Merge pull request #49 from flaxandteal/fix/31-return-tuple

Fix/31 return tuple

src/dewret/renderers/cwl.py

@@ -22,7 +22,7 @@
 from dataclasses import dataclass, is_dataclass, fields as dataclass_fields
 from collections.abc import Mapping
 from contextvars import ContextVar
-from typing import TypedDict, NotRequired, get_args, Union, cast, Any, Unpack
+from typing import TypedDict, NotRequired, get_args, Union, cast, Any, Iterable, Unpack
 from types import UnionType
 
 from dewret.workflow import (
@@ -38,7 +38,9 @@
 )
 from dewret.utils import RawType, flatten, DataclassProtocol
 
-InputSchemaType = Union[str, "CommandInputSchema", list[str], list["InputSchemaType"]]
+InputSchemaType = Union[
+    str, "CommandInputSchema", list[str], list["InputSchemaType"], dict[str, str]
+]
 
 
 @dataclass
@@ -174,7 +176,7 @@ def render(self) -> dict[str, RawType]:
         }
 
 
-def cwl_type_from_value(val: RawType | Unset) -> str | list[str]:
+def cwl_type_from_value(val: RawType | Unset) -> str | list[str] | dict[str, Any]:
     """Find a CWL type for a given (possibly Unset) value.
 
     Args:
@@ -191,7 +193,7 @@ def cwl_type_from_value(val: RawType | Unset) -> str | list[str]:
     return to_cwl_type(raw_type)
 
 
-def to_cwl_type(typ: type) -> str | list[str]:
+def to_cwl_type(typ: type) -> str | dict[str, Any] | list[str]:
     """Map Python types to CWL types.
 
     Args:
@@ -201,24 +203,37 @@ def to_cwl_type(typ: type) -> str | list[str]:
         CWL specification type name, or a list
         if a union.
     """
-    if isinstance(typ, UnionType):
-        return [to_cwl_type(item) for item in get_args(typ)]
-
     if typ == int:
         return "int"
     elif typ == bool:
         return "boolean"
     elif typ == dict or attrs_has(typ):
         return "record"
-    elif typ == list:
-        return "array"
     elif typ == float:
-        return "double"
+        return "float"
     elif typ == str:
         return "string"
+    elif typ == bytes:
+        return "bytes"
+    elif configuration("allow_complex_types"):
+        return typ if isinstance(typ, str) else typ.__name__
+    elif isinstance(typ, UnionType):
+        return [to_cwl_type(item) for item in get_args(typ)]
+    elif isinstance(typ, Iterable):
+        try:
+            basic_types = get_args(typ)
+            if len(basic_types) > 1:
+                return {
+                    "type": "array",
+                    "items": [{"type": to_cwl_type(t)} for t in basic_types],
+                }
+            else:
+                return {"type": "array", "items": to_cwl_type(basic_types[0])}
+        except IndexError as err:
+            raise TypeError(
+                f"Cannot render complex type ({typ}) to CWL, have you enabled allow_complex_types configuration?"
+            ) from err
     else:
-        if configuration("allow_complex_types"):
-            return typ if isinstance(typ, str) else typ.__name__
         raise TypeError(f"Cannot render complex type ({typ}) to CWL")
 
 

src/dewret/workflow.py

@@ -8,7 +8,7 @@
 #
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# with WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
@@ -465,7 +465,7 @@ def assimilate(cls, left: Workflow, right: Workflow) -> "Workflow":
         new.tasks.update(right.tasks)
 
         for step in new.steps:
-            step.__workflow__ = new
+            step.set_workflow(new, with_arguments=True)
 
         # TODO: should we combine as a result array?
         result = left.result or right.result
@@ -742,22 +742,25 @@ def __eq__(self, other: object) -> bool:
             and self.arguments == other.arguments
         )
 
-    def set_workflow(self, workflow: Workflow) -> None:
-        """Move the step reference to another workflow.
+    def set_workflow(self, workflow: Workflow, with_arguments: bool = True) -> None:
+        """Move the step reference to a different workflow.
 
-        Primarily intended to be called by its step, as a cascade.
-        It will attempt to update its arguments, similarly.
+        This method is primarily intended to be called by a step, allowing it to
+        switch to a new workflow. It also updates the workflow reference for any
+        arguments that are steps themselves, if specified.
 
         Args:
-            workflow: the new target workflow.
+            workflow: The new target workflow to which the step should be moved.
+            with_arguments: If True, also update the workflow reference for the step's arguments.
         """
         self.__workflow__ = workflow
-        for argument in self.arguments.values():
-            if hasattr(argument, "__workflow__"):
-                try:
-                    argument.__workflow__ = workflow
-                except AttributeError:
-                    ...
+        if with_arguments:
+            for argument in self.arguments.values():
+                if hasattr(argument, "__workflow__"):
+                    try:
+                        argument.__workflow__ = workflow
+                    except AttributeError:
+                        ...
 
     @property
     def return_type(self) -> Any:
@@ -1011,6 +1014,7 @@ class StepReference(Generic[U], Reference):
     """
 
     step: BaseStep
+    _tethered_workflow: Workflow | None
     _field: str | None
     typ: type[U]
 
@@ -1039,6 +1043,7 @@ def __init__(
         self.step = step
         self._field = field
         self.typ = typ
+        self._tethered_workflow = None
 
     def __str__(self) -> str:
         """Global description of the reference."""
@@ -1048,7 +1053,7 @@ def __repr__(self) -> str:
         """Hashable reference to the step (and field)."""
         return f"{self.step.id}/{self.field}"
 
-    def __getattr__(self, attr: str) -> "StepReference"[Any]:
+    def __getattr__(self, attr: str) -> "StepReference[Any]":
         """Reference to a field within this result, if possible.
 
         If the result is an attrs-class or dataclass, this will pull out an individual
@@ -1119,7 +1124,24 @@ def __workflow__(self) -> Workflow:
         Returns:
             Workflow that the referee is related to.
         """
-        return self.step.__workflow__
+        return self._tethered_workflow or self.step.__workflow__
+
+    @__workflow__.setter
+    def __workflow__(self, workflow: Workflow) -> None:
+        """Sets related workflow.
+
+        We update the tethered workflow. If the step is missing from
+        this workflow then, by construction, it should have at least
+        been through an indexing process once, so we should be able
+        to get it back by name.
+
+        Args:
+            workflow: workflow to update the step
+        """
+        self._tethered_workflow = workflow
+        if self._tethered_workflow:
+            if self.step not in self._tethered_workflow.steps:
+                self.step = self._tethered_workflow._indexed_steps[self.step.id]
 
     @__workflow__.setter
     def __workflow__(self, workflow: Workflow) -> None:

tests/_lib/extra.py

@@ -23,7 +23,7 @@ def double(num: int | float) -> int | float:
 
 @task()
 def mod10(num: int) -> int:
-    """Double an integer."""
+    """Remainder of an integer divided by 10."""
     return num % 10
 
 
@@ -37,3 +37,9 @@ def sum(left: int | float, right: int | float) -> int | float:
 def triple_and_one(num: int | float) -> int | float:
     """Triple a number by doubling and adding again, then add 1."""
     return sum(left=sum(left=double(num=num), right=num), right=1)
+
+
+@task()
+def tuple_float_return() -> tuple[float, float]:
+    """Return a tuple of floats."""
+    return 48.856667, 2.351667

tests/test_cwl.py

@@ -7,7 +7,14 @@
 from dewret.utils import hasher
 from dewret.workflow import param
 
-from ._lib.extra import increment, double, mod10, sum, triple_and_one
+from ._lib.extra import (
+    increment,
+    double,
+    mod10,
+    sum,
+    triple_and_one,
+    tuple_float_return,
+)
 
 
 @task()
@@ -54,7 +61,7 @@ def test_basic_cwl() -> None:
           out:
             label: out
             outputSource: pi-{hsh}/out
-            type: double
+            type: float
         steps:
           pi-{hsh}:
             run: pi
@@ -272,7 +279,7 @@ def test_cwl_with_subworkflow() -> None:
             outputSource: sum-1-2/out
             type:
             - int
-            - double
+            - float
         steps:
           double-1-1:
             in:
@@ -328,7 +335,9 @@ def test_cwl_references() -> None:
           out:
             label: out
             outputSource: double-{hsh_double}/out
-            type: [int, double]
+            type: 
+            - int
+            - float
         steps:
           increment-{hsh_increment}:
             run: increment
@@ -370,7 +379,9 @@ def test_complex_cwl_references() -> None:
           out:
             label: out
             outputSource: sum-1/out
-            type: [int, double]
+            type: 
+            - int
+            - float
         steps:
           increment-1:
             run: increment
@@ -471,7 +482,7 @@ def test_cwl_with_subworkflow_and_raw_params() -> None:
             label: num
             type: [
               int,
-              double
+              float
             ]
           sum-1-2-right:
             default: 1
@@ -483,7 +494,7 @@ def test_cwl_with_subworkflow_and_raw_params() -> None:
             outputSource: sum-1-2/out
             type:
             - int
-            - double
+            - float
         steps:
           double-1-1:
             in:
@@ -511,3 +522,33 @@ def test_cwl_with_subworkflow_and_raw_params() -> None:
             - out
             run: sum
     """)
+
+
+def test_tuple_floats() -> None:
+    """Checks whether we can return a tuple.
+
+    Produces CWL that has a tuple of 2 values of type float.
+    """
+    result = tuple_float_return()
+    workflow = construct(result, simplify_ids=True)
+    rendered = render(workflow)
+    print(yaml.dump(rendered))
+    assert rendered == yaml.safe_load("""
+        cwlVersion: 1.2
+        class: Workflow
+        inputs: {}
+        outputs:
+          out:
+            label: out
+            outputSource: tuple_float_return-1/out
+            type: 
+              items: 
+                - type: float
+                - type: float
+              type: array
+        steps:
+          tuple_float_return-1:
+            run: tuple_float_return
+            in: {}
+            out: [out]
+    """)

tests/test_modularity.py

@@ -31,7 +31,7 @@ def test_nested_task() -> None:
         inputs:
           JUMP:
             label: JUMP
-            type: double
+            type: float
             default: 1.0
           increase-3-num:
             default: 23
@@ -45,7 +45,7 @@ def test_nested_task() -> None:
           out:
             label: out
             outputSource: sum-1/out
-            type: [int, double]
+            type: [int, float]
         steps:
           increase-1:
             run: increase