style: fix doc lints, introduce ruff linting

.github/workflows/unix_unit_tests.yml

@@ -54,6 +54,14 @@
           shell: bash -el {0}
           run: |
             pip install --verbose '.[opt, parallel, test, gui]'
+        - name: Lint with ruff
+          shell: bash -el {0}
+          run: |
+            ruff check --no-fix
+        - name: Check formatting with ruff
+          shell: bash -el {0}
+          run: |
+            ruff format --check
         - name: Test with pytest
           shell: bash -el {0}
           run: |

Makefile

@@ -16,8 +16,13 @@ check-manifest:
 format:
 	ruff format
 
+lint:
+	ruff check
+
 modl:
 	cd hnn_core/mod/ && nrnivmodl
 
 test:
+	ruff format --check
+	ruff check --no-fix
 	pytest .

doc/conf.py

@@ -16,7 +16,6 @@
 import sys
 
 # sys.path.insert(0, os.path.abspath('.'))
-import sphinx_gallery
 from sphinx_gallery.sorting import ExampleTitleSortKey, ExplicitOrder
 
 import sphinx_bootstrap_theme

examples/howto/plot_connectivity.py

@@ -10,12 +10,10 @@
 
 # sphinx_gallery_thumbnail_number = 2
 
-import os.path as op
 
 ###############################################################################
 # Let us import ``hnn_core``.
 
-import hnn_core
 from hnn_core import jones_2009_model, simulate_dipole
 
 ###############################################################################

examples/howto/plot_firing_pattern.py

@@ -16,7 +16,6 @@
 ###############################################################################
 # Let us import ``hnn_core``.
 
-import hnn_core
 from hnn_core import read_spikes, jones_2009_model, simulate_dipole
 
 ###############################################################################

examples/howto/plot_hnn_animation.py

@@ -11,10 +11,8 @@
 ###############################################################################
 # First, we'll import the necessary modules for instantiating a network and
 # running a simulation that we would like to animate.
-import os.path as op
 
-import hnn_core
-from hnn_core import jones_2009_model, simulate_dipole, read_params
+from hnn_core import jones_2009_model, simulate_dipole
 from hnn_core.network_models import add_erp_drives_to_jones_model
 
 ###############################################################################

examples/howto/plot_simulate_mpi_backend.py

@@ -18,9 +18,7 @@
 
 ###############################################################################
 # Let us import hnn_core
-import os.path as op
 
-import hnn_core
 from hnn_core import simulate_dipole, jones_2009_model
 
 ###############################################################################

examples/workflows/plot_simulate_alpha.py

@@ -20,12 +20,10 @@
 #          Nick Tolley <[email protected]>
 #          Christopher Bailey <[email protected]>
 
-import os.path as op
 
 ###############################################################################
 # Let us import hnn_core
 
-import hnn_core
 from hnn_core import simulate_dipole, jones_2009_model
 
 ###############################################################################
@@ -72,7 +70,7 @@
 # included in our biophysical model. We can confirm that what we simulate is
 # indeed 10 Hz activity by plotting the power spectral density (PSD).
 import matplotlib.pyplot as plt
-from hnn_core.viz import plot_dipole, plot_psd
+from hnn_core.viz import plot_psd
 
 fig, axes = plt.subplots(2, 1, constrained_layout=True)
 tmin, tmax = 10, 300  # exclude the initial burn-in period from the plots

examples/workflows/plot_simulate_evoked.py

@@ -21,15 +21,10 @@
 
 # sphinx_gallery_thumbnail_number = 3
 
-import os.path as op
-import tempfile
-
-import matplotlib.pyplot as plt
 
 ###############################################################################
 # Let us import hnn_core
 
-import hnn_core
 from hnn_core import simulate_dipole, jones_2009_model
 from hnn_core.viz import plot_dipole
 

pyproject.toml

@@ -12,3 +12,11 @@ ignore-words-list = 'tha,nam,sherif,dout'
 exclude = ["*.ipynb"]
 [tool.ruff.format]
 quote-style = "single"
+[tool.ruff.lint]
+exclude = ["__init__.py"]
+# We don't include rule "W504", which was in our old flake8 "setup.cfg" file for 2 reasons: it is an
+# invalid option for the ruff linter, and the ruff formatter already applies that rule.
+ignore = [
+   "E402",  # Needed for notes at beginning of example scripts
+   "E722",  # From original flake8 'setup.cfg' file, needed in viz.py
+]