[WIP] Introduce ruff code-format style

.github/workflows/unix_unit_tests.yml

@@ -54,15 +54,19 @@
           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 --no-fix
+        - name: Check formatting with ruff
+          shell: bash -el {0}
+          run: |
+            ruff format --check
         - name: Test with pytest
           shell: bash -el {0}
           run: |
             python -m pytest ./hnn_core/tests/  --cov=hnn_core --cov-report=xml
         - name:  Upload coverage to Codecov
           shell: bash -el {0}
           run: |
-            bash <(curl -s https://codecov.io/bash) -f ./coverage.xml
+            bash <(curl -s https://codecov.io/bash) -f ./coverage.xml

Makefile

@@ -7,24 +7,22 @@
 
 all: modl
 
-modl:
-	cd hnn_core/mod/ && nrnivmodl
-
 clean :
 	rm -rf hnn_core/mod/x86_64/*
 
 check-manifest:
 	check-manifest
 
-test: flake
-	pytest .
+format:
+	ruff format
+
+lint:
+	ruff check
 
-flake:
-	@if command -v flake8 > /dev/null; then \
-		echo "Running flake8"; \
-		flake8 hnn_core --count; \
-	else \
-		echo "flake8 not found, please install it!"; \
-		exit 1; \
-	fi;
-	@echo "flake8 passed"
+modl:
+	cd hnn_core/mod/ && nrnivmodl
+
+test:
+	ruff format --check
+	ruff check --no-fix
+	pytest .

dev_scripts/convert_params.py

@@ -31,7 +31,7 @@ def download_folder_contents(owner, repo, path):
     -------
     Path to temporary directory or None
     """
-    url = f"https://api.github.com/repos/{owner}/{repo}/contents/{path}"
+    url = f'https://api.github.com/repos/{owner}/{repo}/contents/{path}'
 
     try:
         response = requests.get(url)
@@ -47,7 +47,7 @@ def download_folder_contents(owner, repo, path):
             file_name = os.path.join(temp_dir, item['name'])
             with open(file_name, 'wb') as f:
                 f.write(requests.get(download_url).content)
-                print(f"Downloaded: {file_name}")
+                print(f'Downloaded: {file_name}')
     return temp_dir
 
 
@@ -70,36 +70,38 @@ def convert_param_files_from_repo(owner, repo, repo_path, local_path):
     # Download param files
     temp_dir = download_folder_contents(owner, repo, repo_path)
     # Get list of json and param files
-    file_list = [Path(temp_dir, f)
-                 for f in os.listdir(temp_dir)
-                 if f.endswith('.param') or f.endswith('.json')]
+    file_list = [
+        Path(temp_dir, f)
+        for f in os.listdir(temp_dir)
+        if f.endswith('.param') or f.endswith('.json')
+    ]
     # Assign output location and names
     output_dir = Path(local_path)
     if not os.path.exists(output_dir):
         os.makedirs(output_dir)
-    output_filenames = [Path(output_dir, f.name.split('.')[0])
-                        for f in file_list]
+    output_filenames = [Path(output_dir, f.name.split('.')[0]) for f in file_list]
 
-    [convert_to_json(file, outfile)
-     for (file, outfile) in zip(file_list, output_filenames)]
+    [
+        convert_to_json(file, outfile)
+        for (file, outfile) in zip(file_list, output_filenames)
+    ]
 
     # Delete downloads
     shutil.rmtree(temp_dir)
 
 
 if __name__ == '__main__':
-
     # hnn param files
-    convert_param_files_from_repo(owner='jonescompneurolab',
-                                  repo='hnn',
-                                  repo_path='param',
-                                  local_path=(root_path /
-                                              'network_configuration'),
-                                  )
+    convert_param_files_from_repo(
+        owner='jonescompneurolab',
+        repo='hnn',
+        repo_path='param',
+        local_path=(root_path / 'network_configuration'),
+    )
     # hnn-core json files
-    convert_param_files_from_repo(owner='jonescompneurolab',
-                                  repo='hnn-core',
-                                  repo_path='hnn_core/param',
-                                  local_path=(root_path /
-                                              'network_configuration'),
-                                  )
+    convert_param_files_from_repo(
+        owner='jonescompneurolab',
+        repo='hnn-core',
+        repo_path='hnn_core/param',
+        local_path=(root_path / 'network_configuration'),
+    )

doc/conf.py

@@ -14,8 +14,8 @@
 #
 import os
 import sys
+
 # sys.path.insert(0, os.path.abspath('.'))
-import sphinx_gallery
 from sphinx_gallery.sorting import ExampleTitleSortKey, ExplicitOrder
 
 import sphinx_bootstrap_theme
@@ -57,7 +57,7 @@
     'sphinx.ext.intersphinx',
     'numpydoc',
     'sphinx_copybutton',
-    'gh_substitutions'  # custom extension, see ./sphinxext/gh_substitutions.py
+    'gh_substitutions',  # custom extension, see ./sphinxext/gh_substitutions.py
 ]
 
 # generate autosummary even if no references
@@ -68,7 +68,7 @@
 default_role = 'autolink'  # XXX silently allows bad syntax, someone should fix
 
 # Sphinx-Copybutton configuration
-copybutton_prompt_text = r">>> |\.\.\. |\$ "
+copybutton_prompt_text = r'>>> |\.\.\. |\$ '
 copybutton_prompt_is_regexp = True
 
 # Add any paths that contain templates here, relative to this directory.
@@ -113,13 +113,13 @@
 html_theme_options = {
     'navbar_sidebarrel': False,
     'navbar_links': [
-        ("Examples", "auto_examples/index"),
-        ("API", "api"),
-        ("Glossary", "glossary"),
-        ("What's new", "whats_new"),
-        ("GitHub", "https://github.com/jonescompneurolab/hnn-core", True)
+        ('Examples', 'auto_examples/index'),
+        ('API', 'api'),
+        ('Glossary', 'glossary'),
+        ("What's new", 'whats_new'),
+        ('GitHub', 'https://github.com/jonescompneurolab/hnn-core', True),
     ],
-    'bootswatch_theme': "yeti"
+    'bootswatch_theme': 'yeti',
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,
@@ -150,15 +150,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -168,19 +165,15 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'hnn-core.tex', 'hnn-core Documentation',
-     'Mainak Jas', 'manual'),
+    (master_doc, 'hnn-core.tex', 'hnn-core Documentation', 'Mainak Jas', 'manual'),
 ]
 
 
 # -- Options for manual page output ------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'hnn-core', 'hnn-core Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, 'hnn-core', 'hnn-core Documentation', [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -189,17 +182,23 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'hnn-core', 'hnn-core Documentation',
-     author, 'hnn-core', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        'hnn-core',
+        'hnn-core Documentation',
+        author,
+        'hnn-core',
+        'One line description of project.',
+        'Miscellaneous',
+    ),
 ]
 
 intersphinx_mapping = {
     'python': ('https://docs.python.org/3', None),
     'mne': ('https://mne.tools/dev', None),
     'numpy': ('https://numpy.org/devdocs', None),
     'scipy': ('https://scipy.github.io/devdocs', None),
-    'matplotlib': ('https://matplotlib.org', None)
+    'matplotlib': ('https://matplotlib.org', None),
 }
 intersphinx_timeout = 5
 
@@ -209,7 +208,7 @@
     'https://doi.org/10.1152/jn.00535.2009',
     'https://doi.org/10.1152/jn.00122.2010',
     'https://doi.org/10.1101/2021.04.16.440210',
-    'https://groups.google.com/g/hnnsolver'
+    'https://groups.google.com/g/hnnsolver',
 ]
 
 # Resolve binder filepath_prefix. From the docs:
@@ -224,29 +223,28 @@
     filepath_prefix = 'v{}'.format(version)
 
 sphinx_gallery_conf = {
-    'first_notebook_cell': ("import pyvista as pv\n"
-                            "from mne.viz import set_3d_backend\n"
-                            "set_3d_backend('notebook')\n"
-                            "pv.set_jupyter_backend('client')"
-                            ),
+    'first_notebook_cell': (
+        'import pyvista as pv\n'
+        'from mne.viz import set_3d_backend\n'
+        "set_3d_backend('notebook')\n"
+        "pv.set_jupyter_backend('client')"
+    ),
     'doc_module': 'hnn_core',
     # path to your examples scripts
     'examples_dirs': '../examples',
     # path where to save gallery generated examples
     'gallery_dirs': 'auto_examples',
     'backreferences_dir': 'generated',
-    'reference_url': {
-        'hnn_core': None
-    },
+    'reference_url': {'hnn_core': None},
     'within_subsection_order': ExampleTitleSortKey,
-    'subsection_order': ExplicitOrder(['../examples/workflows/',
-                                       '../examples/howto/']),
-    'binder': {'org': 'jonescompneurolab',
-               'repo': 'hnn-core',
-               'branch': 'gh-pages',
-               'binderhub_url': 'https://mybinder.org',
-               'filepath_prefix': filepath_prefix,
-               'notebooks_dir': 'notebooks',
-               'dependencies': 'Dockerfile'
-               }
+    'subsection_order': ExplicitOrder(['../examples/workflows/', '../examples/howto/']),
+    'binder': {
+        'org': 'jonescompneurolab',
+        'repo': 'hnn-core',
+        'branch': 'gh-pages',
+        'binderhub_url': 'https://mybinder.org',
+        'filepath_prefix': filepath_prefix,
+        'notebooks_dir': 'notebooks',
+        'dependencies': 'Dockerfile',
+    },
 }

doc/sphinxext/gh_substitutions.py

@@ -6,6 +6,7 @@
 https://doughellmann.com/blog/2010/05/09/defining-custom-roles-in-sphinx/
 
 """
+
 from docutils.nodes import reference
 from docutils.parsers.rst.roles import set_classes