fix for --generate_cwl_workflow and corresponding test

Author: Vasu Jaganath

src/sophios/main.py

@@ -205,6 +205,11 @@ def main() -> None:
         # we need to copy the output files manually. See comment above.
         if args.cwl_runner == 'cwltool' and args.copy_output_files:
             run_local.copy_output_files(yaml_stem)
+    elif args.generate_cwl_workflow:
+        io.write_to_disk(rose_tree, Path('autogenerated/'), True, args.inputs_file)
+    else:
+        print('Please specify either --generate_cwl_workflow (compile) or --run_local (run)')
+        sys.exit(1)
 
 
 if __name__ == '__main__':

tests/test_cli_flags.py

@@ -1,10 +1,7 @@
 import pathlib
 import subprocess
-import yaml
 import shutil
-
-from sophios.main import main
-from sophios.cli import get_args
+import yaml
 
 
 def test_generate_cwl_workflow() -> None:
@@ -19,17 +16,16 @@ def test_generate_cwl_workflow() -> None:
 
     yaml_path = str(pathlib.Path(__file__).parent.parent.resolve() / "docs/tutorials/helloworld.wic")
 
-    args = ["sophios", "--yaml", yaml_path, "--generate_cwl_workflow"]
+    cmd = ["sophios", "--yaml", yaml_path, "--generate_cwl_workflow"]
 
     # run sophios with args
-    subprocess.run(args)
+    subprocess.run(cmd, check=False)
 
-    with open("autogenerated/helloworld.cwl", "r") as cwl_file:
+    with open("autogenerated/helloworld.cwl", "r", encoding='utf-8') as cwl_file:
         result_dict = yaml.safe_load(cwl_file)
 
-    with open(
-        str(pathlib.Path(__file__).parent.resolve() / "data/cwl/helloworld.cwl"), "r"
-    ) as cwl_file:
+    with open(str(pathlib.Path(__file__).parent.resolve() / "data/cwl/helloworld.cwl"), "r",
+              encoding='utf-8') as cwl_file:
         actual_dict = yaml.safe_load(cwl_file)
 
     assert result_dict == actual_dict