Merge branch 'channel_specific_epoch_rejection' of github.com:CarinaFo/mne-python into channel_specific_epoch_rejection

Author: CarinaFo

.circleci/config.yml

@@ -43,8 +43,8 @@ jobs:
             brew install python@3.11
             which python
             which pip
-            pip install --upgrade pip setuptools wheel
-            pip install --upgrade --only-binary "numpy,scipy,dipy,statsmodels" -ve . -r requirements.txt -r requirements_testing.txt -r requirements_testing_extra.txt PyQt6
+            pip install --upgrade pip
+            pip install --upgrade --only-binary "numpy,scipy,dipy,statsmodels" -ve .[full,test_extra]
             # 3D too slow on Apple's software renderer, and numba causes us problems
             pip uninstall -y vtk pyvista pyvistaqt numba
             mkdir -p test-results
@@ -266,6 +266,9 @@ jobs:
       - restore_cache:
           keys:
             - data-cache-ucl-opm-auditory
+      - restore_cache:
+          keys:
+            - data-cache-phantom-kit
       - run:
           name: Get data
           # This limit could be increased, but this is helpful for finding slow ones
@@ -431,6 +434,10 @@ jobs:
           key: data-cache-ucl-opm-auditory
           paths:
             - ~/mne_data/auditory_OPM_stationary  # (4 G)
+      - save_cache:
+          key: data-cache-phantom-kit
+          paths:
+            - ~/mne_data/MNE-phantom-KIT-data  # (1 G)
 
 
   linkcheck:

.github/workflows/tests.yml

@@ -59,9 +59,6 @@ jobs:
           - os: ubuntu-latest
             python: '3.10'
             kind: conda
-          - os: ubuntu-latest
-            python: '3.10'
-            kind: notebook
           - os: ubuntu-latest
             python: '3.11'
             kind: pip-pre
@@ -87,7 +84,6 @@ jobs:
         with:
           qt: true
           pyvista: false
-        if: matrix.kind != 'notebook'
       # Python (if pip)
       - uses: actions/setup-python@v4
         with:
@@ -103,19 +99,13 @@ jobs:
           miniforge-variant: Mambaforge
           use-mamba: ${{ matrix.kind != 'conda' }}
         if: ${{ !startswith(matrix.kind, 'pip') }}
-      - name: 'Install OSMesa VTK variant'
-        run: |
-          # TODO: As of 2023/02/28, notebook tests need a pinned mesalib
-          mamba install -c conda-forge "vtk>=9.2=*osmesa*" "vtk-base>=9.2=*osmesa*" "mesalib=23.1.4" "numpy=1.24.4" "numba=0.57.1"
-          mamba list
-        if: matrix.kind == 'notebook'
       - run: ./tools/github_actions_dependencies.sh
       # Minimal commands on Linux (macOS stalls)
       - run: ./tools/get_minimal_commands.sh
         if: ${{ startswith(matrix.os, 'ubuntu') }}
       - run: ./tools/github_actions_install.sh
       - run: ./tools/github_actions_infos.sh
-      # Check Qt on non-notebook
+      # Check Qt
       - run: ./tools/check_qt_import.sh $MNE_QT_BACKEND
         if: ${{ env.MNE_QT_BACKEND != '' }}
       - name: Run tests with no testing data

.pre-commit-config.yaml

@@ -1,13 +1,13 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 23.10.1
+    rev: 23.11.0
     hooks:
       - id: black
         args: [--quiet]
 
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.4
+    rev: v0.1.5
     hooks:
       - id: ruff
         name: ruff mne
@@ -16,13 +16,13 @@ repos:
 
   # Ruff tutorials and examples
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.4
+    rev: v0.1.5
     hooks:
       - id: ruff
         name: ruff tutorials and examples
         # D103: missing docstring in public function
         # D400: docstring first line must end with period
-        args: ["--ignore=D103,D400"]
+        args: ["--ignore=D103,D400", "--fix"]
         files: ^tutorials/|^examples/
 
   # Codespell
@@ -37,7 +37,7 @@ repos:
 
   # yamllint
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.32.0
+    rev: v1.33.0
     hooks:
       - id: yamllint
         args: [--strict, -c, .yamllint.yml]
@@ -47,7 +47,6 @@ repos:
     rev: v6.2.0
     hooks:
       - id: rstcheck
+        additional_dependencies:
+          - tomli
         files: ^doc/.*\.(rst|inc)$
-        # https://github.com/rstcheck/rstcheck/issues/199
-        # https://github.com/rstcheck/rstcheck/issues/200
-        exclude: ^doc/(help/faq|install/manual_install|install/mne_c|install/advanced|install/updating|_includes/channel_interpolation|_includes/inverse|_includes/ssp)\.rst$

MANIFEST.in

@@ -1,12 +1,6 @@
 include *.rst
 include LICENSE.txt
 include SECURITY.md
-include requirements.txt
-include requirements_base.txt
-include requirements_hdf5.txt
-include requirements_testing.txt
-include requirements_testing_extra.txt
-include requirements_doc.txt
 include mne/__init__.py
 
 recursive-include examples *.py

Makefile

@@ -24,8 +24,8 @@ clean-cache:
 
 clean: clean-build clean-pyc clean-so clean-ctags clean-cache
 
-wheel_quiet:
-	$(PYTHON) setup.py -q sdist bdist_wheel
+wheel:
+	$(PYTHON) -m build
 
 sample_data:
 	@python -c "import mne; mne.datasets.sample.data_path(verbose=True);"
@@ -57,7 +57,7 @@ codespell:  # running manually
 check-manifest:
 	check-manifest -q --ignore .circleci/config.yml,doc,logo,mne/io/*/tests/data*,mne/io/tests/data,mne/preprocessing/tests/data,.DS_Store,mne/_version.py
 
-check-readme: clean wheel_quiet
+check-readme: clean wheel
 	twine check dist/*
 
 nesting:

azure-pipelines.yml

@@ -51,8 +51,8 @@ stages:
             displayName: 'Get Python'
           - bash: |
               set -eo pipefail
-              python -m pip install --progress-bar off --upgrade pip setuptools wheel
-              python -m pip install --progress-bar off -r requirements_base.txt -r requirements_hdf5.txt -r requirements_testing.txt
+              python -m pip install --progress-bar off --upgrade pip build
+              python -m pip install --progress-bar off -ve .[hdf5,test]
               python -m pip uninstall -yq pytest-qt  # don't want to set up display, etc. for this
               pre-commit install --install-hooks
             displayName: Install dependencies
@@ -107,8 +107,8 @@ stages:
             displayName: 'Get Python'
           - bash: |
               set -e
-              python -m pip install --progress-bar off --upgrade pip setuptools wheel
-              python -m pip install --progress-bar off "mne-qt-browser[opengl] @ git+https://github.com/mne-tools/mne-qt-browser.git@main" pyvista scikit-learn pytest-error-for-skips python-picard "PyQt6!=6.5.1" qtpy nibabel
+              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@main" pyvista scikit-learn pytest-error-for-skips python-picard "PyQt6!=6.5.1" qtpy nibabel sphinx-gallery
               python -m pip uninstall -yq mne
               python -m pip install --progress-bar off --upgrade -e .[test]
             displayName: 'Install dependencies with pip'
@@ -166,11 +166,10 @@ stages:
             displayName: 'Get Python'
           - bash: |
               set -e
-              python -m pip install --progress-bar off --upgrade pip setuptools wheel
+              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 -r requirements.txt -r requirements_testing.txt -r requirements_testing_extra.txt
-              python -m pip install -e .
+              python -m pip install --progress-bar off --upgrade -ve .[full,test_extra]
             displayName: 'Install dependencies with pip'
           - bash: |
               set -e

doc/_includes/channel_interpolation.rst

@@ -22,12 +22,11 @@ In short, data repair using spherical spline interpolation :footcite:`PerrinEtAl
 Spherical splines assume that the potential :math:`V(\boldsymbol{r_i})` at any point :math:`\boldsymbol{r_i}` on the surface of the sphere can be represented by:
 
 .. math:: V(\boldsymbol{r_i}) = c_0 + \sum_{j=1}^{N}c_{i}g_{m}(cos(\boldsymbol{r_i}, \boldsymbol{r_{j}}))
-   :label: model
+   :name: model
 
 where the :math:`C = (c_{1}, ..., c_{N})^{T}` are constants which must be estimated. The function :math:`g_{m}(\cdot)` of order :math:`m` is given by:
 
 .. math:: g_{m}(x) = \frac{1}{4 \pi}\sum_{n=1}^{\infty} \frac{2n + 1}{(n(n + 1))^m}P_{n}(x)
-   :label: legendre
 
 where :math:`P_{n}(x)` are `Legendre polynomials`_ of order :math:`n`.
 
@@ -36,22 +35,22 @@ where :math:`P_{n}(x)` are `Legendre polynomials`_ of order :math:`n`.
 To estimate the constants :math:`C`, we must solve the following two equations simultaneously:
 
 .. math:: G_{ss}C + T_{s}c_0 = X
-   :label: matrix_form
+   :name: matrix_form
 
 .. math:: {T_s}^{T}C = 0
-   :label: constraint
+   :name: constraint
 
 where :math:`G_{ss} \in R^{N \times N}` is a matrix whose entries are :math:`G_{ss}[i, j] = g_{m}(cos(\boldsymbol{r_i}, \boldsymbol{r_j}))` and :math:`X \in R^{N \times 1}` are the potentials :math:`V(\boldsymbol{r_i})` measured at the good channels. :math:`T_{s} = (1, 1, ..., 1)^\top` is a column vector of dimension :math:`N`. Equation :eq:`matrix_form` is the matrix formulation of Equation :eq:`model` and equation :eq:`constraint` is like applying an average reference to the data. From equation :eq:`matrix_form` and :eq:`constraint`, we get:
 
 .. math:: \begin{bmatrix} c_0 \\ C \end{bmatrix} = {\begin{bmatrix} {T_s}^{T} && 0 \\ T_s && G_{ss} \end{bmatrix}}^{-1} \begin{bmatrix} 0 \\ X \end{bmatrix} = C_{i}X
-   :label: estimate_constant
+   :name: estimate_constant
 
 :math:`C_{i}` is the same as matrix :math:`{\begin{bmatrix} {T_s}^{T} && 0 \\ T_s && G_{ss} \end{bmatrix}}^{-1}` but with its first column deleted, therefore giving a matrix of dimension :math:`(N + 1) \times N`.
 
 Now, to estimate the potentials :math:`\hat{X} \in R^{M \times 1}` at the bad channels, we have to do:
 
 .. math:: \hat{X} = G_{ds}C + T_{d}c_0
-   :label: estimate_data
+   :name: estimate_data
 
 where :math:`G_{ds} \in R^{M \times N}` computes :math:`g_{m}(\boldsymbol{r_i}, \boldsymbol{r_j})` between the bad and good channels. :math:`T_{d} = (1, 1, ..., 1)^\top` is a column vector of dimension :math:`M`. Plugging in equation :eq:`estimate_constant` in :eq:`estimate_data`, we get
 

doc/_includes/inverse.rst

@@ -70,7 +70,7 @@ this by writing :math:`R' = R/ \lambda^2 = R \lambda^{-2}`, which yields the
 inverse operator
 
 .. math::
-   :label: inv_m
+   :name: inv_m
 
     M &= R' G^\top (G R' G^\top + C)^{-1} \\
       &= R \lambda^{-2} G^\top (G R \lambda^{-2} G^\top + C)^{-1} \\
@@ -106,12 +106,12 @@ The MNE software employs data whitening so that a 'whitened' inverse operator
 assumes the form
 
 .. math::    \tilde{M} = M C^{^1/_2} = R \tilde{G}^\top (\tilde{G} R \tilde{G}^\top + \lambda^2 I)^{-1}\ ,
-   :label: inv_m_tilde
+   :name: inv_m_tilde
 
 where
 
 .. math:: \tilde{G} = C^{-^1/_2}G
-   :label: inv_g_tilde
+   :name: inv_g_tilde
 
 is the spatially whitened gain matrix. We arrive at the whitened inverse
 operator equation :eq:`inv_m_tilde` by making the substitution for
@@ -128,7 +128,7 @@ operator equation :eq:`inv_m_tilde` by making the substitution for
 The expected current values are
 
 .. math::
-   :label: inv_j_hat_t
+   :name: inv_j_hat_t
 
     \hat{j}(t) &= Mx(t) \\
                &= M C^{^1/_2} C^{-^1/_2} x(t) \\
@@ -137,7 +137,7 @@ The expected current values are
 knowing :eq:`inv_m_tilde` and taking
 
 .. math::
-   :label: inv_tilde_x_t
+   :name: inv_tilde_x_t
 
     \tilde{x}(t) = C^{-^1/_2}x(t)
 
@@ -151,7 +151,7 @@ to raw data. To reflect the decrease of noise due to averaging, this matrix,
 C_0 / L`.
 
 .. note::
-   When EEG data are included, the gain matrix :math:`G` needs to be average referenced when computing the linear inverse operator :math:`M`. This is incorporated during creating the spatial whitening operator :math:`C^{-^1/_2}`, which includes any projectors on the data. EEG data average reference (using a projector) is mandatory for source modeling and is checked when calculating the inverse operator. 
+   When EEG data are included, the gain matrix :math:`G` needs to be average referenced when computing the linear inverse operator :math:`M`. This is incorporated during creating the spatial whitening operator :math:`C^{-^1/_2}`, which includes any projectors on the data. EEG data average reference (using a projector) is mandatory for source modeling and is checked when calculating the inverse operator.
 
 As shown above, regularization of the inverse solution is equivalent to a
 change in the variance of the current amplitudes in the Bayesian *a priori*
@@ -224,7 +224,7 @@ computational convenience we prefer to take another route, which employs the
 singular-value decomposition (SVD) of the matrix
 
 .. math::
-   :label: inv_a
+   :name: inv_a
 
     A &= \tilde{G} R^{^1/_2} \\
       &= U \Lambda V^\top
@@ -238,7 +238,7 @@ Combining the SVD from :eq:`inv_a` with the inverse equation :eq:`inv_m` it is
 easy to show that
 
 .. math::
-   :label: inv_m_tilde_svd
+   :name: inv_m_tilde_svd
 
     \tilde{M} &= R \tilde{G}^\top (\tilde{G} R \tilde{G}^\top + \lambda^2 I)^{-1} \\
               &= R^{^1/_2} A^\top (A A^\top + \lambda^2 I)^{-1} \\
@@ -253,23 +253,23 @@ where the elements of the diagonal matrix :math:`\Gamma` are simply
 .. `reginv` in our code:
 
 .. math::
-   :label: inv_gamma_k
+   :name: inv_gamma_k
 
     \gamma_k = \frac{\lambda_k}{\lambda_k^2 + \lambda^2}\ .
 
 From our expected current equation :eq:`inv_j_hat_t` and our whitened
 measurement equation :eq:`inv_tilde_x_t`, if we take
 
 .. math::
-   :label: inv_w_t
+   :name: inv_w_t
 
     w(t) &= U^\top \tilde{x}(t) \\
          &= U^\top C^{-^1/_2} x(t)\ ,
 
 we can see that the expression for the expected current is just
 
 .. math::
-   :label: inv_j_hat_t_svd
+   :name: inv_j_hat_t_svd
 
     \hat{j}(t) &= R^{^1/_2} V \Gamma w(t) \\
                &= \sum_k {\bar{v_k} \gamma_k w_k(t)}\ ,
@@ -314,7 +314,7 @@ normalization factors, it's convenient to reuse our "weighted eigenleads"
 definition from equation :eq:`inv_j_hat_t` in matrix form as
 
 .. math::
-   :label: inv_eigenleads_weighted
+   :name: inv_eigenleads_weighted
 
     \bar{V} = R^{^1/_2} V\ .
 

doc/_includes/ssp.rst

@@ -30,13 +30,13 @@ Without loss of generality we can always decompose any :math:`n`-channel
 measurement :math:`b(t)` into its signal and noise components as
 
 .. math::    b(t) = b_s(t) + b_n(t)
-   :label: additive_model
+   :name: additive_model
 
 Further, if we know that :math:`b_n(t)` is well characterized by a few field
 patterns :math:`b_1 \dotso b_m`, we can express the disturbance as
 
 .. math::    b_n(t) = Uc_n(t) + e(t)\ ,
-   :label: pca
+   :name: pca
 
 where the columns of :math:`U` constitute an orthonormal basis for :math:`b_1
 \dotso b_m`, :math:`c_n(t)` is an :math:`m`-component column vector, and the
@@ -48,12 +48,12 @@ such that the conditions described above are satisfied. We can now construct
 the orthogonal complement operator
 
 .. math::    P_{\perp} = I - UU^\top
-   :label: projector
+   :name: projector
 
 and apply it to :math:`b(t)` in Equation :eq:`additive_model` yielding
 
 .. math::    b_{s}(t) \approx P_{\perp}b(t)\ ,
-   :label: result
+   :name: result
 
 since :math:`P_{\perp}b_n(t) = P_{\perp}(Uc_n(t) + e(t)) \approx 0` and
 :math:`P_{\perp}b_{s}(t) \approx b_{s}(t)`. The projection operator
@@ -102,12 +102,12 @@ typical in EEG analysis to subtract the average reference from all the sensor
 signals :math:`b^{1}(t), ..., b^{n}(t)`. That is:
 
 .. math::	{b}^{j}_{s}(t) = b^{j}(t) - \frac{1}{n}\sum_{k}{b^k(t)}
-   :label: eeg_proj
+   :name: eeg_proj
 
 where the noise term :math:`b_{n}^{j}(t)` is given by
 
 .. math:: 	b_{n}^{j}(t) = \frac{1}{n}\sum_{k}{b^k(t)}
-   :label: noise_term
+   :name: noise_term
 
 Thus, the projector vector :math:`P_{\perp}` will be given by
 :math:`P_{\perp}=\frac{1}{n}[1, 1, ..., 1]`

doc/api/datasets.rst

@@ -40,10 +40,11 @@ Datasets
    spm_face.data_path
    ucl_opm_auditory.data_path
    visual_92_categories.data_path
+   phantom_kit.data_path
    phantom_4dbti.data_path
    phantom_kernel.data_path
    refmeg_noise.data_path
    ssvep.data_path
    erp_core.data_path
    epilepsy_ecog.data_path
-   eyelink.data_path
+   eyelink.data_path