diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml
new file mode 100644
index 0000000..7a86879
--- /dev/null
+++ b/.github/workflows/build-docs.yml
@@ -0,0 +1,85 @@
+name: build-docs
+
+on:
+ push:
+ branches: [ main ]
+ pull_request:
+ branches: [ main ]
+
+jobs:
+ doc-build:
+ runs-on: ubuntu-latest
+ env:
+ DISPLAY: ":99"
+ OPENBLAS_NUM_THREADS: 4
+ MNE_3D_BACKEND: pyvista
+ _MNE_BRAIN_TRACES_AUTO: false
+
+ steps:
+ - uses: actions/checkout@v4
+
+ - name: Set up Python 3.12
+ uses: actions/setup-python@v5
+ with:
+ python-version: 3.12
+
+ - name: Merge with upstream
+ run: |
+ echo $(git log -1 --pretty=%B) | tee gitlog.txt
+ echo ${CI_PULL_REQUEST//*pull\//} | tee merge.txt
+ if [[ $(cat merge.txt) != "" ]]; then
+ echo "Merging $(cat merge.txt)";
+ git remote add upstream git://github.com/AaltoImagingLanguage/conpy.git;
+ git pull --ff-only upstream "refs/pull/$(cat merge.txt)/merge";
+ git fetch upstream main;
+ fi
+
+ - name: Install 3D rendering libraries
+ run: |
+ sudo apt-get update
+ sudo apt-get install libosmesa6 libglx-mesa0 libopengl0 libglx0 libdbus-1-3
+
+ - name: Spin up Xvfb
+ run: |
+ /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1400x900x24 -ac +extension GLX +render -noreset;
+
+ - name: Install PyQt6 dependencies
+ run: |
+ sudo apt-get install qt6-base-dev libx11-xcb-dev libxcb-cursor0
+
+ - name: Cache Pip
+ id: cache-pip
+ uses: actions/cache@v4
+ with:
+ path: ~/.cache/pip
+ key: pip-cache
+
+ - name: Install Python dependencies
+ run: |
+ python -m pip install --user --upgrade --progress-bar off pip wheel
+ python -m pip install --user --upgrade --progress-bar off -r requirements-dev.txt
+ python -m pip install --user -e .
+
+ # Look at what we have and fail early if there is some library conflict
+ - name: Check installation
+ run: |
+ which python
+ python -c "import mne; mne.sys_info()"
+ python -c "import numpy; numpy.show_config()"
+ python -c "import conpy"
+
+ - name: Download example data
+ run: |
+ python -c "import mne; mne.datasets.sample.data_path(download=True)"
+
+ # Build docs
+ - name: make html
+ run: |
+ cd doc;
+ make html;
+
+ - name: Save HTML as artifact
+ uses: actions/upload-artifact@v4
+ with:
+ name: doc-dev
+ path: doc/_build/html
diff --git a/.github/workflows/unit-tests.yml b/.github/workflows/unit-tests.yml
new file mode 100644
index 0000000..5d474f8
--- /dev/null
+++ b/.github/workflows/unit-tests.yml
@@ -0,0 +1,37 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: unit-tests
+
+on:
+ push:
+ branches: [ main ]
+ pull_request:
+ branches: [ main ]
+
+jobs:
+ unit-tests:
+
+ runs-on: ubuntu-latest
+
+ steps:
+ - uses: actions/checkout@v4
+ - name: Set up Python 3.12
+ uses: actions/setup-python@v5
+ with:
+ python-version: 3.12
+ - name: Install dependencies
+ run: |
+ python -m pip install --upgrade pip
+ pip install ruff pytest tqdm pytest-cov
+ pip install -r requirements-dev.txt
+
+ - name: Lint with ruff
+ run: |
+ # stop the build if there are Python syntax errors or undefined names
+ ruff check conpy
+
+ - name: Test with pytest
+ run: |
+ pip install -e .
+ pytest --cov-report term-missing --cov conpy tests
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..dfada97
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,20 @@
+repos:
+ # Ruff conpy
+ - repo: https://github.com/astral-sh/ruff-pre-commit
+ rev: v0.13.1
+ hooks:
+ - id: ruff
+ name: ruff-lint
+ files: ^conpy/
+ - id: ruff-format
+ files: ^conpy|^doc/|^examples/
+
+ # Codespell
+ - repo: https://github.com/codespell-project/codespell
+ rev: v2.4.1
+ hooks:
+ - id: codespell
+ additional_dependencies:
+ - tomli
+ files: ^conpy/|^doc/|^examples/
+ types_or: [python, bib, rst]
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
deleted file mode 100644
index 247744c..0000000
--- a/azure-pipelines.yml
+++ /dev/null
@@ -1,54 +0,0 @@
-trigger:
-- master
-
-jobs:
-- job: 'Test'
- pool:
- vmImage: 'Ubuntu-16.04'
- steps:
- - bash: |
- echo "##vso[task.prependpath]$CONDA/bin"
- sudo chown -R $USER /usr/share/miniconda
- conda env create --quiet --file environment.yml
- . /usr/share/miniconda/etc/profile.d/conda.sh
- conda activate conpy
- displayName: 'Setup python environment'
-
- - script: python setup.py develop --user
- displayName: 'Install conpy'
-
- - bash: |
- . /usr/share/miniconda/etc/profile.d/conda.sh
- conda activate conpy
- /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1400x900x24 -ac +extension GLX +render -noreset
- export DISPLAY=:99.0
- python -c "import mne; mne.sys_info()"
- python -c "from mayavi import mlab; import matplotlib.pyplot as plt; mlab.figure(); plt.figure()"
- displayName: 'Start X Virtual Frame Buffer'
-
- - script: |
- . /usr/share/miniconda/etc/profile.d/conda.sh
- conda activate conpy
- python -c "import mne; print(mne.datasets.sample.data_path(update_path=True, verbose=False))";
- python -c "import mne; print(mne.datasets.testing.data_path(update_path=True, verbose=False))";
- pytest tests --doctest-modules --junitxml=junit/test-results.xml --cov=com --cov-report=xml --cov-report=html
- displayName: 'Run unit tests'
-
- - task: PublishTestResults@2
- inputs:
- testResultsFiles: '**/test-results.xml'
- testRunTitle: 'Python $(python.version)'
- condition: succeededOrFailed()
-
- - bash: |
- . /usr/share/miniconda/etc/profile.d/conda.sh
- conda activate conpy
- export DISPLAY=:99.0
- cd doc
- make html
- displayName: 'Build documentation'
-
- - task: PublishPipelineArtifact@0
- inputs:
- artifactName: 'doc'
- targetPath: 'doc/_build/html'
diff --git a/conpy/connectivity.py b/conpy/connectivity.py
index 0018e64..44c4d26 100644
--- a/conpy/connectivity.py
+++ b/conpy/connectivity.py
@@ -28,7 +28,7 @@
from .viz import plot_connectivity
-class BaseConnectivity(object):
+class _BaseConnectivity(object):
"""Base class for connectivity objects.
Contains implementation of methods that are defined for all connectivity
@@ -98,6 +98,7 @@ def __init__(
self.source_degree = np.asarray(_compute_degree(pairs, n_sources))
def __repr__(self):
+ """Obtain a string representation."""
return "<{} | n_sources={}, n_conns={}, subject={}>".format(
self.__class__.__name__, self.n_sources, self.n_connections, self.subject
)
@@ -212,7 +213,7 @@ def threshold(self, thresh, crit=None, direction="above", copy=False):
mask = crit < thresh
else:
raise ValueError(
- 'The direction parameter must be either "above" ' 'or "below".'
+ 'The direction parameter must be either "above" or "below".'
)
if copy:
@@ -252,7 +253,7 @@ def is_compatible(self, other):
Whether the given connectivity object is compatible with this one.
"""
return (
- isinstance(other, BaseConnectivity)
+ isinstance(other, _BaseConnectivity)
and other.n_sources == self.n_sources
and np.array_equal(other.pairs, self.pairs)
)
@@ -356,7 +357,7 @@ def _compute_degree(pairs, n_sources):
return out_degree, in_degree
-class VertexConnectivity(BaseConnectivity):
+class VertexConnectivity(_BaseConnectivity):
"""Estimation of connectivity between vertices.
Parameters
@@ -397,9 +398,7 @@ def __init__(
self, data, pairs, vertices, vertex_degree=None, subject=None, directed=False
):
if len(vertices) != 2:
- raise ValueError(
- "The `vertices` parameter should be a list of " "two arrays."
- )
+ raise ValueError("The `vertices` parameter should be a list of two arrays.")
self.vertices = [np.asarray(v) for v in vertices]
n_vertices = len(self.vertices[0]) + len(self.vertices[1])
@@ -420,7 +419,7 @@ def make_stc(self, summary="sum", weight_by_degree=True):
summary : 'sum' | 'degree' | 'absmax'
How to summarize the adjacency data:
- 'sum' : sum the strenghts of both the incoming and outgoing connections
+ 'sum' : sum the strengths of both the incoming and outgoing connections
for each source.
'degree': count the number of incoming and outgoing connections for each
source.
@@ -474,7 +473,7 @@ def make_stc(self, summary="sum", weight_by_degree=True):
else:
raise ValueError(
- 'The summary parameter must be "degree", or ' '"sum", or "absmax".'
+ 'The summary parameter must be "degree", or "sum", or "absmax".'
)
data = np.asarray(data, dtype="float").ravel()
@@ -578,8 +577,7 @@ def summary(c, f, t):
return np.abs(c[f, :][:, t]).max()
elif not isinstance(summary, types.FunctionType):
raise ValueError(
- 'The summary parameter must be "degree", "sum" '
- '"absmax" or a function.'
+ 'The summary parameter must be "degree", "sum" "absmax" or a function.'
)
logger.info("Computing out- and in-degree for each label...")
@@ -718,7 +716,7 @@ def to_original_src(
)
-class LabelConnectivity(BaseConnectivity):
+class LabelConnectivity(_BaseConnectivity):
"""Estimation of all-to-all connectivity, parcellated into labels.
Parameters
@@ -1001,7 +999,7 @@ def one_to_all_connectivity_pairs(src_or_fwd, ref_point, min_dist=0):
-------
vert_from : ndarray, shape (n_pairs,)
For each pair, the index of the first vertex. This is always the index
- of the refence point.
+ of the reference point.
vert_to : ndarray, shape (n_pairs,)
For each pair, the index of the second vertex.
@@ -1236,7 +1234,7 @@ def dics_connectivity(
if n_orient == 1:
raise ValueError(
- "A forward operator with free or tangential " "orientation must be used."
+ "A forward operator with free or tangential orientation must be used."
)
elif n_orient == 3:
# Convert forward to tangential orientation for more speed.
diff --git a/conpy/forward.py b/conpy/forward.py
index b2f3a87..c449bf6 100644
--- a/conpy/forward.py
+++ b/conpy/forward.py
@@ -322,11 +322,11 @@ def restrict_src_to_vertices(
vert_no_lh, vert_no_rh = vertno_or_idx
if check_vertno:
if not (
- np.all(np.in1d(vert_no_lh, src[0]["vertno"]))
- and np.all(np.in1d(vert_no_rh, src[1]["vertno"]))
+ np.all(np.isin(vert_no_lh, src[0]["vertno"]))
+ and np.all(np.isin(vert_no_rh, src[1]["vertno"]))
):
raise ValueError(
- "One or more vertices were not present in" " SourceSpaces."
+ "One or more vertices were not present in SourceSpaces."
)
else:
@@ -404,9 +404,9 @@ def _make_radial_coord_system(points, origin):
Parameters
----------
points : ndarray, shape (n_points, 3)
- For each point, the XYZ carthesian coordinates.
+ For each point, the XYZ Cartesian coordinates.
origin : (x, y, z)
- A tuple (or other array-like) containing the XYZ carthesian coordinates
+ A tuple (or other array-like) containing the XYZ Cartesian coordinates
of the point of origin. This can for example be the center of a sphere
fitted through the points.
@@ -497,7 +497,7 @@ def forward_to_tangential(fwd, center=None):
fwd : instance of Forward
The forward solution to convert.
center : tuple of float (x, y, z) | None
- The carthesian coordinates of the center of the brain. By default, a
+ The Cartesian coordinates of the center of the brain. By default, a
sphere is fitted through all the points in the source space.
Returns
@@ -512,13 +512,13 @@ def forward_to_tangential(fwd, center=None):
if fwd["sol"]["ncol"] // n_sources == 2:
raise ValueError(
- "Forward solution already seems to be in tangential " "orientation."
+ "Forward solution already seems to be in tangential orientation."
)
# Compute two dipole directions tangential to a sphere that has its origin
# in the center of the brain.
if center is None:
- _, center = _fit_sphere(fwd["source_rr"], disp=False)
+ _, center = _fit_sphere(fwd["source_rr"])
_, tan1, tan2 = _make_radial_coord_system(fwd["source_rr"], center)
# Make sure the forward solution is in head orientation for this
diff --git a/conpy/stats.py b/conpy/stats.py
index ed1c6e8..5d1745e 100644
--- a/conpy/stats.py
+++ b/conpy/stats.py
@@ -43,9 +43,7 @@ def group_connectivity_ttest(cond1, cond2, df=None, tail=None):
p-values for all connections.
"""
if len(cond1) != len(cond2):
- raise ValueError(
- "The number of subjects in each condition must be " "the same."
- )
+ raise ValueError("The number of subjects in each condition must be the same.")
n_subjects = len(cond1)
# Check compatibility of the connection objects
@@ -53,8 +51,7 @@ def group_connectivity_ttest(cond1, cond2, df=None, tail=None):
for con in cond1[1:] + cond2:
if not np.array_equal(pairs1, con.pairs):
raise ValueError(
- "Not all Connectivity objects have the same "
- "connection pairs defined."
+ "Not all Connectivity objects have the same connection pairs defined."
)
# Perform a paired t-test
@@ -126,7 +123,7 @@ def cluster_threshold(
)
# Restrict the connections to only those found in the big bundles
- mask = np.in1d(clust_no, big_clusters)
+ mask = np.isin(clust_no, big_clusters)
data = con.data[mask]
pairs = [p[mask] for p in con.pairs]
@@ -177,7 +174,7 @@ def cluster_permutation_test(
experimental condition. Each connectivity object should define the same
connections.
cluster_threshold : float
- The threshold to use for forming the intial bundles. Only connections
+ The threshold to use for forming the initial bundles. Only connections
with a t-value that is either higher than ``cluster_threshold`` or
lower than ``-cluster_threshold`` are kept.
tail : -1 | 0 | 1
@@ -236,7 +233,7 @@ def cluster_permutation_test(
Only returned when ``return_details=True`` is specified.
bundle_ps : ndarray, shape (n_bundles,) (optional)
For each found bundle, the p-value based on the permutation test,
- indicative for the likelyhood that the null-hypothesis holds.
+ indicative for the likelihood that the null-hypothesis holds.
Only returned when ``return_details=True`` is specified.
H0 : ndarray, shape (n_permutations,) (optional)
The maximum observed t-value during each random permutation.
@@ -253,22 +250,19 @@ def cluster_permutation_test(
bioRxiv, 245530, 1-25. https://doi.org/10.1101/245530
"""
if len(cond1) != len(cond2):
- raise ValueError(
- "The number of subjects in each condition must be " "the same."
- )
+ raise ValueError("The number of subjects in each condition must be the same.")
n_subjects = len(cond1)
# Check compatibility of the connection objects
for con in cond1 + cond2:
if not isinstance(con, VertexConnectivity):
raise ValueError(
- "All connectivity objects must by of type " "VertexConnectivity."
+ "All connectivity objects must by of type VertexConnectivity."
)
if not np.array_equal(con.pairs, cond1[0].pairs):
raise ValueError(
- "Not all Connectivity objects have the same "
- "connection pairs defined."
+ "Not all Connectivity objects have the same connection pairs defined."
)
if tail not in [-1, 0, 1]:
@@ -382,7 +376,7 @@ def _do_single_permutation(
Parameters
----------
Xs : ndarray, shape(n_subjects, n_connections)
- The connectivity data: a constrast between two conditions.
+ The connectivity data: a contrast between two conditions.
cluster_threshold : float
The initial t-value threshold to prune connections.
tail : -1 | 0 | 1
diff --git a/conpy/utils.py b/conpy/utils.py
index a2a22bd..1bbe2f8 100644
--- a/conpy/utils.py
+++ b/conpy/utils.py
@@ -14,12 +14,7 @@
)
from mne.utils import get_subjects_dir, warn
-try:
- # MNE-Python 0.18 and up
- from mne.rank import estimate_rank
-except ImportError:
- # Older verions of MNE-Python
- from mne.utils import estimate_rank
+from mne.rank import estimate_rank
def _make_diagonal_noise_matrix(csd, reg):
@@ -74,11 +69,11 @@ def _find_indices_1d(haystack, needles, check_needles=True):
haystack = np.asarray(haystack)
needles = np.asarray(needles)
if haystack.ndim != 1 or needles.ndim != 1:
- raise ValueError("Both the haystack and the needles arrays should be " "1D.")
+ raise ValueError("Both the haystack and the needles arrays should be 1D.")
if check_needles and len(np.setdiff1d(needles, haystack)) > 0:
raise IndexError(
- "One or more values where not present in the given " "haystack array."
+ "One or more values where not present in the given haystack array."
)
sorted_ind = np.argsort(haystack)
@@ -292,7 +287,7 @@ def reg_pinv(x, reg=0, rank="full", rcond=1e-15):
# Warn the user if both all parameters were kept at their defaults and the
# matrix is rank deficient.
if rank_after < len(x) and reg == 0 and rank == "full" and rcond == 1e-15:
- warn("Covariance matrix is rank-deficient and no regularization is " "done.")
+ warn("Covariance matrix is rank-deficient and no regularization is done.")
elif isinstance(rank, int) and rank > len(x):
raise ValueError(
"Invalid value for the rank parameter (%d) given "
diff --git a/doc/Makefile b/doc/Makefile
index c45dc8f..12f327e 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -42,7 +42,7 @@ help:
clean:
rm -rf $(BUILDDIR)/*
rm -rf auto_examples/
- rm -rf generated/*
+ rm -rf functions/*
rm -rf modules/*
html-noplot:
diff --git a/doc/_templates/layout.html b/doc/_templates/layout.html
deleted file mode 100644
index a99c912..0000000
--- a/doc/_templates/layout.html
+++ /dev/null
@@ -1,17 +0,0 @@
-{%- extends 'pydata_sphinx_theme/layout.html' %}
-
-{% block extrahead %}
-
- {{ super() }}
-{% endblock %}
-
-{% block docs_body %}
-
- {% block body %} {% endblock %}
-
-{% endblock %}
-
-{%- block scripts_end %}
- {{ super() }}
-
-{%- endblock %}
diff --git a/doc/api.rst b/doc/api.rst
index e13dc3f..622cfff 100644
--- a/doc/api.rst
+++ b/doc/api.rst
@@ -11,14 +11,15 @@ Forward models
==============
.. autosummary::
- :toctree: generated/
+ :toctree: functions
+ :template: function.rst
- forward_to_tangential
- restrict_forward_to_sensor_range
- restrict_forward_to_vertices
- restrict_src_to_vertices
- select_shared_vertices
- select_vertices_in_sensor_range
+ forward_to_tangential
+ restrict_forward_to_sensor_range
+ restrict_forward_to_vertices
+ restrict_src_to_vertices
+ select_shared_vertices
+ select_vertices_in_sensor_range
Connectivity
@@ -29,17 +30,18 @@ Connectivity
Classes:
.. autosummary::
- :toctree: generated/
- :template: class.rst
+ :toctree: functions/
+ :template: class.rst
- LabelConnectivity
- VertexConnectivity
+ LabelConnectivity
+ VertexConnectivity
Functions:
.. autosummary::
- :toctree: generated/
+ :toctree: functions
+ :template: function.rst
all_to_all_connectivity_pairs
dics_connectivity
@@ -53,7 +55,8 @@ Statistics
.. currentmodule:: conpy.stats
.. autosummary::
- :toctree: generated/
+ :toctree: functions
+ :template: function.rst
cluster_threshold
group_connectivity_ttest
@@ -66,7 +69,8 @@ Utilities
.. currentmodule:: conpy.utils
.. autosummary::
- :toctree: generated/
+ :toctree: functions
+ :template: function.rst
get_morph_src_mapping
reg_pinv
diff --git a/doc/conf.py b/doc/conf.py
index c40345b..e8448d7 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -15,6 +15,7 @@
import mne.viz._brain
import conpy
+from intersphinx_registry import get_intersphinx_mapping
from numpydoc import docscrape, numpydoc # noqa
# -- General configuration ------------------------------------------------
@@ -162,12 +163,12 @@
# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {
- "python": ("https://docs.python.org/3/", None),
"mne": ("https://mne.tools/stable/", None),
- "conpy": ("https://users.aalto.fi/~vanvlm1/conpy/", None),
- "numpy": ("https://docs.scipy.org/doc/numpy/", None),
- "scipy": ("https://scipy.github.io/devdocs", None),
}
+intersphinx_mapping.update(
+ get_intersphinx_mapping(packages={"matplotlib", "numpy", "python", "scipy"})
+)
+
sphinx_gallery_conf = {
"examples_dirs": "../examples",
@@ -175,4 +176,6 @@
"backreferences_dir": "generated",
"image_scrapers": ["matplotlib", mne.viz._brain._BrainScraper()],
"reference_url": dict(mne=None),
+ "filename_pattern": r".*\.py",
+ "within_subsection_order": "FileNameSortKey",
}
diff --git a/doc/index.rst b/doc/index.rst
index 089bdd3..24a42fc 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -6,7 +6,7 @@
Conpy
==========
-A Python library implementing the DICS beamformer for connectivity analysis and power mapping on the cortex. This is a Python reimplementation of the MATLAB code originally developed for [1]_. This repository also holds the code complementing our submittion to the Frontiers Research Topic: `From raw MEG/EEG to publication: how to perform MEG/EEG group analysis with free academic software `_
+A Python library implementing the DICS beamformer for connectivity analysis and power mapping on the cortex. This is a Python reimplementation of the MATLAB code originally developed for [1]_. This repository also holds the code complementing our submission to the Frontiers Research Topic: `From raw MEG/EEG to publication: how to perform MEG/EEG group analysis with free academic software `_
`Marijn van Vliet, Mia LiljestroĢm, Susanna Aro, Riitta Salmelin and Jan Kujala. Analysis of functional connectivity and oscillatory power using DICS: from raw MEG data to group-level statistics in Python. `_
diff --git a/examples/plot_simulation.py b/examples/plot_simulation.py
index 0af0ca1..cf7121a 100644
--- a/examples/plot_simulation.py
+++ b/examples/plot_simulation.py
@@ -296,7 +296,7 @@ def coh_signal_gen():
# Excellent! Both methods found our two simulated sources. Of course, with a
# signal-to-noise ratio (SNR) of 1, it isn't very hard to find them. You can
# try playing with the SNR and see how the MNE-dSPM and DICS results hold up in
-# the presense of increasing noise.
+# the presence of increasing noise.
###############################################################################
# One-to-all connectivity
diff --git a/requirements-dev.txt b/requirements-dev.txt
new file mode 100644
index 0000000..0d5b210
--- /dev/null
+++ b/requirements-dev.txt
@@ -0,0 +1,29 @@
+doit
+h5io
+h5py
+intersphinx_registry
+matplotlib
+mne
+mne-connectivity
+nibabel
+nilearn
+numpy
+numpydoc
+numpydoc
+pillow
+pooch
+pre-commit
+pydata_sphinx_theme
+pydata_sphinx_theme
+pyside6
+pytest
+pytest-cov
+pytest-xdist
+pyvista
+pyvistaqt
+scikit-learn
+scipy
+seaborn
+sphinx_gallery
+tqdm
+vtk
diff --git a/requirements.txt b/requirements.txt
index 8df8b9c..5663ff5 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,13 +3,9 @@ numpydoc>=0.7
doit>=0.30
setuptools>=61.0
matplotlib>=1.5
-mne>=1.0
+mne[all]>=1.0
+mne-connectivity
nibabel
tqdm
h5py
h5io
-pytest>=3.2
-sphinx
-sphinx_gallery>=0.1
-sphinx_bootstrap_theme>=0.6
-intersphinx_registry