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Fix Numpy pickle warnings #1334

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Merged
j-c-c merged 2 commits into from
Oct 22, 2025
Merged

Fix Numpy pickle warnings #1334

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44609d4
update test data files
j-c-c Oct 21, 2025
42c6aaf
save data files with npz format. Refactor tests to handle npz diction…
j-c-c Oct 22, 2025
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Binary file removed tests/saved_test_data/clean70SRibosome_cov2d_covar.npy
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Binary file added tests/saved_test_data/clean70SRibosome_cov2d_covar.npz
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Binary file removed tests/saved_test_data/clean70SRibosome_cov2d_covarctf.npy
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Binary file removed tests/saved_test_data/clean70SRibosome_cov2d_covarctf_shrink.npy
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20 changes: 8 additions & 12 deletions tests/test_covar2d.py
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Original file line number Diff line number Diff line change
Expand Up @@ -128,15 +128,14 @@ def test_get_mean(cov2d_fixture):

def test_get_covar(cov2d_fixture):
results = np.load(
os.path.join(DATA_DIR, "clean70SRibosome_cov2d_covar.npy"),
allow_pickle=True,
os.path.join(DATA_DIR, "clean70SRibosome_cov2d_covar.npz"),
)

cov2d, coef_clean = cov2d_fixture[1], cov2d_fixture[2]

covar_coef = cov2d._get_covar(coef_clean.asnumpy())

for im, mat in enumerate(results.tolist()):
for im, mat in enumerate(results.values()):
np.testing.assert_allclose(mat, covar_coef[im], rtol=1e-05)


Expand Down Expand Up @@ -210,13 +209,12 @@ def test_shrinkage(cov2d_fixture, shrinker):
cov2d, coef_clean = cov2d_fixture[1], cov2d_fixture[2]

results = np.load(
os.path.join(DATA_DIR, "clean70SRibosome_cov2d_covar.npy"),
allow_pickle=True,
os.path.join(DATA_DIR, "clean70SRibosome_cov2d_covar.npz"),
)

covar_coef = cov2d.get_covar(coef_clean, covar_est_opt={"shrinker": shrinker})

for im, mat in enumerate(results.tolist()):
for im, mat in enumerate(results.values()):
np.testing.assert_allclose(
mat, covar_coef[im], atol=utest_tolerance(cov2d.dtype)
)
Expand Down Expand Up @@ -288,12 +286,11 @@ def test_get_covar_ctf(cov2d_fixture, ctf_enabled):
sim, cov2d, _, coef, h_ctf_fb, h_idx = cov2d_fixture

results = np.load(
os.path.join(DATA_DIR, "clean70SRibosome_cov2d_covarctf.npy"),
allow_pickle=True,
os.path.join(DATA_DIR, "clean70SRibosome_cov2d_covarctf.npz"),
)

covar_coef_ctf = cov2d.get_covar(coef, h_ctf_fb, h_idx, noise_var=NOISE_VAR)
for im, mat in enumerate(results.tolist()):
for im, mat in enumerate(results.values()):
# These tolerances were adjusted slightly (1e-8 to 3e-8) to accomodate MATLAB CTF repro changes
np.testing.assert_allclose(mat, covar_coef_ctf[im], rtol=3e-05, atol=3e-08)

Expand All @@ -306,8 +303,7 @@ def test_get_covar_ctf_shrink(cov2d_fixture, ctf_enabled):
pytest.skip(reason="Reference file n/a.")

results = np.load(
os.path.join(DATA_DIR, "clean70SRibosome_cov2d_covarctf_shrink.npy"),
allow_pickle=True,
os.path.join(DATA_DIR, "clean70SRibosome_cov2d_covarctf_shrink.npz"),
)

covar_opt = {
Expand All @@ -328,5 +324,5 @@ def test_get_covar_ctf_shrink(cov2d_fixture, ctf_enabled):
covar_est_opt=covar_opt,
)

for im, mat in enumerate(results.tolist()):
for im, mat in enumerate(results.values()):
np.testing.assert_allclose(mat, covar_coef_ctf_shrink[im])