Release v0.8.12

Author: markgeejw

flake.lock

@@ -0,0 +1,21 @@
+{
+  description = "A basic flake with a shell";
+  inputs.nixpkgs.url = "github:NixOS/nixpkgs/nixpkgs-unstable";
+  inputs.systems.url = "github:nix-systems/default";
+  inputs.flake-utils = {
+    url = "github:numtide/flake-utils";
+    inputs.systems.follows = "systems";
+  };
+
+  outputs =
+    { nixpkgs, flake-utils, ... }:
+    flake-utils.lib.eachDefaultSystem (
+      system:
+      let
+        pkgs = nixpkgs.legacyPackages.${system};
+      in
+      {
+        devShells.default = pkgs.mkShell { packages = [ pkgs.bashInteractive ]; };
+      }
+    );
+}

flake.nix

@@ -11,14 +11,16 @@
 from openprotein.models.base import ProteinModel
 from openprotein.protein import Protein
 
+from .boltzgen_schema import BoltzGenDesignSpec
+
 
 class BoltzGenRequest(BaseModel):
     "Specification for an BoltzGen request."
 
     n: int = 1
     # protein: Protein
     structure_text: str | None = None
-    design_spec: dict[str, Any]
+    design_spec: BoltzGenDesignSpec | dict[str, Any]
     diffusion_batch_size: int | None = None
     step_scale: float | None = None
     noise_scale: float | None = None
@@ -120,7 +122,7 @@ def get_metadata(self) -> ModelMetadata:
 
     def generate(
         self,
-        design_spec: dict[str, Any],
+        design_spec: BoltzGenDesignSpec | dict[str, Any],
         structure_file: str | bytes | BinaryIO | None = None,
         n: int = 1,
         diffusion_batch_size: int | None = None,
@@ -133,12 +135,22 @@ def generate(
 
         Parameters
         ----------
-        design_spec : dict[str, Any]
-            The BoltzGen design specification to run. This is the Python representation
-            of the BoltzGen yaml request specification.
-        structure_file : BinaryIO, optional
-            An input PDB file (as a file-like object) used for inpainting or other
-            guided design tasks where parts of an existing structure are provided.
+        design_spec : BoltzGenDesignSpec | dict[str, Any]
+            The BoltzGen design specification to run. Can be a typed BoltzGenDesignSpec
+            object or a dict representing the BoltzGen yaml request specification.
+            
+            Note: If the design_spec includes FileEntity objects with `path` fields,
+            those paths are placeholders. The actual structure file content must be
+            provided via the `structure_file` parameter below, as the platform backend
+            currently only accepts structure files this way.
+        structure_file : str | bytes | BinaryIO | None, optional
+            An input PDB/CIF file used for inpainting or other guided design tasks
+            where parts of an existing structure are provided. This parameter provides
+            the actual structure content that corresponds to any FileEntity `path`
+            fields in the design_spec. Can be:
+            - A file path (str) to read from
+            - Raw file content (bytes)
+            - A file-like object (BinaryIO)
         n : int, optional
             The number of unique design trajectories to run (default is 1).
         diffusion_batch_size : int, optional
@@ -163,6 +175,10 @@ def generate(
             A future object that can be used to retrieve the results of the design
             job upon completion.
         """
+        # Validate design_spec if it's a dict
+        if isinstance(design_spec, dict):
+            design_spec = BoltzGenDesignSpec.model_validate(design_spec)
+        
         request = BoltzGenRequest(
             n=n,
             design_spec=design_spec,