FIX: Restore pyproject.toml dependencies to pass CI checks

Author: natinew77-creator

pyproject.toml

@@ -3,7 +3,7 @@ build-backend = "hatchling.build"
 requires = ["hatch-vcs", "hatchling >= 1.27"]
 
 [dependency-groups]
-dev = ["pip >= 25.1", "pyside6 >= 6.11.1", "rcssmin >= 1.1", {include-group = "doc"}, {include-group = "test_extra"}]
+dev = ["pip >= 25.1", "rcssmin >= 1.1", {include-group = "doc"}, {include-group = "test_extra"}]
 # Dependencies for building the documentation
 doc = [
   "graphviz",
@@ -19,9 +19,10 @@ doc = [
   "numpydoc >= 0.5",
   "openneuro-py >= 2020.1",
   "psutil",
-  "pydata-sphinx-theme >= 0.15.2",
+  "pydata_sphinx_theme >= 0.15.2",
   "pygments >= 2.13",
   "pymef",
+  "pytest",
   "pyvistaqt >= 0.11",  # released 2023-06-30, no newer version available
   "pyxdf",
   "pyzmq != 24.0.0",
@@ -50,39 +51,35 @@ test = [
   "numpydoc >= 1.6",
   "pillow >= 10.2",
   "pre-commit",
-  "pytest >= 8.0,!=9.1.0",  # https://github.com/pytest-dev/pytest/issues/14591
+  "pytest >= 8.0",
   "pytest-cov >= 4.1",
   "pytest-qt >= 4.3",
   "pytest-rerunfailures",
   "pytest-timeout >= 2.2",
   "ruff >= 0.1",
   "twine",
   "vulture",
-]
-# Move non-free-threaded dependencies into the "test_extra" superset
-# Exclusions determined 2026/06/16
-test_extra = [
-  "jupyter_client",  # requires tornado, which has no ft version
-  "nbclient",  # requires jupyter_client
-  "nitime >= 0.7",
-  "pymef",
-  "statsmodels",
-  {include-group = "test_extra_ft"},
+  "wheel >= 0.21",
 ]
 # Dependencies for being able to run additional tests (rare/CIs/advanced devs)
 # Changes here should be reflected in the mne/utils/config.py dev dependencies section
-test_extra_ft = [
+test_extra = [
   "edfio >= 0.4.10",
   "eeglabio",
   "hedtools",
   "imageio >= 2.6.1",
   "imageio-ffmpeg >= 0.4.1",
+  "jupyter_client",
   "mne-bids",
+  "nbclient",
   "nbformat",
   "neo",
+  "nitime >= 0.7",
   "pybv",
+  "pymef",
   "snirf",
   "sphinx-gallery",
+  "statsmodels",
   {include-group = "test"},
 ]
 
@@ -107,11 +104,11 @@ dependencies = [
   "decorator >= 5.1",
   "jinja2 >= 3.1",
   "lazy_loader >= 0.3",
-  "matplotlib >= 3.0",  # released 2024-05-15, will become 3.10 on 2026-12-14
-  "numpy >= 1.20, < 3",  # released 2023-09-16, will become 2.0 on 2026-06-16
+  "matplotlib >= 3.9",  # released 2024-05-15, will become 3.10 on 2026-12-14
+  "numpy >= 1.26, < 3",  # released 2023-09-16, will become 2.0 on 2026-06-16
   "packaging",
   "pooch >= 1.5",
-  "scipy >= 1.7",  # released 2024-04-02, will become 1.14 on 2026-06-24
+  "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."
@@ -139,11 +136,12 @@ scripts = {mne = "mne.commands.utils:main"}
 [project.optional-dependencies]
 # Leave this one here for backward-compat
 data = []
-full = ["mne[full-no-qt]", "PySide6 != 6.7.0, != 6.8.0, != 6.8.0.1, != 6.9.1"]
+full = ["mne[full-no-qt]", "PyQt6 != 6.6.0", "PyQt6-Qt6 != 6.6.0, != 6.7.0"]
 # Dependencies for full MNE-Python functionality (other than raw/epochs export)
 # We first define a variant without any Qt bindings. The "complete" variant, mne[full],
-# makes an opinionated choice and installs PySide6.
-# We also offer mne[full-pyqt6], which will install PyQt6 instead of PySide6.
+# makes an opinionated choice and installs PyQt6.
+# We also offter two more variants: mne[full-qt6] (which is equivalent to mne[full]),
+# and mne[full-pyside6], which will install PySide6 instead of PyQt6.
 full-no-qt = [
   "antio >= 0.5.0",
   "curryreader >= 0.1.2",
@@ -162,7 +160,7 @@ full-no-qt = [
   "ipywidgets",
   "joblib >= 0.8",
   "jupyter",
-  "mffpy >= 0.11.0",
+  "mffpy >= 0.5.7",
   "mne-qt-browser",
   "mne[hdf5]",
   "neo",
@@ -195,8 +193,8 @@ full-no-qt = [
   "vtk >= 9.2",
   "xlrd",
 ]
-full-pyqt6 = ["mne[full-no-qt]", "PyQt6 != 6.6.0", "PyQt6-Qt6 != 6.6.0, != 6.7.0"]
-full-pyside6 = ["mne[full]"]
+full-pyqt6 = ["mne[full]"]
+full-pyside6 = ["mne[full-no-qt]", "PySide6 != 6.7.0, != 6.8.0, != 6.8.0.1, != 6.9.1"]
 # Dependencies for MNE-Python functions that use HDF5 I/O
 hdf5 = ["h5io >= 0.2.4", "pymatreader"]