Prettify array assertion failure messages (#3117)

Author: dweindl

python/tests/adapters/test_fiddy.py

@@ -15,6 +15,7 @@
 from fiddy import MethodId, Type, get_derivative
 from fiddy.derivative_check import NumpyIsCloseDerivativeCheck
 from fiddy.success import Consistency
+from numpy.testing import assert_allclose
 from petab import v1
 
 # Absolute and relative tolerances for finite difference gradient checks.
@@ -85,13 +86,13 @@ def test_run_amici_simulation_to_functions(problem_generator):
     test_derivative = derivative.value
 
     # The test derivative is close to the expected derivative.
-    assert np.isclose(
+    assert_allclose(
         test_derivative,
         expected_derivative,
         rtol=1e-1,
         atol=1e-1,
         equal_nan=True,
-    ).all()
+    )
 
     # Same as above assert.
     check = NumpyIsCloseDerivativeCheck(

python/tests/test_bngl.py

@@ -11,6 +11,7 @@
 from amici.importers.bngl import bngl2amici
 from amici.sim.sundials import run_simulation
 from amici.testing import TemporaryDirectoryWinSafe, skip_on_valgrind
+from numpy.testing import assert_allclose
 from pysb.importers.bngl import model_from_bngl
 from pysb.simulator import ScipyOdeSimulator
 
@@ -113,4 +114,4 @@ def test_compare_to_pysb_simulation(example):
         rdata = run_simulation(model_amici, solver)
 
         # check agreement of species simulation
-        assert np.isclose(rdata.x, pysb_simres.species, 1e-4, 1e-4).all()
+        assert_allclose(rdata.x, pysb_simres.species, 1e-4, 1e-4)

python/tests/test_edata.py

@@ -10,6 +10,7 @@
     run_simulation,
 )
 from amici.testing import skip_on_valgrind
+from numpy.testing import assert_allclose
 
 
 @skip_on_valgrind
@@ -51,5 +52,5 @@ def test_edata_sensi_unscaling(model_units_module):  # noqa: F811
     rdata1 = run_simulation(model, solver, edata1)
 
     # The initial state sensitivities are as specified.
-    assert np.isclose(rdata0.sx0.flatten(), sx0).all()
-    assert np.isclose(rdata1.sx0.flatten(), sx0).all()
+    assert_allclose(rdata0.sx0.flatten(), sx0)
+    assert_allclose(rdata1.sx0.flatten(), sx0)

python/tests/test_pysb.py

@@ -57,29 +57,32 @@ def test_compare_to_sbml_import(
         [rdata_sbml, rdata_pysb], [model_sbml, model_pysb], ["sbml", "pysb"]
     ):
         # check equilibrium fixed parameters
-        assert np.isclose(
+        assert_allclose(
             [sum(rdata["x_ss"][[1, 3]]), sum(rdata["x_ss"][[2, 4]])],
             edata.fixed_parameters_pre_equilibration,
             atol=1e-6,
             rtol=1e-6,
-        ).all(), f"{importer} preequilibration"
+            err_msg=f"{importer} preequilibration",
+        )
 
         # check equilibrium initial parameters
-        assert np.isclose(
+        assert_allclose(
             sum(rdata["x_ss"][[0, 3, 4, 5]]),
             model.get_free_parameter_by_name("PROT_0"),
             atol=1e-6,
             rtol=1e-6,
-        ), f"{importer} preequilibration"
+            err_msg=f"{importer} preequilibration",
+        )
 
         # check reinitialization with fixed parameter after
         # presimulation
-        assert np.isclose(
+        assert_allclose(
             [rdata["x0"][1], rdata["x0"][2]],
             edata.fixed_parameters,
             atol=1e-6,
             rtol=1e-6,
-        ).all(), f"{importer} presimulation"
+            err_msg=f"{importer} presimulation",
+        )
 
     skip_attrs = [
         "ptr",
@@ -216,9 +219,7 @@ def test_compare_to_pysb_simulation(example):
                 rdata = run_simulation(model_pysb, solver)
 
                 # check agreement of species simulations
-                assert np.isclose(
-                    rdata["x"], pysb_simres.species, 1e-4, 1e-4
-                ).all()
+                assert_allclose(rdata["x"], pysb_simres.species, 1e-4, 1e-4)
 
                 if example not in [
                     "fricker_2010_apoptosis",