tech debt cleanup (PolusAI#325)

Co-authored-by: Vasu Jaganath <[email protected]>

Author: vjaganat90

src/sophios/api/pythonapi.py

@@ -15,7 +15,7 @@
 from sophios import run_local as run_local_module
 from sophios.cli import get_args
 from sophios.utils_graphs import get_graph_reps
-from sophios.wic_types import CompilerInfo, RoseTree, StepId, Tool, Tools, YamlTree, Json, Cwl, NodeData
+from sophios.wic_types import CompilerInfo, RoseTree, StepId, Tool, Tools, YamlTree, Json
 
 from ._types import ScatterMethod
 

src/sophios/api/utils/ict/ict_spec/metadata/objects.py

@@ -88,13 +88,13 @@ def __eq__(self, other: Any) -> bool:  # type: ignore
         raise TypeError(msg)
 
 
-@DOI.__eq__.register(str)  # type: ignore  # pylint: disable=no-member
-def _(self, other):
+@DOI.__eq__.register(str)  # type: ignore # pylint: disable=no-member
+def _(self: Author, other: str) -> Any:
     return self.root == other
 
 
-@DOI.__eq__.register(DOI)  # type: ignore  # pylint: disable=no-member
-def _(self, other):
+@DOI.__eq__.register(DOI)  # type: ignore # pylint: disable=no-member
+def _(self: Author, other: DOI) -> Any:
     return self.root == other.root
 
 

src/sophios/cli.py

@@ -132,8 +132,8 @@ def get_args(yaml_path: str = '', suppliedargs: list[str] = []) -> argparse.Name
     Returns:
         argparse.Namespace: The mocked command line arguments
     """
-    defaultargs = ['wic', '--yaml', yaml_path]  # ignore --yaml
+    defaultargs = ['sophios', '--yaml', yaml_path]  # ignore --yaml
     testargs = defaultargs + suppliedargs
     with patch.object(sys, 'argv', testargs):
-        args: argparse.Namespace = parser.parse_args()
+        args = parser.parse_args()
     return args

src/sophios/schemas/wic_schema.py

@@ -639,8 +639,8 @@ def compile_workflow_generate_schema(homedir: str,
     graphdata = GraphData(str(yml_path))
     graph = GraphReps(graph_gv, graph_nx, graphdata)
     args = get_args(str(yml_path), ['--allow_raw_cwl'] if allow_raw_cwl else [])
-    compiler_info = sophios.compiler.compile_workflow(yaml_tree, args, [], [graph], {}, {}, {}, {},
-                                                      tools_cwl, True, relative_run_path=True, testing=True)
+    compiler_info = compiler.compile_workflow(yaml_tree, args, [], [graph], {}, {}, {}, {},
+                                              tools_cwl, True, relative_run_path=True, testing=True)
     rose_tree = compiler_info.rose
     sub_node_data: NodeData = rose_tree.data