Merge pull request #101 from ArcanaFramework/relative-copy-check

Update to match refactor of Pydra API

Author: tclose

.github/workflows/ci-cd.yml

@@ -47,7 +47,7 @@ jobs:
     - name: Install Extras Package
       run: python3 -m pip install -e ./extras[test]
     - name: Install development Pydra
-      run: pip install --no-deps git+https://github.com/nipype/pydra.git@new-syntax
+      run: pip install --no-deps git+https://github.com/nipype/pydra.git@develop
     - name: MyPy
       run: mypy --install-types --non-interactive --no-warn-unused-ignores .
     - name: Pytest

extras/fileformats/extras/application/archive.py

@@ -5,7 +5,7 @@
 import tarfile
 import zipfile
 from pathlib import Path
-from pydra.design import python
+from pydra.compose import python
 from fileformats.generic import FsObject
 from fileformats.core.utils import set_cwd
 from fileformats.core.typing import PathType

extras/fileformats/extras/application/serialization.py

@@ -2,7 +2,7 @@
 import typing as ty
 import tempfile
 import yaml
-from pydra.design import python
+from pydra.compose import python
 from fileformats.core import FileSet, converter, extra_implementation
 from fileformats.application import TextSerialization, Json, Yaml
 from fileformats.application.serialization import SerializationType

extras/fileformats/extras/generic/converters.py

@@ -1,7 +1,7 @@
 import tempfile
 from pathlib import Path
 import typing as ty
-from pydra.design import python
+from pydra.compose import python
 from fileformats.core import converter, FileSet
 from fileformats.generic import DirectoryOf, SetOf, TypedDirectory, TypedSet
 

extras/fileformats/extras/image/converters.py

@@ -1,7 +1,7 @@
 from pathlib import Path
 import typing as ty
 import tempfile
-from pydra.design import python
+from pydra.compose import python
 from fileformats.core import converter
 from fileformats.image.raster import RasterImage, Bitmap, Gif, Jpeg, Png, Tiff
 

fileformats/core/converter_helpers.py

@@ -6,7 +6,7 @@
 from .datatype import DataType
 
 if ty.TYPE_CHECKING:
-    from pydra.engine.specs import TaskDef
+    from pydra.compose.base import Task
     import fileformats.core
     from . import mixin
 
@@ -120,17 +120,17 @@ def register_converter(
             prev_def = cls.converters[prev_registered[0]]
             # task, task_kwargs, _ = converter_spec
             # prev_task, prev_kwargs = prev_tuple
-            if converter.task_def == prev_def.task_def:
+            if converter.task == prev_def.task:
                 logger.warning(
                     "Ignoring duplicate registrations of the same converter %s",
-                    converter.task_def,
+                    converter.task,
                 )
                 return  # actually the same task but just imported twice for some reason
-            generic_type = tuple(prev_def.task_def.wildcard_classifiers())[0]  # type: ignore
+            generic_type = tuple(prev_def.task.wildcard_classifiers())[0]  # type: ignore
             raise FormatDefinitionError(
                 f"Cannot register converter from {source_format} to the generic type "
-                f"'{generic_type}', {converter.task_def} "
-                f"because there is already one registered, {prev_def.task_def}"
+                f"'{generic_type}', {converter.task} "
+                f"because there is already one registered, {prev_def.task}"
             )
 
         cls.converters[source_format] = converter  # type: ignore
@@ -140,19 +140,19 @@ class Converter:
     """Specification of a converter task, including the task callable, its arguments and
     the classifiers"""
 
-    task_def: "TaskDef[ty.Any]"
+    task: "Task[ty.Any]"
     classifiers: ty.Tuple[ty.Type[Classifier], ...]
     in_file: str
     out_file: str
 
     def __init__(
         self,
-        task_def: "TaskDef[T]",
+        task: "Task[T]",
         classifiers: ty.Tuple[ty.Type[Classifier], ...] = (),
         in_file: str = "in_file",
         out_file: str = "out_file",
     ):
-        self.task_def = task_def
+        self.task = task
         self.classifiers = classifiers
         self.in_file = in_file
         self.out_file = out_file
@@ -162,7 +162,7 @@ def __eq__(self, other: object) -> bool:
 
         return (
             isinstance(other, Converter)
-            and self.task_def == other.task_def
+            and self.task == other.task
             and hash_function(self.classifiers) == hash_function(other.classifiers)
             and self.in_file == other.in_file
             and self.out_file == other.out_file

fileformats/core/extras.py

@@ -18,7 +18,7 @@
     from typing import Self
 
 if ty.TYPE_CHECKING:
-    from pydra.engine.specs import TaskDef
+    from pydra.compose.base import Task
 
 T = ty.TypeVar("T")
 ExtraImplementation = ty.TypeVar("ExtraImplementation", bound=ty.Callable[..., ty.Any])
@@ -190,21 +190,21 @@ def type_match(mtype: ty.Union[str, type], ftype: ty.Union[str, type]) -> bool:
 
 
 def converter(
-    task_type: ty.Optional[ty.Type["TaskDef[T]"]] = None,
+    task_type: ty.Optional[ty.Type["Task[T]"]] = None,
     source_format: FormatType = None,
     target_format: FormatType = None,
     in_file: str = "in_file",
     out_file: str = "out_file",
     **converter_kwargs: ty.Any,
 ) -> ty.Union[
-    ty.Type["TaskDef[T]"], ty.Callable[[ty.Type["TaskDef[T]"]], ty.Type["TaskDef[T]"]]
+    ty.Type["Task[T]"], ty.Callable[[ty.Type["Task[T]"]], ty.Type["Task[T]"]]
 ]:
     """Decorator that registers a task as a converter between a source and target format
     pair
 
     Parameters
     ----------
-    task_type : pydra.engine.core.TaskBase, optional
+    task_type : pydra.compose.base.Task, optional
         the Pydra task to register as a converter, if provided the decorator is assumed
         to wrap the task spec directly, otherwise a wrapping decorator is returned instead
     source_format: type, optional
@@ -235,8 +235,8 @@ def converter(
         converter_kwargs["in_file"] = converter_kwargs.pop("in_file_")
 
     def decorator(
-        task_type: ty.Type["TaskDef[T]"],
-    ) -> ty.Type["TaskDef[T]"]:
+        task_type: ty.Type["Task[T]"],
+    ) -> ty.Type["Task[T]"]:
         out_file_local = out_file
         source: FormatType
         target: FormatType

fileformats/core/fileset.py

@@ -525,8 +525,8 @@ def convert(
             assert isinstance(fileset, cls)
             return copy(fileset)
         kwargs[converter.in_file] = fileset
-        task_def = attrs.evolve(converter.task_def, **kwargs)
-        outputs = task_def()
+        task = attrs.evolve(converter.task, **kwargs)
+        outputs = task()
         out_file = getattr(outputs, converter.out_file)
         if not isinstance(out_file, cls):
             out_file = cls(out_file)
@@ -584,9 +584,7 @@ def get_converter(
                     available_converters = [available_converters[0]]
                 else:
                     available_converters[0] == available_converters[1]
-                    available_str = "\n".join(
-                        str(a.task_def) for a in available_converters
-                    )
+                    available_str = "\n".join(str(a.task) for a in available_converters)
                     raise FormatConversionError(
                         f"Ambiguous converters found between '{cls.mime_like}' and "
                         f"'{source_format.mime_like}':\n{available_str}"
@@ -684,18 +682,18 @@ def register_converter(
             prev_converter = cls.converters[source_format]
             # task, task_kwargs = converter_spec
             # prev_task, prev_kwargs = prev_tuple
-            if converter.task_def == prev_converter.task_def:
+            if converter.task == prev_converter.task:
                 logger.warning(
                     "Ignoring duplicate registrations of the same converter %s",
-                    converter.task_def,
+                    converter.task,
                 )
                 return  # actually the same task but just imported twice for some reason
             raise FormatConversionError(
                 f"Cannot register converter from {source_format.__name__} "
-                f"to {cls.__name__}, {converter.task_def}, because there is already "
-                f"one registered from {prev_converter.task_def}:"
-                f"\n\n{converter.task_def}\n\n"
-                f"and {prev_converter.task_def}\n\n"
+                f"to {cls.__name__}, {converter.task}, because there is already "
+                f"one registered from {prev_converter.task}:"
+                f"\n\n{converter.task}\n\n"
+                f"and {prev_converter.task}\n\n"
             )
         converters_dict[source_format] = converter
 

fileformats/core/mixin.py

@@ -661,15 +661,15 @@ def register_converter(
                     if converter == prev_converter:
                         logger.warning(
                             "Ignoring duplicate registrations of the same converter %s",
-                            converter.task_def,
+                            converter.task,
                         )
                         return  # actually the same task but just imported twice for some reason
                     prev_unclassified = prev.unclassified
                     unclassified = cls.unclassified  # type: ignore[attr-defined]
                     raise FormatDefinitionError(
                         f"Cannot register converter from {prev_unclassified} "
                         f"to {unclassified} with non-wildcard classifiers "
-                        f"{list(prev.non_wildcard_classifiers())}, {converter.task_def}, "
+                        f"{list(prev.non_wildcard_classifiers())}, {converter.task}, "
                         f"because there is already one registered, {prev_converter.task}"
                     )
             converters_dict = cls.unclassified.get_converters_dict()  # type: ignore[attr-defined]

fileformats/core/tests/test_classifiers.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 import decimal
 import pytest
-from pydra.design import python
+from pydra.compose import python
 from fileformats.core import from_mime, DataType, FileSet
 from fileformats.core import converter
 from fileformats.application import Zip