feat: replace flake8 with faster ruff

Note: for anyone doing testing on an existing install, this DOES require
that you will have to install the `ruff` Python package. Alternatively,
you can also install `ruff` by re-installing the development packages
the same way you originally installed `flake8`, via:

`pip install --editable "<your_hnn_dir>[dev]"`

.github/workflows/unix_unit_tests.yml

@@ -54,10 +54,10 @@
           shell: bash -el {0}
           run: |
             pip install --verbose '.[opt, parallel, test, gui]'
-        - name: Lint with flake8
+        - name: Lint with ruff
           shell: bash -el {0}
           run: |
-            flake8 --count hnn_core
+            ruff check hnn_core
         - name: Test non-MPI, embarrassingly parallel tests with pytest
           shell: bash -el {0}
           run: |

Makefile

@@ -16,16 +16,15 @@ clean :
 check-manifest:
 	check-manifest
 
-test: flake
+test: lint
 	pytest ./hnn_core/tests/ -m "not uses_mpi" -n auto
 	pytest ./hnn_core/tests/ -m "uses_mpi"
 
-flake:
-	@if command -v flake8 > /dev/null; then \
-		echo "Running flake8"; \
-		flake8 hnn_core --count; \
+lint:
+	@if command -v ruff > /dev/null; then \
+		echo "Running ruff check"; \
+		ruff check hnn_core; \
 	else \
-		echo "flake8 not found, please install it!"; \
+		echo "ruff not found, please install it!"; \
 		exit 1; \
 	fi;
-	@echo "flake8 passed"

pyproject.toml

@@ -7,3 +7,13 @@ check-hidden = true
 # in jupyter notebooks - images and also some embedded outputs
 ignore-regex = '^\s*"image/\S+": ".*|.*%22%3A%20.*'
 ignore-words-list = 'tha,nam,sherif,dout'
+
+[tool.ruff]
+exclude = ["*.ipynb"]
+[tool.ruff.lint]
+exclude = ["__init__.py"]
+# We don't include rule "W504", which was in our old flake8 "setup.cfg" file, because the ruff
+# linter does not detect it.
+ignore = [
+   "E722",  # From original flake8 'setup.cfg' file, needed in gui.py and viz.py
+]

setup.cfg

@@ -1,7 +1,3 @@
-[flake8]
-exclude = __init__.py
-ignore = E722, W504
-
 [check-manifest]
 ignore =
     .circleci/*

setup.py

@@ -77,7 +77,7 @@ def run(self):
     extras = {
         'opt': ['scikit-learn'],
         'parallel': ['joblib', 'psutil'],
-        'test': ['flake8', 'pytest', 'pytest-cov', 'pytest-xdist'],
+        'test': ['pytest', 'pytest-cov', 'pytest-xdist', 'ruff'],
         'docs': ['mne', 'nibabel', 'pooch', 'tdqm',
                  'sphinx', 'sphinx-gallery',
                  'sphinx_bootstrap_theme', 'sphinx-copybutton',