Add volume_size parameter to ComputeCurvatures

Author: rycwo

.github/workflows/python-package.yml

@@ -20,8 +20,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install -r requirements.txt
-          python -m pip install requests-toolbelt ruff mypy typing_extensions types-networkx types-requests pytest networkx
+          python -m pip install -r requirements-test.txt
       - name: Lint with Ruff
         run: ruff check --output-format=github .
       - run: |

examples/run_workflow.py

@@ -1,6 +1,8 @@
 """Helper script to dispatch workflows."""
 from argparse import ArgumentParser, FileType
 from metafold import MetafoldClient
+from pathlib import Path
+from pprint import pprint
 import json
 import os
 import sys
@@ -17,7 +19,7 @@ def main():
 
     parser.add_argument(
         "--asset-uploads", nargs="*",
-        type=FileType("rb"), help="assets to upload before dispatch")
+        type=Path, help="assets to upload before dispatch")
 
     project_id = os.environ.get("METAFOLD_PROJECT_ID")
     parser.add_argument("-p", "--project-id", default=project_id)
@@ -60,19 +62,24 @@ def main():
 
     if args.asset_uploads:
         print("Uploading assets…")
-        for f in args.asset_uploads:
-            m.assets.create(f)
+        for p in args.asset_uploads:
+            m.assets.create(p.resolve())
 
     print("Running workflow…")
     definition = args.workflow.read()
     w = m.workflows.run(definition, assets=assets, parameters=params)
 
     print(f"Workflow completed: {w.state}")
 
-    if w.state == "failure":
-        for job_id in w.jobs:
-            j = m.jobs.get(job_id)
-            if j.state == "failure":
+    for job_id in w.jobs:
+        j = m.jobs.get(job_id)
+        match j.state:
+            case "success":
+                if j.outputs and j.outputs.assets:
+                    pprint(j.outputs.assets)
+                if j.outputs and j.outputs.params:
+                    pprint(j.outputs.params)
+            case "failure":
                 print(f"Job {j.id} failed: {j.error}")
 
     return 0

metafold/api.py

@@ -35,7 +35,7 @@ def optional(f: Callable[[T], U]) -> Callable[[Optional[T]], Optional[U]]:
     @wraps(f)
     def decorator(v: Optional[T]) -> Optional[U]:
         if v is None:
-            return v
+            return None
         return f(v)
 
     return decorator

metafold/func.py

@@ -106,6 +106,7 @@ def __call__(self, eval_: Evaluator) -> TypedResult[Literal[FuncType.FLOAT]]:
 class ComputeCurvatures_Parameters(TypedDict, total=False):
     spacing_type: ComputeCurvatures_Enum_spacing_type
     step_size: float
+    volume_size: Vec3f
 
 
 class ComputeCurvatures(TypedFunc[Literal[FuncType.VEC3F]]):

metafold/jobs.py

@@ -5,7 +5,8 @@
 from metafold.client import Client
 from metafold.exceptions import PollTimeout
 from requests import Response
-from typing import Any, Optional, TypeAlias, TypedDict, Union
+from typing import Any, Optional, TypedDict, Union
+from typing_extensions import TypeAlias
 
 
 def _assets(v: list[Union[dict[str, Any], Asset]]) -> list[Asset]:
@@ -37,7 +38,7 @@ class IO:
     """
     params: Optional[dict[str, Any]] = None
     assets: Optional[dict[str, Asset]] = field(
-        converter=optional(_assets_dict), default=None)
+        converter=lambda v: optional(_assets_dict)(v), default=None)
 
     @staticmethod
     def from_dict(d: IODict) -> "IO":
@@ -69,13 +70,16 @@ class Job:
     type: str
     state: str
     created: datetime = field(converter=asdatetime)
-    started: Optional[datetime] = field(converter=optional_datetime, default=None)
-    finished: Optional[datetime] = field(converter=optional_datetime, default=None)
+    started: Optional[datetime] = field(
+        converter=lambda v: optional_datetime(v), default=None)
+    finished: Optional[datetime] = field(
+        converter=lambda v: optional_datetime(v), default=None)
     error: Optional[str] = None
     inputs: IO = field(converter=lambda v: v if isinstance(v, IO) else IO.from_dict(v))
     outputs: IO = field(converter=lambda v: v if isinstance(v, IO) else IO.from_dict(v))
     # NOTE(ryan): Deprecated
-    assets: Optional[list[Asset]] = field(converter=optional(_assets), default=None)
+    assets: Optional[list[Asset]] = field(
+        converter=lambda v: optional(_assets)(v), default=None)
     parameters: dict[str, Any]
     meta: dict[str, Any]
 

metafold/workflows.py

@@ -24,8 +24,10 @@ class Workflow:
     jobs: list[str] = field(factory=list)
     state: str
     created: datetime = field(converter=asdatetime)
-    started: Optional[datetime] = field(converter=optional_datetime, default=None)
-    finished: Optional[datetime] = field(converter=optional_datetime, default=None)
+    started: Optional[datetime] = field(
+        converter=lambda v: optional_datetime(v), default=None)
+    finished: Optional[datetime] = field(
+        converter=lambda v: optional_datetime(v), default=None)
     definition: str
 
 
@@ -101,7 +103,7 @@ def run(
         r: Response = self._client.post(f"/projects/{project_id}/workflows", json=payload)
         url = r.json()["link"]
         try:
-            r: Response = self._client.poll(url, timeout)
+            r = self._client.poll(url, timeout)
         except PollTimeout as e:
             raise RuntimeError(
                 f"Workflow failed to complete within {timeout} seconds"

requirements-test.txt

@@ -0,0 +1,14 @@
+attrs~=23.2
+auth0-python~=4.7
+numpy~=1.23
+requests~=2.31
+scipy~=1.11
+
+mypy
+networkx
+pytest
+requests-toolbelt
+ruff
+types-networkx
+types-requests
+typing_extensions