Release 1.1.0

Also:
- 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.

Author: nsoranzo

CHANGELOG.md

@@ -1,11 +1,28 @@
-### BioBlend v
+### BioBlend v1.1.0 - 2023-02-21
 
 * 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.
 
-* Improvements to tests
+* Add ``py.typed`` marker file to distributed packages (as per PEP 561) to
+  declare type checking support.
+
+* Improvements to tests and documentation.
 
 ### BioBlend v1.0.0 - 2022-10-13
 

bioblend/__init__.py

@@ -13,7 +13,7 @@
 )
 
 # Current version of the library
-__version__ = "1.0.0"
+__version__ = "1.0.1"
 
 # default chunk size (in bytes) for reading remote data
 try:

bioblend/galaxy/libraries/__init__.py

@@ -3,7 +3,6 @@
 """
 import logging
 import time
-import warnings
 from typing import (
     Any,
     Dict,
@@ -280,33 +279,24 @@ def get_folders(
         :type library_id: str
         :param library_id: library id to use
 
-        :type folder_id: str
-        :param folder_id: filter for folder by folder id
-
-          .. deprecated:: 0.16.0
-             To get details of a folder for which you know the ID, use the much
-             more efficient :meth:`show_folder` instead.
-
         :type name: str
         :param name: Folder name to filter on. For ``name`` specify the full
                      path of the folder starting from the library's root
                      folder, e.g. ``/subfolder/subsubfolder``.
 
         :rtype: list
         :return: list of dicts each containing basic information about a folder
+
+        .. versionchanged:: 1.1.0
+           Using the deprecated ``folder_id`` parameter now raises a
+           ``ValueError`` exception.
         """
         if folder_id is not None:
-            warnings.warn(
-                "The folder_id parameter is deprecated, use the show_folder() method to view details of a folder for which you know the ID.",
-                category=FutureWarning,
+            raise ValueError(
+                "The folder_id parameter has been removed, use the show_folder() method to view details of a folder for which you know the ID."
             )
-        if folder_id is not None and name is not None:
-            raise ValueError("Provide only one argument between name or folder_id, but not both")
         library_contents = self.show_library(library_id=library_id, contents=True)
-        if folder_id is not None:
-            folder = next((_ for _ in library_contents if _["type"] == "folder" and _["id"] == folder_id), None)
-            folders = [folder] if folder is not None else []
-        elif name is not None:
+        if name is not None:
             folders = [_ for _ in library_contents if _["type"] == "folder" and _["name"] == name]
         else:
             folders = [_ for _ in library_contents if _["type"] == "folder"]
@@ -319,13 +309,6 @@ def get_libraries(
         Get all libraries, or select a subset by specifying optional arguments
         for filtering (e.g. a library name).
 
-        :type library_id: str
-        :param library_id: filter for library by library id
-
-          .. deprecated:: 0.16.0
-             To get details of a library for which you know the ID, use the much
-             more efficient :meth:`show_library` instead.
-
         :type name: str
         :param name: Library name to filter on.
 
@@ -336,18 +319,16 @@ def get_libraries(
 
         :rtype: list
         :return: list of dicts each containing basic information about a library
+
+        .. versionchanged:: 1.1.0
+           Using the deprecated ``library_id`` parameter now raises a
+           ``ValueError`` exception.
         """
         if library_id is not None:
-            warnings.warn(
-                "The library_id parameter is deprecated, use the show_library() method to view details of a library for which you know the ID.",
-                category=FutureWarning,
+            raise ValueError(
+                "The library_id parameter has been removed, use the show_library() method to view details of a library for which you know the ID."
             )
-        if library_id is not None and name is not None:
-            raise ValueError("Provide only one argument between name or library_id, but not both")
         libraries = self._get(params={"deleted": deleted})
-        if library_id is not None:
-            library = next((_ for _ in libraries if _["id"] == library_id), None)
-            libraries = [library] if library is not None else []
         if name is not None:
             libraries = [_ for _ in libraries if _["name"] == name]
         return libraries

bioblend/galaxy/tools/__init__.py

@@ -1,7 +1,6 @@
 """
 Contains possible interaction dealing with Galaxy tools.
 """
-import warnings
 from os.path import basename
 from typing import (
     Any,
@@ -37,13 +36,6 @@ def get_tools(
         Get all tools, or select a subset by specifying optional arguments for
         filtering (e.g. a tool name).
 
-        :type tool_id: str
-        :param tool_id: id of the requested tool
-
-          .. deprecated:: 0.16.0
-             To get details of a tool for which you know the ID, use the much
-             more efficient :meth:`show_tool` instead.
-
         :type name: str
         :param name: Tool name to filter on.
 
@@ -55,19 +47,17 @@ def get_tools(
         :return: List of tool descriptions.
 
         .. seealso:: bioblend.galaxy.toolshed.get_repositories()
+
+        .. versionchanged:: 1.1.0
+           Using the deprecated ``tool_id`` parameter now raises a
+           ``ValueError`` exception.
         """
         if tool_id is not None:
-            warnings.warn(
-                "The tool_id parameter is deprecated, use the show_tool() method to view details of a tool for which you know the ID.",
-                category=FutureWarning,
+            raise ValueError(
+                "The tool_id parameter has been removed, use the show_tool() method to view details of a tool for which you know the ID."
             )
-        if tool_id is not None and name is not None:
-            raise ValueError("Provide only one argument between name or tool_id, but not both")
         tools = self._raw_get_tool(in_panel=False, trackster=trackster)
-        if tool_id is not None:
-            tool = next((_ for _ in tools if _["id"] == tool_id), None)
-            tools = [tool] if tool is not None else []
-        elif name is not None:
+        if name is not None:
             tools = [_ for _ in tools if _["name"] == name]
         return tools
 

bioblend/galaxy/workflows/__init__.py

@@ -3,7 +3,6 @@
 """
 import json
 import os
-import warnings
 from typing import (
     Any,
     Dict,
@@ -36,13 +35,6 @@ def get_workflows(
         Get all workflows, or select a subset by specifying optional arguments
         for filtering (e.g. a workflow name).
 
-        :type workflow_id: str
-        :param workflow_id: Encoded workflow ID
-
-          .. deprecated:: 0.16.0
-             To get details of a workflow for which you know the ID, use the
-             much more efficient :meth:`show_workflow` instead.
-
         :type name: str
         :param name: Workflow name to filter on.
 
@@ -57,22 +49,19 @@ def get_workflows(
                      'name': 'Simple',
                      'url': '/api/workflows/92c56938c2f9b315'}]
 
+        .. versionchanged:: 1.1.0
+           Using the deprecated ``workflow_id`` parameter now raises a
+           ``ValueError`` exception.
         """
         if workflow_id is not None:
-            warnings.warn(
-                "The workflow_id parameter is deprecated, use the show_workflow() method to view details of a workflow for which you know the ID.",
-                category=FutureWarning,
+            raise ValueError(
+                "The workflow_id parameter has been removed, use the show_workflow() method to view details of a workflow for which you know the ID."
             )
-        if workflow_id is not None and name is not None:
-            raise ValueError("Provide only one argument between name or workflow_id, but not both")
         params: Dict[str, Any] = {}
         if published:
             params["show_published"] = True
         workflows = self._get(params=params)
-        if workflow_id is not None:
-            workflow = next((_ for _ in workflows if _["id"] == workflow_id), None)
-            workflows = [workflow] if workflow is not None else []
-        elif name is not None:
+        if name is not None:
             workflows = [_ for _ in workflows if _["name"] == name]
         return workflows