add github workflows

.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

.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

.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]

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.

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