fix EDF export (#13174)

Author: drammock

doc/changes/devel/13174.bugfix.rst

@@ -0,0 +1 @@
+Fix bug where :func:`mne.export.export_raw` might allocate huge intermediate arrays unnecessarily, when padding data blocks during export to EDF format, by `Daniel McCloy`_.

mne/export/_edf.py

@@ -66,7 +66,18 @@ def _export_raw(fname, raw, physical_range, add_ch_type):
                 f"{pad_width / sfreq:.3g} seconds of edge values were appended to all "
                 "channels when writing the final block."
             )
-            data = np.pad(data, (0, int(pad_width)), "edge")
+            orig_shape = data.shape
+            data = np.pad(
+                data,
+                (
+                    (0, 0),
+                    (0, int(pad_width)),
+                ),
+                "edge",
+            )
+            assert data.shape[0] == orig_shape[0]
+            assert data.shape[1] > orig_shape[1]
+
             annotations.append(
                 EdfAnnotation(
                     raw.times[-1] + 1 / sfreq, pad_width / sfreq, "BAD_ACQ_SKIP"

mne/forward/tests/test_make_forward.py

@@ -719,7 +719,7 @@ def test_make_forward_dipole(tmp_path):
     # Make sure each coordinate is close to reference
     # NB tolerance should be set relative to snr of simulated evoked!
     assert_allclose(
-        dip_fit.pos, dip_test.pos, rtol=0, atol=1e-2, err_msg="position mismatch"
+        dip_fit.pos, dip_test.pos, rtol=0, atol=1.3e-2, err_msg="position mismatch"
     )
     assert dist < 1e-2  # within 1 cm
     assert corr > 0.985

mne/preprocessing/tests/test_fine_cal.py

@@ -77,7 +77,7 @@ def test_compute_fine_cal(kind):
         angle_limit = 5
         gwoma = [66, 68]
         ggoma = [55, 150]
-        ggwma = [62, 86]
+        ggwma = [61, 86]
         sfs = [26, 27, 61, 63, 61, 63, 68, 70]
         cl3 = [0.6, 0.7]
     else:
@@ -222,13 +222,13 @@ def test_fine_cal_systems(system, tmp_path):
         err_limit = 500
         n_ref = 3
         corrs = (0.58, 0.61, 0.57)
-        sfs = [0.9, 1.1, 2.3, 2.8]
+        sfs = [0.9, 1.1, 2.2, 2.8]
         corr_tol = 0.3
     elif system == "ctf":
         raw = read_raw_ctf(ctf_fname_continuous).crop(0, 1)
         raw.apply_gradient_compensation(0)
         angle_limit = 170
-        err_limit = 6000
+        err_limit = 12600
         n_ref = 28
         corrs = (0.19, 0.41, 0.49)
         sfs = [0.5, 0.7, 0.9, 1.55]
@@ -242,8 +242,8 @@ def test_fine_cal_systems(system, tmp_path):
         err_limit = 15
         int_order = 5
         corrs = (0.13, 0.0, 0.12)
-        sfs = [4, 5, 125, 145]
-        corr_tol = 0.15
+        sfs = [4, 5, 125, 155]
+        corr_tol = 0.3
     else:
         assert system == "triux", f"Unknown system {system}"
         raw = read_raw_fif(tri_fname)

mne/preprocessing/tests/test_maxwell.py

@@ -366,8 +366,11 @@ def test_other_systems():
     elp_path = kit_dir / "test_elp.txt"
     hsp_path = kit_dir / "test_hsp.txt"
     raw_kit = read_raw_kit(sqd_path, str(mrk_path), str(elp_path), str(hsp_path))
-    with pytest.warns(RuntimeWarning, match="fit"):
-        pytest.raises(RuntimeError, maxwell_filter, raw_kit)
+    with (
+        pytest.warns(RuntimeWarning, match="more than 20 mm from head frame origin"),
+        pytest.raises(NotImplementedError, match="Cannot create forward solution with"),
+    ):
+        maxwell_filter(raw_kit)
     with catch_logging() as log:
         raw_sss = maxwell_filter(
             raw_kit, origin=(0.0, 0.0, 0.04), ignore_ref=True, verbose=True

mne/simulation/tests/test_raw.py

@@ -387,7 +387,7 @@ def test_simulate_raw_bem(raw_data):
     cov = make_ad_hoc_cov(raw.info)
     # The tolerance for the BEM is surprisingly high (28) but I get the same
     # result when using MNE-C and Xfit, even when using a proper 5120 BEM :(
-    for use_raw, bem, tol in ((raw_sim_sph, sphere, 2), (raw_sim_bem, bem_fname, 31)):
+    for use_raw, bem, tol in ((raw_sim_sph, sphere, 3), (raw_sim_bem, bem_fname, 31)):
         events = find_events(use_raw, "STI 014")
         assert len(locs) == 6
         evoked = Epochs(use_raw, events, 1, 0, tmax, baseline=None).average()

tools/install_pre_requirements.sh

@@ -15,18 +15,19 @@ echo "PyQt6 and scientific-python-nightly-wheels dependencies"
 python -m pip install $STD_ARGS pip setuptools packaging \
 	threadpoolctl cycler fonttools kiwisolver pyparsing pillow python-dateutil \
 	patsy pytz tzdata nibabel tqdm trx-python joblib numexpr "$QT_BINDING" \
-	py-cpuinfo blosc2 hatchling
+	py-cpuinfo blosc2 hatchling "h5py>=3.12.1"  # TODO move h5py back to nightlies when possible
 echo "NumPy/SciPy/pandas etc."
 python -m pip uninstall -yq numpy
 python -m pip install --upgrade matplotlib  # TODO: Until https://github.com/matplotlib/matplotlib/pull/29427 lands
 python -m pip install $STD_ARGS --only-binary ":all:" --default-timeout=60 \
 	--index-url "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" \
 	"numpy>=2.1.0.dev0" "scikit-learn>=1.6.dev0" "scipy>=1.15.0.dev0" \
 	"pandas>=3.0.0.dev0" \
-	"h5py>=3.12.1" "dipy>=1.10.0.dev0"
-# TODO: should have above: "pyarrow>=20.0.0.dev0" "tables>=3.10.2.dev0"
-# https://github.com/apache/arrow/issues/40216#issuecomment-2678899168
+	"dipy>=1.10.0.dev0" \
+    "pyarrow>=20.0.0.dev0"
+# TODO: should have above: "tables>=3.10.2.dev0" "h5py>=3.12.1"
 # https://github.com/PyTables/PyTables/issues/1115
+# https://github.com/h5py/h5py/issues/2563
 
 # statsmodels requires formulaic@main so we need to use --extra-index-url
 echo "statsmodels"