MAINT: Update dependency specifiers (#13899)

mne-bot · autofix-ci[bot] · larsoner · web-flow · commit 990b0b5bfaa9 · 2026-05-18T16:54:53.000Z
Co-authored-by: autofix-ci[bot] &lt;114827586+autofix-ci[bot]@users.noreply.github.com&gt;
Co-authored-by: Eric Larson &lt;larson.eric.d@gmail.com&gt;
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -114,7 +114,7 @@ stages:
           - bash: |
               set -eo pipefail
               python -m pip install --progress-bar off --upgrade pip
-              python -m pip install --progress-bar off "mne-qt-browser[opengl] @ git+https://github.com/mne-tools/mne-qt-browser.git" pyvista scikit-learn python-picard qtpy nibabel sphinx-gallery "PySide6!=6.8.0,!=6.8.0.1,!=6.8.1.1,!=6.9.1" pandas neo pymatreader antio defusedxml curryreader pymef
+              python -m pip install --progress-bar off "mne-qt-browser @ https://github.com/mne-tools/mne-qt-browser/archive/refs/heads/main.zip" pyvista scikit-learn python-picard qtpy nibabel sphinx-gallery "PySide6!=6.8.0,!=6.8.0.1,!=6.8.1.1,!=6.9.1" pandas neo pymatreader antio defusedxml curryreader pymef
               python -m pip uninstall -yq mne
               python -m pip install --progress-bar off --upgrade -e . --group=test
             displayName: 'Install dependencies with pip'
@@ -164,7 +164,7 @@ stages:
               python -m pip install --progress-bar off --upgrade pip
               python -m pip install --progress-bar off --upgrade --pre --only-binary=\"numpy,scipy,matplotlib,vtk\" numpy scipy matplotlib vtk
               python -c "import vtk"
-              python -m pip install --progress-bar off --upgrade -ve .[full] --group=test_extra
+              python -m pip install --progress-bar off --upgrade -ve .[full] --group=test_extra "mne-qt-browser @ https://github.com/mne-tools/mne-qt-browser/archive/refs/heads/main.zip"
             displayName: 'Install dependencies with pip'
           - bash: |
               set -e
diff --git a/doc/changes/dev/13899.dependency.rst b/doc/changes/dev/13899.dependency.rst
@@ -0,0 +1,5 @@
+Updated minimum for:
+
+- Core dependency ``matplotlib >= 3.9``
+
+Changes implemented via CI action created by `Thomas Binns`_.
diff --git a/environment.yml b/environment.yml
@@ -27,7 +27,7 @@ dependencies:
   - jupyter
   - lazy_loader >=0.3
   - mamba
-  - matplotlib >=3.8
+  - matplotlib >=3.9
   - mffpy >=0.5.7
   - mne-qt-browser
   - nest-asyncio2
diff --git a/mne/fixes.py b/mne/fixes.py
@@ -57,7 +57,9 @@ def _compare_version(version_a, operator, version_b):
 
 
 ###############################################################################
-# NumPy 2.5 deprecates .shape assignment, but .reshape(copy=False) requires 2.1+
+# NumPy 2.5 removes .shape assignment, but .reshape(copy=False) requires 2.1+
+
+# TODO VERSION remove on NumPy 2.1+
 
 
 def _reshape_view(arr, shape):
@@ -66,10 +68,8 @@ def _reshape_view(arr, shape):
     This function provides compatibility across NumPy versions for reshaping
     arrays as views. On NumPy >= 2.1, it uses ``reshape(copy=False)`` which
     explicitly fails if a view cannot be created. On older versions, it uses
-    direct shape assignment which has the same behavior but is deprecated in
-    NumPy 2.5+.
-
-    Can be removed once NumPy 2.1 is the minimum supported version.
+    direct shape assignment which has the same behavior but is being removed
+    as of NumPy 2.5+.
 
     Parameters
     ----------
@@ -765,8 +765,7 @@ def minimum_phase(h, method="homomorphic", n_fft=None, *, half=True):
     return h_minimum[:n_out]
 
 
-# SciPy 1.15 deprecates sph_harm for sph_harm_y and using it will trigger a
-# DeprecationWarning. This is a backport of the new function for older SciPy versions.
+# TODO VERSION SciPy 1.15+ (sph_harm -> sph_harm_y)
 def sph_harm_y(n, m, theta, phi, *, diff_n=0):
     """Wrap scipy.special.sph_harm for sph_harm_y."""
     # Can be removed once we no longer support scipy < 1.15.0
diff --git a/mne/time_frequency/tfr.py b/mne/time_frequency/tfr.py
@@ -1939,7 +1939,7 @@ def plot(
         cnorm=None,
         cmap=None,
         colorbar=True,
-        title=None,  # don't deprecate this one; has (useful) option title="auto"
+        title=None,  # keep: has (useful) option title="auto"
         mask=None,
         mask_style=None,
         mask_cmap="Greys",
@@ -2481,7 +2481,7 @@ def plot_topo(
         vmax=None,
         layout=None,
         cmap="RdBu_r",
-        title=None,  # don't deprecate; topo titles aren't standard (color, size, just.)
+        title=None,  # keep: topo titles aren't standard (color, size, just.)
         dB=False,
         colorbar=True,
         layout_scale=0.945,
@@ -3432,7 +3432,7 @@ def plot(
         cnorm=None,
         cmap=None,
         colorbar=True,
-        title=None,  # don't deprecate this one; has (useful) option title="auto"
+        title=None,  # keep: has (useful) option title="auto"
         mask=None,
         mask_style=None,
         mask_cmap="Greys",
@@ -3484,7 +3484,7 @@ def plot_topo(
         vmax=None,
         layout=None,
         cmap=None,
-        title=None,  # don't deprecate; topo titles aren't standard (color, size, just.)
+        title=None,  # keep: topo titles aren't standard (color, size, just.)
         dB=False,
         colorbar=True,
         layout_scale=0.945,
diff --git a/mne/utils/dataframe.py b/mne/utils/dataframe.py
@@ -58,10 +58,10 @@ def _convert_times(
 
 
 def _inplace(df, method, **kwargs):
-    # TODO VERSION can be removed once pandas>=3.0 is required
+    # TODO VERSION remove on pandas 3.0+
     # Handle transition: inplace=True (pandas <1.5) → copy=False (>=1.5)
     # and 3.0 warning:
-    # E   DeprecationWarning: The copy keyword is deprecated and will be removed in a
+    #     The copy keyword will be removed in a
     #     future version. Copy-on-Write is active in pandas since 3.0 which utilizes a
     #     lazy copy mechanism that defers copies until necessary. Use .copy() to make
     #     an eager copy if necessary.
diff --git a/mne/utils/spectrum.py b/mne/utils/spectrum.py
@@ -106,7 +106,7 @@ def _split_psd_kwargs(*, plot_fun=None, kwargs=None):
 
 
 def _convert_old_birthday_format(info):
-    """Convert deprecated birthday tuple to datetime."""
+    """Convert old birthday tuple to datetime."""
     subject_info = info.get("subject_info")
     if subject_info is not None:
         birthday = subject_info.get("birthday")
diff --git a/mne/viz/backends/_utils.py b/mne/viz/backends/_utils.py
@@ -193,7 +193,9 @@ def _init_mne_qtapp(enable_icon=True, pg_app=False, splash=False):
     out = app
     if splash:
         pixmap = QPixmap(f"{icons_path}/mne_splash.png")
-        pixmap.setDevicePixelRatio(QGuiApplication.primaryScreen().devicePixelRatio())
+        screen = QGuiApplication.primaryScreen()
+        ratio = screen.devicePixelRatio() if screen else 1
+        pixmap.setDevicePixelRatio(ratio)
         args = (pixmap,)
         if _should_raise_window():
             args += (Qt.WindowStaysOnTopHint,)
diff --git a/pyproject.toml b/pyproject.toml
@@ -102,7 +102,7 @@ dependencies = [
   "decorator >= 5.1",
   "jinja2 >= 3.1",
   "lazy_loader >= 0.3",
-  "matplotlib >= 3.8",  # released 2023-09-15, will become 3.9 on 2026-05-15
+  "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",
diff --git a/tools/azure_dependencies.sh b/tools/azure_dependencies.sh
@@ -5,7 +5,7 @@ SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
 STD_ARGS="--progress-bar off --upgrade "
 python -m pip install $STD_ARGS pip setuptools wheel
 if [ "${TEST_MODE}" == "pip" ]; then
-	python -m pip install $STD_ARGS --only-binary="numba,llvmlite,numpy,scipy,vtk,dipy,openmeeg" -e .[full] --group=test
+	python -m pip install $STD_ARGS --only-binary="numba,llvmlite,numpy,scipy,vtk,dipy,openmeeg" -e .[full] --group=test "mne-qt-browser @ https://github.com/mne-tools/mne-qt-browser/archive/refs/heads/main.zip"
 elif [ "${TEST_MODE}" == "pip-pre" ]; then
 	${SCRIPT_DIR}/install_pre_requirements.sh
 	python -m pip install $STD_ARGS --pre -e . --group=test_extra
diff --git a/tools/install_pre_requirements.sh b/tools/install_pre_requirements.sh
@@ -46,15 +46,15 @@ echo "::endgroup::"
 
 echo "::group::Everything else"
 python -m pip install $STD_ARGS \
-	"git+https://github.com/pyvista/pyvista" \
-	"git+https://github.com/pyvista/pyvistaqt" \
+	"pyvista @ https://github.com/pyvista/pyvista/archive/refs/heads/main.zip" \
+	"pyvistaqt @ https://github.com/pyvista/pyvistaqt/archive/refs/heads/main.zip" \
 	"git+https://github.com/nilearn/nilearn" \
 	"git+https://github.com/pierreablin/picard" \
 	"git+https://github.com/the-siesta-group/edfio" \
-	https://gitlab.com/obob/pymatreader/-/archive/master/pymatreader-master.zip \
-	git+https://github.com/mne-tools/mne-qt-browser \
+	"https://gitlab.com/obob/pymatreader/-/archive/master/pymatreader-master.zip" \
 	git+https://github.com/pyqtgraph/pyqtgraph \
-	git+https://github.com/mne-tools/mne-bids \
+	"mne-qt-browser @ https://github.com/mne-tools/mne-qt-browser/archive/refs/heads/main.zip" \
+	"mne-bids @ https://github.com/mne-tools/mne-bids/archive/refs/heads/main.zip" \
 	git+https://github.com/nipy/nibabel \
 	git+https://github.com/joblib/joblib \
 	git+https://github.com/h5io/h5io \
diff --git a/tools/pylock.ci-old.toml b/tools/pylock.ci-old.toml
@@ -231,9 +231,9 @@ wheels = [{ url = "https://files.pythonhosted.org/packages/af/cd/ce6e848bbf2c323
 
 [[packages]]
 name = "matplotlib"
-version = "3.8.0"
-sdist = { url = "https://files.pythonhosted.org/packages/23/e1/77016194621fb1356aafeb2186f07b5dede62ea2043bf03f82325c4fccc5/matplotlib-3.8.0.tar.gz", upload-time = 2023-09-15T04:49:03Z, size = 35864435, hashes = { sha256 = "df8505e1c19d5c2c26aff3497a7cbd3ccfc2e97043d1e4db3e76afa399164b69" } }
-wheels = [{ url = "https://files.pythonhosted.org/packages/b5/24/aaccf324ce862bb82277e8814d2aebbb2a2c160d04e95aa2b8c9dc3137a9/matplotlib-3.8.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", upload-time = 2023-09-15T04:50:03Z, size = 11610560, hashes = { sha256 = "d670b9348e712ec176de225d425f150dc8e37b13010d85233c539b547da0be39" } }]
+version = "3.9.0"
+sdist = { url = "https://files.pythonhosted.org/packages/c5/a4/a7236bf8b0137deff48737c6ccf2154ef4486e57c6a5b7c309bf515992bd/matplotlib-3.9.0.tar.gz", upload-time = 2024-05-15T23:38:15Z, size = 36069890, hashes = { sha256 = "e6d29ea6c19e34b30fb7d88b7081f869a03014f66fe06d62cc77d5a6ea88ed7a" } }
+wheels = [{ url = "https://files.pythonhosted.org/packages/a7/68/16e7b9154fae61fb29f0f3450b39b855b89e6d2c598d67302e70f96883af/matplotlib-3.9.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", upload-time = 2024-05-15T23:37:12Z, size = 8296303, hashes = { sha256 = "eaf3978060a106fab40c328778b148f590e27f6fa3cd15a19d6892575bce387d" } }]
 
 [[packages]]
 name = "matplotlib-inline"
