Release v0.6.1

Author: markgeejw

Makefile

@@ -1,4 +1,4 @@
-VERSION ?= 0.6.0
+VERSION ?= 0.6.1
 SHELL := /bin/bash
 
 .PHONY: releasehere

anaconda_build/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: openprotein-python
-  version: "0.6.0"
+  version: "0.6.1"
 
 source:
   path: ../

openprotein/schemas/design.py

@@ -150,29 +150,46 @@ def __init__(self, sequence: str):
         self.sequence = sequence
         self.mutations = self.initialize(sequence)
 
-    def initialize(self, sequence: str) -> dict[int, list[str]]:
+    def initialize(self, sequence: str) -> dict[int, set[str]]:
         """Initialize with no changes allowed to the sequence."""
-        return {i: [aa] for i, aa in enumerate(sequence, start=1)}
+        return {i: {aa} for i, aa in enumerate(sequence, start=1)}
 
-    def allow(self, positions: int | list[int], amino_acids: list[str] | str) -> None:
+    def allow(
+        self,
+        amino_acids: list[str] | str | None = None,
+        positions: int | list[int] | None = None,
+    ) -> None:
         """Allow specific amino acids at given positions."""
         if isinstance(positions, int):
             positions = [positions]
+        elif positions is None:
+            positions = [i + 1 for i in range(len(self.sequence))]
         if isinstance(amino_acids, str):
             amino_acids = list(amino_acids)
+        elif amino_acids is None:
+            amino_acids = list(self.sequence)
 
         for position in positions:
             if position in self.mutations:
-                self.mutations[position].extend(amino_acids)
+                for aa in amino_acids:
+                    self.mutations[position].add(aa)
             else:
-                self.mutations[position] = amino_acids
+                self.mutations[position] = set(amino_acids)
 
-    def remove(self, positions: int | list[int], amino_acids: list[str] | str) -> None:
+    def remove(
+        self,
+        amino_acids: list[str] | str | None = None,
+        positions: int | list[int] | None = None,
+    ) -> None:
         """Remove specific amino acids from being allowed at given positions."""
         if isinstance(positions, int):
             positions = [positions]
+        elif positions is None:
+            positions = [i + 1 for i in range(len(self.sequence))]
         if isinstance(amino_acids, str):
             amino_acids = list(amino_acids)
+        elif amino_acids is None:
+            amino_acids = list(self.sequence)
 
         for position in positions:
             if position in self.mutations:
@@ -182,4 +199,4 @@ def remove(self, positions: int | list[int], amino_acids: list[str] | str) -> No
 
     def as_dict(self) -> dict[int, list[str]]:
         """Convert the internal mutations representation into a dictionary."""
-        return self.mutations
+        return {i: list(aa) for i, aa in self.mutations.items()}

openprotein/schemas/predictor.py

@@ -44,7 +44,7 @@ class PredictorMetadata(BaseModel):
     status: JobStatus
     model_spec: ModelSpec
     training_dataset: Dataset
-    traingraphs: list["TrainGraph"]
+    traingraphs: list["TrainGraph"] | None = None
 
     def is_done(self):
         return self.status.done()

pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "openprotein_python"
 packages = [{ include = "openprotein" }]
-version = "0.6.0"
+version = "0.6.1"
 description = "OpenProtein Python interface."
 license = "MIT"
 readme = "README.md"