MAINT: Update dependency specifiers

.github/workflows/spec_zero.yml

@@ -64,8 +64,9 @@ jobs:
           git config --global user.email "50266005+mne-bot@users.noreply.github.com"
           git config --global user.name "mne[bot]"
           git checkout -b spec_zero
+          git add doc/changes/dev/dependency.rst  # one new file, others changed
           git commit -am "mne[bot]: Update dependency specifiers"
           git push origin spec_zero
-          PR_NUM=$(gh pr create --base main --head spec_zero --title "MAINT: Update dependency specifiers" --body "Created by spec_zero [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }}). <br> <br> *Adjustments may need to be made to shims in \`mne/fixes.py\` in this or another PR. \`git grep TODO VERSION\` is a good starting point for finding potential updates.*" --label "no-changelog-entry-needed")
+          PR_NUM=$(gh pr create --base main --head spec_zero --title "MAINT: Update dependency specifiers" --body "Created by spec_zero [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }}). <br> <br> *It is very likely that `tools/environment_old.yml` needs to be updated.* <br> <br> *Adjustments may need to be made to shims in \`mne/fixes.py\` and elswhere in this or another PR. \`git grep TODO VERSION\` is a good starting point for finding potential updates.*")
           echo "Opened https://github.com/mne-tools/mne-python/pull/${PR_NUM}" >> $GITHUB_STEP_SUMMARY
         if: steps.status.outputs.dirty == 'true'

.github/workflows/tests.yml

@@ -154,6 +154,8 @@ jobs:
         if: ${{ !startswith(matrix.kind, 'pip') }}
         timeout-minutes: 20
       - run: bash ./tools/github_actions_dependencies.sh
+      - run: python ./tools/github_actions_check_old.py
+        if: matrix.kind == 'old'
       # Minimal commands on Linux (macOS stalls)
       - run: bash ./tools/get_minimal_commands.sh
         if: startswith(matrix.os, 'ubuntu') && matrix.kind != 'minimal' && matrix.kind != 'old'

doc/changes/dev/13611.dependency.rst

@@ -0,0 +1,8 @@
+Updated minimum for:
+
+- Core dependency ``scipy >= 1.12``
+- Optional dependency ``pandas >= 2.2``
+- Optional dependency ``pyobjc-framework-Cocoa >= 5.2.0; platform_system == "Darwin"``
+- Optional dependency ``scikit-learn >= 1.4``
+
+Changed implemented via CI action created by `Thomas Binns`_.

environment.yml

@@ -36,7 +36,7 @@ dependencies:
   - numpy >=1.26,<3
   - openmeeg >=2.5.7
   - packaging
-  - pandas >=2.1
+  - pandas >=2.2
   - pillow
   - pip
   - pooch >=1.5
@@ -50,8 +50,8 @@ dependencies:
   - pyvistaqt >=0.11
   - qdarkstyle !=3.2.2
   - qtpy
-  - scikit-learn >=1.3
-  - scipy >=1.11
+  - scikit-learn >=1.4
+  - scipy >=1.12
   - sip
   - snirf
   - statsmodels

mne/decoding/_fixes.py

@@ -3,6 +3,7 @@
 # Copyright the MNE-Python contributors.
 
 try:
+    # TODO VERSION remove once we require sklearn 1.6+
     from sklearn.utils.validation import validate_data
 except ImportError:
     from sklearn.utils.validation import check_array, check_X_y

mne/decoding/tests/test_csp.py

@@ -495,5 +495,5 @@ def test_csp_component_ordering():
 @parametrize_with_checks([CSP(), SPoC()])
 def test_sklearn_compliance(estimator, check):
     """Test compliance with sklearn."""
-    pytest.importorskip("sklearn", minversion="1.4")  # TODO VERSION remove on 1.4+
+    pytest.importorskip("sklearn", minversion="1.5")  # TODO VERSION remove on 1.5+
     check(estimator)

mne/decoding/tests/test_ems.py

@@ -97,5 +97,5 @@ def test_ems():
 @parametrize_with_checks([EMS()])
 def test_sklearn_compliance(estimator, check):
     """Test compliance with sklearn."""
-    pytest.importorskip("sklearn", minversion="1.4")  # TODO VERSION remove on 1.4+
+    pytest.importorskip("sklearn", minversion="1.6")  # TODO VERSION remove on 1.6+
     check(estimator)

mne/decoding/tests/test_receptive_field.py

@@ -590,7 +590,7 @@ def test_linalg_warning():
 @parametrize_with_checks([TimeDelayingRidge(0, 10, 1.0, 0.1, "laplacian", n_jobs=1)])
 def test_tdr_sklearn_compliance(estimator, check):
     """Test sklearn estimator compliance."""
-    pytest.importorskip("sklearn", minversion="1.4")  # TODO VERSION remove on 1.4+
+    pytest.importorskip("sklearn", minversion="1.6")  # TODO VERSION remove on 1.6+
     ignores = (
         # TDR convolves and thus its output cannot be invariant when
         # shuffled or subsampled.
@@ -606,7 +606,7 @@ def test_tdr_sklearn_compliance(estimator, check):
 @parametrize_with_checks([ReceptiveField(-1, 2, 1.0, estimator=Ridge(), patterns=True)])
 def test_rf_sklearn_compliance(estimator, check):
     """Test sklearn RF compliance."""
-    pytest.importorskip("sklearn", minversion="1.4")  # TODO VERSION remove on 1.4+
+    pytest.importorskip("sklearn", minversion="1.6")  # TODO VERSION remove on 1.6+
     ignores = (
         # RF does time-lagging, so its output cannot be invariant when
         # shuffled or subsampled.

mne/decoding/tests/test_ssd.py

@@ -621,7 +621,7 @@ def test_get_spectral_ratio():
 )
 def test_sklearn_compliance(estimator, check):
     """Test LinearModel compliance with sklearn."""
-    pytest.importorskip("sklearn", minversion="1.4")  # TODO VERSION remove on 1.4+
+    pytest.importorskip("sklearn", minversion="1.6")  # TODO VERSION remove on 1.6+
     ignores = (
         # Checks below fail because what sklearn passes as (n_samples, n_features)
         # is considered (n_channels, n_times) by SSD and creates problems

mne/decoding/tests/test_time_frequency.py

@@ -57,5 +57,5 @@ def test_timefrequency_basic():
 @parametrize_with_checks([TimeFrequency([300, 400], 1000.0, n_cycles=0.25)])
 def test_sklearn_compliance(estimator, check):
     """Test LinearModel compliance with sklearn."""
-    pytest.importorskip("sklearn", minversion="1.4")  # TODO VERSION remove on 1.4+
+    pytest.importorskip("sklearn", minversion="1.6")  # TODO VERSION remove on 1.6+
     check(estimator)

mne/decoding/tests/test_transformer.py

@@ -339,7 +339,7 @@ def test_bad_triage():
 )
 def test_sklearn_compliance(estimator, check):
     """Test LinearModel compliance with sklearn."""
-    pytest.importorskip("sklearn", minversion="1.4")  # TODO VERSION remove on 1.4+
+    pytest.importorskip("sklearn", minversion="1.6")  # TODO VERSION remove on 1.6+
     ignores = []
     if estimator.__class__.__name__ == "FilterEstimator":
         ignores += [

mne/decoding/transformer.py

@@ -20,7 +20,7 @@
 from ..fixes import _reshape_view
 from ..time_frequency import psd_array_multitaper
 from ..utils import _check_option, _validate_type, check_version, fill_doc
-from ._fixes import validate_data  # TODO VERSION remove with sklearn 1.4+
+from ._fixes import validate_data
 
 
 class MNETransformerMixin(TransformerMixin):
@@ -44,7 +44,7 @@ def _check_data(
         if isinstance(epochs_data, BaseEpochs):
             epochs_data = epochs_data.get_data(copy=False)
         kwargs = dict(dtype=np.float64, allow_nd=True, order="C")
-        if check_version("sklearn", "1.4"):  # TODO VERSION sklearn 1.4+
+        if check_version("sklearn", "1.5"):  # TODO VERSION sklearn 1.5+
             kwargs["force_writeable"] = True
         if hasattr(self, "n_features_in_") and check_n_features:
             if y is None:

mne/preprocessing/nirs/tests/test_beer_lambert_law.py

@@ -43,6 +43,8 @@
 )
 def test_beer_lambert(fname, fmt, tmp_path):
     """Test converting raw CW amplitude files."""
+    if fname.suffix == ".snirf":
+        pytest.importorskip("h5py")
     match fmt:
         case "nirx":
             raw_volt = read_raw_nirx(fname)

mne/preprocessing/nirs/tests/test_nirs.py

@@ -40,12 +40,18 @@
 )
 
 
+def read_raw_snirf_safe(fname):
+    """Wrap to read_raw_snirf, skipping if h5py is not installed."""
+    pytest.importorskip("h5py")
+    return read_raw_snirf(fname)
+
+
 @testing.requires_testing_data
 @pytest.mark.parametrize(
     "fname, readerfn",
     [
         (fname_nirx_15_0, read_raw_nirx),
-        (fname_labnirs_multi_wavelength, read_raw_snirf),
+        (fname_labnirs_multi_wavelength, read_raw_snirf_safe),
     ],
 )
 def test_fnirs_picks(fname, readerfn):
@@ -121,7 +127,7 @@ def _fnirs_check_bads(info):
         (fname_nirx_15_0, read_raw_nirx),
         (fname_nirx_15_2_short, read_raw_nirx),
         (fname_nirx_15_2, read_raw_nirx),
-        (fname_labnirs_multi_wavelength, read_raw_snirf),
+        (fname_labnirs_multi_wavelength, read_raw_snirf_safe),
     ],
 )
 def test_fnirs_check_bads(fname, readerfn):
@@ -166,7 +172,7 @@ def test_fnirs_check_bads(fname, readerfn):
         (fname_nirx_15_0, read_raw_nirx),
         (fname_nirx_15_2_short, read_raw_nirx),
         (fname_nirx_15_2, read_raw_nirx),
-        (fname_labnirs_multi_wavelength, read_raw_snirf),
+        (fname_labnirs_multi_wavelength, read_raw_snirf_safe),
     ],
 )
 def test_fnirs_spread_bads(fname, readerfn):
@@ -210,7 +216,7 @@ def test_fnirs_spread_bads(fname, readerfn):
         (fname_nirx_15_0, read_raw_nirx),
         (fname_nirx_15_2_short, read_raw_nirx),
         (fname_nirx_15_2, read_raw_nirx),
-        (fname_labnirs_multi_wavelength, read_raw_snirf),
+        (fname_labnirs_multi_wavelength, read_raw_snirf_safe),
     ],
 )
 def test_fnirs_channel_frequency_ordering(fname, readerfn):
@@ -598,7 +604,7 @@ def test_order_agnostic(nirx_snirf):
         (fname_nirx_15_0, read_raw_nirx),
         (fname_nirx_15_2_short, read_raw_nirx),
         (fname_nirx_15_2, read_raw_nirx),
-        (fname_labnirs_multi_wavelength, read_raw_snirf),
+        (fname_labnirs_multi_wavelength, read_raw_snirf_safe),
     ],
 )
 def test_nirs_channel_grouping(fname, readerfn):

mne/preprocessing/nirs/tests/test_optical_density.py

@@ -27,6 +27,8 @@
 )
 def test_optical_density(fname, readerfn):
     """Test return type for optical density."""
+    if fname.suffix == ".snirf":
+        pytest.importorskip("h5py")
     raw_volt = readerfn(fname, preload=False)
     _validate_type(raw_volt, BaseRaw, "raw")
 

mne/preprocessing/nirs/tests/test_scalp_coupling_index.py

@@ -85,6 +85,7 @@ def test_scalp_coupling_index_multi_wavelength():
     Similar to test in test_scalp_coupling_index, considers cases
     specific to multi-wavelength data.
     """
+    pytest.importorskip("h5py")
     raw = optical_density(read_raw_snirf(fname_labnirs_multi_wavelength))
     times = np.arange(raw.n_times) / raw.info["sfreq"]
     signal = np.sin(2 * np.pi * 1.0 * times) + 1

mne/tests/test_annotations.py

@@ -1051,6 +1051,8 @@ def dummy_annotation_file(tmp_path_factory, ch_names, fmt, with_extras):
 @pytest.mark.parametrize("with_extras", [True, False])
 def test_io_annotation(dummy_annotation_file, tmp_path, fmt, ch_names, with_extras):
     """Test CSV, TXT, and FIF input/output (which support ch_names)."""
+    if with_extras:
+        pytest.importorskip("pandas")
     annot = read_annotations(dummy_annotation_file)
     assert annot.orig_time == _ORIG_TIME
     kwargs = dict(orig_time=_ORIG_TIME)

mne/tests/test_chpi.py

@@ -51,6 +51,7 @@
     _record_warnings,
     assert_meg_snr,
     catch_logging,
+    check_version,
     object_diff,
     verbose,
 )
@@ -884,6 +885,9 @@ def assert_slopes_correlated(actual_meas, desired_meas, *, lim=(0.99, 1.0)):
 @testing.requires_testing_data
 def test_refit_hpi_locs_basic():
     """Test that HPI locations can be refit."""
+    if not check_version("scipy", "1.13"):
+        # TODO VERSION remove when scipy >= 1.13 is required
+        pytest.xfail("SciPy 1.12 has an lwork bug affecting this test")
     raw = read_raw_fif(chpi_fif_fname, allow_maxshield="yes").crop(0, 2).load_data()
     # These should be similar (and both should work)
     locs = compute_chpi_amplitudes(raw, t_step_min=2, t_window=1)

pyproject.toml

@@ -97,7 +97,7 @@ dependencies = [
   "numpy >= 1.26, < 3",  # released 2023-09-16, will become 2.0 on 2026-06-16
   "packaging",
   "pooch >= 1.5",
-  "scipy >= 1.11",  # released 2023-06-28, will become 1.12 on 2026-01-19
+  "scipy >= 1.12",  # released 2024-01-20, will become 1.13 on 2026-04-02
   "tqdm",
 ]
 description = "MNE-Python project for MEG and EEG data analysis."
@@ -155,7 +155,7 @@ full-no-qt = [
   "nilearn",
   "numba",
   "openmeeg >= 2.5.7",
-  "pandas >= 2.1",  # released 2023-08-30, will become 2.2 on 2026-01-19
+  "pandas >= 2.2",  # released 2024-01-20, will become 2.3 on 2027-06-05
   "pillow",  # for `Brain.save_image` and `mne.Report`
   "pyarrow",  # only needed to avoid a deprecation warning in pandas
   "pybv",
@@ -165,7 +165,7 @@ full-no-qt = [
   "pyvistaqt >= 0.11",  # released 2023-06-30, no newer version available
   "qdarkstyle != 3.2.2",
   "qtpy",
-  "scikit-learn >= 1.3",  # released 2023-06-30, will become 1.4 on 2026-01-17
+  "scikit-learn >= 1.4",  # released 2024-01-18, will become 1.5 on 2026-05-21
   "sip",
   "snirf",
   "statsmodels",

tools/dev/spec_zero_update_versions.py

@@ -9,6 +9,7 @@
 adopted.
 
 MNE-Python's policy differs from SPEC0 in the following ways:
+
 - Python versions are supported for at least 3 years after release, but possibly longer
   at the discretion of the MNE-Python maintainers based on, e.g., maintainability,
   features.
@@ -23,6 +24,7 @@
   https://github.com/mne-tools/mne-python/pull/13451#discussion_r2445337934
 
 For example, in October 2025:
+
 - The latest version of NumPy available 2 years prior was 1.26.1 (released October
   2023), making the latest minor release 1.26, which would be pinned. Support for 1.26
   would be dropped in June 2026 in favour of 2.0, which was released in June 2024.
@@ -39,6 +41,8 @@
 import collections
 import datetime
 import re
+from copy import deepcopy
+from pathlib import Path
 
 import requests
 from packaging.requirements import Requirement
@@ -60,6 +64,8 @@
 SUPPORT_TIME = datetime.timedelta(days=365 * 2)
 CURRENT_DATE = datetime.datetime.now()
 
+project_root = Path(__file__).parent.parent.parent
+
 
 def get_release_and_drop_dates(package):
     """Get release and drop dates for a given package from pypi.org."""
@@ -70,7 +76,7 @@ def get_release_and_drop_dates(package):
         headers={"Accept": "application/vnd.pypi.simple.v1+json"},
         timeout=10,
     ).json()
-    print("OK")
+    print("OK", flush=True)
     file_date = collections.defaultdict(list)
     for f in response["files"]:
         if f["filename"].endswith(".tar.gz") or f["filename"].endswith(".zip"):
@@ -99,7 +105,7 @@ def get_release_and_drop_dates(package):
 
 
 def update_specifiers(dependencies, releases):
-    """Update dependency version specifiers."""
+    """Update dependency version specifiers inplace."""
     for idx, dep in enumerate(dependencies):
         req = Requirement(dep)
         pkg_name = req.name
@@ -153,7 +159,6 @@ def update_specifiers(dependencies, releases):
                 dependencies._value[idx], min_ver_release, next_ver, next_ver_release
             )
         dependencies[idx] = _prettify_requirement(req)
-    return dependencies
 
 
 def _as_minor_version(ver):
@@ -239,19 +244,47 @@ def _find_specifier_order(specifiers):
 }
 
 # Get dependencies from pyproject.toml
-pyproject = TOMLFile("pyproject.toml")
+pyproject = TOMLFile(project_root / "pyproject.toml")
 pyproject_data = pyproject.read()
-project_info = pyproject_data.get("project")
+project_info = pyproject_data["project"]
 core_dependencies = project_info["dependencies"]
-opt_dependencies = project_info.get("optional-dependencies", {})
+opt_dependencies = project_info["optional-dependencies"]
 
 # Update version specifiers
-core_dependencies = update_specifiers(core_dependencies, package_releases)
+changed = []
+old_deps = deepcopy(core_dependencies)
+update_specifiers(core_dependencies, package_releases)
+changed.extend(
+    [
+        f"Core dependency ``{new}``"
+        for new, old in zip(core_dependencies, old_deps)
+        if new != old
+    ]
+)
 for key in opt_dependencies:
-    opt_dependencies[key] = update_specifiers(opt_dependencies[key], package_releases)
-pyproject_data["project"]["dependencies"] = core_dependencies
-if opt_dependencies:
-    pyproject_data["project"]["optional-dependencies"] = opt_dependencies
+    old_deps = deepcopy(opt_dependencies[key])
+    update_specifiers(opt_dependencies[key], package_releases)
+    changed.extend(
+        [
+            f"Optional dependency ``{new}``"
+            for new, old in zip(opt_dependencies[key], old_deps)
+            if new != old
+        ]
+    )
+
+# Need to write a changelog entry if versions were updated
+if changed:
+    changelog_text = "Updated minimum for:\n\n"
+    changelog_text += "\n".join(f"- {change}" for change in changed)
+    print(changelog_text, flush=True)
+    # no reason to print this but it should go in the changelog
+    changelog_text += (
+        "\n\nChanged implemented via CI action created by `Thomas Binns`_.\n"
+    )
+    changelog_path = project_root / "doc" / "changes" / "dev" / "dependency.rst"
+    changelog_path.write_text(changelog_text, encoding="utf-8")
+else:
+    print("No dependency versions needed updating.", flush=True)
 
 # Save updated pyproject.toml (replace ugly \" with ' first)
 pyproject_data = parse(pyproject_data.as_string().replace('\\"', "'"))