From a253b17f8156d81a7ee4ba7de495dac68ab01ea1 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <dweindl@users.noreply.github.com>
Date: Fri, 5 Jan 2024 09:18:23 +0100
Subject: [PATCH 1/6] pre-commit ruff (#2257)

Replace black&isort by [ruff](https://docs.astral.sh/ruff/) (faster, additional functionality).

* Enable (99%) black-compatible formatting
* Enable linting with autofixing
* Fix some linting issues
* `pre-commit run --all-files`
---
 .pre-commit-config.yaml                       | 30 +++++++++----------
 documentation/conf.py                         |  2 +-
 python/sdist/amici/__init__.py                | 11 ++++---
 python/sdist/amici/__init__.template.py       |  4 +--
 python/sdist/amici/de_export.py               |  2 +-
 python/sdist/amici/gradient_check.py          |  4 +--
 python/sdist/amici/import_utils.py            |  6 ++--
 python/sdist/amici/petab/util.py              |  7 +++--
 python/sdist/amici/plotting.py                |  3 +-
 python/sdist/amici/pysb_import.py             |  4 +--
 python/sdist/amici/sbml_import.py             |  9 +++---
 python/sdist/amici/sbml_utils.py              |  2 +-
 python/sdist/amici/splines.py                 |  5 +++-
 python/sdist/amici/swig_wrappers.py           |  2 +-
 python/sdist/pyproject.toml                   |  5 ++++
 python/tests/conftest.py                      |  1 -
 .../lotka_volterra/model/writer.py            |  1 -
 python/tests/test_edata.py                    |  4 +--
 python/tests/test_pysb.py                     |  1 +
 tests/conftest.py                             |  5 +++-
 .../generateTestConfig/example_steadystate.py |  2 +-
 21 files changed, 62 insertions(+), 48 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 521ff54f85..84438209b1 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,12 +1,6 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
-  hooks:
-    - id: isort
-      name: isort (python)
-      args: ["--profile", "black", "--filter-files", "--line-length", "79"]
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.4.0
   hooks:
@@ -16,15 +10,21 @@ repos:
     args: [--allow-multiple-documents]
   - id: end-of-file-fixer
   - id: trailing-whitespace
-- repo: https://github.com/psf/black
-  rev: 23.7.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.1.11
   hooks:
-    - id: black-jupyter
-      # It is recommended to specify the latest version of Python
-      # supported by your project here, or alternatively use
-      # pre-commit's default_language_version, see
-      # https://pre-commit.com/#top_level-default_language_version
-      language_version: python3.11
-      args: ["--line-length", "79"]
+    # Run the linter.
+    - id: ruff
+      args:
+        - --fix
+        - --config
+        - python/sdist/pyproject.toml
+
+    # Run the formatter.
+    - id: ruff-format
+      args:
+        - --config
+        - python/sdist/pyproject.toml
 
 exclude: '^(ThirdParty|models)/'
diff --git a/documentation/conf.py b/documentation/conf.py
index 6576601208..c880530e00 100644
--- a/documentation/conf.py
+++ b/documentation/conf.py
@@ -5,7 +5,6 @@
 # This file does only contain a selection of the most common options. For a
 # full list see the documentation:
 # http://www.sphinx-doc.org/en/stable/config
-
 import os
 import re
 import subprocess
@@ -18,6 +17,7 @@
 import exhale_multiproject_monkeypatch
 import mock
 import pandas as pd
+import sphinx
 import sympy as sp
 from exhale import configs as exhale_configs
 from sphinx.transforms.post_transforms import ReferencesResolver
diff --git a/python/sdist/amici/__init__.py b/python/sdist/amici/__init__.py
index 4ee6f05637..b06ea6d0f3 100644
--- a/python/sdist/amici/__init__.py
+++ b/python/sdist/amici/__init__.py
@@ -107,18 +107,21 @@ def _imported_from_setup() -> bool:
         #  from .swig_wrappers
         hdf5_enabled = "readSolverSettingsFromHDF5" in dir()
         # These modules require the swig interface and other dependencies
-        from .numpy import ExpDataView, ReturnDataView
+        from .numpy import ExpDataView, ReturnDataView  # noqa: F401
         from .pandas import *
         from .swig_wrappers import *
 
     # These modules don't require the swig interface
     from typing import Protocol, runtime_checkable
 
-    from .de_export import DEExporter, DEModel
-    from .sbml_import import SbmlImporter, assignmentRules2observables
+    from .de_export import DEExporter, DEModel  # noqa: F401
+    from .sbml_import import (  # noqa: F401
+        SbmlImporter,
+        assignmentRules2observables,
+    )
 
     @runtime_checkable
-    class ModelModule(Protocol):
+    class ModelModule(Protocol):  # noqa: F811
         """Type of AMICI-generated model modules.
 
         To enable static type checking."""
diff --git a/python/sdist/amici/__init__.template.py b/python/sdist/amici/__init__.template.py
index c37ac0f962..f5e49b03dd 100644
--- a/python/sdist/amici/__init__.template.py
+++ b/python/sdist/amici/__init__.template.py
@@ -15,7 +15,7 @@
         "version currently installed."
     )
 
-from .TPL_MODELNAME import *
-from .TPL_MODELNAME import getModel as get_model
+from .TPL_MODELNAME import *  # noqa: F403, F401
+from .TPL_MODELNAME import getModel as get_model  # noqa: F401
 
 __version__ = "TPL_PACKAGE_VERSION"
diff --git a/python/sdist/amici/de_export.py b/python/sdist/amici/de_export.py
index 63c9c05072..dddb748cab 100644
--- a/python/sdist/amici/de_export.py
+++ b/python/sdist/amici/de_export.py
@@ -587,7 +587,7 @@ def smart_multiply(
 
 
 def smart_is_zero_matrix(
-    x: Union[sp.MutableDenseMatrix, sp.MutableSparseMatrix]
+    x: Union[sp.MutableDenseMatrix, sp.MutableSparseMatrix],
 ) -> bool:
     """A faster implementation of sympy's is_zero_matrix
 
diff --git a/python/sdist/amici/gradient_check.py b/python/sdist/amici/gradient_check.py
index 27e2d671d3..5372fcc853 100644
--- a/python/sdist/amici/gradient_check.py
+++ b/python/sdist/amici/gradient_check.py
@@ -6,7 +6,7 @@
 """
 
 import copy
-from typing import Callable, List, Optional, Sequence
+from typing import List, Optional, Sequence
 
 import numpy as np
 
@@ -331,7 +331,7 @@ def _check_results(
     """
 
     result = rdata[field]
-    if type(result) is float:
+    if type(result) is float:  # noqa E721
         result = np.array(result)
 
     _check_close(
diff --git a/python/sdist/amici/import_utils.py b/python/sdist/amici/import_utils.py
index 2dfc60d0c5..9f75fcff75 100644
--- a/python/sdist/amici/import_utils.py
+++ b/python/sdist/amici/import_utils.py
@@ -72,7 +72,7 @@ class ObservableTransformation(str, enum.Enum):
 
 
 def noise_distribution_to_observable_transformation(
-    noise_distribution: Union[str, Callable]
+    noise_distribution: Union[str, Callable],
 ) -> ObservableTransformation:
     """
     Parse noise distribution string and extract observable transformation
@@ -93,7 +93,7 @@ def noise_distribution_to_observable_transformation(
 
 
 def noise_distribution_to_cost_function(
-    noise_distribution: Union[str, Callable]
+    noise_distribution: Union[str, Callable],
 ) -> Callable[[str], str]:
     """
     Parse noise distribution string to a cost function definition amici can
@@ -423,7 +423,7 @@ def _parse_special_functions(sym: sp.Expr, toplevel: bool = True) -> sp.Expr:
 
 
 def _denest_piecewise(
-    args: Sequence[Union[sp.Expr, sp.logic.boolalg.Boolean, bool]]
+    args: Sequence[Union[sp.Expr, sp.logic.boolalg.Boolean, bool]],
 ) -> Tuple[Union[sp.Expr, sp.logic.boolalg.Boolean, bool]]:
     """
     Denest piecewise functions that contain piecewise as condition
diff --git a/python/sdist/amici/petab/util.py b/python/sdist/amici/petab/util.py
index d30c1a6e9b..8f309e4071 100644
--- a/python/sdist/amici/petab/util.py
+++ b/python/sdist/amici/petab/util.py
@@ -1,6 +1,6 @@
 """Various helper functions for working with PEtab problems."""
 import re
-from typing import Dict, Tuple, Union
+from typing import TYPE_CHECKING, Dict, Tuple, Union
 
 import libsbml
 import pandas as pd
@@ -9,6 +9,9 @@
 from petab.mapping import resolve_mapping
 from petab.models import MODEL_TYPE_PYSB, MODEL_TYPE_SBML
 
+if TYPE_CHECKING:
+    pysb = None
+
 
 def get_states_in_condition_table(
     petab_problem: petab.Problem,
@@ -63,7 +66,7 @@ def get_states_in_condition_table(
             spm = pysb.pattern.SpeciesPatternMatcher(
                 model=petab_problem.model.model
             )
-        except NotImplementedError as e:
+        except NotImplementedError:
             raise NotImplementedError(
                 "Requires https://github.com/pysb/pysb/pull/570. "
                 "To use this functionality, update pysb via "
diff --git a/python/sdist/amici/plotting.py b/python/sdist/amici/plotting.py
index edf4a33156..895f83814a 100644
--- a/python/sdist/amici/plotting.py
+++ b/python/sdist/amici/plotting.py
@@ -56,8 +56,7 @@ def plot_state_trajectories(
     elif model is not None and prefer_names:
         labels = np.asarray(model.getStateNames())[list(state_indices)]
         labels = [
-            l if l else model.getStateIds()[ix]
-            for ix, l in enumerate(labels)
+            l if l else model.getStateIds()[ix] for ix, l in enumerate(labels)
         ]
     elif model is not None:
         labels = np.asarray(model.getStateIds())[list(state_indices)]
diff --git a/python/sdist/amici/pysb_import.py b/python/sdist/amici/pysb_import.py
index aa1dc7cd9b..5862d515a1 100644
--- a/python/sdist/amici/pysb_import.py
+++ b/python/sdist/amici/pysb_import.py
@@ -410,7 +410,7 @@ def _process_pysb_species(pysb_model: pysb.Model, ode_model: DEModel) -> None:
                 sp.Symbol(f"__s{ix}"), f"{specie}", init, xdot[ix]
             )
         )
-    logger.debug(f"Finished Processing PySB species ")
+    logger.debug("Finished Processing PySB species ")
 
 
 @log_execution_time("processing PySB parameters", logger)
@@ -1353,7 +1353,7 @@ def has_fixed_parameter_ic(
 
 
 def extract_monomers(
-    complex_patterns: Union[pysb.ComplexPattern, List[pysb.ComplexPattern]]
+    complex_patterns: Union[pysb.ComplexPattern, List[pysb.ComplexPattern]],
 ) -> List[str]:
     """
     Constructs a list of monomer names contained in complex patterns.
diff --git a/python/sdist/amici/sbml_import.py b/python/sdist/amici/sbml_import.py
index 124dfc7a63..d8361c04ab 100644
--- a/python/sdist/amici/sbml_import.py
+++ b/python/sdist/amici/sbml_import.py
@@ -21,7 +21,6 @@
     List,
     Optional,
     Sequence,
-    Set,
     Tuple,
     Union,
 )
@@ -1165,7 +1164,7 @@ def _process_reactions(self):
                     # accounts for possibly variable compartments.
                     self.stoichiometric_matrix[
                         species["index"], reaction_index
-                    ] += (sign * stoichiometry * species["conversion_factor"])
+                    ] += sign * stoichiometry * species["conversion_factor"]
             if reaction.isSetId():
                 sym_math = self._local_symbols[reaction.getId()]
             else:
@@ -2360,9 +2359,9 @@ def _replace_in_all_expressions(
         # rule (at the end of the _process_species method), hence needs to be
         # processed here too.
         self.compartments = {
-            smart_subs(c, old, new)
-            if replace_identifiers
-            else c: smart_subs(v, old, self._make_initial(new))
+            smart_subs(c, old, new) if replace_identifiers else c: smart_subs(
+                v, old, self._make_initial(new)
+            )
             for c, v in self.compartments.items()
         }
 
diff --git a/python/sdist/amici/sbml_utils.py b/python/sdist/amici/sbml_utils.py
index 66c9d01bbc..75bcb82a18 100644
--- a/python/sdist/amici/sbml_utils.py
+++ b/python/sdist/amici/sbml_utils.py
@@ -519,7 +519,7 @@ def mathml2sympy(
 
 
 def _parse_logical_operators(
-    math_str: Union[str, float, None]
+    math_str: Union[str, float, None],
 ) -> Union[str, float, None]:
     """
     Parses a math string in order to replace logical operators by a form
diff --git a/python/sdist/amici/splines.py b/python/sdist/amici/splines.py
index fdb0912045..657170c2f5 100644
--- a/python/sdist/amici/splines.py
+++ b/python/sdist/amici/splines.py
@@ -1510,7 +1510,10 @@ def spline_user_functions(
         "AmiciSplineSensitivity": [
             (
                 lambda *args: True,
-                lambda spline_id, x, param_id, *p: f"sspl_{spline_ids.index(spline_id)}_{p_index[param_id]}",
+                lambda spline_id,
+                x,
+                param_id,
+                *p: f"sspl_{spline_ids.index(spline_id)}_{p_index[param_id]}",
             )
         ],
     }
diff --git a/python/sdist/amici/swig_wrappers.py b/python/sdist/amici/swig_wrappers.py
index f56f3bd5d2..4983a28f23 100644
--- a/python/sdist/amici/swig_wrappers.py
+++ b/python/sdist/amici/swig_wrappers.py
@@ -54,7 +54,7 @@ def _capture_cstdout():
 
 
 def _get_ptr(
-    obj: Union[AmiciModel, AmiciExpData, AmiciSolver, AmiciReturnData]
+    obj: Union[AmiciModel, AmiciExpData, AmiciSolver, AmiciReturnData],
 ) -> Union[
     "amici_swig.Model",
     "amici_swig.ExpData",
diff --git a/python/sdist/pyproject.toml b/python/sdist/pyproject.toml
index 011064fbdb..91b8484af6 100644
--- a/python/sdist/pyproject.toml
+++ b/python/sdist/pyproject.toml
@@ -15,3 +15,8 @@ build-backend = "setuptools.build_meta"
 
 [tool.black]
 line-length = 79
+
+[tool.ruff]
+line-length = 79
+ignore = ["E402", "F403", "F405", "E741"]
+extend-include = ["*.ipynb"]
diff --git a/python/tests/conftest.py b/python/tests/conftest.py
index 9ab64b91d7..1da7cb31b3 100644
--- a/python/tests/conftest.py
+++ b/python/tests/conftest.py
@@ -2,7 +2,6 @@
 import copy
 import importlib
 import os
-import shutil
 import sys
 
 import amici
diff --git a/python/tests/petab_test_problems/lotka_volterra/model/writer.py b/python/tests/petab_test_problems/lotka_volterra/model/writer.py
index 76b98c3deb..c6abebaebe 100644
--- a/python/tests/petab_test_problems/lotka_volterra/model/writer.py
+++ b/python/tests/petab_test_problems/lotka_volterra/model/writer.py
@@ -1,6 +1,5 @@
 from pathlib import Path
 
-import petab
 import yaml2sbml
 
 yaml2sbml_yaml = "lotka_volterra.yaml"
diff --git a/python/tests/test_edata.py b/python/tests/test_edata.py
index 9c4d9b9edc..27c67de61e 100644
--- a/python/tests/test_edata.py
+++ b/python/tests/test_edata.py
@@ -2,11 +2,11 @@
 import amici
 import numpy as np
 from amici.testing import skip_on_valgrind
-from test_sbml_import import model_units_module
+from test_sbml_import import model_units_module  # noqa: F401
 
 
 @skip_on_valgrind
-def test_edata_sensi_unscaling(model_units_module):
+def test_edata_sensi_unscaling(model_units_module):  # noqa: F811
     """
     ExpData parameters should be used for unscaling initial state
     sensitivities.
diff --git a/python/tests/test_pysb.py b/python/tests/test_pysb.py
index 52ca3a320f..2911b05fc9 100644
--- a/python/tests/test_pysb.py
+++ b/python/tests/test_pysb.py
@@ -1,4 +1,5 @@
 """PYSB model tests"""
+# flake8: noqa: F821
 
 import importlib
 import logging
diff --git a/tests/conftest.py b/tests/conftest.py
index 9e90400518..7d98a09abb 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -3,10 +3,13 @@
 import re
 import sys
 from pathlib import Path
-from typing import List, Set, Tuple
+from typing import TYPE_CHECKING, List, Set, Tuple
 
 import pytest
 
+if TYPE_CHECKING:
+    from _pytest.reports import TestReport
+
 # stores passed SBML semantic test suite IDs
 passed_ids = []
 
diff --git a/tests/generateTestConfig/example_steadystate.py b/tests/generateTestConfig/example_steadystate.py
index 07fab49dfe..80e8a776d2 100755
--- a/tests/generateTestConfig/example_steadystate.py
+++ b/tests/generateTestConfig/example_steadystate.py
@@ -2,7 +2,7 @@
 import sys
 
 import numpy as np
-from example import AmiciExample, dict2attrs
+from example import AmiciExample
 
 
 class ExampleSteadystate(AmiciExample):

From 68a6625eadf54a214bb0eda333139e84a3b7a46a Mon Sep 17 00:00:00 2001
From: Daniel Weindl <dweindl@users.noreply.github.com>
Date: Fri, 5 Jan 2024 09:32:50 +0100
Subject: [PATCH 2/6] Doc: Update edata.h (#2254)

---
 include/amici/edata.h | 61 ++++++++++++++++++++++---------------------
 1 file changed, 31 insertions(+), 30 deletions(-)

diff --git a/include/amici/edata.h b/include/amici/edata.h
index f8639ca2eb..78bcba0fc7 100644
--- a/include/amici/edata.h
+++ b/include/amici/edata.h
@@ -14,24 +14,24 @@ class ReturnData;
 
 /**
  * @brief ExpData carries all information about experimental or
- * condition-specific data
+ * condition-specific data.
  */
 class ExpData : public SimulationParameters {
 
   public:
     /**
-     * @brief default constructor
+     * @brief Default constructor.
      */
     ExpData() = default;
 
     /**
-     * @brief Copy constructor, needs to be declared to be generated in
-     * swig
+     * @brief Copy constructor.
      */
+    // needs to be declared to be wrapped by SWIG
     ExpData(ExpData const&) = default;
 
     /**
-     * @brief constructor that only initializes dimensions
+     * @brief Constructor that only initializes dimensions.
      *
      * @param nytrue Number of observables
      * @param nztrue Number of event outputs
@@ -154,6 +154,16 @@ class ExpData : public SimulationParameters {
     /**
      * @brief Set output timepoints.
      *
+     * If the number of timepoint increases, this will grow the
+     * observation/sigma matrices and fill new entries with NaN.
+     * If the number of timepoints decreases, this will shrink the
+     * observation/sigma matrices.
+     *
+     * Note that the mapping from timepoints to measurements will not be
+     * preserved. E.g., say there are measurements at t = 2, and this
+     * function is called with [1, 2], then the old measurements will belong to
+     * t = 1.
+     *
      * @param ts timepoints
      */
     void setTimepoints(std::vector<realtype> const& ts);
@@ -225,7 +235,7 @@ class ExpData : public SimulationParameters {
     void setObservedDataStdDev(std::vector<realtype> const& observedDataStdDev);
 
     /**
-     * @brief Set indentical standard deviation for all measurements.
+     * @brief Set identical standard deviation for all measurements.
      *
      * @param stdDev standard deviation (dimension: scalar)
      */
@@ -278,8 +288,7 @@ class ExpData : public SimulationParameters {
     realtype const* getObservedDataStdDevPtr(int it) const;
 
     /**
-     * @brief set function that copies observed event data from input to
-     * ExpData::observedEvents
+     * @brief Set observed event data.
      *
      * @param observedEvents observed data (dimension: nmaxevent x nztrue,
      * row-major)
@@ -287,8 +296,7 @@ class ExpData : public SimulationParameters {
     void setObservedEvents(std::vector<realtype> const& observedEvents);
 
     /**
-     * @brief set function that copies observed event data for specific event
-     * observable
+     * @brief Set observed event data for specific event observable.
      *
      * @param observedEvents observed data (dimension: nmaxevent)
      * @param iz observed event data index
@@ -296,8 +304,7 @@ class ExpData : public SimulationParameters {
     void setObservedEvents(std::vector<realtype> const& observedEvents, int iz);
 
     /**
-     * @brief get function that checks whether event data at specified indices
-     * has been set
+     * @brief Check whether event data at specified indices has been set.
      *
      * @param ie event index
      * @param iz event observable index
@@ -306,25 +313,23 @@ class ExpData : public SimulationParameters {
     bool isSetObservedEvents(int ie, int iz) const;
 
     /**
-     * @brief get function that copies data from ExpData::mz to output
+     * @brief Get observed event data.
      *
      * @return observed event data
      */
     std::vector<realtype> const& getObservedEvents() const;
 
     /**
-     * @brief get function that returns a pointer to observed data at ieth
-     * occurrence
+     * @brief Get pointer to observed data at ie-th occurrence.
      *
      * @param ie event occurrence
      *
-     * @return pointer to observed event data at ieth occurrence
+     * @return pointer to observed event data at ie-th occurrence
      */
     realtype const* getObservedEventsPtr(int ie) const;
 
     /**
-     * @brief set function that copies data from input to
-     * ExpData::observedEventsStdDev
+     * @brief Set standard deviation of observed event data.
      *
      * @param observedEventsStdDev standard deviation of observed event data
      */
@@ -332,16 +337,14 @@ class ExpData : public SimulationParameters {
     setObservedEventsStdDev(std::vector<realtype> const& observedEventsStdDev);
 
     /**
-     * @brief set function that sets all ExpData::observedDataStdDev to the
-     * input value
+     * @brief Set standard deviation of observed event data.
      *
      * @param stdDev standard deviation (dimension: scalar)
      */
     void setObservedEventsStdDev(realtype stdDev);
 
     /**
-     * @brief set function that copies standard deviation of observed data for
-     * specific observable
+     * @brief Set standard deviation of observed data for a specific observable.
      *
      * @param observedEventsStdDev standard deviation of observed data
      * (dimension: nmaxevent)
@@ -352,8 +355,7 @@ class ExpData : public SimulationParameters {
     );
 
     /**
-     * @brief set function that sets all standard deviation of a specific
-     * observable to the input value
+     * @brief Set all standard deviations of a specific event-observable.
      *
      * @param stdDev standard deviation (dimension: scalar)
      * @param iz observed data index
@@ -361,8 +363,8 @@ class ExpData : public SimulationParameters {
     void setObservedEventsStdDev(realtype stdDev, int iz);
 
     /**
-     * @brief get function that checks whether standard deviation of even data
-     * at specified indices has been set
+     * @brief Check whether standard deviation of event data
+     * at specified indices has been set.
      *
      * @param ie event index
      * @param iz event observable index
@@ -371,16 +373,15 @@ class ExpData : public SimulationParameters {
     bool isSetObservedEventsStdDev(int ie, int iz) const;
 
     /**
-     * @brief get function that copies data from ExpData::observedEventsStdDev
-     * to output
+     * @brief Get standard deviation of observed event data.
      *
      * @return standard deviation of observed event data
      */
     std::vector<realtype> const& getObservedEventsStdDev() const;
 
     /**
-     * @brief get function that returns a pointer to standard deviation of
-     * observed event data at ie-th occurrence
+     * @brief Get pointer to standard deviation of
+     * observed event data at ie-th occurrence.
      *
      * @param ie event occurrence
      *

From 9886c690f3c5619148a6fd9541e7d3741bbf108a Mon Sep 17 00:00:00 2001
From: Daniel Weindl <dweindl@users.noreply.github.com>
Date: Sat, 6 Jan 2024 10:40:32 +0100
Subject: [PATCH 3/6] Fix swig shadow warning + other linting issues (#2261)

Fixes swig warning
```
include/amici/simulation_parameters.h:71: Warning 509: Overloaded method amici::SimulationParameters::SimulationParameters(std::vector< amici::realtype,std::allocator< amici::realtype > >,std::vector< amici::realtype,std::allocator< amici::realtype > >,std::vector< amici::realtype,std::allocator< amici::realtype > >) effectively ignored,
include/amici/simulation_parameters.h:54: Warning 509: as it is shadowed by amici::SimulationParameters::SimulationParameters(std::vector< amici::realtype,std::allocator< amici::realtype > >,std::vector< amici::realtype,std::allocator< amici::realtype > >,std::vector< int,std::allocator< int > >).
```

and some other linting warnings.
---
 include/amici/logging.h               | 2 +-
 include/amici/model.h                 | 2 +-
 include/amici/simulation_parameters.h | 6 ++++++
 src/steadystateproblem.cpp            | 6 +++---
 4 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/include/amici/logging.h b/include/amici/logging.h
index 0118bedd28..6af039d4c4 100644
--- a/include/amici/logging.h
+++ b/include/amici/logging.h
@@ -83,7 +83,7 @@ struct LogItem {
         , message(message){};
 
     /** Severity level */
-    LogSeverity severity;
+    LogSeverity severity = LogSeverity::error;
 
     /** Short identifier for the logged event */
     std::string identifier;
diff --git a/include/amici/model.h b/include/amici/model.h
index f5421bed3d..3d2645028a 100644
--- a/include/amici/model.h
+++ b/include/amici/model.h
@@ -1437,7 +1437,7 @@ class Model : public AbstractModel, public ModelDimensions {
     std::vector<int> const& getReinitializationStateIdxs() const;
 
     /** Flag indicating Matlab- or Python-based model generation */
-    bool pythonGenerated;
+    bool pythonGenerated = false;
 
     /**
      * @brief getter for dxdotdp (matlab generated)
diff --git a/include/amici/simulation_parameters.h b/include/amici/simulation_parameters.h
index ca0e127c5c..55db090184 100644
--- a/include/amici/simulation_parameters.h
+++ b/include/amici/simulation_parameters.h
@@ -35,6 +35,11 @@ class SimulationParameters {
               this->parameters.size(), ParameterScaling::none
           )) {}
 
+#ifndef SWIGPYTHON
+    /*
+     * include/amici/simulation_parameters.h:71: Warning 509: Overloaded method amici::SimulationParameters::SimulationParameters(std::vector< amici::realtype,std::allocator< amici::realtype > >,std::vector< amici::realtype,std::allocator< amici::realtype > >,std::vector< amici::realtype,std::allocator< amici::realtype > >) effectively ignored,
+     * include/amici/simulation_parameters.h:54: Warning 509: as it is shadowed by amici::SimulationParameters::SimulationParameters(std::vector< amici::realtype,std::allocator< amici::realtype > >,std::vector< amici::realtype,std::allocator< amici::realtype > >,std::vector< int,std::allocator< int > >).
+     */
     /**
      * @brief Constructor
      * @param fixedParameters Model constants
@@ -69,6 +74,7 @@ class SimulationParameters {
               this->parameters.size(), ParameterScaling::none
           ))
         , ts_(std::move(timepoints)) {}
+#endif
 
     /**
      * @brief Set reinitialization of all states based on model constants for
diff --git a/src/steadystateproblem.cpp b/src/steadystateproblem.cpp
index 4576b43363..98c36589f7 100644
--- a/src/steadystateproblem.cpp
+++ b/src/steadystateproblem.cpp
@@ -601,8 +601,6 @@ void SteadystateProblem::applyNewtonsMethod(Model& model, bool newton_retry) {
     int& i_newtonstep = numsteps_.at(newton_retry ? 2 : 0);
     i_newtonstep = 0;
     gamma_ = 1.0;
-    bool update_direction = true;
-    bool step_successful = false;
 
     if (model.nx_solver == 0)
         return;
@@ -613,6 +611,8 @@ void SteadystateProblem::applyNewtonsMethod(Model& model, bool newton_retry) {
     bool converged = false;
     wrms_ = getWrms(model, SensitivityMethod::none);
     converged = newton_retry ? false : wrms_ < conv_thresh;
+    bool update_direction = true;
+
     while (!converged && i_newtonstep < max_steps_) {
 
         /* If Newton steps are necessary, compute the initial search
@@ -634,7 +634,7 @@ void SteadystateProblem::applyNewtonsMethod(Model& model, bool newton_retry) {
         /* Compute new xdot and residuals */
         realtype wrms_tmp = getWrms(model, SensitivityMethod::none);
 
-        step_successful = wrms_tmp < wrms_;
+        bool step_successful = wrms_tmp < wrms_;
         if (step_successful) {
             /* If new residuals are smaller than old ones, update state */
             wrms_ = wrms_tmp;

From 30ed2f0feb338cb30207f1ff7784280e26ab17de Mon Sep 17 00:00:00 2001
From: Daniel Weindl <dweindl@users.noreply.github.com>
Date: Sat, 6 Jan 2024 10:46:19 +0100
Subject: [PATCH 4/6] Fix `SwigPtrView.__getattr__` (#2259)

`hasattr` didn't work with SwigPtrView, because calling `__getattr__` for a missing attribute resulted in a KeyError via `__missing__`. However, hasattr expects an attribute error in that case. Fixed. Added tests.
---
 python/sdist/amici/numpy.py         |  5 ++++-
 python/tests/test_swig_interface.py | 25 +++++++++++++++++++++++++
 2 files changed, 29 insertions(+), 1 deletion(-)

diff --git a/python/sdist/amici/numpy.py b/python/sdist/amici/numpy.py
index 93b04603be..b259aca2a0 100644
--- a/python/sdist/amici/numpy.py
+++ b/python/sdist/amici/numpy.py
@@ -80,7 +80,10 @@ def __getattr__(self, item) -> Union[np.ndarray, float]:
 
         :returns: value
         """
-        return self.__getitem__(item)
+        try:
+            return self.__getitem__(item)
+        except KeyError as e:
+            raise AttributeError(item) from e
 
     def __init__(self, swigptr):
         """
diff --git a/python/tests/test_swig_interface.py b/python/tests/test_swig_interface.py
index 3eabafd49b..ffec95b77b 100644
--- a/python/tests/test_swig_interface.py
+++ b/python/tests/test_swig_interface.py
@@ -6,6 +6,8 @@
 import copy
 import numbers
 
+import pytest
+
 import amici
 import numpy as np
 
@@ -500,3 +502,26 @@ def test_model_is_deepcopyable(pysb_example_presimulation_module):
         assert model1.t0() == model2.t0()
         model2.setT0(100 + model2.t0())
         assert model1.t0() != model2.t0()
+
+
+def test_rdataview(sbml_example_presimulation_module):
+    """Test some SwigPtrView functionality via ReturnDataView."""
+    model_module = sbml_example_presimulation_module
+    model = model_module.getModel()
+    rdata = amici.runAmiciSimulation(model, model.getSolver())
+    assert isinstance(rdata, amici.ReturnDataView)
+
+    # fields are accessible via dot notation and [] operator,
+    #  __contains__ and __getattr__ are implemented correctly
+    with pytest.raises(AttributeError):
+        _ = rdata.nonexisting_attribute
+
+    with pytest.raises(KeyError):
+        _ = rdata["nonexisting_attribute"]
+
+    assert not hasattr(rdata, "nonexisting_attribute")
+    assert "x" in rdata
+    assert rdata.x == rdata["x"]
+
+    # field names are included by dir()
+    assert "x" in dir(rdata)

From 66f4ba540cba7fa562baa0f5b93b670526416b32 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <dweindl@users.noreply.github.com>
Date: Sat, 6 Jan 2024 11:43:57 +0100
Subject: [PATCH 5/6] GHA: Split macOS C++ / Python test jobs (#2260)

Currently, macOS jobs run for >1h, this can be rather annoying.
Splitting current tests into two separate jobs. Now we have 33' + 23' instead of 1h20'.

Also:
* cleanup some bash scripts
* manage dependencies via pyproject.toml
* move h5py dependency to extras
* parallelize model compilation on macos
---
 .../install-macos-dependencies/action.yml     | 31 ++++++++++
 .github/workflows/test_python_cplusplus.yml   | 60 +++++++++++++++----
 python/sdist/setup.cfg                        |  6 +-
 scripts/installAmiciSource.sh                 | 32 +++++-----
 scripts/run-python-tests.sh                   | 12 ++--
 scripts/run-valgrind-py.sh                    |  3 +-
 6 files changed, 109 insertions(+), 35 deletions(-)
 create mode 100644 .github/actions/install-macos-dependencies/action.yml

diff --git a/.github/actions/install-macos-dependencies/action.yml b/.github/actions/install-macos-dependencies/action.yml
new file mode 100644
index 0000000000..b19cac1052
--- /dev/null
+++ b/.github/actions/install-macos-dependencies/action.yml
@@ -0,0 +1,31 @@
+name: Install AMICI dependencies for MacOS
+description: Install AMICI dependencies for MacOS
+
+runs:
+  using: "composite"
+  steps:
+    # use all available cores
+    - run: echo "AMICI_PARALLEL_COMPILE=" >> $GITHUB_ENV
+      shell: bash
+
+    # AMICI repository root
+    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
+      shell: bash
+
+    # BioNetGen path
+    - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
+      shell: bash
+
+    # CMake hints
+    # Ensure CMake is using the python version that we will use for the python tests later on
+    - run: echo "PYTHON_EXECUTABLE=${Python3_ROOT_DIR}/bin/python3" >> $GITHUB_ENV
+      shell: bash
+    - run: echo "OpenMP_ROOT=$(brew --prefix)/opt/libomp" >> $GITHUB_ENV
+      shell: bash
+    - run: echo "BOOST_ROOT=$(brew --prefix)/opt/boost" >> $GITHUB_ENV
+      shell: bash
+
+    # install amici dependencies
+    - name: homebrew
+      run: brew install hdf5 swig gcc libomp boost
+      shell: bash
diff --git a/.github/workflows/test_python_cplusplus.yml b/.github/workflows/test_python_cplusplus.yml
index 496779c6ec..5aa47173b8 100644
--- a/.github/workflows/test_python_cplusplus.yml
+++ b/.github/workflows/test_python_cplusplus.yml
@@ -218,8 +218,8 @@ jobs:
 
     # TODO: Include notebooks in coverage report
 
-  osx:
-    name: Tests OSX
+  macos_cpp_py:
+    name: Tests MacOS C++/Python
     runs-on: macos-latest
 
     steps:
@@ -231,16 +231,11 @@ jobs:
     - uses: actions/checkout@v3
     - run: git fetch --prune --unshallow
 
-    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
-    - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
-    # Ensure CMake is using the python version that we will use for the python tests later on
-    - run: echo "PYTHON_EXECUTABLE=${Python3_ROOT_DIR}/bin/python3" >> $GITHUB_ENV
-    - run: echo "OpenMP_ROOT=$(brew --prefix)/opt/libomp" >> $GITHUB_ENV
-    - run: echo "BOOST_ROOT=$(brew --prefix)/opt/boost" >> $GITHUB_ENV
+    - name: Install dependencies
+      uses: ./.github/actions/install-macos-dependencies
 
-    # install amici dependencies
     - name: homebrew
-      run: brew install hdf5 swig gcc cppcheck libomp boost
+      run: brew install cppcheck
 
     - name: Build AMICI
       run: scripts/buildAll.sh
@@ -254,8 +249,47 @@ jobs:
     - name: cppcheck
       run: scripts/run-cppcheck.sh
 
-    - name: Python tests
-      run: scripts/run-python-tests.sh
-
     - name: C++ tests
       run: scripts/run-cpp-tests.sh
+
+    - name: Python tests
+      run: |
+        scripts/run-python-tests.sh \
+          test_pregenerated_models.py \
+          test_splines_short.py \
+          test_misc.py
+
+
+  macos_python:
+    name: Tests MacOS Python
+    runs-on: macos-latest
+
+    steps:
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+
+    - uses: actions/checkout@v3
+    - run: git fetch --prune --unshallow
+
+    - name: Install dependencies
+      uses: ./.github/actions/install-macos-dependencies
+
+    - name: Install python package
+      run: |
+        pip show numpy > /dev/null || python3 -m pip install numpy
+        scripts/installAmiciSource.sh
+
+    - name: Check OpenMP support
+      run: source build/venv/bin/activate && python -c "import amici; import sys; sys.exit(not amici.compiledWithOpenMP())"
+
+    - name: Get BioNetGen
+      run: scripts/buildBNGL.sh
+
+    - name: Python tests
+      run: |
+        scripts/run-python-tests.sh \
+          --ignore=test_pregenerated_models.py \
+          --ignore=test_splines_short.py \
+          --ignore=test_misc.py
diff --git a/python/sdist/setup.cfg b/python/sdist/setup.cfg
index 8e8797fda7..5ae8e1e742 100644
--- a/python/sdist/setup.cfg
+++ b/python/sdist/setup.cfg
@@ -34,7 +34,6 @@ install_requires =
     numpy>=1.23.2; python_version=='3.11'
     numpy; python_version>='3.12'
     python-libsbml
-    h5py
     pandas>=2.0.2
     wurlitzer
     toposort
@@ -47,6 +46,7 @@ zip_safe = False
 petab = petab>=0.2.1
 pysb = pysb>=1.13.1
 test =
+    h5py
     pytest
     pytest-cov
     pytest-rerunfailures
@@ -56,9 +56,13 @@ test =
     # see https://github.com/sys-bio/antimony/issues/92
     #  unsupported x86_64 / x86_64h
     antimony!=2.14; platform_system=='Darwin' and platform_machine in 'x86_64h'
+    scipy
 vis =
     matplotlib
     seaborn
+examples =
+    jupyter
+    scipy
 
 [options.package_data]
 amici =
diff --git a/scripts/installAmiciSource.sh b/scripts/installAmiciSource.sh
index 4e693468b7..bbb4bf4a83 100755
--- a/scripts/installAmiciSource.sh
+++ b/scripts/installAmiciSource.sh
@@ -1,35 +1,37 @@
 #!/bin/bash
-#
-# Build libamici
-#
+# Create a virtual environment and perform an editable amici installation
 set -e
 
 SCRIPT_PATH=$(dirname $BASH_SOURCE)
-AMICI_PATH=$(cd $SCRIPT_PATH/.. && pwd)
+AMICI_PATH=$(cd "$SCRIPT_PATH/.." && pwd)
 
+venv_dir="${AMICI_PATH}/build/venv"
 # Disabled until cmake package is made compatible with updated setup.py
 #make python-wheel
 #pip3 install --user --prefix= `ls -t ${AMICI_PATH}/build/python/amici-*.whl | head -1`
 
 # test install from setup.py
 set +e
-python3 -m venv ${AMICI_PATH}/build/venv --clear
+mkdir -p "${venv_dir}"
+python3 -m venv "${venv_dir}" --clear
 # in case this fails (usually due to missing ensurepip, try getting pip
 # manually
 if [[ $? ]]; then
     set -e
-    python3 -m venv ${AMICI_PATH}/build/venv --clear --without-pip
-    source ${AMICI_PATH}/build/venv/bin/activate
-    curl https://bootstrap.pypa.io/get-pip.py -o ${AMICI_PATH}/build/get-pip.py
-    python3 ${AMICI_PATH}/build/get-pip.py
+    python3 -m venv "${venv_dir}" --clear --without-pip
+    source "${venv_dir}/bin/activate"
+    get_pip=${AMICI_PATH}/build/get-pip.py
+    curl "https://bootstrap.pypa.io/get-pip.py" -o "${get_pip}"
+    python3 "${get_pip}"
+    rm "${get_pip}"
 else
     set -e
-    source ${AMICI_PATH}/build/venv/bin/activate
+    source "${venv_dir}/bin/activate"
 fi
 
-pip install --upgrade pip wheel
-pip install --upgrade pip scipy matplotlib coverage pytest \
-  pytest-cov cmake_build_extension numpy
-pip install git+https://github.com/FFroehlich/pysb@fix_pattern_matching # pin to PR for SPM with compartments
-AMICI_BUILD_TEMP="${AMICI_PATH}/python/sdist/build/temp" pip install --verbose -e ${AMICI_PATH}/python/sdist[petab,test,vis] --no-build-isolation
+python -m pip install --upgrade pip wheel
+python -m pip install --upgrade pip setuptools cmake_build_extension numpy
+python -m pip install git+https://github.com/FFroehlich/pysb@fix_pattern_matching # pin to PR for SPM with compartments
+AMICI_BUILD_TEMP="${AMICI_PATH}/python/sdist/build/temp" \
+  python -m pip install --verbose -e "${AMICI_PATH}/python/sdist[petab,test,vis]" --no-build-isolation
 deactivate
diff --git a/scripts/run-python-tests.sh b/scripts/run-python-tests.sh
index 982aa02f0f..d58a1c8dec 100755
--- a/scripts/run-python-tests.sh
+++ b/scripts/run-python-tests.sh
@@ -1,7 +1,8 @@
 #!/bin/bash
-# Test python model wrapping inside virtual environment
+# Run Python test suite inside virtual environment
+# Usage: ./run-python-tests.sh [additional pytest arguments]
 
-script_path=$(dirname $BASH_SOURCE)
+script_path=$(dirname "${BASH_SOURCE[0]}")
 amici_path=$(cd "$script_path"/.. && pwd)
 
 set -e
@@ -12,7 +13,10 @@ fi
 
 cd "${amici_path}"/python/tests
 source "${amici_path}"/build/venv/bin/activate
-pip install scipy h5py pytest pytest-cov
 
 # PEtab tests are run separately
-pytest --ignore-glob=*petab* --ignore-glob=*test_splines.py
+pytest \
+  --ignore-glob=*petab* \
+  --ignore-glob=*test_splines.py \
+  --durations=10 \
+  $@
diff --git a/scripts/run-valgrind-py.sh b/scripts/run-valgrind-py.sh
index d9e6158d51..c2a6239ad4 100755
--- a/scripts/run-valgrind-py.sh
+++ b/scripts/run-valgrind-py.sh
@@ -2,7 +2,7 @@
 # Without arguments: run Python test suite under valgrind
 # With arguments: run whatever was passed as arguments under valgrind
 
-script_path=$(dirname $BASH_SOURCE)
+script_path=$(dirname "${BASH_SOURCE[0]}")
 amici_path=$(cd "$script_path"/.. && pwd)
 
 set -e
@@ -16,7 +16,6 @@ if [ $# -eq 0 ]
     # No arguments supplied, run all tests
     cd "${amici_path}"/python/tests
     source "${amici_path}"/build/venv/bin/activate
-    pip install scipy h5py pytest pytest-rerunfailures
     command=(python -m pytest -vv --ignore-glob=*petab* -W 'ignore:Signature ')
     #                                                    ^ ignores the following warning that occurs only under valgrind,
     # e.g. `valgrind python -c "import h5py"`:

From 3d01ebbdd5d243b715a845f1ce4bd6cca10a08aa Mon Sep 17 00:00:00 2001
From: Daniel Weindl <dweindl@users.noreply.github.com>
Date: Sun, 7 Jan 2024 14:10:21 +0100
Subject: [PATCH 6/6] Use Model.setAlwaysCheckFinite(True) in debug builds
 (#2262)

* Use Model.setAlwaysCheckFinite(True) in debug builds

So that we automatically use the additional checks in our tests.

Closes #2235

* Fix sparse-`unravel_index` for the case where no indices/ptrs have been set (this is the case for matlab-generated models).
---
 include/amici/model.h               |  4 ++++
 python/tests/test_swig_interface.py | 12 +++++++----
 src/sundials_matrix_wrapper.cpp     | 33 +++++++++++++++++------------
 tests/cpp/unittests/testMisc.cpp    | 12 ++++++++++-
 4 files changed, 42 insertions(+), 19 deletions(-)

diff --git a/include/amici/model.h b/include/amici/model.h
index 3d2645028a..d355ea7fee 100644
--- a/include/amici/model.h
+++ b/include/amici/model.h
@@ -2020,7 +2020,11 @@ class Model : public AbstractModel, public ModelDimensions {
      * Indicates whether the result of every call to `Model::f*` should be
      * checked for finiteness
      */
+#ifdef NDEBUG
     bool always_check_finite_{false};
+#else
+    bool always_check_finite_{true};
+#endif
 
     /** indicates whether sigma residuals are to be added for every datapoint */
     bool sigma_res_{false};
diff --git a/python/tests/test_swig_interface.py b/python/tests/test_swig_interface.py
index ffec95b77b..536c107458 100644
--- a/python/tests/test_swig_interface.py
+++ b/python/tests/test_swig_interface.py
@@ -68,10 +68,7 @@ def test_copy_constructors(pysb_example_presimulation_module):
 model_instance_settings0 = {
     # setting name: [default value, custom value]
     "AddSigmaResiduals": [False, True],
-    "AlwaysCheckFinite": [
-        False,
-        True,
-    ],
+    "AlwaysCheckFinite": [False, True],
     # Skipped due to model dependency in `'InitialStates'`.
     "FixedParameters": None,
     "InitialStates": [
@@ -132,6 +129,13 @@ def test_model_instance_settings(pysb_example_presimulation_module):
     i_getter = 0
     i_setter = 1
 
+    # the default setting for AlwaysCheckFinite depends on whether the amici
+    # extension has been built in debug mode
+    model_instance_settings0["AlwaysCheckFinite"] = [
+        model0.getAlwaysCheckFinite(),
+        not model0.getAlwaysCheckFinite(),
+    ]
+
     # All settings are tested.
     assert set(model_instance_settings0) == set(
         amici.swig_wrappers.model_instance_settings
diff --git a/src/sundials_matrix_wrapper.cpp b/src/sundials_matrix_wrapper.cpp
index b5c7300628..a86574cd82 100644
--- a/src/sundials_matrix_wrapper.cpp
+++ b/src/sundials_matrix_wrapper.cpp
@@ -793,20 +793,25 @@ unravel_index(sunindextype i, SUNMatrix m) {
     }
 
     if (mat_id == SUNMATRIX_SPARSE) {
-        gsl_ExpectsDebug(i < SM_NNZ_S(m));
-        sunindextype row = SM_INDEXVALS_S(m)[i];
-        sunindextype i_colptr = 0;
-        while (SM_INDEXPTRS_S(m)[i_colptr] < SM_NNZ_S(m)) {
-            if (SM_INDEXPTRS_S(m)[i_colptr + 1] > i) {
-                sunindextype col = i_colptr;
-                gsl_EnsuresDebug(row >= 0);
-                gsl_EnsuresDebug(row < SM_ROWS_S(m));
-                gsl_EnsuresDebug(col >= 0);
-                gsl_EnsuresDebug(col < SM_COLUMNS_S(m));
-                return {row, col};
-            }
-            ++i_colptr;
-        }
+        auto nnz = SM_NNZ_S(m);
+        auto ncols = SM_COLUMNS_S(m);
+        auto index_vals = SM_INDEXVALS_S(m);
+        auto index_ptrs = SM_INDEXPTRS_S(m);
+        gsl_ExpectsDebug(i < nnz);
+        sunindextype row = index_vals[i];
+        sunindextype col = 0;
+        while (col < ncols && index_ptrs[col + 1] <= i)
+            ++col;
+
+        // This can happen if indexvals / indexptrs haven't been set.
+        if(col == ncols)
+            return {-1, -1};
+
+        gsl_EnsuresDebug(row >= 0);
+        gsl_EnsuresDebug(row < SM_ROWS_S(m));
+        gsl_EnsuresDebug(col >= 0);
+        gsl_EnsuresDebug(col < ncols);
+        return {row, col};
     }
 
     throw amici::AmiException("Unimplemented SUNMatrix type for unravel_index");
diff --git a/tests/cpp/unittests/testMisc.cpp b/tests/cpp/unittests/testMisc.cpp
index 14af3a7a82..f18de96b79 100644
--- a/tests/cpp/unittests/testMisc.cpp
+++ b/tests/cpp/unittests/testMisc.cpp
@@ -689,7 +689,7 @@ TEST(UnravelIndex, UnravelIndexSunMatSparse)
     // [2, 0]
     // data [1, 2, 3]
     // colptrs [0, 2, 3]
-    // rowidxs [2, 3, 1]
+    // rowidxs [2, 3, 0]
     D.set_data(0, 0, 0);
     D.set_data(1, 0, 0);
     D.set_data(2, 0, 1);
@@ -708,6 +708,16 @@ TEST(UnravelIndex, UnravelIndexSunMatSparse)
     SUNMatDestroy(S);
 }
 
+
+TEST(UnravelIndex, UnravelIndexSunMatSparseMissingIndices)
+{
+    // Sparse matrix without any indices set
+    SUNMatrixWrapper mat = SUNMatrixWrapper(2, 3, 2, CSC_MAT);
+    EXPECT_EQ(unravel_index(0, mat.get()), std::make_pair((sunindextype) -1, (sunindextype) -1));
+    EXPECT_EQ(unravel_index(1, mat.get()), std::make_pair((sunindextype) -1, (sunindextype) -1));
+}
+
+
 TEST(ReturnCodeToStr, ReturnCodeToStr)
 {
     EXPECT_EQ("AMICI_SUCCESS", simulation_status_to_str(AMICI_SUCCESS));