test(conftest): introduce new custom absolute tolerance

add "atol=custom_atol" for every assert_allclose statement that did not have it previously

test/conftest.py

@@ -15,6 +15,7 @@
 from PyDynamic import make_semiposdef
 from PyDynamic.misc.tools import normalize_vector_or_matrix
 
+custom_atol = 1e2 * np.finfo(np.float64).eps
 
 def _check_for_ci_to_switch_off_performance_related_healthchecks():
     if _running_in_ci():

test/test_DFT.py

@@ -31,6 +31,7 @@
     hypothesis_float_vector,
     hypothesis_not_negative_float_strategy,
     VectorAndCompatibleMatrix,
+    custom_atol,
 )
 
 
@@ -259,7 +260,7 @@ def test_DFT_MC(params):
     )
 
     # compare analytical and numerical result
-    assert_allclose(X, X_MC, rtol=1e-1)
+    assert_allclose(X, X_MC, rtol=1e-1, atol=custom_atol)
     assert_allclose(X_cov, X_MC_cov, atol=8e-1)
 
 
@@ -322,11 +323,11 @@ def test_iDFT_resampling_sensitivity(params):
     x_resampled_numpy = np.fft.irfft(ri2c(X), n=Nx)
 
     # check resampled signal against numpy implementation
-    assert_allclose(x_resampled_numpy, x_resampled, atol=1e-14)
+    assert_allclose(x_resampled_numpy, x_resampled, atol=custom_atol)
 
     # check sensitivities against numpy implementation
     C = np.hstack((sens["Cc"], sens["Cs"]))
-    assert_allclose(x_resampled_numpy, C @ X / Nx, atol=1e-14)
+    assert_allclose(x_resampled_numpy, C @ X / Nx, atol=custom_atol)
 
 
 @pytest.mark.slow
@@ -406,6 +407,7 @@ def test_apply_window_with_known_result(known_inputs_and_outputs_for_apply_windo
     assert_allclose(
         actual=_apply_window(**known_inputs_and_outputs_for_apply_window["inputs"]),
         desired=known_inputs_and_outputs_for_apply_window["outputs"],
+        atol=custom_atol,
     )
 
 

test/test_DFT_deconv.py

@@ -14,6 +14,7 @@
     hypothesis_float_vector,
     hypothesis_nonzero_complex_vector,
     hypothesis_positive_powers_of_two,
+    custom_atol,
 )
 
 
@@ -86,11 +87,13 @@ def test_dft_deconv(
         x_deconv + x_deconv_shift_away_from_zero,
         monte_carlo_mean + x_deconv_shift_away_from_zero,
         rtol=6.8e-2,
+        atol=custom_atol,
     )
     assert_allclose(
         u_deconv + u_deconv_shift_away_from_zero,
         monte_carlo_cov + u_deconv_shift_away_from_zero,
         rtol=4.98e-1,
+        atol=custom_atol,
     )
 
 
@@ -209,4 +212,4 @@ def test_reveal_bug_in_dft_deconv_up_to_1_9(
         n_monte_carlo_runs=n_monte_carlo_runs,
         operator=complex_deconvolution_on_sets,
     )
-    assert_allclose(u_deconv + 1, y_divided_by_h_mc_cov + 1)
+    assert_allclose(u_deconv + 1, y_divided_by_h_mc_cov + 1, atol=custom_atol)

test/test_interpolate.py

@@ -7,9 +7,10 @@
 from hypothesis import assume, given
 from hypothesis.strategies import composite
 from numpy.testing import assert_allclose
+from PyDynamic.uncertainty.interpolate import interp1d_unc, make_equidistant
 from pytest import raises
 
-from PyDynamic.uncertainty.interpolate import interp1d_unc, make_equidistant
+from .conftest import custom_atol
 
 _MIN_NODES_FOR_CUBIC_SPLINE = 4
 
@@ -595,7 +596,11 @@ def test_returnc_with_extrapolation_check_c_interp1d_unc(
 
     # Check if each row of sensitivities sum to one, which should hold for the
     # Lagrangians and proves equality with one for extrapolation sensitivities.
-    assert_allclose(np.sum(C, 1), np.ones_like(interp_inputs["x_new"]))
+    assert_allclose(
+        np.sum(C, 1),
+        np.ones_like(interp_inputs["x_new"]),
+        atol=custom_atol,
+    )
 
 
 @given(

test/test_lsfir/conftest.py

@@ -8,14 +8,15 @@
 import scipy.signal as dsp
 from hypothesis.strategies import composite
 from numpy.testing import assert_allclose, assert_almost_equal
-
 from PyDynamic.misc.SecondOrderSystem import sos_phys2filter
 from PyDynamic.misc.tools import (
     complex_2_real_imag,
     make_semiposdef,
     real_imag_2_complex,
 )
+
 from ..conftest import (
+    custom_atol,
     hypothesis_float_vector,
     scale_matrix_or_vector_to_convex_combination,
 )
@@ -101,6 +102,7 @@ def monte_carlo(
         np.load(
             os.path.join(reference_array_path, "test_LSFIR_H.npz"),
         )["H"],
+        atol=custom_atol,
     )
     uAbs = np.std(np.abs(HMC), axis=0)
     assert_allclose(
@@ -109,6 +111,7 @@ def monte_carlo(
             os.path.join(reference_array_path, "test_LSFIR_uAbs.npz"),
         )["uAbs"],
         rtol=3.5e-2,
+        atol=custom_atol,
     )
     uPhas = np.std(np.angle(HMC), axis=0)
     assert_allclose(
@@ -117,6 +120,7 @@ def monte_carlo(
             os.path.join(reference_array_path, "test_LSFIR_uPhas.npz"),
         )["uPhas"],
         rtol=4.3e-2,
+        atol=custom_atol,
     )
     UH = np.cov(np.hstack((np.real(HMC), np.imag(HMC))), rowvar=False)
     UH = make_semiposdef(UH)
@@ -145,10 +149,16 @@ def digital_filter(measurement_system, sampling_freq):
         measurement_system["S0"], measurement_system["delta"], measurement_system["f0"]
     )
     assert_almost_equal(bc, [20465611686.098896])
-    assert_allclose(ac, np.array([1.00000000e00, 4.52389342e03, 5.11640292e10]))
+    assert_allclose(
+        ac,
+        np.array([1.00000000e00, 4.52389342e03, 5.11640292e10]),
+        atol=custom_atol,
+    )
     b, a = dsp.bilinear(bc, ac, sampling_freq)
     assert_allclose(
-        b, np.array([0.019386043211510096, 0.03877208642302019, 0.019386043211510096])
+        b,
+        np.array([0.019386043211510096, 0.03877208642302019, 0.019386043211510096]),
+        atol=custom_atol,
     )
     assert_allclose(a, np.array([1.0, -1.7975690550957188, 0.9914294872108197]))
     return {"b": b, "a": a}
@@ -168,5 +178,6 @@ def complex_freq_resp(
         np.load(
             os.path.join(reference_array_path, "test_LSFIR_Hf.npz"),
         )["Hf"],
+        atol=custom_atol,
     )
     return Hf

test/test_lsfir/test_LSFIR.py

@@ -19,6 +19,7 @@
 from .conftest import weights
 from ..conftest import (
     hypothesis_dimension,
+    custom_atol,
 )
 
 
@@ -48,7 +49,7 @@ def simulated_measurement_input_and_output(
                 "test_LSFIR_x.npz",
             ),
         )["x"],
-        atol=1e2*np.finfo(np.float64).eps,
+        atol=custom_atol,
     )
     y = dsp.lfilter(digital_filter["b"], digital_filter["a"], x)
     noise = 1e-3
@@ -74,6 +75,7 @@ def LSFIR_filter_fit(monte_carlo, freqs, sampling_freq):
                 "test_LSFIR_bF.npz",
             ),
         )["bF"],
+        atol=custom_atol,
     )
     assert_allclose(
         UbF,
@@ -85,6 +87,7 @@ def LSFIR_filter_fit(monte_carlo, freqs, sampling_freq):
             ),
         )["UbF"],
         rtol=3e-1,
+        atol=custom_atol,
     )
     return {"bF": bF, "UbF": UbF, "N": N, "tau": tau}
 
@@ -103,6 +106,7 @@ def fir_low_pass(measurement_system, sampling_freq):
                 "test_LSFIR_blow.npz",
             ),
         )["blow"],
+        atol=custom_atol,
     )
     return {"blow": blow, "lshift": lshift}
 
@@ -119,6 +123,7 @@ def shift(simulated_measurement_input_and_output, LSFIR_filter_fit, fir_low_pass
                 "test_LSFIR_shift.npz",
             ),
         )["shift"],
+        atol=custom_atol,
     )
     return shift
 
@@ -239,6 +244,7 @@ def test_digital_deconvolution_FIR_example_figure_5(
                 "test_LSFIR_HbF.npz",
             ),
         )["HbF"],
+        atol=custom_atol,
     )
     plt.semilogy(
         freqs * 1e-3,
@@ -660,4 +666,4 @@ def test_compare_invLSFIR_to_LSFIR(monte_carlo, freqs, sampling_freq, filter_ord
         tau=filter_order // 2,
         inv=True,
     )[0]
-    assert_allclose(b_fir, b_fir_inv_lsfir)
+    assert_allclose(b_fir, b_fir_inv_lsfir, atol=custom_atol)

test/test_lsfir/test_compare_different_dtypes.py

@@ -8,6 +8,7 @@
 )
 from ..conftest import (
     hypothesis_dimension,
+    custom_atol,
 )
 
 
@@ -43,5 +44,5 @@ def test(monte_carlo, complex_H_with_UH, freqs, sampling_freq, filter_order):
         UH=monte_carlo["UH"],
         mc_runs=10000,
     )
-    assert_allclose(b_real_imaginary, b_complex, rtol=4e-2)
-    assert_allclose(ub_real_imaginary, ub_complex, rtol=6e-1)
+    assert_allclose(b_real_imaginary, b_complex, rtol=4e-2, atol=custom_atol)
+    assert_allclose(ub_real_imaginary, ub_complex, rtol=6e-1, atol=custom_atol)

test/test_lsfir/test_compare_inv_ls_fir_to_unc_mc_ls_fir.py

@@ -9,6 +9,7 @@
 )
 from ..conftest import (
     hypothesis_dimension,
+    custom_atol,
 )
 
 
@@ -40,5 +41,5 @@ def test(monte_carlo, freqs, sampling_freq, filter_order):
         UH=monte_carlo["UH"],
         mc_runs=10000,
     )
-    assert_allclose(b_fir_mc, b_fir, rtol=4e-2)
-    assert_allclose(Ub_fir_mc, Ub_fir, atol=6e-1, rtol=6e-1)
+    assert_allclose(b_fir_mc, b_fir, rtol=4e-2, atol=custom_atol)
+    assert_allclose(Ub_fir_mc, Ub_fir, rtol=6e-1, atol=6e-1)

test/test_lsfir/test_compare_inv_ls_fir_unc_to_ls_fir.py

@@ -9,6 +9,7 @@
 )
 from ..conftest import (
     hypothesis_dimension,
+    custom_atol,
 )
 
 
@@ -39,5 +40,5 @@ def test(monte_carlo, freqs, sampling_freq, filter_order):
         inv=True,
         UH=monte_carlo["UH"],
     )
-    assert_allclose(b_fir_mc, b_fir)
+    assert_allclose(b_fir_mc, b_fir, atol=custom_atol)
     assert_allclose(Ub_fir_mc, Ub_fir, atol=6e-1, rtol=6e-1)

test/test_lsfir/test_compare_ls_fir_with_svd_and_with_mc.py

@@ -8,6 +8,7 @@
 )
 from ..conftest import (
     hypothesis_dimension,
+    custom_atol,
 )
 
 
@@ -42,5 +43,5 @@ def test(monte_carlo, freqs, sampling_freq, filter_order):
         UH=monte_carlo["UH"],
         mc_runs=10000,
     )
-    assert_allclose(b_fir_mc, b_fir_svd, rtol=9e-2)
-    assert_allclose(Ub_fir_mc, Ub_fir_svd, atol=6e-1, rtol=6e-1)
+    assert_allclose(b_fir_mc, b_fir_svd, rtol=9e-2, atol=custom_atol)
+    assert_allclose(Ub_fir_mc, Ub_fir_svd, rtol=6e-1, atol=6e-1)

test/test_lsfir/test_compare_ls_fir_zero_to_none_uncertainties.py

@@ -9,6 +9,7 @@
 )
 from ..conftest import (
     hypothesis_dimension,
+    custom_atol,
 )
 
 
@@ -42,7 +43,7 @@ def test_compare_LSFIR_with_zero_to_None_uncertainties_with_svd_for_fitting_one_
         inv=True,
         UH=None,
     )[0]
-    assert_allclose(b_fir_svd, b_fir_none)
+    assert_allclose(b_fir_svd, b_fir_none, atol=custom_atol)
 
 
 @given(hypothesis_dimension(min_value=4, max_value=8))
@@ -76,7 +77,7 @@ def test_compare_LSFIR_with_zero_to_None_uncertainties_and_mc_for_fitting_one_ov
         inv=True,
         UH=None,
     )[0]
-    assert_allclose(b_fir_mc, b_fir_none)
+    assert_allclose(b_fir_mc, b_fir_none, atol=custom_atol)
 
 
 @given(hypothesis_dimension(min_value=4, max_value=8))
@@ -110,4 +111,4 @@ def test_compare_LSFIR_with_zero_to_None_uncertainties_and_mc_for_fitting_H_dire
         inv=False,
         UH=None,
     )[0]
-    assert_allclose(b_fir_mc, b_fir_none)
+    assert_allclose(b_fir_mc, b_fir_none, atol=custom_atol)