[MAINT] Run black, isort, ruff, and other auto-linters on entire pack…

…age (mne-tools#159)

* Repackage with pyrpoject.toml

Signed-off-by: Adam Li <[email protected]>

* Fix CIs

Signed-off-by: Adam Li <[email protected]>

* Add version

Signed-off-by: Adam Li <[email protected]>

* Try to fix ci again

Signed-off-by: Adam Li <[email protected]>

* Fix the pyproject toml and otehr files

Signed-off-by: Adam Li <[email protected]>

* Fix circleCI and style

Signed-off-by: Adam Li <[email protected]>

* Fix statsmodels install

Signed-off-by: Adam Li <[email protected]>

* Run precommit

Signed-off-by: Adam Li <[email protected]>

* Ran black and isort and ruff

Signed-off-by: Adam Li <[email protected]>

* Sort pyrpoject

Signed-off-by: Adam Li <[email protected]>

* Fix

Signed-off-by: Adam Li <[email protected]>

* Don't need to test install

Signed-off-by: Adam Li <[email protected]>

---------

Signed-off-by: Adam Li <[email protected]>

.codespellignore

@@ -1,3 +1,6 @@
 raison
 fro
-nd
+nd
+manuel
+ba
+master

.github/workflows/code-style.yaml

@@ -44,4 +44,4 @@ jobs:
       - name: Run toml-sort
         run: toml-sort pyproject.toml --check
       - name: Run yamllint
-        run: yamllint . -c .yamllint.yaml --strict
+        run: yamllint . -c .yamllint.yml --strict

.github/workflows/unit_tests.yml

@@ -11,64 +11,6 @@ on:
       - "*"
 
 jobs:
-  # Run installation tests
-  install:
-    runs-on: install-${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.11"]
-        include:
-          # An old one
-          - os: ubuntu-latest
-            python-version: "3.9"
-    steps:
-      - uses: actions/checkout@v4
-      - uses: pyvista/setup-headless-display-action@main
-        with:
-          qt: true
-          pyvista: false
-      - uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
-        run: |
-          pip install --upgrade pip setuptools wheel
-          pip install --upgrade .[test]
-      - run: mne sys_info
-      - name: Build sdist
-        run: python setup.py sdist
-      - name: Install sdist
-        run: pip install ./dist/mne-connectivity-*
-        shell: bash -e {0}
-      - name: Clean up working directory
-        run: rm -rf ./*
-        shell: bash -e {0}
-      - name: Try importing mne_connectivity
-        run: python -c 'import mne_connectivity; print(mne_connectivity.__version__)'
-      - name: Remove sdist install
-        run: pip uninstall -y mne-connectivity
-      # build with build wheet
-      - uses: actions/checkout@v4
-      - name: Build wheel
-        run: python setup.py bdist_wheel
-      - name: Install wheel
-        run: pip install ./dist/mne_connectivity-*.whl
-        shell: bash -e {0}
-      - name: Clean up working directory
-        run: rm -rf ./*
-        shell: bash -e {0}
-      - name: Try importing mne_connectivity
-        run: python -c 'import mne_connectivity; print(mne_connectivity.__version__)'
-      - name: Remove wheel install
-        run: pip uninstall -y mne-connectivity
-      - uses: actions/checkout@v4
-      - name: Test extras install
-        run: |
-          pip install .[full]
-          python -c 'import mne_connectivity; print(mne_connectivity.__version__)'
-
   # Run unit tests
   test:
     runs-on: ${{ matrix.os }}

.pre-commit-config.yaml

@@ -0,0 +1,55 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 23.11.0
+    hooks:
+      - id: black
+        args: [--quiet]
+
+  # Ruff mne_connectivity
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.6
+    hooks:
+      - id: ruff
+        name: ruff mne_connectivity
+        args: ["--fix"]
+        files: ^mne_connectivity/
+
+  # Ruff tutorials and examples
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.6
+    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", "--fix"]
+        files: ^tutorials/|^examples/
+
+  # Codespell
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli
+        files: ^mne_connectivity/|^doc/|^examples/|^tutorials/
+        types_or: [python, bib, rst, inc]
+
+  # yamllint
+  - repo: https://github.com/adrienverge/yamllint.git
+    rev: v1.33.0
+    hooks:
+      - id: yamllint
+        args: [--strict, -c, .yamllint.yml]
+
+  # rstcheck
+  - repo: https://github.com/rstcheck/rstcheck.git
+    rev: v6.2.0
+    hooks:
+      - id: rstcheck
+        additional_dependencies:
+          - tomli
+        files: ^doc/.*\.(rst|inc)$
+
+ci:
+  autofix_prs: false

CONTRIBUTING.md

@@ -27,10 +27,10 @@ First, you should [fork](https://help.github.com/en/github/getting-started-with-
 
 
 ### Install Python packages required to run tests
-Install the following packages for testing purposes, plus all optonal MNE-connectivity
+Install the following packages for testing purposes, plus all optional MNE-connectivity
 dependencies to ensure you will be able to run all tests.
 
-    $ pip install -r requirements_testing.txt
+    $ pip install .[test]
 
 ### Invoke pytest
 Now you can finally run the tests by running `pytest` in the
@@ -44,7 +44,7 @@ Now you can finally run the tests by running `pytest` in the
 The documentation can be built using sphinx. For that, please additionally
 install the following:
 
-    $ pip install -r requirements_doc.txt
+    $ pip install .[doc]
 
 To build the documentation locally, one can run:
 

benchmarks/bench_var.py

@@ -9,8 +9,8 @@
 """
 import numpy as np
 from memory_profiler import profile
-
 from statsmodels.tsa.vector_ar.var_model import VAR
+
 from mne_connectivity import vector_auto_regression
 
 
@@ -29,10 +29,10 @@ def run_sm_experiment(sample_data):
     """Run RAM expeirment with statsmodels."""
     # statsmodels feeds in (n_samples, n_channels)
     sm_var = VAR(endog=sample_data.squeeze().T)
-    sm_params = sm_var.fit(maxlags=5, trend='n')
+    sm_params = sm_var.fit(maxlags=5, trend="n")
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     rng = np.random.RandomState(0)
     n_epochs, n_signals, n_times = 1, 50, 100
     data = rng.randn(n_epochs, n_signals, n_times)