metafold 0.10.0__tar.gz → 0.12.dev0__tar.gz

{metafold-0.10.0 → metafold-0.12.dev0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: metafold
-Version: 0.10.0
+Version: 0.12.dev0
 Summary: Metafold SDK for Python
 Author-email: Metafold 3D <info@metafold3d.com>
 License: Copyright 2024 Metafold 3D
@@ -21,13 +21,11 @@ Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Requires-Python: >=3.9
+Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: attrs~=23.2
@@ -35,18 +33,13 @@ Requires-Dist: auth0-python~=4.7
 Requires-Dist: numpy~=2.0
 Requires-Dist: requests~=2.31
 Requires-Dist: scipy~=1.11
-Provides-Extra: docs
-Requires-Dist: sphinx~=7.2; extra == "docs"
-Requires-Dist: sphinx_rtd_theme~=2.0; extra == "docs"
-Provides-Extra: lint
-Requires-Dist: mypy~=1.10; extra == "lint"
-Requires-Dist: types-requests~=2.31; extra == "lint"
-Provides-Extra: test
-Requires-Dist: pytest~=7.3; extra == "test"
-Requires-Dist: requests-toolbelt~=1.0; extra == "test"
-Provides-Extra: networkx
-Requires-Dist: networkx~=3.2; extra == "networkx"
-Requires-Dist: types-networkx~=3.2; extra == "networkx"
+Provides-Extra: simulation
+Requires-Dist: dotenv>=0.9.9; extra == "simulation"
+Requires-Dist: pandas>=2.3.3; extra == "simulation"
+Requires-Dist: plyfile>=1.1.3; extra == "simulation"
+Requires-Dist: pyyaml>=6.0.3; extra == "simulation"
+Requires-Dist: simulation-configurator==0.1.1; extra == "simulation"
+Requires-Dist: tables>=3.11.1; extra == "simulation"
 Dynamic: license-file
 
 # Metafold SDK for Python
@@ -58,7 +51,7 @@ Dynamic: license-file
 
 ## Installation
 
-```
+```console
 pip install metafold
 ```
 
@@ -83,3 +76,13 @@ Read the [documentation][] for more info or play around with one of the
 [examples](examples).
 
 [documentation]: https://Metafold3d.github.io/metafold-python/
+
+## Development
+
+This project uses [uv](https://docs.astral.sh/uv/) to manage dependencies.
+
+### Run tests
+
+```console
+uv run pytest ./tests
+```

{metafold-0.10.0 → metafold-0.12.dev0}/README.md

@@ -7,7 +7,7 @@
 
 ## Installation
 
-```
+```console
 pip install metafold
 ```
 
@@ -32,3 +32,13 @@ Read the [documentation][] for more info or play around with one of the
 [examples](examples).
 
 [documentation]: https://Metafold3d.github.io/metafold-python/
+
+## Development
+
+This project uses [uv](https://docs.astral.sh/uv/) to manage dependencies.
+
+### Run tests
+
+```console
+uv run pytest ./tests
+```

{metafold-0.10.0 → metafold-0.12.dev0}/metafold/__init__.py

@@ -4,7 +4,6 @@ from metafold.assets import AssetsEndpoint
 from metafold.jobs import JobsEndpoint
 from metafold.workflows import WorkflowsEndpoint
 from metafold.auth import AuthProvider
-from typing import Optional
 
 
 class MetafoldClient(Client):
@@ -22,10 +21,10 @@ class MetafoldClient(Client):
 
     def __init__(
         self,
-        access_token: Optional[str] = None,
-        project_id: Optional[str] = None,
-        client_id: Optional[str] = None,
-        client_secret: Optional[str] = None,
+        access_token: str | None = None,
+        project_id: str | None = None,
+        client_id: str | None = None,
+        client_secret: str | None = None,
         auth_domain: str = "metafold3d.us.auth0.com",
         base_url: str = "https://api.metafold3d.com/",
     ) -> None:

{metafold-0.10.0 → metafold-0.12.dev0}/metafold/api.py

@@ -1,9 +1,9 @@
 from datetime import datetime, timezone
 from functools import wraps
-from typing import Any, Callable, Optional, TypeVar, Union
+from typing import Any, Callable, TypeVar
 
 
-def asdatetime(s: Union[str, datetime]) -> datetime:
+def asdatetime(s: str | datetime) -> datetime:
     """Parse Metafold API datetime.
 
     Note datetime strings returned by the Metafold API are RFC 1123 formatted,
@@ -30,10 +30,10 @@ T = TypeVar("T")
 U = TypeVar("U")
 
 
-def optional(f: Callable[[T], U]) -> Callable[[Optional[T]], Optional[U]]:
+def optional(f: Callable[[T], U]) -> Callable[[T | None], U | None]:
     """Decorator to generate converters that accept optional values."""
     @wraps(f)
-    def decorator(v: Optional[T]) -> Optional[U]:
+    def decorator(v: T | None) -> U | None:
         if v is None:
             return None
         return f(v)

{metafold-0.10.0 → metafold-0.12.dev0}/metafold/assets.py

@@ -4,7 +4,7 @@ from metafold.api import asdatetime, asdict
 from metafold.client import Client
 from os import PathLike
 from requests import Response
-from typing import IO, Optional, Union
+from typing import IO
 import requests
 
 
@@ -29,7 +29,7 @@ class Asset:
     created: datetime = field(converter=asdatetime)
     modified: datetime = field(converter=asdatetime)
     project_id: str
-    job_id: Optional[str] = None
+    job_id: str | None = None
 
 
 class AssetsEndpoint:
@@ -40,9 +40,9 @@ class AssetsEndpoint:
 
     def list(
         self,
-        sort: Optional[str] = None,
-        q: Optional[str] = None,
-        project_id: Optional[str] = None,
+        sort: str | None = None,
+        q: str | None = None,
+        project_id: str | None = None,
     ) -> list[Asset]:
         """List assets.
 
@@ -63,7 +63,7 @@ class AssetsEndpoint:
         r: Response = self._client.get(url, params=payload)
         return [Asset(**a) for a in r.json()]
 
-    def get(self, asset_id: str, project_id: Optional[str] = None) -> Asset:
+    def get(self, asset_id: str, project_id: str | None = None) -> Asset:
         """Get an asset.
 
         Args:
@@ -78,28 +78,44 @@ class AssetsEndpoint:
         r: Response = self._client.get(url)
         return Asset(**r.json())
 
-    def download_file(
-        self, asset_id: str, path: Union[str, PathLike],
-        project_id: Optional[str] = None,
+    def download(
+        self, asset_id: str, f: IO[bytes],
+        project_id: str | None = None,
     ):
         """Download an asset.
 
         Args:
             asset_id: ID of asset to download.
-            path: Path to downloaded file.
+            f: File-like object open for writing in binary mode.
             project_id: Asset project ID.
         """
         project_id = self._client.project_id(project_id)
         url = f"/projects/{project_id}/assets/{asset_id}"
         r: Response = self._client.get(url, params={"download": "true"})
         r = requests.get(r.json()["link"], stream=True)
-        with open(path, "wb") as f:
+        try:
             for chunk in r.iter_content(chunk_size=65536):  # 64 KiB
                 f.write(chunk)
+        finally:
+            f.close()
+
+    def download_file(
+        self, asset_id: str, path: str | PathLike,
+        project_id: str | None = None,
+    ):
+        """Download an asset.
+
+        Args:
+            asset_id: ID of asset to download.
+            path: Path to downloaded file.
+            project_id: Asset project ID.
+        """
+        with open(path, "wb") as f:
+            self.download(asset_id, f, project_id)
 
     def create(
-        self, f: Union[str, bytes, PathLike, IO[bytes]],
-        project_id: Optional[str] = None,
+        self, f: str | bytes | PathLike | IO[bytes],
+        project_id: str | None = None,
     ) -> Asset:
         """Upload an asset.
 
@@ -119,7 +135,7 @@ class AssetsEndpoint:
             fp.close()
         return Asset(**r.json())
 
-    def delete(self, asset_id: str, project_id: Optional[str] = None) -> None:
+    def delete(self, asset_id: str, project_id: str | None = None) -> None:
         """Delete an asset.
 
         Args:
@@ -131,7 +147,7 @@ class AssetsEndpoint:
         self._client.delete(url)
 
 
-def _open_file(f: Union[str, bytes, PathLike, IO[bytes]]) -> IO[bytes]:
+def _open_file(f: str | bytes | PathLike | IO[bytes]) -> IO[bytes]:
     if isinstance(f, (str, bytes, PathLike)):
         return open(f, "rb")
     return f

{metafold-0.10.0 → metafold-0.12.dev0}/metafold/auth.py

@@ -1,7 +1,6 @@
 from auth0.authentication import GetToken  # type: ignore
 from collections import namedtuple
 from datetime import datetime, timedelta, timezone
-from typing import Optional
 
 Token = namedtuple("Token", ["access_token", "expires_at"])
 
@@ -23,7 +22,7 @@ class AuthProvider:
             self._client_id,
             client_secret=client_secret,
         )
-        self._token: Optional[Token] = None
+        self._token: Token | None = None
 
     def get_token(self) -> str:
         now = datetime.now(timezone.utc)

{metafold-0.10.0 → metafold-0.12.dev0}/metafold/client.py

@@ -1,7 +1,7 @@
 from metafold.auth import AuthProvider
 from metafold.exceptions import PollTimeout
 from requests import HTTPError, Response, Session
-from typing import Any, Callable, Optional, Union
+from typing import Any, Callable
 from urllib.parse import urljoin
 import platform
 import time
@@ -13,9 +13,9 @@ class Client:
     def __init__(
         self,
         base_url: str,
-        access_token: Optional[str] = None,
-        project_id: Optional[str] = None,
-        auth: Optional[AuthProvider] = None
+        access_token: str | None = None,
+        project_id: str | None = None,
+        auth: AuthProvider | None = None
     ) -> None:
         if bool(auth) == bool(access_token):
             raise ValueError(
@@ -34,7 +34,7 @@ class Client:
                 "Authorization": f"Bearer {access_token}",
             })
 
-    def project_id(self, id: Optional[str] = None) -> str:
+    def project_id(self, id: str | None = None) -> str:
         id = id or self._default_project
         if not id:
             raise ValueError(
@@ -79,8 +79,8 @@ class Client:
 
     def poll(
         self, url: str,
-        timeout: Union[int, float] = 120,
-        every: Union[int, float] = 1,
+        timeout: int | float = 120,
+        every: int | float = 1,
         ) -> Response:
         """Poll the given URL in regular intervals.
 

{metafold-0.10.0 → metafold-0.12.dev0}/metafold/jobs.py

@@ -5,15 +5,14 @@ from metafold.assets import Asset
 from metafold.client import Client
 from metafold.exceptions import PollTimeout
 from requests import Response
-from typing import Any, Optional, TypedDict, Union
-from typing_extensions import TypeAlias
+from typing import Any, TypeAlias, TypedDict
 
 
-def _assets(v: list[Union[dict[str, Any], Asset]]) -> list[Asset]:
+def _assets(v: list[dict[str, Any] | Asset]) -> list[Asset]:
     return [a if isinstance(a, Asset) else Asset(**a) for a in v]
 
 
-AssetDict: TypeAlias = dict[str, Union[dict[str, Any], Asset]]
+AssetDict: TypeAlias = dict[str, dict[str, Any] | Asset]
 
 
 def _assets_dict(v: AssetDict) -> dict[str, Asset]:
@@ -24,8 +23,8 @@ def _assets_dict(v: AssetDict) -> dict[str, Asset]:
 
 
 class IODict(TypedDict):
-    params: Optional[dict[str, Any]]
-    assets: Optional[dict[str, AssetDict]]
+    params: dict[str, Any] | None
+    assets: dict[str, AssetDict] | None
 
 
 @frozen(kw_only=True)
@@ -36,8 +35,8 @@ class IO:
         params: JSON-encoded parameter values.
         assets: Related assets.
     """
-    params: Optional[dict[str, Any]] = None
-    assets: Optional[dict[str, Asset]] = field(
+    params: dict[str, Any] | None = None
+    assets: dict[str, Asset] | None = field(
         converter=lambda v: optional(_assets_dict)(v), default=None)
 
     @staticmethod
@@ -69,22 +68,22 @@ class Job:
         meta: (Deprecated) Additional metadata generated by the job.
     """
     id: str
-    name: Optional[str] = None
+    name: str | None = None
     type: str
     state: str
     created: datetime = field(converter=asdatetime)
-    started: Optional[datetime] = field(
+    started: datetime | None = field(
         converter=lambda v: optional_datetime(v), default=None)
-    finished: Optional[datetime] = field(
+    finished: datetime | None = field(
         converter=lambda v: optional_datetime(v), default=None)
-    error: Optional[str] = None
+    error: str | None = 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))
     needs: list[str]
-    project_id: Optional[str] = None
-    workflow_id: Optional[str] = None
+    project_id: str | None = None
+    workflow_id: str | None = None
     # NOTE(ryan): Deprecated
-    assets: Optional[list[Asset]] = field(
+    assets: list[Asset] | None = field(
         converter=lambda v: optional(_assets)(v), default=None)
     parameters: dict[str, Any]
     meta: dict[str, Any]
@@ -98,9 +97,9 @@ class JobsEndpoint:
 
     def list(
         self,
-        sort: Optional[str] = None,
-        q: Optional[str] = None,
-        project_id: Optional[str] = None,
+        sort: str | None = None,
+        q: str | None = None,
+        project_id: str | None = None,
     ) -> list[Job]:
         """List jobs.
 
@@ -121,7 +120,7 @@ class JobsEndpoint:
         r: Response = self._client.get(url, params=payload)
         return [Job(**j) for j in r.json()]
 
-    def get(self, job_id: str, project_id: Optional[str] = None) -> Job:
+    def get(self, job_id: str, project_id: str | None = None) -> Job:
         """Get a job.
 
         Args:
@@ -138,9 +137,9 @@ class JobsEndpoint:
 
     def run(
         self, type: str, params: dict[str, Any],
-        name: Optional[str] = None,
-        timeout: Union[int, float] = 120,
-        project_id: Optional[str] = None,
+        name: str | None = None,
+        timeout: int | float = 120,
+        project_id: str | None = None,
     ) -> Job:
         """Dispatch a new job and wait for a result.
 
@@ -167,8 +166,8 @@ class JobsEndpoint:
 
     def run_status(
         self, type: str, params: dict[str, Any],
-        name: Optional[str] = None,
-        project_id: Optional[str] = None,
+        name: str | None = None,
+        project_id: str | None = None,
     ) -> str:
         """Dispatch a new job and return immediately without waiting for result.
 
@@ -193,8 +192,8 @@ class JobsEndpoint:
 
     def update(
         self, job_id: str,
-        name: Optional[str] = None,
-        project_id: Optional[str] = None,
+        name: str | None = None,
+        project_id: str | None = None,
     ) -> Job:
         """Update a job.
 
@@ -212,7 +211,7 @@ class JobsEndpoint:
         r: Response = self._client.patch(url, data=payload)
         return Job(**r.json())
 
-    def delete(self, job_id: str, project_id: Optional[str] = None):
+    def delete(self, job_id: str, project_id: str | None = None):
         """Delete a job.
 
         Args: