Remove parameters deprecated in v0.5.3 .

bioblend/galaxy/histories/__init__.py

@@ -361,15 +361,11 @@ def create_dataset_collection(self, history_id, collection_description):
         return Client._post(self, payload, id=history_id, contents=True)
 
     def download_dataset(self, history_id, dataset_id, file_path,
-                         use_default_filename=True, to_ext=None):
+                         use_default_filename=True):
         """
         Download a ``dataset_id`` from history with ``history_id`` to a
         file on the local file system, saving it to ``file_path``.
 
-        :type to_ext: str
-        :param to_ext: this parameter is deprecated and ignored, it will be
-          removed in BioBlend 0.6
-
         Refer to ``bioblend.galaxy.dataset.DatasetClient.download_dataset()``
         for the other available parameters.
         """

bioblend/galaxy/objects/client.py

@@ -285,15 +285,12 @@ def get_previews(self, name=None, published=False):
         return [wrappers.WorkflowPreview(_, gi=self.obj_gi) for _ in dicts]
 
     # the 'deleted' option is not available for workflows
-    def list(self, name=None, deleted=False, published=False):
+    def list(self, name=None, published=False):
         """
         Get workflows owned by the user of this Galaxy instance.
 
         :type name: str
         :param name: return only workflows with this name
-        :type deleted: bool
-        :param deleted: this parameter is deprecated and ignored, it will be
-          removed in BioBlend 0.6
         :type published: bool
         :param published: if ``True``, return also published workflows
 

bioblend/galaxy/workflows/__init__.py

@@ -11,7 +11,8 @@ def __init__(self, galaxy_instance):
         self.module = 'workflows'
         super(WorkflowClient, self).__init__(galaxy_instance)
 
-    def get_workflows(self, workflow_id=None, name=None, deleted=False, published=False):
+    # the 'deleted' option is not available for workflows
+    def get_workflows(self, workflow_id=None, name=None, published=False):
         """
         Get all workflows or filter the specific one(s) via the provided ``name``
         or ``workflow_id``. Provide only one argument, ``name`` or ``workflow_id``,
@@ -25,10 +26,6 @@ def get_workflows(self, workflow_id=None, name=None, deleted=False, published=Fa
           ``workflow_id``). If multiple names match the given name, all the
           workflows matching the argument will be returned.
 
-        :type deleted: bool
-        :param deleted: this parameter is deprecated and ignored, it will be
-          removed in BioBlend 0.6
-
         :type published: bool
         :param published: if ``True``, return also published workflows