[6/11] Define typed cloning recipes and explicit material demands

pyproject.toml

@@ -24,6 +24,7 @@ dependencies = [
     "pint>=0.24,<0.27",
     "sbol3==1.2.0.post0",
     "rdflib>=6.1.1,<7",
+    "biopython==1.84",
 ]
 
 [project.urls]
@@ -91,5 +92,5 @@ check_untyped_defs = true
 disallow_untyped_defs = true
 
 [[tool.mypy.overrides]]
-module = ["opentrons.*", "pylabrobot.*", "sbol3.*"]
+module = ["opentrons.*", "pylabrobot.*", "sbol3.*", "Bio.*"]
 ignore_missing_imports = true

scripts/check_install.py

@@ -20,6 +20,7 @@
 def main() -> None:
     # Verify public modules and subpackages are present in the installed distribution.
     import_module("lab.experiments.cloning")
+    import_module("lab.experiments.cloning.routes")
     import_module("lab.part")
     import_module("lab.samples")
     import_module("lab.provenance")

src/lab/experiments/cloning/__init__.py

@@ -5,6 +5,14 @@
 """
 
 from lab.experiments.cloning.decks import assembly_deck, plating_deck, transformation_deck
+from lab.experiments.cloning.methods import (
+    AssemblyMethod,
+    CloningMethods,
+    ExternalPreparationMethod,
+    PlatingMethod,
+    Reagent,
+    TransformationMethod,
+)
 from lab.experiments.cloning.stages import (
     AssemblyLayout,
     AssemblyReaction,
@@ -21,6 +29,14 @@
     record_plating,
     record_transformation,
 )
+from lab.experiments.cloning.systems import (
+    AssemblyRecipe,
+    CloningSystem,
+    ExternalPreparationRecipe,
+    FragmentSelection,
+    PlatingRecipe,
+    TransformationRecipe,
+)
 from lab.experiments.cloning.types import (
     BSAI,
     Assembly,
@@ -32,6 +48,18 @@
 from lab.experiments.cloning.workflow import golden_gate
 
 __all__ = [
+    "AssemblyRecipe",
+    "CloningSystem",
+    "ExternalPreparationRecipe",
+    "FragmentSelection",
+    "PlatingRecipe",
+    "TransformationRecipe",
+    "AssemblyMethod",
+    "CloningMethods",
+    "ExternalPreparationMethod",
+    "PlatingMethod",
+    "Reagent",
+    "TransformationMethod",
     "Assembly",
     "AssemblyLayout",
     "AssemblyReaction",