Release 13.0.1

.readthedocs.yml

@@ -16,6 +16,7 @@ python:
       path: .
       extra_requirements:
         - doc
+        - petab
 
 build:
   os: "ubuntu-22.04"

CHANGELOG.rst

@@ -7,6 +7,22 @@ Release Notes
 0.13 Series
 ...........
 
+0.13.1 (2026-10-26)
+-------------------
+
+Documentation:
+
+* Install the ``petab`` extra on Read the Docs and mock optional PEtab/BasiCO
+  imports in autodoc, so the PEtab API reference renders.
+* Minor documentation improvements.
+* Fix broken links and docstring formatting.
+
+Tests:
+
+* Load PEtab benchmark models via ``benchmark_models_petab`` instead of
+  cloning the benchmark repository.
+
+
 0.13.0 (2026-07-30)
 -------------------
 

doc/conf.py

@@ -55,6 +55,8 @@
     'sphinxcontrib.jquery',
 ]
 
+autodoc_mock_imports = ['PEtab', 'BasiCO']
+
 # default autodoc options
 # list for special-members seems not to be possible before 1.8
 autodoc_default_options = {

pyabc/distance/ot.py

@@ -59,9 +59,9 @@ class WassersteinDistance(Distance):
 
     .. [#bernton2019]
         Bernton, E., Jacob, P.E., Gerber, M. and Robert, C.P.,
-        2019.
         Approximate Bayesian computation with the Wasserstein distance.
-        arXiv preprint arXiv:1905.03747.
+        Journal of the Royal Statistical Society Series B: Statistical Methodology, Volume 81, Issue 2, April 2019, Pages 235–269.
+        https://doi.org/10.1111/rssb.12312.
     """
 
     def __init__(

pyabc/petab/amici.py

@@ -177,10 +177,10 @@ class AmiciPetabImporter(PetabImporter):
     amici_model:
         A corresponding compiled AMICI model that allows simulating data for
         parameters. If not provided, one is created using
-        `amici.importers.petab.v1.import_petab_problem`.
+        :func:`amici.importers.petab.v1.import_petab_problem`.
     amici_solver:
         An AMICI solver to simulate the model. If not provided, one is created
-        using `amici_model.create_solver()`.
+        using ``amici_model.create_solver()``.
     """
 
     def __init__(
@@ -216,7 +216,7 @@ def create_model(
             Whether to return the simulations also (large, can be stored
             in database).
         return_rdatas:
-            Whether to return the full `list[amici.sim.sundials.ExpData]`
+            Whether to return the full ``list[amici.sim.sundials.ExpData]``
             objects (large, cannot be stored in database).
 
         Returns

pyabc/version.py

@@ -1 +1 @@
-__version__ = '0.13.0'
+__version__ = '0.13.1'

test/petab/test_petab.py

@@ -1,13 +1,11 @@
 import itertools
-import os
 import sys
 
+import benchmark_models_petab
 import cloudpickle as pickle
-import git
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
-import petab.v1 as petab
 import petab.v1.C as C
 import pytest
 import scipy.stats
@@ -285,38 +283,11 @@ def test_get_bounds():
         )
 
 
-benchmark_dir = 'doc/examples/tmp/benchmark-models-petab'
-
-
-def download_benchmark_repo():
-    # download archive
-    if not os.path.exists(benchmark_dir):
-        git.Repo.clone_from(
-            'https://github.com/benchmarking-initiative'
-            '/benchmark-models-petab.git',
-            benchmark_dir,
-            depth=1,
-        )
-    g = git.Git(benchmark_dir)
-
-    # update repo if online
-    try:
-        g.pull()
-    except git.exc.GitCommandError:
-        pass
-
-
 def boehm_model_importer():
     """Import Boehm model."""
-    download_benchmark_repo()
-
     # create problem
     model_name = 'Boehm_JProteomeRes2014'
-    petab_problem = petab.Problem.from_yaml(
-        os.path.join(
-            benchmark_dir, 'Benchmark-Models', model_name, model_name + '.yaml'
-        )
-    )
+    petab_problem = benchmark_models_petab.get_problem(model_name)
 
     # compile amici
     output_folder = f'amici_models/{model_name}'

tox.ini

@@ -133,7 +133,7 @@ deps =
 commands =
     python -m pip install --upgrade pip
     # install an old pyabc version
-    python -m pip install pyabc==0.10.13 numpy==1.23.5 pandas==1.5.0 sqlalchemy==1.4.48
+    python -m pip install pyabc==0.10.13 numpy==1.23.5 pandas==1.5.0 sqlalchemy==1.4.48 pyarrow<26
     python test/migrate/create_test_db.py
     # back to latest (this repo)
     python -m pip install --upgrade .