Merge remote-tracking branch 'upstream/main' into deploy

* upstream/main: (56 commits)
  [CI] Fix CIs (mne-tools#164)
  Fix azure
  Fix CIs
  New dev for v0.7
  [RELEASE] V0.6 (mne-tools#162)
  Try azure again
  [CI] Fix azure (mne-tools#161)
  Add gitblame
  [MAINT] Run black, isort, ruff, and other auto-linters on entire package (mne-tools#159)
  [MAINT] Replace setup.py with pyproject.toml (mne-tools#160)
  [BUG] Fixed issue w/ different rank-indices length (mne-tools#158)
  [MAINT] Refactor bivariate and multivariate methods into separate files (mne-tools#156)
  [MAINT] Fix failing unit tests & update CI packages (mne-tools#157)
  fixed grammar mistake
  switched to array indices & added inline comments
  updated default non-zero rank tolerance
  removed redundant list creation
  removed redundant ignored word
  switched to masked indices for multivariate conn
  updated time
  ...

.codespellignore

@@ -0,0 +1,6 @@
+raison
+fro
+nd
+manuel
+ba
+master

.flake8

@@ -0,0 +1,28 @@
+[flake8]
+max-line-length = 100
+
+ignore =
+    # these rules don't play well with black
+    # whitespace before ':'
+    E203
+    # line break before binary operator
+    W503
+    E241,E305,W504,W605,E731
+
+exclude =
+    .git
+    .github
+    .venv
+    .mypy_cache
+    .pytest_cache
+    .circleci
+    paper
+    setup.py
+    doc
+    benchmarks
+    build
+
+per-file-ignores =
+    # __init__.py files are allowed to have unused imports
+    */__init__.py:F401
+    */**/__init__.py:F401

.git-blame-ignore-revs

@@ -0,0 +1 @@
+0c216d35127f48792caabdc3cca170874a443eee  # black, isort, ruff

.github/workflows/cffconvert.yml

@@ -0,0 +1,22 @@
+name: cffconvert
+
+on:
+  push:
+    paths:
+      - CITATION.cff
+  pull_request:
+    paths:
+      - CITATION.cff
+
+jobs:
+  validate:
+    name: "validate"
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out a copy of the repository
+        uses: actions/checkout@v4
+
+      - name: Check whether the citation metadata from CITATION.cff is valid
+        uses: citation-file-format/[email protected]
+        with:
+          args: "--validate"

.github/workflows/code-style.yaml

@@ -0,0 +1,47 @@
+name: code-style
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+on:  # yamllint disable-line rule:truthy
+  pull_request:
+  push:
+    branches: [main, maint/0.2, maint/0.3, maint/0.4]
+  workflow_dispatch:
+
+jobs:
+  style:
+    timeout-minutes: 10
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+          architecture: 'x64'
+      - name: Install dependencies
+        run: |
+          python -m pip install --progress-bar off --upgrade pip setuptools
+          python -m pip install --progress-bar off .[style]
+      - name: Run isort
+        uses: isort/isort-action@master
+      - name: Run black
+        uses: psf/black@stable
+        with:
+          options: "--check --verbose"
+      - name: Run Ruff
+        run: ruff check .
+      - name: Run codespell
+        uses: codespell-project/actions-codespell@master
+        with:
+          check_filenames: true
+          check_hidden: true
+          skip: './.git,./build,./.mypy_cache,./.pytest_cache,./mne_icalabel/iclabel/network/assets'
+          ignore_words_file: ./.codespellignore
+      # - name: Run pydocstyle
+      #   run: pydocstyle .
+      - name: Run toml-sort
+        run: toml-sort pyproject.toml --check
+      - name: Run yamllint
+        run: yamllint . -c .yamllint.yml --strict

.github/workflows/linux_conda.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-20.04
     defaults:
       run:
-        shell: bash
+        shell: bash -el {0}
     env:
       CONDA_ENV: 'environment.yml'
       DISPLAY: ':99.0'
@@ -27,47 +27,29 @@ jobs:
       PYTHONUNBUFFERED: '1'
       PYTHON_VERSION: '3.9'
     steps:
-      - uses: actions/checkout@v2
-      - run: |
-          curl https://raw.githubusercontent.com/mne-tools/mne-python/main/tools/setup_xvfb.sh -o setup_xvfb.sh
-          chmod +x setup_xvfb.sh
-          ./setup_xvfb.sh
-        name: 'Setup xvfb'
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v4
+      - uses: pyvista/setup-headless-display-action@main
+        with:
+          qt: true
+          pyvista: false
+      - uses: mamba-org/setup-micromamba@v1
         with:
-          activate-environment: 'mne'
-          python-version: ${{ env.PYTHON_VERSION }}
           environment-file: ${{ env.CONDA_ENV }}
-        name: 'Setup conda'
-      - shell: bash -el {0}
-        run: |
-          conda activate mne
+          create-args: >- # beware the >- instead of |, we don't split on newlines but on spaces
+            python=${{ env.PYTHON_VERSION }}
+      - run: |
           curl https://raw.githubusercontent.com/mne-tools/mne-python/main/tools/get_minimal_commands.sh -o get_minimal_commands.sh
           chmod +x get_minimal_commands.sh
           source ./get_minimal_commands.sh
-          pip install -r requirements_testing.txt
+          pip install .[test]
         name: 'Install dependencies'
-
-      - shell: bash -el {0}
-        name: Install MNE (main)
-        run: |
-          git clone --depth 1 https://github.com/mne-tools/mne-python.git -b main
-          pip install -e ./mne-python
-
-      - shell: bash -el {0}
-        run: |
-          python setup.py build
-          python setup.py install
-        name: 'Install MNE'
-
-      - shell: bash -el {0}
-        run: |
+      - run: pip install git+https://github.com/mne-tools/mne-python@main
+      - run: pip install -e .
+      - run: |
           which mne
           mne sys_info -pd
           python -c "import numpy; numpy.show_config()"
         name: 'Show infos'
-
       - name: Run pytest
-        run: |
-          python -m pytest . --cov=mne_connectivity --cov-report=xml --cov-config=setup.cfg --verbose --ignore mne-python
-        shell: bash -el {0}
+        run: python -m pytest . --cov=mne_connectivity --cov-report=xml --cov-config=pyproject.toml --verbose --ignore mne-python
+      - uses: codecov/codecov-action@v3

.github/workflows/publish_release.yml

@@ -8,25 +8,25 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
-    
+
     steps:
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.10
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.10
 
-    - name: Checkout code
-      uses: actions/checkout@v2
+      - name: Checkout code
+        uses: actions/checkout@v2
 
-    - name: Install dependencies
-      run: |
-        pip install -r requirements.txt
-        pip install twine wheel
+      - name: Install dependencies
+        run: |
+          pip install .[build]
+          pip install twine wheel
 
-    - name: Build and publish to PyPi
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run: |
-        python setup.py sdist bdist_wheel
-        python -m twine upload --repository pypi dist/*
+      - name: Build and publish to PyPi
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: |
+          python setup.py sdist bdist_wheel
+          python -m twine upload --repository pypi dist/*