finished off the workflow tutorial for now

nipype · Dec 28, 2024 · 8e88ed2 · 8e88ed2
1 parent a8ed05e
commit 8e88ed2
Showing 1 changed file with 86 additions and 8 deletions.
diff --git a/new-docs/source/tutorial/workflow.ipynb b/new-docs/source/tutorial/workflow.ipynb
@@ -4,14 +4,22 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Workflow design"
+    "# Workflow design\n",
+    "\n",
+    "In Pydra, workflows are DAG of component tasks to be executed on specified inputs.\n",
+    "Workflow specifications are dataclasses, which interchangeable with Python and shell tasks\n",
+    "specifications and executed in the same way."
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Given two task specifications, `Add` and `Mul`"
+    "## Constructor functions\n",
+    "\n",
+    "Workflows are typically defined using the `pydra.design.workflow.define` decorator on \n",
+    "a \"constructor\" function that generates the workflow. For example, given two task\n",
+    "specifications, `Add` and `Mul`."
    ]
   },
   {
@@ -47,7 +55,7 @@
    "outputs": [],
    "source": [
     "@workflow.define\n",
-    "def MyTestWorkflow(a, b):\n",
+    "def BasicWorkflow(a, b):\n",
     "    add = workflow.add(Add(a=a, b=b))\n",
     "    mul = workflow.add(Mul(a=add.out, b=b))\n",
     "    return mul.out"
@@ -72,7 +80,7 @@
     "from fileformats import image, video\n",
     "\n",
     "@workflow.define\n",
-    "def MyTestShellWorkflow(\n",
+    "def ShellWorkflow(\n",
     "    input_video: video.Mp4,\n",
     "    watermark: image.Png,\n",
     "    watermark_dims: tuple[int, int] = (10, 10),\n",
@@ -209,7 +217,7 @@
     "    return float(value)\n",
     "\n",
     "@workflow.define\n",
-    "class MyLibraryWorkflow(WorkflowSpec[\"MyLibraryWorkflow.Outputs\"]):\n",
+    "class LibraryWorkflow(WorkflowSpec[\"MyLibraryWorkflow.Outputs\"]):\n",
     "\n",
     "    a: int\n",
     "    b: float = workflow.arg(\n",
@@ -248,7 +256,7 @@
     "    return sum(x)\n",
     "\n",
     "@workflow.define\n",
-    "def MySplitWorkflow(a: list[int], b: list[float]) -> list[float]:\n",
+    "def SplitWorkflow(a: list[int], b: list[float]) -> list[float]:\n",
     "    # Multiply over all combinations of the elements of a and b, then combine the results\n",
     "    # for each a element into a list over each b element\n",
     "    mul = workflow.add(Mul()).split(x=a, y=b).combine(\"x\")\n",
@@ -271,7 +279,7 @@
    "outputs": [],
    "source": [
     "@workflow.define\n",
-    "def MySplitThenCombineWorkflow(a: list[int], b: list[float], c: float) -> list[float]:\n",
+    "def SplitThenCombineWorkflow(a: list[int], b: list[float], c: float) -> list[float]:\n",
     "    mul = workflow.add(Mul()).split(x=a, y=b)\n",
     "    add = workflow.add(Add(x=mul.out, y=c)).combine(\"Mul.x\")\n",
     "    sum = workflow.add(Sum(x=add.out))\n",
@@ -301,7 +309,7 @@
    "outputs": [],
    "source": [
     "@workflow.define\n",
-    "def MyConditionalWorkflow(\n",
+    "def ConditionalWorkflow(\n",
     "    input_video: video.Mp4,\n",
     "    watermark: image.Png,\n",
     "    watermark_dims: tuple[int, int] | None = None,\n",
@@ -371,6 +379,76 @@
     "placeholders see [Conditional construction](../explanation/conditional-lazy.html)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Typing\n",
+    "\n",
+    "Pydra utilizes Python type annotations to implement strong type-checking, which is performed\n",
+    "when values or upstream outputs are assigned to task specification inputs.\n",
+    "\n",
+    "Task input and output fields do not need to be assigned types, since they will default to `typing.Any`.\n",
+    "However, if they are assigned a type and a value or output from an upstream node conflicts\n",
+    "with the type, a `TypeError` will be raised at construction time.\n",
+    "\n",
+    "Note that the type-checking \"assumes the best\", and will pass if the upstream field is typed\n",
+    "by `Any` or a super-class of the field being assigned to. For example, an input of\n",
+    "`fileformats.generic.File` passed to a field expecting a `fileformats.image.Png` file type,\n",
+    "because `Png` is a subtype of `File`, where as `fileformats.image.Jpeg` input would fail\n",
+    "since it is clearly not the intended type.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from fileformats import generic\n",
+    "\n",
+    "Mp4Handbrake = shell.define(\n",
+    "    \"HandBrakeCLI -i <in_video:video/mp4> -o <out|out_video:video/mp4> \"\n",
+    "    \"--width <width:int> --height <height:int>\",\n",
+    ")\n",
+    "\n",
+    "\n",
+    "QuicktimeHandbrake = shell.define(\n",
+    "    \"HandBrakeCLI -i <in_video:video/quicktime> -o <out|out_video:video/quicktime> \"\n",
+    "    \"--width <width:int> --height <height:int>\",\n",
+    ")\n",
+    "\n",
+    "@workflow.define\n",
+    "def TypeErrorWorkflow(\n",
+    "    input_video: video.Mp4,\n",
+    "    watermark: generic.File,\n",
+    "    watermark_dims: tuple[int, int] = (10, 10),\n",
+    ") -> video.Mp4:\n",
+    "\n",
+    "    add_watermark = workflow.add(\n",
+    "        shell.define(\n",
+    "            \"ffmpeg -i <in_video> -i <watermark:image/png> \"\n",
+    "            \"-filter_complex <filter> <out|out_video:video/mp4>\"\n",
+    "        )(\n",
+    "            in_video=input_video,\n",
+    "            watermark=watermark,  # Type is OK because generic.File is superclass of image.Png\n",
+    "            filter=\"overlay={}:{}\".format(*watermark_dims),\n",
+    "        ),\n",
+    "        name=\"add_watermark\",\n",
+    "    )\n",
+    "\n",
+    "    try:\n",
+    "        handbrake = workflow.add(\n",
+    "            QuicktimeHandbrake(in_video=add_watermark.out_video, width=1280, height=720),\n",
+    "        )  # This will raise a TypeError because the input video is an Mp4\n",
+    "    except TypeError:\n",
+    "        handbrake = workflow.add(\n",
+    "            Mp4Handbrake(in_video=add_watermark.out_video, width=1280, height=720),\n",
+    "        )  # The type of the input video is now correct\n",
+    "\n",
+    "    return handbrake.output_video"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},