Implement workflow_id configuration option

This commit implements the first in-notebook configuration option:
adding

xcengine_config = dict(
  workflow_id = "foo"
)

will now set the specified string as the ID of the Workflow object
within a generated CWL file.

Author: pont-us

test/data/paramtest.ipynb

@@ -151,7 +151,8 @@
    "outputs": [],
    "source": [
     "parameter_1 = my_constant * 2\n",
-    "parameter_2 = \"default value\""
+    "parameter_2 = \"default value\"\n",
+    "xcengine_config = dict(workflow_id=\"my-workflow\")"
    ]
   }
  ],
@@ -171,7 +172,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.13.3"
   }
  },
  "nbformat": 4,

test/test_core.py

@@ -165,11 +165,10 @@ def test_script_creator_convert_notebook_to_script(tmp_path, clear):
     # TODO test execution as well?
 
 
-def test_script_creator_cwl(tmp_path):
-    nb_path = pathlib.Path(__file__).parent / "data" / "noparamtest.ipynb"
-    script_creator = ScriptCreator(
-        nb_path
-    )
+@pytest.mark.parametrize("nb_name", ["noparamtest", "paramtest"])
+def test_script_creator_cwl(tmp_path, nb_name):
+    nb_path = pathlib.Path(__file__).parent / "data" / f"{nb_name}.ipynb"
+    script_creator = ScriptCreator(nb_path)
     image_tag = "foo"
     cwl_path = tmp_path / "test.cwl"
     cwl = script_creator.create_cwl(image_tag)
@@ -188,10 +187,14 @@ def test_script_creator_cwl(tmp_path):
     cli_tools = [n for n in graph if n["class"] == "CommandLineTool"]
     assert len(cli_tools) == 1
     cli_tool = cli_tools[0]
-    assert cli_tool["requirements"]["DockerRequirement"]["dockerPull"] == image_tag
+    assert (
+        cli_tool["requirements"]["DockerRequirement"]["dockerPull"]
+        == image_tag
+    )
     assert cli_tool["hints"]["DockerRequirement"]["dockerPull"] == image_tag
     workflows = [n for n in graph if n["class"] == "Workflow"]
     assert len(workflows) == 1
     workflow = workflows[0]
-    assert workflow["id"] == nb_path.stem
-
+    assert workflow["id"] == (
+        nb_path.stem if nb_name == "noparamtest" else "my-workflow"
+    )

test/test_parameters.py

@@ -143,12 +143,14 @@ def test_parameters_get_cwl_step_inputs(notebook_parameters):
 
 
 def test_parameters_from_code(expected_vars):
-    parameters = xcengine.parameters.NotebookParameters.from_code("""
+    parameters = xcengine.parameters.NotebookParameters.from_code(
+        """
 some_int = 42
 some_float = 3.14159
 some_string = "foo"
 some_bool = False
-    """)
+    """
+    )
     assert parameters.params == expected_vars
     assert parameters.config == {}
 

xcengine/cli.py

@@ -150,11 +150,18 @@ def build(
             )
             image = image_builder.build()
     if eoap:
+
         class IndentDumper(yaml.Dumper):
             def increase_indent(self, flow=False, indentless=False):
                 return super(IndentDumper, self).increase_indent(flow, False)
 
-        eoap.write_text(yaml.dump(image_builder.create_cwl(), sort_keys=False, Dumper=IndentDumper))
+        eoap.write_text(
+            yaml.dump(
+                image_builder.create_cwl(),
+                sort_keys=False,
+                Dumper=IndentDumper,
+            )
+        )
     print(f"Built image with tags {image.tags}")
 
 

xcengine/core.py

@@ -123,7 +123,9 @@ def create_cwl(self, image_tag: str) -> dict[str, Any]:
             "$graph": [
                 {
                     "class": "Workflow",
-                    "id": self.nb_path.stem,
+                    "id": self.nb_params.config.get(
+                        "workflow_id", self.nb_path.stem
+                    ),
                     "label": "xcengine notebook",
                     "doc": "xcengine notebook",
                     "requirements": [],
@@ -149,9 +151,7 @@ def create_cwl(self, image_tag: str) -> dict[str, Any]:
                     "requirements": {
                         "DockerRequirement": {"dockerPull": image_tag}
                     },
-                    "hints": {
-                        "DockerRequirement": {"dockerPull": image_tag}
-                    },
+                    "hints": {"DockerRequirement": {"dockerPull": image_tag}},
                     "baseCommand": [
                         "/usr/local/bin/_entrypoint.sh",
                         "python",

xcengine/parameters.py

@@ -22,9 +22,9 @@ class NotebookParameters:
     config: dict[str, Any]
 
     def __init__(
-            self,
-            params: dict[str, tuple[type, Any]],
-            config: dict[str, Any] = None
+        self,
+        params: dict[str, tuple[type, Any]],
+        config: dict[str, Any] = None,
     ):
         self.params = params
         self.config = {} if config is None else config
@@ -86,7 +86,11 @@ def extract_variables(
     def make_param_tuple(cls, key: str, value: Any) -> tuple[type, Any]:
         return (
             t := type(value),
-            value if t in {int, float, str, bool} or key == cls.config_var_name else None,
+            (
+                value
+                if t in {int, float, str, bool} or key == cls.config_var_name
+                else None
+            ),
         )
 
     def get_cwl_workflow_inputs(self) -> dict[str, dict[str, Any]]: