fixed up all import errors

Author: tclose

.gitignore

@@ -22,5 +22,4 @@ cov.xml
 .ipynb_checkpoints
 
 # This can be generated in-tree. We never want to commit it.
-pydra/_version.py
-pydra/engine/_version.py
+pydra/utils/_version.py

docs/source/tutorial/2-advanced-execution.ipynb

@@ -371,8 +371,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pydra.engine.core import Job\n",
-    "from pydra.engine.specs import TaskHooks, Result\n",
+    "from pydra.engine.job import Job\n",
+    "from pydra.engine.hooks import TaskHooks\n",
+    "from pydra.engine.result import Result\n",
     "import os\n",
     "import platform\n",
     "\n",

docs/source/tutorial/5-shell.ipynb

@@ -355,13 +355,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pydra.engine.specs import ShellTask, ShellOutputs\n",
     "from pydra.utils.typing import MultiInputObj\n",
     "from fileformats.generic import FsObject, Directory\n",
     "\n",
     "\n",
     "@shell.define\n",
-    "class Cp(ShellTask[\"Cp.Outputs\"]):\n",
+    "class Cp(shell.Task[\"Cp.Outputs\"]):\n",
     "\n",
     "    executable = \"cp\"\n",
     "\n",
@@ -371,8 +370,7 @@
     "    int_arg: int | None = shell.arg(argstr=\"--int-arg\", default=None)\n",
     "    tuple_arg: tuple[int, str] | None = shell.arg(argstr=\"--tuple-arg\", default=None)\n",
     "\n",
-    "    @shell.outputs\n",
-    "    class Outputs(ShellOutputs):\n",
+    "    class Outputs(shell.Outputs):\n",
     "        out_dir: Directory = shell.outarg(path_template=\"{out_dir}\")"
    ]
   },

docs/source/tutorial/7-canonical-form.ipynb

@@ -34,8 +34,8 @@
     "Default values can also be set directly, as with Attrs classes.\n",
     "\n",
     "In order to allow static type-checkers to check the type of outputs of tasks added\n",
-    "to workflows, it is also necessary to explicitly extend from the `pydra.engine.specs.PythonTask`\n",
-    "and `pydra.engine.specs.PythonOutputs` classes (they are otherwise set as bases by the\n",
+    "to workflows, it is also necessary to explicitly extend from the `pydra.engine.python.Task`\n",
+    "and `pydra.engine.python.Outputs` classes (they are otherwise set as bases by the\n",
     "`define` method implicitly). Thus the \"canonical form\" of Python task is as\n",
     "follows"
    ]
@@ -47,13 +47,12 @@
    "outputs": [],
    "source": [
     "from pprint import pprint\n",
-    "from pydra.engine.helpers import fields_dict\n",
-    "from pydra.engine.specs import PythonTask, PythonOutputs\n",
+    "from pydra.utils import fields_dict\n",
     "from pydra.compose import python\n",
     "\n",
     "\n",
     "@python.define\n",
-    "class CanonicalPythonTask(PythonTask[\"CanonicalPythonTask.Outputs\"]):\n",
+    "class CanonicalPythonTask(python.Task[\"CanonicalPythonTask.Outputs\"]):\n",
     "    \"\"\"Canonical Python task class for testing\n",
     "\n",
     "    Args:\n",
@@ -65,7 +64,7 @@
     "    a: int\n",
     "    b: float = 2.0  # set default value\n",
     "\n",
-    "    class Outputs(PythonOutputs):\n",
+    "    class Outputs(python.Outputs):\n",
     "        \"\"\"\n",
     "        Args:\n",
     "            c: Sum of a and b\n",
@@ -102,7 +101,7 @@
     "\n",
     "\n",
     "@python.define\n",
-    "class CanonicalPythonTask(PythonTask[\"CanonicalPythonTask.Outputs\"]):\n",
+    "class CanonicalPythonTask(python.Task[\"CanonicalPythonTask.Outputs\"]):\n",
     "    \"\"\"Canonical Python task class for testing\n",
     "\n",
     "    Args:\n",
@@ -114,7 +113,7 @@
     "    a: int = python.arg(allowed_values=[1, 2, 3, 4, 5])\n",
     "    b: float = python.arg(default=2.0, validator=attrs.validators.not_(0))\n",
     "\n",
-    "    class Outputs(PythonOutputs):\n",
+    "    class Outputs(python.Outputs):\n",
     "        \"\"\"\n",
     "        Args:\n",
     "            c: Sum of a and b\n",
@@ -153,12 +152,11 @@
     "from pathlib import Path\n",
     "from fileformats import generic\n",
     "from pydra.compose import shell\n",
-    "from pydra.engine.specs import ShellTask, ShellOutputs\n",
     "from pydra.utils.typing import MultiInputObj\n",
     "\n",
     "\n",
     "@shell.define\n",
-    "class CpWithSize(ShellTask[\"CpWithSize.Outputs\"]):\n",
+    "class CpWithSize(shell.Task[\"CpWithSize.Outputs\"]):\n",
     "\n",
     "    executable = \"cp\"\n",
     "\n",
@@ -168,7 +166,7 @@
     "    int_arg: int | None = shell.arg(argstr=\"--int-arg\")\n",
     "    tuple_arg: tuple[int, str] | None = shell.arg(argstr=\"--tuple-arg\")\n",
     "\n",
-    "    class Outputs(ShellOutputs):\n",
+    "    class Outputs(shell.Outputs):\n",
     "\n",
     "        @staticmethod\n",
     "        def get_file_size(out_file: Path) -> int:\n",
@@ -201,7 +199,6 @@
    "outputs": [],
    "source": [
     "from pydra.compose import python, workflow\n",
-    "from pydra.engine.specs import WorkflowTask, WorkflowOutputs\n",
     "\n",
     "\n",
     "# Example python tasks\n",
@@ -216,7 +213,7 @@
     "\n",
     "\n",
     "@workflow.define\n",
-    "class CanonicalWorkflowTask(WorkflowTask[\"CanonicalWorkflowTask.Outputs\"]):\n",
+    "class CanonicalWorkflowTask(workflow.Task[\"CanonicalWorkflowTask.Outputs\"]):\n",
     "\n",
     "    @staticmethod\n",
     "    def a_converter(value):\n",
@@ -236,7 +233,7 @@
     "        mul = workflow.add(Mul(a=add.out, b=b))\n",
     "        return mul.out\n",
     "\n",
-    "    class Outputs(WorkflowOutputs):\n",
+    "    class Outputs(workflow.Outputs):\n",
     "        out: float"
    ]
   }

pydra/_version.py

@@ -0,0 +1 @@
+__version__ = "1.0.0"

pydra/compose/base/builder.py

@@ -12,13 +12,13 @@
     from_list_if_single,
     ensure_list,
     PYDRA_ATTR_METADATA,
-    is_lazy,
 )
 from pydra.utils.typing import (
     MultiInputObj,
     MultiInputFile,
     MultiOutputObj,
     MultiOutputFile,
+    is_lazy,
 )
 from .field import Field, Arg, Out
 

pydra/compose/base/task.py

@@ -5,13 +5,8 @@
 from typing import Self
 import attrs.validators
 from pydra.utils.typing import is_optional, is_fileset_or_union
-from pydra.utils.general import (
-    list_fields,
-    is_lazy,
-)
-from pydra.utils.typing import (
-    StateArray,
-)
+from pydra.utils.general import list_fields
+from pydra.utils.typing import StateArray, is_lazy
 from pydra.utils.hash import hash_function
 import os
 import itertools
@@ -183,7 +178,7 @@ def __call__(
         audit_flags: AuditFlag = AuditFlag.NONE,
         messengers: ty.Iterable[Messenger] | None = None,
         messenger_args: dict[str, ty.Any] | None = None,
-        hooks: TaskHooks | None = None,
+        hooks: "TaskHooks | None" = None,
         **kwargs: ty.Any,
     ) -> OutputsType:
         """Create a job from this task and execute it to produce a result.

pydra/compose/python.py

@@ -16,7 +16,7 @@
 if ty.TYPE_CHECKING:
     from pydra.engine.job import Job
 
-__all__ = ["arg", "out", "define", "PythonTask", "PythonOutputs"]
+__all__ = ["arg", "out", "define", "Task", "Outputs"]
 
 
 @attrs.define
@@ -103,7 +103,7 @@ def define(
     outputs_bases: ty.Sequence[type] = (),
     auto_attribs: bool = True,
     xor: ty.Sequence[str | None] | ty.Sequence[ty.Sequence[str | None]] = (),
-) -> "PythonTask":
+) -> "Task":
     """
     Create an interface for a function or a class.
 
@@ -124,20 +124,19 @@ def define(
 
     Returns
     -------
-    PythonTask
+    Task
         The task class for the Python function
     """
-    from pydra.engine.specs import PythonTask, PythonOutputs
 
-    def make(wrapped: ty.Callable | type) -> PythonTask:
+    def make(wrapped: ty.Callable | type) -> Task:
         if inspect.isclass(wrapped):
             klass = wrapped
             function = klass.function
             name = klass.__name__
             check_explicit_fields_are_none(klass, inputs, outputs)
             parsed_inputs, parsed_outputs = extract_fields_from_class(
-                PythonTask,
-                PythonOutputs,
+                Task,
+                Outputs,
                 klass,
                 arg,
                 out,
@@ -176,8 +175,8 @@ def make(wrapped: ty.Callable | type) -> PythonTask:
         )
 
         defn = build_task_class(
-            PythonTask,
-            PythonOutputs,
+            Task,
+            Outputs,
             parsed_inputs,
             parsed_outputs,
             name=name,
@@ -197,16 +196,16 @@ def make(wrapped: ty.Callable | type) -> PythonTask:
 
 
 @attrs.define(kw_only=True, auto_attribs=False, eq=False, repr=False)
-class PythonOutputs(base.Outputs):
+class Outputs(base.Outputs):
 
     @classmethod
-    def _from_task(cls, job: "Job[PythonTask]") -> ty.Self:
+    def _from_task(cls, job: "Job[Task]") -> ty.Self:
         """Collect the outputs of a job from a combination of the provided inputs,
         the objects in the output directory, and the stdout and stderr of the process.
 
         Parameters
         ----------
-        job : Job[PythonTask]
+        job : Job[Task]
             The job whose outputs are being collected.
         outputs_dict : dict[str, ty.Any]
             The outputs of the job, as a dictionary
@@ -222,15 +221,15 @@ def _from_task(cls, job: "Job[PythonTask]") -> ty.Self:
         return outputs
 
 
-PythonOutputsType = ty.TypeVar("OutputType", bound=PythonOutputs)
+PythonOutputsType = ty.TypeVar("OutputType", bound=Outputs)
 
 
 @attrs.define(kw_only=True, auto_attribs=False, eq=False, repr=False)
-class PythonTask(base.Task[PythonOutputsType]):
+class Task(base.Task[PythonOutputsType]):
 
     _task_type = "python"
 
-    def _run(self, job: "Job[PythonTask]", rerun: bool = True) -> None:
+    def _run(self, job: "Job[Task]", rerun: bool = True) -> None:
         # Prepare the inputs to the function
         inputs = attrs_values(self)
         del inputs["function"]

pydra/compose/shell/__init__.py

@@ -1,5 +1,5 @@
 from .field import arg, out, outarg
 from .builder import define
-from .task import ShellTask, ShellOutputs
+from .task import Task, Outputs
 
-__all__ = ["arg", "out", "outarg", "define", "ShellTask", "ShellOutputs"]
+__all__ = ["arg", "out", "outarg", "define", "Task", "Outputs"]

pydra/compose/shell/builder.py

@@ -30,7 +30,7 @@
     is_optional,
 )
 from . import field
-from .task import ShellTask, ShellOutputs
+from .task import Task, Outputs
 
 
 EXECUTABLE_HELP_STRING = (
@@ -62,7 +62,7 @@ def define(
     auto_attribs: bool = True,
     name: str | None = None,
     xor: ty.Sequence[str | None] | ty.Sequence[ty.Sequence[str | None]] = (),
-) -> "ShellTask":
+) -> "Task":
     """Create a task for a shell command. Can be used either as a decorator on
     the "canonical" dataclass-form of a task or as a function that takes a
     "shell-command template string" of the form
@@ -115,13 +115,13 @@ def define(
 
     Returns
     -------
-    ShellTask
+    Task
         The interface for the shell command
     """
 
     def make(
         wrapped: ty.Callable | type | None = None,
-    ) -> ShellTask:
+    ) -> Task:
 
         if inspect.isclass(wrapped):
             klass = wrapped
@@ -147,8 +147,8 @@ def make(
             class_name = klass.__name__
             check_explicit_fields_are_none(klass, inputs, outputs)
             parsed_inputs, parsed_outputs = extract_fields_from_class(
-                ShellTask,
-                ShellOutputs,
+                Task,
+                Outputs,
                 klass,
                 field.arg,
                 field.out,
@@ -189,12 +189,8 @@ def make(
                 class_name = f"_{class_name}"
 
             # Add in fields from base classes
-            parsed_inputs.update(
-                {n: getattr(ShellTask, n) for n in ShellTask.BASE_NAMES}
-            )
-            parsed_outputs.update(
-                {n: getattr(ShellOutputs, n) for n in ShellOutputs.BASE_NAMES}
-            )
+            parsed_inputs.update({n: getattr(Task, n) for n in Task.BASE_NAMES})
+            parsed_outputs.update({n: getattr(Outputs, n) for n in Outputs.BASE_NAMES})
 
         if "executable" in parsed_inputs:
             raise ValueError(
@@ -236,8 +232,8 @@ def make(
                 outpt.default = NO_DEFAULT
 
         defn = build_task_class(
-            ShellTask,
-            ShellOutputs,
+            Task,
+            Outputs,
             parsed_inputs,
             parsed_outputs,
             name=class_name,
@@ -582,7 +578,7 @@ class _InputPassThrough:
 
     name: str
 
-    def __call__(self, inputs: ShellTask) -> ty.Any:
+    def __call__(self, inputs: Task) -> ty.Any:
         return getattr(inputs, self.name)