MAINT: Bump minimums (mne-tools#11557)

Author: larsoner

.github/workflows/compat_old.yml

@@ -18,7 +18,7 @@ jobs:
       run:
         shell: bash
     env:
-      CONDA_DEPENDENCIES: 'numpy=1.18 scipy=1.6.3 matplotlib=3.1 pandas=1.0 scikit-learn=0.22'
+      CONDA_DEPENDENCIES: 'numpy=1.20.2 scipy=1.6.3 matplotlib=3.4 pandas=1.2.4 scikit-learn=0.24.2'
       DISPLAY: ':99.0'
       MNE_LOGGING_LEVEL: 'warning'
       OPENBLAS_NUM_THREADS: '1'

README.rst

@@ -94,28 +94,36 @@ Dependencies
 The minimum required dependencies to run MNE-Python are:
 
 - Python >= 3.8
-- NumPy >= 1.18.1
+- NumPy >= 1.20.2
 - SciPy >= 1.6.3
-- Matplotlib >= 3.1.0
+- Matplotlib >= 3.4.0
 - pooch >= 1.5
 - tqdm
 - Jinja2
 - decorator
 
 For full functionality, some functions require:
 
-- Scikit-learn >= 0.22.0
+- Scikit-learn >= 0.24.2
 - joblib >= 0.15 (for parallelization control)
-- Numba >= 0.48.0
-- NiBabel >= 2.5.0
+- mne-qt-browser >= 0.1 (for fast raw data visualization)
+- Qt5 >= 5.12 via one of the following bindings (for fast raw data visualization and interactive 3D visualization):
+
+  - PyQt6 >= 6.0
+  - PySide6 >= 6.0
+  - PyQt5 >= 5.12
+  - PySide2 >= 5.12
+
+- Numba >= 0.53.1
+- NiBabel >= 3.2.1
 - OpenMEEG >= 2.5.5
-- Pandas >= 1.0.0
+- Pandas >= 1.2.4
 - Picard >= 0.3
-- CuPy >= 7.1.1 (for NVIDIA CUDA acceleration)
-- DIPY >= 1.1.0
-- Imageio >= 2.6.1
-- PyVista >= 0.32
-- pyvistaqt >= 0.4
+- CuPy >= 9.0.0 (for NVIDIA CUDA acceleration)
+- DIPY >= 1.4.0
+- Imageio >= 2.8.0
+- PyVista >= 0.32 (for 3D visualization)
+- pyvistaqt >= 0.4 (for 3D visualization)
 - mffpy >= 0.5.7
 - h5py
 - h5io

doc/conf.py

@@ -631,7 +631,8 @@ def append_attr_meth_examples(app, what, name, obj, options, lines):
     'navigation_with_keys': False,
     'show_toc_level': 1,
     'navbar_end': ['theme-switcher', 'version-switcher', 'navbar-icon-links'],
-    'footer_items': ['copyright'],
+    'footer_start': ['copyright'],
+    'footer_end': [],
     'secondary_sidebar_items': ['page-toc'],
     'analytics': dict(google_analytics_id='G-5TBCPCRB6X'),
     'switcher': {

mne/decoding/tests/test_base.py

@@ -10,7 +10,7 @@
 
 from mne import create_info, EpochsArray
 from mne.fixes import is_regressor, is_classifier
-from mne.utils import requires_sklearn, requires_version
+from mne.utils import requires_sklearn
 from mne.decoding.base import (_get_inverse_funcs, LinearModel, get_coef,
                                cross_val_multiscore, BaseEstimator)
 from mne.decoding.search_light import SlidingEstimator
@@ -268,7 +268,7 @@ def test_get_coef_multiclass(n_features, n_targets):
     lm.fit(X, Y, sample_weight=np.ones(len(Y)))
 
 
-@requires_version('sklearn', '0.22')  # roc_auc_ovr_weighted
+@requires_sklearn
 @pytest.mark.parametrize('n_classes, n_channels, n_times', [
     (4, 10, 2),
     (4, 3, 2),

mne/fixes.py

@@ -94,84 +94,6 @@ def _csc_matrix_cast(x):
     return csc_matrix(x)
 
 
-###############################################################################
-# Backporting nibabel's read_geometry
-
-def _get_read_geometry():
-    """Get the geometry reading function."""
-    try:
-        import nibabel as nib
-        has_nibabel = True
-    except ImportError:
-        has_nibabel = False
-    if has_nibabel:
-        from nibabel.freesurfer import read_geometry
-    else:
-        read_geometry = _read_geometry
-    return read_geometry
-
-
-def _read_geometry(filepath, read_metadata=False, read_stamp=False):
-    """Backport from nibabel."""
-    from .surface import _fread3, _fread3_many
-    volume_info = dict()
-
-    TRIANGLE_MAGIC = 16777214
-    QUAD_MAGIC = 16777215
-    NEW_QUAD_MAGIC = 16777213
-    with open(filepath, "rb") as fobj:
-        magic = _fread3(fobj)
-        if magic in (QUAD_MAGIC, NEW_QUAD_MAGIC):  # Quad file
-            nvert = _fread3(fobj)
-            nquad = _fread3(fobj)
-            (fmt, div) = (">i2", 100.) if magic == QUAD_MAGIC else (">f4", 1.)
-            coords = np.fromfile(fobj, fmt, nvert * 3).astype(np.float64) / div
-            coords = coords.reshape(-1, 3)
-            quads = _fread3_many(fobj, nquad * 4)
-            quads = quads.reshape(nquad, 4)
-            #
-            #   Face splitting follows
-            #
-            faces = np.zeros((2 * nquad, 3), dtype=np.int64)
-            nface = 0
-            for quad in quads:
-                if (quad[0] % 2) == 0:
-                    faces[nface] = quad[0], quad[1], quad[3]
-                    nface += 1
-                    faces[nface] = quad[2], quad[3], quad[1]
-                    nface += 1
-                else:
-                    faces[nface] = quad[0], quad[1], quad[2]
-                    nface += 1
-                    faces[nface] = quad[0], quad[2], quad[3]
-                    nface += 1
-
-        elif magic == TRIANGLE_MAGIC:  # Triangle file
-            create_stamp = fobj.readline().rstrip(b'\n').decode('utf-8')
-            fobj.readline()
-            vnum = np.fromfile(fobj, ">i4", 1)[0]
-            fnum = np.fromfile(fobj, ">i4", 1)[0]
-            coords = np.fromfile(fobj, ">f4", vnum * 3).reshape(vnum, 3)
-            faces = np.fromfile(fobj, ">i4", fnum * 3).reshape(fnum, 3)
-
-            if read_metadata:
-                volume_info = _read_volume_info(fobj)
-        else:
-            raise ValueError("File does not appear to be a Freesurfer surface")
-
-    coords = coords.astype(np.float64)
-
-    ret = (coords, faces)
-    if read_metadata:
-        if len(volume_info) == 0:
-            warnings.warn('No volume information contained in the file')
-        ret += (volume_info,)
-    if read_stamp:
-        ret += (create_stamp,)
-
-    return ret
-
-
 ###############################################################################
 # NumPy Generator (NumPy 1.17)
 
@@ -234,36 +156,6 @@ def _read_volume_info(fobj):
     return volume_info
 
 
-def _serialize_volume_info(volume_info):
-    """An implementation of nibabel.freesurfer.io._serialize_volume_info, since
-    old versions of nibabel (<=2.1.0) don't have it."""
-    keys = ['head', 'valid', 'filename', 'volume', 'voxelsize', 'xras', 'yras',
-            'zras', 'cras']
-    diff = set(volume_info.keys()).difference(keys)
-    if len(diff) > 0:
-        raise ValueError('Invalid volume info: %s.' % diff.pop())
-
-    strings = list()
-    for key in keys:
-        if key == 'head':
-            if not (np.array_equal(volume_info[key], [20]) or np.array_equal(
-                    volume_info[key], [2, 0, 20])):
-                warnings.warn("Unknown extension code.")
-            strings.append(np.array(volume_info[key], dtype='>i4').tobytes())
-        elif key in ('valid', 'filename'):
-            val = volume_info[key]
-            strings.append('{} = {}\n'.format(key, val).encode('utf-8'))
-        elif key == 'volume':
-            val = volume_info[key]
-            strings.append('{} = {} {} {}\n'.format(
-                key, val[0], val[1], val[2]).encode('utf-8'))
-        else:
-            val = volume_info[key]
-            strings.append('{} = {:0.10g} {:0.10g} {:0.10g}\n'.format(
-                key.ljust(6), val[0], val[1], val[2]).encode('utf-8'))
-    return b''.join(strings)
-
-
 ##############################################################################
 # adapted from scikit-learn
 
@@ -877,28 +769,9 @@ def stable_cumsum(arr, axis=None, rtol=1e-05, atol=1e-08):
     return out
 
 
-# This shim can be removed once NumPy 1.19.0+ is required (1.18.4 has sign bug)
-def svd(a, hermitian=False):
-    if hermitian:  # faster
-        s, u = np.linalg.eigh(a)
-        sgn = np.sign(s)
-        s = np.abs(s)
-        sidx = np.argsort(s)[..., ::-1]
-        sgn = np.take_along_axis(sgn, sidx, axis=-1)
-        s = np.take_along_axis(s, sidx, axis=-1)
-        u = np.take_along_axis(u, sidx[..., None, :], axis=-1)
-        # singular values are unsigned, move the sign into v
-        vt = (u * sgn[..., np.newaxis, :]).swapaxes(-2, -1).conj()
-        np.abs(s, out=s)
-        return u, s, vt
-    else:
-        return np.linalg.svd(a)
-
-
 ###############################################################################
 # From nilearn
 
-
 def _crop_colorbar(cbar, cbar_vmin, cbar_vmax):
     """
     crop a colorbar to show from cbar_vmin to cbar_vmax
@@ -915,31 +788,18 @@ def _crop_colorbar(cbar, cbar_vmin, cbar_vmax):
     new_tick_locs = np.linspace(cbar_vmin, cbar_vmax,
                                 len(cbar_tick_locs))
 
-    # matplotlib >= 3.2.0 no longer normalizes axes between 0 and 1
-    # See https://matplotlib.org/3.2.1/api/prev_api_changes/api_changes_3.2.0.html
-    # _outline was removed in
-    # https://github.com/matplotlib/matplotlib/commit/03a542e875eba091a027046d5ec652daa8be6863
-    # so we use the code from there
-    if _compare_version(matplotlib.__version__, '>=', '3.2.0'):
-        cbar.ax.set_ylim(cbar_vmin, cbar_vmax)
-        X = cbar._mesh()[0]
-        X = np.array([X[0], X[-1]])
-        Y = np.array([[cbar_vmin, cbar_vmin], [cbar_vmax, cbar_vmax]])
-        N = X.shape[0]
-        ii = [0, 1, N - 2, N - 1, 2 * N - 1, 2 * N - 2, N + 1, N, 0]
-        x = X.T.reshape(-1)[ii]
-        y = Y.T.reshape(-1)[ii]
-        xy = (np.column_stack([y, x])
-              if cbar.orientation == 'horizontal' else
-              np.column_stack([x, y]))
-        cbar.outline.set_xy(xy)
-    else:
-        cbar.ax.set_ylim(cbar.norm(cbar_vmin), cbar.norm(cbar_vmax))
-        outline = cbar.outline.get_xy()
-        outline[:2, 1] += cbar.norm(cbar_vmin)
-        outline[2:6, 1] -= (1. - cbar.norm(cbar_vmax))
-        outline[6:, 1] += cbar.norm(cbar_vmin)
-        cbar.outline.set_xy(outline)
+    cbar.ax.set_ylim(cbar_vmin, cbar_vmax)
+    X = cbar._mesh()[0]
+    X = np.array([X[0], X[-1]])
+    Y = np.array([[cbar_vmin, cbar_vmin], [cbar_vmax, cbar_vmax]])
+    N = X.shape[0]
+    ii = [0, 1, N - 2, N - 1, 2 * N - 1, 2 * N - 2, N + 1, N, 0]
+    x = X.T.reshape(-1)[ii]
+    y = Y.T.reshape(-1)[ii]
+    xy = (np.column_stack([y, x])
+            if cbar.orientation == 'horizontal' else
+            np.column_stack([x, y]))
+    cbar.outline.set_xy(xy)
 
     cbar.set_ticks(new_tick_locs)
     cbar.update_ticks()
@@ -951,7 +811,7 @@ def _crop_colorbar(cbar, cbar_vmin, cbar_vmax):
 # Here we choose different defaults to speed things up by default
 try:
     import numba
-    if _compare_version(numba.__version__, '<', '0.48'):
+    if _compare_version(numba.__version__, '<', '0.53.1'):
         raise ImportError
     prange = numba.prange
     def jit(nopython=True, nogil=True, fastmath=True, cache=True,

mne/surface.py

@@ -13,15 +13,13 @@
 from collections import OrderedDict
 from glob import glob
 from os import path as op
-from struct import pack
 import time
 import warnings
 
 import numpy as np
 
 from .channels.channels import _get_meg_system
-from .fixes import (_serialize_volume_info, _get_read_geometry, jit,
-                    prange, bincount)
+from .fixes import jit, prange, bincount
 from .io.constants import FIFF
 from .io.pick import pick_types
 from .parallel import parallel_func
@@ -810,6 +808,7 @@ def read_surface(fname, read_metadata=False, return_dict=False,
     write_surface
     read_tri
     """
+    from ._freesurfer import _import_nibabel
     fname = _check_fname(fname, 'read', True)
     _check_option('file_format', file_format, ['auto', 'freesurfer', 'obj'])
 
@@ -820,7 +819,9 @@ def read_surface(fname, read_metadata=False, return_dict=False,
             file_format = 'freesurfer'
 
     if file_format == 'freesurfer':
-        ret = _get_read_geometry()(fname, read_metadata=read_metadata)
+        _import_nibabel('read surface geometry')
+        from nibabel.freesurfer import read_geometry
+        ret = read_geometry(fname, read_metadata=read_metadata)
     elif file_format == 'obj':
         ret = _read_wavefront_obj(fname)
         if read_metadata:
@@ -1185,6 +1186,7 @@ def write_surface(fname, coords, faces, create_stamp='', volume_info=None,
     read_surface
     read_tri
     """
+    from ._freesurfer import _import_nibabel
     fname = _check_fname(fname, overwrite=overwrite)
     _check_option('file_format', file_format, ['auto', 'freesurfer', 'obj'])
 
@@ -1195,35 +1197,13 @@ def write_surface(fname, coords, faces, create_stamp='', volume_info=None,
             file_format = 'freesurfer'
 
     if file_format == 'freesurfer':
-        try:
-            import nibabel as nib
-            has_nibabel = True
-        except ImportError:
-            has_nibabel = False
-        if has_nibabel:
-            nib.freesurfer.io.write_geometry(fname, coords, faces,
-                                             create_stamp=create_stamp,
-                                             volume_info=volume_info)
-            return
-        if len(create_stamp.splitlines()) > 1:
-            raise ValueError("create_stamp can only contain one line")
-
-        with open(fname, 'wb') as fid:
-            fid.write(pack('>3B', 255, 255, 254))
-            strs = ['%s\n' % create_stamp, '\n']
-            strs = [s.encode('utf-8') for s in strs]
-            fid.writelines(strs)
-            vnum = len(coords)
-            fnum = len(faces)
-            fid.write(pack('>2i', vnum, fnum))
-            fid.write(np.array(coords, dtype='>f4').tobytes())
-            fid.write(np.array(faces, dtype='>i4').tobytes())
-
-            # Add volume info, if given
-            if volume_info is not None and len(volume_info) > 0:
-                fid.write(_serialize_volume_info(volume_info))
-
-    elif file_format == 'obj':
+        _import_nibabel('write surface geometry')
+        from nibabel.freesurfer import write_geometry
+        write_geometry(
+            fname, coords, faces, create_stamp=create_stamp,
+            volume_info=volume_info)
+    else:
+        assert file_format == 'obj'
         with open(fname, 'w') as fid:
             for line in create_stamp.splitlines():
                 fid.write(f'# {line}\n')

mne/tests/test_annotations.py

@@ -1062,7 +1062,6 @@ def test_annotations_simple_iteration():
             assert elem == expected_value
 
 
-@requires_version('numpy', '1.12')
 def test_annotations_slices():
     """Test indexing Annotations."""
     NUM_ANNOT = 5

mne/tests/test_surface.py

@@ -118,6 +118,7 @@ def test_compute_nearest():
 @testing.requires_testing_data
 def test_io_surface(tmp_path):
     """Test reading and writing of Freesurfer surface mesh files."""
+    pytest.importorskip('nibabel')
     fname_quad = data_path / "subjects" / "bert" / "surf" / "lh.inflated.nofix"
     fname_tri = data_path / "subjects" / "sample" / "bem" / "inner_skull.surf"
     for fname in (fname_quad, fname_tri):
@@ -155,6 +156,7 @@ def test_io_surface(tmp_path):
 @testing.requires_testing_data
 def test_read_curv():
     """Test reading curvature data."""
+    pytest.importorskip('nibabel')
     fname_curv = data_path / "subjects" / "fsaverage" / "surf" / "lh.curv"
     fname_surf = data_path / "subjects" / "fsaverage" / "surf" / "lh.inflated"
     bin_curv = read_curvature(fname_curv)