MAINT: Bump mins, deprecations (mne-tools#13322)

Co-authored-by: Daniel McCloy <dan@mccloy.info>

Author: larsoner

.github/workflows/tests.yml

@@ -30,7 +30,7 @@ jobs:
           persist-credentials: false
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: '3.13'
       - uses: pre-commit/action@v3.0.1
       - run: pip install mypy numpy scipy vulture
       - run: mypy
@@ -70,16 +70,16 @@ jobs:
             python: '3.13'
             kind: pip
           - os: ubuntu-latest
-            python: '3.12'
+            python: '3.13'
             kind: pip-pre
           - os: ubuntu-latest
-            python: '3.12'
+            python: '3.13'
             kind: conda
           - os: macos-latest  # arm64 (Apple Silicon)
-            python: '3.12'
+            python: '3.13'
             kind: mamba
           - os: macos-13  # latest Intel release
-            python: '3.12'
+            python: '3.13'
             kind: mamba
           - os: windows-latest
             python: '3.10'

.pre-commit-config.yaml

@@ -78,7 +78,7 @@ repos:
         language: python
         entry: ./tools/hooks/sync_dependencies.py
         files: '^(pyproject.toml|tools/hooks/sync_dependencies.py)$'
-        additional_dependencies: ["mne==1.9.0"]
+        additional_dependencies: ["mne==1.10.0"]
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit

README.rst

@@ -73,9 +73,9 @@ The minimum required dependencies to run MNE-Python are:
 .. ↓↓↓ BEGIN CORE DEPS LIST. DO NOT EDIT! HANDLED BY PRE-COMMIT HOOK ↓↓↓
 
 - `Python <https://www.python.org>`__ ≥ 3.10
-- `NumPy <https://numpy.org>`__ ≥ 1.23
-- `SciPy <https://scipy.org>`__ ≥ 1.9
-- `Matplotlib <https://matplotlib.org>`__ ≥ 3.6
+- `NumPy <https://numpy.org>`__ ≥ 1.25
+- `SciPy <https://scipy.org>`__ ≥ 1.11
+- `Matplotlib <https://matplotlib.org>`__ ≥ 3.7
 - `Pooch <https://www.fatiando.org/pooch/latest/>`__ ≥ 1.5
 - `tqdm <https://tqdm.github.io>`__
 - `Jinja2 <https://palletsprojects.com/p/jinja/>`__

environment.yml

@@ -25,17 +25,17 @@ dependencies:
   - jupyter
   - lazy_loader >=0.3
   - mamba
-  - matplotlib >=3.7
+  - matplotlib >=3.8
   - mffpy >=0.5.7
   - mne-qt-browser
   - nibabel
   - nilearn
   - nomkl
   - numba
-  - numpy >=1.25,<3
-  - openmeeg >=2.5.5
+  - numpy >=1.26,<3
+  - openmeeg >=2.5.7
   - packaging
-  - pandas >=2.0
+  - pandas >=2.1
   - pillow
   - pip
   - pooch >=1.5

mne/datasets/sleep_physionet/_utils.py

@@ -2,7 +2,6 @@
 # License: BSD-3-Clause
 # Copyright the MNE-Python contributors.
 
-import inspect
 import os
 import os.path as op
 
@@ -115,16 +114,13 @@ def _update_sleep_temazepam_records(fname=TEMAZEPAM_SLEEP_RECORDS):
     data = data.set_index(("Subject - age - sex", "Nr"))
     data.index.name = "subject"
     data.columns.names = [None, None]
-    kwargs = dict()
-    # TODO VERSION can be removed once we require Pandas 2.1
-    if "future_stack" in inspect.getfullargspec(pd.DataFrame.stack).args:
-        kwargs["future_stack"] = True
     data = (
         data.set_index(
             [("Subject - age - sex", "Age"), ("Subject - age - sex", "M1/F2")],
             append=True,
         )
-        .stack(level=0, **kwargs)
+        # TODO VERSION future_stack goes away w/ Pandas 3.0
+        .stack(level=0, future_stack=True)
         .reset_index()
     )
 

mne/preprocessing/maxwell.py

@@ -236,8 +236,8 @@ def maxwell_filter(
     mag_scale=100.0,
     skip_by_annotation=("edge", "bad_acq_skip"),
     extended_proj=(),
-    st_overlap=None,
-    mc_interp=None,
+    st_overlap=True,
+    mc_interp="hann",
     verbose=None,
 ):
     """Maxwell filter data using multipole moments.
@@ -287,8 +287,7 @@ def maxwell_filter(
     %(extended_proj_maxwell)s
     st_overlap : bool
         If True (default in 1.11), tSSS processing will use a constant
-        overlap-add method. If False (default in 1.10), then
-        non-overlapping windows will be used.
+        overlap-add method. If False, then non-overlapping windows will be used.
 
         .. versionadded:: 1.10
     %(maxwell_mc_interp)s
@@ -456,8 +455,8 @@ def _prep_maxwell_filter(
     skip_by_annotation=("edge", "bad_acq_skip"),
     extended_proj=(),
     reconstruct="in",
-    st_overlap=False,
-    mc_interp="zero",
+    st_overlap=True,
+    mc_interp="hann",
     verbose=None,
 ):
     # There are an absurd number of different possible notations for spherical
@@ -494,25 +493,7 @@ def _prep_maxwell_filter(
         )
     if st_only and st_duration is None:
         raise ValueError("st_duration must not be None if st_only is True")
-    if st_overlap is None:
-        if st_duration is not None:
-            # TODO VERSION 1.10/1.11 deprecation
-            warn(
-                "st_overlap defaults to False in 1.10 but will change to "
-                "True in 1.11. Set it explicitly to avoid this warning.",
-                DeprecationWarning,
-            )
-        st_overlap = False
-    add_channels = head_pos is not None and not st_only
-    if mc_interp is None:
-        if head_pos is not None:
-            # TODO VERSION 1.10/1.11 deprecation
-            warn(
-                'mc_interp defaults to "zero" in 1.10 but will change '
-                'to "hann" in 1.11, set it explicitly to avoid this '
-                "message.",
-                DeprecationWarning,
-            )
+    if head_pos is None and mc_interp:
         mc_interp = "zero"
     add_channels = (head_pos is not None) and (not st_only)
     head_pos = _check_pos(head_pos, coord_frame, raw, st_fixed)
@@ -776,7 +757,7 @@ def _run_maxwell_filter(
         n = end - onset
         assert n > 0
         tsss_valid = n >= st_duration
-        if st_overlap and tsss_valid:
+        if st_overlap and tsss_valid and st_correlation is not None:
             n_overlap = st_duration // 2
             window = "hann"
         else:
@@ -2555,7 +2536,7 @@ def find_bad_channels_maxwell(
     skip_by_annotation=("edge", "bad_acq_skip"),
     h_freq=40.0,
     extended_proj=(),
-    mc_interp=None,
+    mc_interp="hann",
     verbose=None,
 ):
     r"""Find bad channels using Maxwell filtering.
@@ -2754,6 +2735,7 @@ def find_bad_channels_maxwell(
         extended_proj=extended_proj,
         reconstruct="orig",
     )
+    assert params["st_correlation"] is None
     del origin, int_order, ext_order, calibration, cross_talk, coord_frame
     del regularize, ignore_ref, bad_condition, head_pos, mag_scale
     good_meg_picks = params["meg_picks"][params["good_mask"]]

mne/preprocessing/tests/test_fine_cal.py

@@ -222,7 +222,7 @@ 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, 2.1, 2.8]
+        sfs = [0.9, 1.1, 1.9, 2.8]
         corr_tol = 0.3
     elif system == "ctf":
         raw = read_raw_ctf(ctf_fname_continuous).crop(0, 1)
@@ -242,7 +242,7 @@ 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, 155]
+        sfs = [4, 5, 125, 157]
         corr_tol = 0.38
     else:
         assert system == "triux", f"Unknown system {system}"
@@ -278,6 +278,8 @@ def test_fine_cal_systems(system, tmp_path):
         regularize=None,
         bad_condition="ignore",
         int_order=int_order,
+        st_overlap=False,
+        mc_interp="zero",
     )
     raw_sss = maxwell_filter(raw, **kwargs)
     _assert_shielding(raw_sss, raw, *sfs[0:2])

mne/preprocessing/tests/test_maxwell.py

@@ -1622,10 +1622,21 @@ def test_mf_skips():
     ),
     [
         # Neuromag data tested against MF
-        (sample_fname, [], False, False, False, ["MEG 2443"], False, None, "raw"),
+        pytest.param(
+            sample_fname,
+            [],
+            False,
+            False,
+            False,
+            ["MEG 2443"],
+            False,
+            None,
+            "raw",
+            id="Neuromag no bads",
+        ),
         # add 0111 to test picking, add annot to test it, and prepend chs for
         # idx
-        (
+        pytest.param(
             sample_fname,
             ["MEG 0111"],
             True,
@@ -1635,11 +1646,12 @@ def test_mf_skips():
             False,
             None,
             "raw",
+            id="Neuromag with bads and annot",
         ),
         # CTF data seems to be sensitive to linalg lib (?) because some
         # channels are very close to the limit, so we just check that one shows
         # up
-        (
+        pytest.param(
             ctf_fname_continuous,
             [],
             False,
@@ -1649,9 +1661,10 @@ def test_mf_skips():
             False,
             None,
             "raw",
+            id="CTF no bads",
         ),
         # faked
-        (
+        pytest.param(
             ctf_fname_continuous,
             [],
             False,
@@ -1661,10 +1674,33 @@ def test_mf_skips():
             False,
             None,
             "raw",
+            id="CTF ignore ref",
         ),
         # For `return_scores=True`
-        (sample_fname, ["MEG 0111"], True, True, False, ["MEG 2443"], True, 50, "raw"),
-        (sample_fname, ["MEG 0111"], True, True, False, ["MEG 2443"], True, 50, None),
+        pytest.param(
+            sample_fname,
+            ["MEG 0111"],
+            True,
+            True,
+            False,
+            ["MEG 2443"],
+            True,
+            50,
+            "raw",
+            id="Neuromag return scores",
+        ),
+        pytest.param(
+            sample_fname,
+            ["MEG 0111"],
+            True,
+            True,
+            False,
+            ["MEG 2443"],
+            True,
+            50,
+            None,
+            id="Neuromag return scores no meas date",
+        ),
     ],
 )
 def test_find_bad_channels_maxwell(

mne/report/report.py

@@ -1599,7 +1599,6 @@ def add_inverse_operator(
         *,
         subject=None,
         subjects_dir=None,
-        trans=None,
         plot=False,
         tags=("inverse-operator",),
         section=None,
@@ -1619,9 +1618,6 @@ def add_inverse_operator(
             passed on report creation.
         subjects_dir : path-like | None
             The FreeSurfer ``SUBJECTS_DIR``.
-        trans : path-like | instance of Transform | None
-            Deprecated and will be removed in 1.11.
-            The trans stored in the inverse operator will be used instead.
         plot : bool
             If True, plot the source space of the inverse operator.
 
@@ -1637,12 +1633,6 @@ def add_inverse_operator(
         .. versionadded:: 0.24.0
         """
         tags = _check_tags(tags)
-        if trans is not None:
-            warn(
-                "trans is deprecated and will be removed in 1.11, do not pass it "
-                "to add_inverse_operator",
-                category=FutureWarning,
-            )
         self._add_inverse_operator(
             inverse_operator=inverse_operator,
             subject=subject,

mne/utils/config.py

@@ -839,6 +839,8 @@ def sys_info(
         "edfio",
         "mffpy",
         "pybv",
+        "antio",
+        "defusedxml",
         "",
     )
     if dependencies == "developer":
@@ -847,11 +849,9 @@ def sys_info(
             "pytest",
             "statsmodels",
             "numpydoc",
-            "flake8",
             "jupyter_client",
             "nbclient",
             "nbformat",
-            "pydocstyle",
             "nitime",
             "imageio",
             "imageio-ffmpeg",