MAINT: Update dependency specifiers (#13814)

Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com>
Co-authored-by: Thomas S. Binns <t.s.binns@outlook.com>

Author: 3 people

doc/changes/dev/13814.dependency.rst

@@ -0,0 +1,5 @@
+Updated minimum for:
+
+- Core dependency ``scipy >= 1.13``
+
+Changed implemented via CI action created by `Thomas Binns`_.

environment.yml

@@ -51,7 +51,7 @@ dependencies:
   - qdarkstyle !=3.2.2
   - qtpy
   - scikit-learn >=1.4
-  - scipy >=1.12
+  - scipy >=1.13
   - sip
   - snirf
   - statsmodels >=0.6

mne/tests/test_chpi.py

@@ -885,9 +885,11 @@ 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")
+    if not check_version("scipy", "1.14"):
+        # TODO VERSION remove when scipy >= 1.14 is required (gh mne-python #13814)
+        # Test fails on "old" job with SciPy 1.12 and 1.13. Will need to see after
+        # 2026-06-24 whether bumping min SciPy version to 1.14 fixes this.
+        pytest.xfail("SciPy 1.13 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)

mne/viz/backends/_pyvista.py

@@ -213,7 +213,7 @@ def __init__(
         from .._3d import _get_3d_option
 
         # TODO VERSION change whenever PyVista min gets updated:
-        _require_version("pyvista", "use 3D rendering", "0.42")
+        _require_version("pyvista", "use 3D rendering", "0.43")
         multi_samples = _get_3d_option("multi_samples")
         # multi_samples > 1 is broken on macOS + Intel Iris + volume rendering
         if platform.system() == "Darwin":

mne/viz/tests/test_raw.py

@@ -347,9 +347,6 @@ def test_scale_bar(browser_backend):
 def test_plot_raw_selection(raw, browser_backend):
     """Test selection mode of plot_raw()."""
     ismpl = browser_backend.name == "matplotlib"
-    if ismpl and os.getenv("MNE_CI_KIND") == "pip-pre":
-        # TODO VERSION FIX SOON AFTER 2026/01/26!
-        pytest.xfail("Needs mpl gh-31031")
     with raw.info._unlock():
         raw.info["lowpass"] = 10.0  # allow heavy decim during plotting
     browser_backend._close_all()  # ensure all are closed
@@ -794,9 +791,6 @@ def test_plot_misc_auto(browser_backend):
 def test_plot_annotations(raw, browser_backend):
     """Test annotation mode of the plotter."""
     ismpl = browser_backend.name == "matplotlib"
-    if ismpl and os.getenv("MNE_CI_KIND") == "pip-pre":
-        # TODO VERSION FIX SOON AFTER 2026/01/26!
-        pytest.xfail("Needs mpl gh-31031")
     with raw.info._unlock():
         raw.info["lowpass"] = 10.0
     _annotation_helper(raw, browser_backend)

pyproject.toml

@@ -106,7 +106,7 @@ dependencies = [
   "numpy >= 1.26, < 3",  # released 2023-09-16, will become 2.0 on 2026-06-16
   "packaging",
   "pooch >= 1.5",
-  "scipy >= 1.12",  # released 2024-01-20, will become 1.13 on 2026-04-02
+  "scipy >= 1.13",  # released 2024-04-02, will become 1.14 on 2026-06-24
   "tqdm >= 4.66",
 ]
 description = "MNE-Python project for MEG and EEG data analysis."

tools/pylock.ci-old.toml

@@ -67,12 +67,6 @@ wheels = [
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 ]
 
-[[packages]]
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-version = "7.1.2"
-sdist = { url = "https://files.pythonhosted.org/packages/27/6f/be940c8b1f1d69daceeb0032fee6c34d7bd70e3e649ccac0951500b4720e/click-7.1.2.tar.gz", upload-time = 2020-04-27T20:22:45Z, size = 297279, hashes = { sha256 = "d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a" } }
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-
 [[packages]]
 name = "codespell"
 version = "1.9.0"
@@ -463,9 +457,9 @@ wheels = [
 
 [[packages]]
 name = "scipy"
-version = "1.12.0"
-sdist = { url = "https://files.pythonhosted.org/packages/30/85/cdbf2c3c460fe5aae812917866392068a88d02f07de0fe31ce738734c477/scipy-1.12.0.tar.gz", upload-time = 2024-01-20T21:13:43Z, size = 56811768, hashes = { sha256 = "4bf5abab8a36d20193c698b0f1fc282c1d083c94723902c447e5d2f1780936a3" } }
-wheels = [{ url = "https://files.pythonhosted.org/packages/f5/aa/8e6071a5e4dca4ec68b5b22e4991ee74c59c5d372112b9c236ec1faff57d/scipy-1.12.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", upload-time = 2024-01-20T21:10:51Z, size = 38441046, hashes = { sha256 = "5e32847e08da8d895ce09d108a494d9eb78974cf6de23063f93306a3e419960c" } }]
+version = "1.13.0"
+sdist = { url = "https://files.pythonhosted.org/packages/fb/a3/328965862f41ba67d27ddd26205962007ec87d99eec6d364a29bf00ac093/scipy-1.13.0.tar.gz", upload-time = 2024-04-02T21:48:22Z, size = 57204550, hashes = { sha256 = "58569af537ea29d3f78e5abd18398459f195546bb3be23d16677fb26616cc11e" } }
+wheels = [{ url = "https://files.pythonhosted.org/packages/b9/9d/39dbcf49a793157f9d4f5b8961855677eb4dbb4b82700dcee7042ad2310c/scipy-1.13.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", upload-time = 2024-04-02T21:41:39Z, size = 38568731, hashes = { sha256 = "b8434f6f3fa49f631fae84afee424e2483289dfc30a47755b4b4e6b07b2633a4" } }]
 
 [[packages]]
 name = "setuptools"
@@ -565,25 +559,13 @@ version = "3.6.0"
 sdist = { url = "https://files.pythonhosted.org/packages/b7/4d/08c89e34946fce2aec4fbb45c9016efd5f4d7f24af8e5d93296e935631d8/threadpoolctl-3.6.0.tar.gz", upload-time = 2025-03-13T13:49:23Z, size = 21274, hashes = { sha256 = "8ab8b4aa3491d812b623328249fab5302a68d2d71745c8a4c719a2fcaba9f44e" } }
 wheels = [{ url = "https://files.pythonhosted.org/packages/32/d5/f9a850d79b0851d1d4ef6456097579a9005b31fea68726a4ae5f2d82ddd9/threadpoolctl-3.6.0-py3-none-any.whl", upload-time = 2025-03-13T13:49:21Z, size = 18638, hashes = { sha256 = "43a0b8fd5a2928500110039e43a5eed8480b918967083ea48dc3ab9f13c4a7fb" } }]
 
-[[packages]]
-name = "toml-sort"
-version = "0.1.0"
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-
 [[packages]]
 name = "tomli"
 version = "1.1.0"
 marker = "python_full_version <= '3.11'"
 sdist = { url = "https://files.pythonhosted.org/packages/6c/16/f48ab3289015f8f90e2c68fb76531728b3d8e4ce5052ee80ad10e7707eda/tomli-1.1.0.tar.gz", upload-time = 2021-07-23T09:47:07Z, size = 12134, hashes = { sha256 = "33d7984738f8bb699c9b0a816eb646a8178a69eaa792d258486776a5d21b8ca5" } }
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-
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