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notebooks/pMHN-Development-JAX.py

@@ -159,7 +159,6 @@ def generate_loglikelihood(
     theta_link_fn=None,
     omega_link_fn=None,
 ):
-
     if theta_link_fn is None:
         theta_link_fn = _default_theta_link(dataset.n_genes)
     if omega_link_fn is None:

src/pmhn/_simulate/__init__.py

@@ -1,4 +1,5 @@
 """The simulation utilities."""
+
 from pmhn._simulate._jump_chain import (
     simulate_dataset,
     simulate_genotype_known_time,

src/pmhn/_simulate/_jump_chain.py

@@ -1,4 +1,5 @@
 """The jump Markov chain simulation from an underlying Markov process."""
+
 from typing import Optional, Union, Sequence
 
 import numpy as np

src/pmhn/_trees/_backend_jax/_private_api.py

@@ -1,4 +1,5 @@
 """This is *private* API, which is convenient for testing and experimenting."""
+
 import pmhn._trees._backend_jax._rates as rates
 from pmhn._trees._backend_jax._loglikelihood import loglikelihood
 from pmhn._trees._backend_jax._solver import logprob_forward_substitution

src/pmhn/_trees/_backend_jax/_rates.py

@@ -1,4 +1,5 @@
 """Submodule used to construct the rates matrices from wrapped tree."""
+
 import jax
 import jax.numpy as jnp
 from jaxtyping import Array, Float, Int

src/pmhn/_trees/_interfaces.py

@@ -1,4 +1,5 @@
 """Interfaces."""
+
 from typing import TypeAlias
 from anytree import Node
 

src/pmhn/_trees/_io.py

@@ -1,4 +1,5 @@
 """Utilities for parsing data frames into AnyTree trees."""
+
 import dataclasses
 from typing import Any
 

src/pmhn/_trees/_validate.py

@@ -1,4 +1,5 @@
 """Tree validation utilities."""
+
 from pmhn._trees._interfaces import Tree