Add dependency on AnyTree.

pyproject.toml

@@ -17,6 +17,7 @@ matplotlib = "^3.7.1"
 seaborn = "^0.12.2"
 pydantic = "^1.10.9"
 netcdf4 = "^1.6.4"
+anytree = "^2.9.0"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.2.1"

src/pmhn/_trees/__init__.py

@@ -8,7 +8,11 @@
 """
 
 from pmhn._trees._simulate import simulate_trees
+from pmhn._trees._interfaces import Tree
+from pmhn._trees._backend import OriginalTreeMHNBackend
 
 __all__ = [
     "simulate_trees",
+    "Tree",
+    "OriginalTreeMHNBackend",
 ]

src/pmhn/_trees/_backend.py

@@ -7,7 +7,7 @@
 from pmhn._trees._interfaces import Tree
 
 
-class IndividualTreeMHNBackend(Protocol):
+class IndividualTreeMHNBackendInterface(Protocol):
     def loglikelihood(
         self,
         tree: Tree,
@@ -53,3 +53,38 @@ def gradient_and_loglikelihood(
             separately.
         """
         return self.gradient(tree, theta), self.loglikelihood(tree, theta)
+
+
+class OriginalTreeMHNBackend(IndividualTreeMHNBackendInterface):
+    def loglikelihood(
+        self,
+        tree: Tree,
+        theta: np.ndarray,
+    ) -> float:
+        """Calculates loglikelihood `log P(tree | theta)`.
+
+        Args:
+            tree: a tree
+            theta: real-valued (i.e., log-theta) matrix,
+              shape (n_mutations, n_mutations)
+
+        Returns:
+            loglikelihood of the tree
+        """
+        # TODO(Laurenz): This implementation is missing.
+        raise NotImplementedError
+
+    def gradient(self, tree: Tree, theta: np.ndarray) -> np.ndarray:
+        """Calculates the partial derivatives of `log P(tree | theta)`
+        with respect to `theta`.
+
+        Args:
+            tree: a tree
+            theta: real-valued matrix, shape (n_mutations, n_mutatations)
+
+        Returns:
+            gradient `d log P(tree | theta) / d theta`,
+              shape (n_mutations, n_mutations)
+        """
+        # TODO(Laurenz): This implementation is missing.
+        raise NotImplementedError

src/pmhn/_trees/_interfaces.py

@@ -1,11 +1,6 @@
 """Interfaces."""
+from typing import TypeAlias
+from anytree import Node
 
 
-class Tree:
-    """This is a mock class.
-    It will be replaced by the actual Tree class,
-    build around AnyTree's `Node` class:
-    https://anytree.readthedocs.io/
-    """
-
-    pass
+Tree: TypeAlias = Node