MAINT: Update dependency specifiers #13611

larsoner · 2026-01-27T16:45:31Z

@tsbinns the old code both updated inplace and set vars, which is unnecessary (and led to some confusion where I assumed things were not updated inplace because the vars were set). I've changed it just to operate inplace where possible.

-Original file line number
+Diff line change
@@ Expand Up / @@ -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'

-Original file line number
+Diff line change
@@ Expand Up / @@ -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'
@@ Expand Down @@

-Original file line number
+Diff line change
@@ -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`_.

-Original file line number
+Diff line change
@@ Expand Up / @@ -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
@@ Expand All / @@ -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
@@ Expand Down @@

-Original file line number
+Diff line change
@@ Expand Up / @@ -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
@@ Expand Down @@

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-Original file line number
+Diff line change
@@ Expand Up / @@ -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)

-Original file line number
+Diff line change
@@ Expand Up / @@ -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.
@@ Expand All / @@ -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.
@@ Expand Down @@

-Original file line number
+Diff line change
@@ Expand Up / @@ -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):
@@ Expand All / @@ -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:
@@ Expand Down @@

-Original file line number
+Diff line change
@@ Expand Up / @@ -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)
@@ Expand Down @@

-Original file line number
+Diff line change
@@ Expand Up / @@ -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):
@@ Expand Down Expand Up / @@ -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):
@@ Expand Down Expand Up / @@ -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):
@@ Expand Down Expand Up / @@ -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):
@@ Expand Down Expand Up / @@ -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):
@@ Expand Down @@

-Original file line number
+Diff line change
@@ Expand Up / @@ -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
@@ Expand Down @@

-Original file line number
+Diff line change
@@ Expand Up @@
     @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)
@@ Expand Down @@

-Original file line number
+Diff line change
@@ Expand Up / @@ -51,6 +51,7 @@ @@
         _record_warnings,
         assert_meg_snr,
         catch_logging,
+        check_version,
         object_diff,
         verbose,
     )
@@ Expand Down Expand Up @@
     @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)
@@ Expand Down @@

-Original file line number
+Diff line change
@@ Expand Up / @@ -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."
@@ Expand Down Expand Up / @@ -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",
@@ Expand All / @@ -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",
@@ Expand Down @@

-Original file line number
+Diff line change
@@ Expand Up / @@ -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.
@@ Expand All / @@ -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
 ), 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.
@@ Expand All / @@ -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
@@ Expand All / @@ -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."""
@@ Expand All / @@ -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"):
@@ Expand Down Expand Up / @@ -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
@@ Expand Down Expand Up / @@ -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):
@@ Expand Down Expand Up / @@ -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('\\"', "'"))
@@ Expand Down @@

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larsoner Jan 27, 2026

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