Addresses a bug in padding with random mutations (#65)

* Addresses a bug in padding with random mutations

* Updates the lambo2 test to skip on base env

* Bumps patch version

Author: miguelgondu

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "poli-baselines"
-version = "1.0.1"
+version = "1.0.2"
 description = "poli-baselines, a library of discrete objective optimizers"
 readme = "README.md"
 authors = [{name="Miguel González-Duque", email="miguelgondu@gmail.com"}]
@@ -94,7 +94,7 @@ markers = [
 profile = "black"
 
 [tool.bumpversion]
-current_version = "1.0.1"
+current_version = "1.0.2"
 parse = """(?x)
     (?P<major>0|[1-9]\\d*)\\.
     (?P<minor>0|[1-9]\\d*)\\.

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = poli_baselines
-version = 1.0.1
+version = 1.0.2
 author_email = miguelgondu@gmail.com
 description = Baselines for Discrete Sequence Optimization, focusing on proteins
 long_description = file: readme.md

src/poli_baselines/__init__.py

@@ -1 +1 @@
-__version__ = "1.0.1"
+__version__ = "1.0.2"

src/poli_baselines/core/utils/mutations/random_mutations.py

@@ -25,7 +25,14 @@ def add_random_mutations_to_reach_pop_size(
             f"Expected x to have less elements than the population size. x.shape: {x.shape}, pop_size: {population_size}"
         )
 
-    x_as_1d_array_of_strings = np.array(["".join(x[i, :]) for i in range(b)])
+    if len(x.shape) == 1:
+        # Then the input as an array [b,] of strings
+        x_as_1d_array_of_strings = x
+    elif len(x.shape) == 2:
+        # Then the input as an array [b, L] of strings
+        x_as_1d_array_of_strings = np.array(["".join(x[i, :]) for i in range(b)])
+    else:
+        raise ValueError(f"Expected x to have shape [b,] or [b, L], but got {x.shape}.")
 
     more_mutants = []
     for _ in range(population_size - b):

src/poli_baselines/tests/solvers/bayesian_optimization/test_lambo2.py

@@ -1,8 +1,8 @@
-import importlib
+import importlib.util
 from pathlib import Path
 
 import pytest
-from poli.repository import EhrlichProblemFactory
+from poli.repository import EhrlichHoloProblemFactory
 
 if importlib.util.find_spec("cortex") is None:
     pytest.skip("Cortex is not installed.", allow_module_level=True)
@@ -13,7 +13,7 @@
 def test_lambo2_runs_on_ehrlich():
     from poli_baselines.solvers.bayesian_optimization.lambo2 import LaMBO2
 
-    problem = EhrlichProblemFactory().create(
+    problem = EhrlichHoloProblemFactory().create(
         sequence_length=10,
         n_motifs=2,
         motif_length=4,