split base and shell compose modules into packages

Author: tclose

docs/source/examples/glm.ipynb

@@ -55,7 +55,7 @@
     "import typing as ty\n",
     "from pathlib import Path\n",
     "\n",
-    "from pydra.design import python, workflow\n",
+    "from pydra.compose import python, workflow\n",
     "from pydra.engine.submitter import Submitter\n",
     "from fileformats.generic import File, Directory\n",
     "from fileformats.text import Csv\n",

docs/source/tutorial/4-python.ipynb

@@ -11,7 +11,7 @@
     "\n",
     "## Define decorator\n",
     "\n",
-    "The simplest way to define a Python task is to decorate a function with `pydra.design.python.define`"
+    "The simplest way to define a Python task is to decorate a function with `pydra.compose.python.define`"
    ]
   },
   {
@@ -20,7 +20,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pydra.design import python\n",
+    "from pydra.compose import python\n",
     "\n",
     "\n",
     "# Note that we use PascalCase because the object returned by the decorator is actually a class\n",
@@ -123,7 +123,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pydra.design import python\n",
+    "from pydra.compose import python\n",
     "\n",
     "\n",
     "@python.define\n",

docs/source/tutorial/5-shell.ipynb

@@ -22,7 +22,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pydra.design import shell\n",
+    "from pydra.compose import shell\n",
     "\n",
     "Cp = shell.define(\"cp <in_file> <out|destination>\")"
    ]
@@ -193,7 +193,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pydra.design import shell\n",
+    "from pydra.compose import shell\n",
     "from fileformats.generic import File\n",
     "\n",
     "Gzip = shell.define(\"gzip <out|out_file:application/gzip> <in_files+>\")\n",
@@ -295,7 +295,7 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "from pydra.design import shell\n",
+    "from pydra.compose import shell\n",
     "from pathlib import Path\n",
     "from fileformats.generic import File\n",
     "\n",

docs/source/tutorial/6-workflow.ipynb

@@ -17,7 +17,7 @@
    "source": [
     "## Constructor functions\n",
     "\n",
-    "Workflows are typically defined using the `pydra.design.workflow.define` decorator on \n",
+    "Workflows are typically defined using the `pydra.compose.workflow.define` decorator on \n",
     "a \"constructor\" function that generates the workflow. For example, given two task\n",
     "definitions, `Add` and `Mul`."
    ]
@@ -28,7 +28,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pydra.design import workflow, python\n",
+    "from pydra.compose import workflow, python\n",
     "\n",
     "\n",
     "# Example python tasks\n",
@@ -81,7 +81,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pydra.design import shell\n",
+    "from pydra.compose import shell\n",
     "from fileformats import image, video\n",
     "\n",
     "\n",
@@ -447,7 +447,7 @@
     "from fileformats.medimage import Nifti1\n",
     "import fileformats.medimage_mrtrix3 as mrtrix3\n",
     "from pydra.engine.environments import Docker\n",
-    "from pydra.design import workflow, python\n",
+    "from pydra.compose import workflow, python\n",
     "from pydra.tasks.mrtrix3.v3_0 import MrConvert, MrThreshold\n",
     "\n",
     "MRTRIX2NUMPY_DTYPES = {\n",

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

@@ -7,7 +7,7 @@
     "# Canonical task form\n",
     "\n",
     "Under the hood, all Python, shell and workflow tasks generated by the\n",
-    "`pydra.design.*.define` decorators/functions are translated to\n",
+    "`pydra.compose.*.define` decorators/functions are translated to\n",
     "[dataclasses](https://docs.python.org/3/library/dataclasses.html) by the\n",
     "[Attrs](https://www.attrs.org/en/stable/). While the more compact syntax described\n",
     "in the [Python-tasks](./4-python.html), [Shell-tasks](./5-shell.html) and [Workflow](./6-workflow.html)\n",
@@ -28,7 +28,7 @@
    "source": [
     "## Python-tasks\n",
     "\n",
-    "Python tasks in dataclass form are decorated by `pydra.design.python.define`\n",
+    "Python tasks in dataclass form are decorated by `pydra.compose.python.define`\n",
     "with inputs listed as type annotations. Outputs are similarly defined in a nested class\n",
     "called `Outputs`. The function to be executed should be a staticmethod called `function`.\n",
     "Default values can also be set directly, as with Attrs classes.\n",
@@ -49,7 +49,7 @@
     "from pprint import pprint\n",
     "from pydra.engine.helpers import fields_dict\n",
     "from pydra.engine.specs import PythonTask, PythonOutputs\n",
-    "from pydra.design import python\n",
+    "from pydra.compose import python\n",
     "\n",
     "\n",
     "@python.define\n",
@@ -152,7 +152,7 @@
     "import os\n",
     "from pathlib import Path\n",
     "from fileformats import generic\n",
-    "from pydra.design import shell\n",
+    "from pydra.compose import shell\n",
     "from pydra.engine.specs import ShellTask, ShellOutputs\n",
     "from pydra.utils.typing import MultiInputObj\n",
     "\n",
@@ -200,7 +200,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pydra.design import python, workflow\n",
+    "from pydra.compose import python, workflow\n",
     "from pydra.engine.specs import WorkflowTask, WorkflowOutputs\n",
     "\n",
     "\n",

pydra/compose/base/__init__.py

@@ -0,0 +1,27 @@
+from .field import Field, Arg, Out, NO_DEFAULT
+from .helpers import (
+    ensure_field_objects,
+    parse_doc_string,
+    extract_function_inputs_and_outputs,
+    check_explicit_fields_are_none,
+    extract_fields_from_class,
+    is_set,
+)
+from .task import Task, Outputs
+from .builder import build_task_class
+
+__all__ = [
+    "Field",
+    "Arg",
+    "Out",
+    "NO_DEFAULT",
+    "ensure_field_objects",
+    "parse_doc_string",
+    "extract_function_inputs_and_outputs",
+    "check_explicit_fields_are_none",
+    "extract_fields_from_class",
+    "is_set",
+    "build_task_class",
+    "Task",
+    "Outputs",
+]