Add setup_code parameter to extract_variables

This parameter allows the caller to pass an additional code block
which is run before the parameter-defining block.

This is a first step towards implementing improved parameter
extraction (Issue 9), but will require some work in ScriptCreator
to become useful.

Author: pont-us

examples/dynamic.ipynb

@@ -212,7 +212,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.5"
+   "version": "3.12.8"
   }
  },
  "nbformat": 4,

test/test_core.py

@@ -47,13 +47,13 @@ def test_image_builder_init(init_mock, tmp_path, tag):
     init_mock.assert_called_once_with(nb_path)
 
 
-def test_init_runner_invalid_image_type():
+def test_runner_init_invalid_image_type():
     with pytest.raises(ValueError, match='Invalid type "int"'):
         # noinspection PyTypeChecker
         xcengine.core.ContainerRunner(666, pathlib.Path("/foo"))
 
 
-def test_init_runner_with_string():
+def test_runner_init_with_string():
     image_name = "foo"
     image_mock = Mock(docker.models.images.Image)
     client_mock = Mock(docker.client.DockerClient)
@@ -69,7 +69,7 @@ def get_mock(name):
     assert image_mock == runner.image
 
 
-def test_init_runner_with_image():
+def test_runner_init_with_image():
     runner = xcengine.core.ContainerRunner(
         image := Mock(docker.models.images.Image), pathlib.Path("/foo")
     )

test/test_parameters.py

@@ -156,6 +156,25 @@ def test_parameters_from_code(expected_vars):
     )
 
 
+def test_parameters_from_code_with_setup(expected_vars):
+    assert (
+        xcengine.parameters.NotebookParameters.from_code(
+            """
+some_int = 2 * half_of_some_int
+some_float = 3.14159
+some_string = some_uppercase_string.lower()
+some_bool = not not_some_bool
+    """,
+            setup_code="""
+half_of_some_int = 21
+some_uppercase_string = "FOO"
+not_some_bool = True
+            """
+        ).params
+        == expected_vars
+    )
+
+
 def test_parameters_get_workflow_inputs(notebook_parameters):
     assert notebook_parameters.get_cwl_workflow_inputs() == {
         "some_int": {

xcengine/parameters.py

@@ -35,12 +35,12 @@ def make_cwl_params(self):
             self.cwl_params["product"] = "Directory", None
 
     @classmethod
-    def from_code(cls, code: str) -> "NotebookParameters":
+    def from_code(cls, code: str, setup_code: str | None = None) -> "NotebookParameters":
         # TODO run whole notebook up to params cell, not just the params cell!
         # (Because it might use imports etc. from earlier in the notebook.)
         # This will need some tweaking of the parameter extraction -- see
         # comment therein.
-        return cls(cls.extract_variables(code))
+        return cls(cls.extract_variables(code, setup_code))
 
     @classmethod
     def from_yaml(cls, yaml_content: str | typing.IO) -> "NotebookParameters":
@@ -61,12 +61,17 @@ def from_yaml_file(cls, path: str | os.PathLike) -> "NotebookParameters":
             return cls.from_yaml(fh)
 
     @classmethod
-    def extract_variables(cls, code: str) -> dict[str, tuple[type, Any]]:
-        # TODO: just working on a single code block is insufficient:
-        # We should execute everything up to the params cell, but only extract
-        # variables defined in the params cell.
-        exec(code, globals(), locals_ := {})
-        return {k: cls.make_param_tuple(locals_[k]) for k in (locals_.keys())}
+    def extract_variables(cls, code: str, setup_code: str | None = None) -> dict[str, tuple[type, Any]]:
+        pass
+        if setup_code is None:
+            locals_ = {}
+            old_locals = {}
+        else:
+            exec(setup_code, globals(), locals_ := {})
+            old_locals = locals_.copy()
+        exec(code, globals(), locals_)
+        new_vars = locals_.keys() - old_locals.keys()
+        return {k: cls.make_param_tuple(locals_[k]) for k in new_vars}
 
     @staticmethod
     def make_param_tuple(value: Any) -> tuple[type, Any]: