remove args from inference.py,removing args 2/n

Author: Vasu Jaganath

src/sophios/compiler.py

@@ -209,6 +209,11 @@ def compile_workflow_once(yaml_tree_ast: YamlTree,
 
     tools_lst: List[Tool] = []
 
+    graph_settings = {}
+    graph_settings['graph_dark_theme'] = args.graph_dark_theme
+    graph_settings['graph_inline_depth'] = args.graph_inline_depth
+    graph_settings['graph_label_edges'] = args.graph_label_edges
+
     for i, step_key in enumerate(steps_keys):
         step_name_i = utils.step_name_str(yaml_stem, i, step_key)
         stem = Path(step_key).stem
@@ -315,7 +320,8 @@ def compile_workflow_once(yaml_tree_ast: YamlTree,
                 # Use auto-discovery mechanism (with run tag)
                 tool_i = tools[stepid_runtag]
             else:
-                msg = f"Error! Neither {stepid.stem} nor {stepid_runtag.stem} found!, check your 'search_paths_cwl' in global_config.json"
+                msg = f"Error! Neither {stepid.stem} nor {
+                    stepid_runtag.stem} found!, check your 'search_paths_cwl' in global_config.json"
                 raise Exception(msg)
             # Programmatically modify tool_i here
             graph_dummy = graph  # Just use anything here to satisfy mypy
@@ -604,7 +610,7 @@ def compile_workflow_once(yaml_tree_ast: YamlTree,
                         else:
                             nss_call = namespaces + [step_name_or_key] + nss_call_embedded
 
-                        utils_graphs.add_graph_edge(args, graph_init, nss_def, nss_call, label, color='blue')
+                        utils_graphs.add_graph_edge(graph_settings, graph_init, nss_def, nss_call, label, color='blue')
             elif isinstance(arg_val, Dict) and 'wic_inline_input' in arg_val:
                 arg_val = arg_val['wic_inline_input']
 
@@ -747,7 +753,8 @@ def compile_workflow_once(yaml_tree_ast: YamlTree,
                 insertions: List[StepId] = []
                 in_name_in_inputs_file_workflow: bool = (in_name in inputs_file_workflow)
                 arg_key_in_yaml_tree_inputs: bool = (arg_key in yaml_tree.get('inputs', {}))
-                steps[i] = inference.perform_edge_inference(args, tools, tools_lst, steps_keys,
+                inference_use_naming_conventions = args.inference_use_naming_conventions
+                steps[i] = inference.perform_edge_inference(inference_use_naming_conventions, graph_settings, tools, tools_lst, steps_keys,
                                                             yaml_stem, i, steps, arg_key, graph, is_root, namespaces,
                                                             vars_workflow_output_internal, input_mapping_copy, output_mapping_copy, inputs_workflow, in_name,
                                                             in_name_in_inputs_file_workflow, arg_key_in_yaml_tree_inputs, insertions, wic_steps, testing)

src/sophios/inference.py

@@ -1,4 +1,3 @@
-import argparse
 from pathlib import Path
 from typing import Any, Dict, List, Tuple
 
@@ -31,7 +30,8 @@ def types_match(in_type: Any, out_type: Any) -> bool:
     return False
 
 
-def perform_edge_inference(args: argparse.Namespace,
+def perform_edge_inference(inference_use_naming_conventions: bool,
+                           graph_settings: Dict[str, Any],
                            tools: Tools,
                            tools_lst: List[Tool],
                            steps_keys: List[str],
@@ -56,7 +56,8 @@ def perform_edge_inference(args: argparse.Namespace,
     NOTE: steps[i], vars_workflow_output_internal, inputs_workflow are mutably updated.
 
     Args:
-        args (argparse.Namespace): The command line arguments
+        inference_use_naming_conventions (bool): If to do inference using naming conventions
+        graph_settings(Dict[str,Any]) : The settings needed for graphviz graph generation
         tools (Tools): The CWL CommandLineTool definitions found using get_tools_cwl()
         tools_lst (List[Tool]): A list of the CWL CommandLineTools or compiled subworkflows for the current workflow.
         steps_keys (List[str]): The name of each step in the current CWL workflow
@@ -183,7 +184,7 @@ def perform_edge_inference(args: argparse.Namespace,
             # By default, simply choose the first (i.e. most-recent) matching format
             out_key = format_matches[0][0]
 
-            if args.inference_use_naming_conventions:  # default False
+            if inference_use_naming_conventions:  # default False
                 if len(format_matches) == 1:
                     # Great! We found a unique format match.
                     out_key = format_matches[0][0]
@@ -276,7 +277,7 @@ def perform_edge_inference(args: argparse.Namespace,
                 # TODO: check this
                 out_key_no_namespace = out_key.split('___')[-1]
                 label = out_key_no_namespace if tool_j.cwl['class'] == 'Workflow' else out_key
-                utils_graphs.add_graph_edge(args, graph, nss1, nss2, label)
+                utils_graphs.add_graph_edge(graph_settings, graph, nss1, nss2, label)
 
             return steps_i  # Short circuit
 

src/sophios/utils_graphs.py

@@ -1,14 +1,14 @@
 import argparse
 from pathlib import Path
-from typing import List
+from typing import List, Dict, Any
 
 import graphviz
 import networkx as nx
 
 from .wic_types import (GraphData, GraphReps, Json, Namespaces, Tool, Tools)
 
 
-def add_graph_edge(args: argparse.Namespace, graph: GraphReps,
+def add_graph_edge(graph_settings: Dict[str, Any], graph: GraphReps,
                    nss1: Namespaces, nss2: Namespaces,
                    label: str, color: str = '') -> None:
     """Adds edges to (all of) our graph representations, with the ability to
@@ -28,10 +28,10 @@ def add_graph_edge(args: argparse.Namespace, graph: GraphReps,
         color (str, optional): The edge color
     """
     if color == '':
-        color = 'black' if args.graph_dark_theme else 'white'
-    nss1 = nss1[:(1 + args.graph_inline_depth)]
+        color = 'black' if graph_settings['graph_dark_theme'] else 'white'
+    nss1 = nss1[:(1 + graph_settings['graph_inline_depth'])]
     edge_node1 = '___'.join(nss1)
-    nss2 = nss2[:(1 + args.graph_inline_depth)]
+    nss2 = nss2[:(1 + graph_settings['graph_inline_depth'])]
     edge_node2 = '___'.join(nss2)
     graph_gv = graph.graphviz
     graph_nx = graph.networkx
@@ -40,7 +40,7 @@ def add_graph_edge(args: argparse.Namespace, graph: GraphReps,
     # Hide internal self-edges
     if edge_node1 != edge_node2:
         attrs = {'color': color}
-        if args.graph_label_edges:
+        if graph_settings['graph_label_edges']:
             attrs['label'] = label
 
         graph_gv.edge(edge_node1, edge_node2, **attrs)