7,7 @@
 )
 
 # Current version of the library
-__version__ = '0.15.0'
+__version__ = '0.16.0'
 
 # default chunk size (in bytes) for reading remote data
 try:

bioblend/galaxy/dataset_collections/__init__.py

@@ -86,15 +86,6 @@ def __init__(self, name, id):
         ))
 
 
-__all__ = (
-    "CollectionDescription",
-    "CollectionElement",
-    "HistoryDatasetElement",
-    "HistoryDatasetCollectionElement",
-    "LibraryDatasetElement",
-)
-
-
 class DatasetCollectionClient(Client):
     module = 'dataset_collections'
 
@@ -217,3 +208,13 @@ def wait_for_dataset_collection(self, dataset_collection_id: str, maxwait: float
 
 class DatasetCollectionTimeoutException(TimeoutException):
     pass
+
+
+__all__ = (
+    "CollectionDescription",
+    "CollectionElement",
+    "DatasetCollectionClient",
+    "HistoryDatasetElement",
+    "HistoryDatasetCollectionElement",
+    "LibraryDatasetElement",
+)

bioblend/galaxy/datasets/__init__.py

@@ -310,6 +310,7 @@ def publish_dataset(self, dataset_id: str, published: bool = False):
 
         :rtype: dict
         :return: Current roles for all available permission types.
+
         .. note::
           This method can only be used with Galaxy ``release_19.05`` or later.
         """
@@ -338,6 +339,7 @@ def update_permissions(self, dataset_id: str, access_ids: Optional[list] = None,
 
         :rtype: dict
         :return: Current roles for all available permission types.
+
         .. note::
           This method can only be used with Galaxy ``release_19.05`` or later.
         """

bioblend/galaxy/invocations/__init__.py

@@ -321,22 +321,19 @@ def get_invocation_step_jobs_summary(self, invocation_id):
         :rtype: list of dicts
         :return: The invocation step jobs summary.
           For example::
-            [
-                {'populated_state': 'ok',
-                 'states': {'ok': 1},
-                 'model': 'Job',
-                 'id': 'e85a3be143d5905b'},
-
-                {'populated_state': 'ok',
-                 'states': {'running': 1},
-                 'model': 'Job',
-                 'id': 'c9468fdb6dc5c5f1'}
-
-                {'populated_state': 'ok',
-                 'states': {'new': 1},
-                 'model': 'Job',
-                 'id': '2a56795cad3c7db3'}
-            ]
+
+            [{'id': 'e85a3be143d5905b',
+              'model': 'Job',
+              'populated_state': 'ok',
+              'states': {'ok': 1}},
+             {'id': 'c9468fdb6dc5c5f1',
+              'model': 'Job',
+              'populated_state': 'ok',
+              'states': {'running': 1}},
+             {'id': '2a56795cad3c7db3',
+              'model': 'Job',
+              'populated_state': 'ok',
+              'states': {'new': 1}}]
         """
         url = self._make_url(invocation_id) + '/step_jobs_summary'
         return self._get(url=url)

bioblend/galaxy/jobs/__init__.py

@@ -193,6 +193,7 @@ def rerun_job(self, job_id, remap=False, tool_inputs_update=None, history_id=Non
 
         :rtype: dict
         :return: Information about outputs and the rerun job
+
         .. note::
           This method can only be used with Galaxy ``release_21.01`` or later.
         """

bioblend/galaxy/objects/wrappers.py

@@ -172,7 +172,7 @@ def __init__(self, step_dict, parent):
 
 class InvocationStep(Wrapper):
     """
-    Abstract base class for invocation steps.
+    Invocation step.
     """
     BASE_ATTRS = Wrapper.BASE_ATTRS + (
         'action',

bioblend/galaxy/tool_dependencies/__init__.py

@@ -32,12 +32,12 @@ def summarize_toolbox(self, index=None, tool_ids=None, resolver_type=None, inclu
 
         :type index_by: str
         :param index_by: By default results are grouped by requirements.  Set to 'tools'
-            to return one entry per tool.
+          to return one entry per tool.
 
         :rtype: list of dicts
         :returns: dictified descriptions of the dependencies, with attribute
-            `dependency_type: None` if no match was found.
-            For example::
+          `dependency_type: None` if no match was found.
+          For example::
 
             [{'requirements': [{'name': 'galaxy_sequence_utils',
                                 'specs': [],
@@ -60,6 +60,7 @@ def summarize_toolbox(self, index=None, tool_ids=None, resolver_type=None, inclu
                           'name': 'bx-python',
                           'version': '0.8.6'}],
               'tool_ids': ['vcf_to_maf_customtrack1']}]
+
         .. note::
           This method can only be used with Galaxy ``release_20.01`` or later and requires
             the user to be an admin. It relies on an experimental API particularly tied to

docs/api_docs/galaxy/all.rst

@@ -27,6 +27,13 @@ Datasets
 
 -----
 
+Dataset collections
+-------------------
+
+.. automodule:: bioblend.galaxy.dataset_collections
+
+-----
+
 Datatypes
 ---------
 
@@ -123,6 +130,13 @@ Tool data tables
 
 -----
 
+Tool dependencies
+-----------------
+
+.. automodule:: bioblend.galaxy.tool_dependencies
+
+-----
+
 ToolShed
 --------