Add flag to only compile workflow to cwl without running (#272)

* Add flag to only compile workflow to cwl without running

* Switch --generate_cwl_workflow to group_run

* Add test for --generate_cwl_workflow

* Update generate cwl test to use helloworld from tutorials

---------

Co-authored-by: Sameeul Bashir Samee <sameeul@gmail.com>

src/sophios/cli.py

@@ -88,7 +88,6 @@
                        help='After generating the cwl file(s), run it on your local machine.')
 group_run.add_argument('--generate_cwl_workflow', required=False, default=False, action="store_true",
                        help='Compile the workflow without pulling the docker image')
-
 parser.add_argument('--cwl_inline_subworkflows', default=False, action="store_true",
                     help='Before generating the cwl file, inline all subworkflows.')
 parser.add_argument('--inference_disable', default=False, action="store_true",

tests/data/cwl/helloworld.cwl

@@ -0,0 +1,24 @@
+#!/usr/bin/env cwl-runner
+# This file was autogenerated using the Workflow Inference Compiler, version 0+unknown
+# https://github.com/PolusAI/workflow-inference-compiler
+steps:
+- id: helloworld__step__1__echo
+  in:
+    message:
+      source: helloworld__step__1__echo___message
+  run: helloworld__step__1__echo/echo.cwl
+  out:
+  - stdout
+cwlVersion: v1.2
+class: Workflow
+$namespaces:
+  edam: https://edamontology.org/
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl
+inputs:
+  helloworld__step__1__echo___message:
+    type: string
+outputs:
+  helloworld__step__1__echo___stdout:
+    type: File
+    outputSource: helloworld__step__1__echo/stdout

tests/test_cli_flags.py

@@ -0,0 +1,35 @@
+import pathlib
+import subprocess
+import yaml
+import shutil
+
+from sophios.main import main
+from sophios.cli import get_args
+
+
+def test_generate_cwl_workflow() -> None:
+    """
+    Test that running sophios with --generate_cwl_workflow produces the correct cwl file
+    """
+    # remove output directory in case it exists to avoid false test pass
+    out_path = pathlib.Path('autogenerated')
+
+    if out_path.exists() and out_path.is_dir():
+        shutil.rmtree(out_path)
+
+    yaml_path = str(pathlib.Path(__file__).parent.parent.resolve() / "docs/tutorials/helloworld.wic")
+
+    args = ["sophios", "--yaml", yaml_path, "--generate_cwl_workflow"]
+
+    # run sophios with args
+    subprocess.run(args)
+
+    with open("autogenerated/helloworld.cwl", "r") 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:
+        actual_dict = yaml.safe_load(cwl_file)
+
+    assert result_dict == actual_dict