Merge pull request #1394 from NeuralEnsemble/black-formatting

Black formatting

Author: apdavison

doc/source/conf.py

@@ -17,13 +17,13 @@
 
 from packaging.version import Version
 
-with open('../../pyproject.toml', mode='r') as f:
+with open("../../pyproject.toml", mode="r") as f:
     txt = f.read()
     neo_release = re.findall('version = "(\S+)"', txt)[0]
 
-neo_version = '.'.join((str(e) for e in Version(neo_release).release[:2]))
+neo_version = ".".join((str(e) for e in Version(neo_release).release[:2]))
 
-AUTHORS = 'Neo authors and contributors <[email protected]>'
+AUTHORS = "Neo authors and contributors <[email protected]>"
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -34,28 +34,33 @@
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.todo',
-              'IPython.sphinxext.ipython_console_highlighting',
-              'IPython.sphinxext.ipython_directive',
-              'matplotlib.sphinxext.plot_directive',
-              'sphinx_gallery.gen_gallery',
-              'sphinx_inline_tabs', "sphinx_design"]
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.doctest",
+    "sphinx.ext.todo",
+    "IPython.sphinxext.ipython_console_highlighting",
+    "IPython.sphinxext.ipython_directive",
+    "matplotlib.sphinxext.plot_directive",
+    "sphinx_gallery.gen_gallery",
+    "sphinx_inline_tabs",
+    "sphinx_design",
+]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix of source filenames.
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The encoding of source files.
 # source_encoding = 'utf-8'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'Neo'
-copyright = '2010-2024, ' + AUTHORS
+project = "Neo"
+copyright = "2010-2024, " + AUTHORS
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -99,7 +104,7 @@
 # show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
 # modindex_common_prefix = []
@@ -115,32 +120,28 @@
 # html_theme = 'scrolls'
 # html_theme = 'agogo'
 # html_theme = 'alabaster'
-html_theme = 'pydata_sphinx_theme'
+html_theme = "pydata_sphinx_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 
 html_theme_options = {
     "logo": {
-      "image_light": "images/neologo_small.png",
-      "image_dark": "images/neologo_small_darkmode.png",
+        "image_light": "images/neologo_small.png",
+        "image_dark": "images/neologo_small_darkmode.png",
     },
-    'icon_links': [
-        {
-            "name": 'GitHub',
-            "url": 'https://github.com/NeuralEnsemble/python-neo',
-            "icon": 'fa-brands fa-square-github'
-        },
+    "icon_links": [
+        {"name": "GitHub", "url": "https://github.com/NeuralEnsemble/python-neo", "icon": "fa-brands fa-square-github"},
         {
             "name": "PyPI",
             "url": "https://pypi.org/project/neo",
             "icon": "fa-solid fa-box",
         },
     ],
-    'icon_links_label': 'External Links',  # for screen reader
-    'use_edit_page_button': False,
-    'navbar_end': ['theme-switcher', 'navbar-icon-links'],
+    "icon_links_label": "External Links",  # for screen reader
+    "use_edit_page_button": False,
+    "navbar_end": ["theme-switcher", "navbar-icon-links"],
 }
 
 # Add any paths that contain custom themes here, relative to this directory.
@@ -155,22 +156,22 @@
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-html_logo = 'images/neologo_small.png'
+html_logo = "images/neologo_small.png"
 
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-html_favicon = 'images/neologo_favicon.png'
+html_favicon = "images/neologo_favicon.png"
 
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['images', '_static']
+html_static_path = ["images", "_static"]
 
 html_css_files = [
-    'css/custom.css',
+    "css/custom.css",
 ]
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
@@ -209,7 +210,7 @@
 # html_file_suffix = ''
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'neodoc'
+htmlhelp_basename = "neodoc"
 
 
 # -- Options for LaTeX output -------------------------------------------------
@@ -223,8 +224,7 @@
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author,
 #  documentclass [howto/manual]).
-latex_documents = [('index', 'neo.tex', 'Neo Documentation',
-                    AUTHORS, 'manual')]
+latex_documents = [("index", "neo.tex", "Neo Documentation", AUTHORS, "manual")]
 
 # The name of an image file (relative to this directory) to place at the
 # top of the title page.
@@ -247,9 +247,11 @@
 
 rst_epilog = """
 .. |neo_github_url| replace:: https://github.com/NeuralEnsemble/python-neo/archive/neo-{}.zip
-""".format(neo_release)
+""".format(
+    neo_release
+)
 
 sphinx_gallery_conf = {
-    'examples_dirs': '../../examples',   # path to your example scripts
-    'gallery_dirs': 'examples',  # path to where to save gallery generated output
+    "examples_dirs": "../../examples",  # path to your example scripts
+    "gallery_dirs": "examples",  # path to where to save gallery generated output
 }

doc/source/images/generate_io_overview.py

@@ -26,89 +26,86 @@
 # dpi = 100
 
 
-default_style = {'shape': 'rectangle',
-                 'color': 'black',
-                 'fontcolor': 'black'}
+default_style = {"shape": "rectangle", "color": "black", "fontcolor": "black"}
 IO_style = default_style.copy()
-IO_style['fontsize'] = '30'
-IO_style['penwidth'] = 6
+IO_style["fontsize"] = "30"
+IO_style["penwidth"] = 6
 
-styles = {'IO': {'ro': IO_style.copy(),
-                 'rw': IO_style.copy(),
-                 'raw': IO_style.copy()
-                 },
-          'main': default_style.copy(),
-          'ext': default_style.copy()}
+styles = {
+    "IO": {"ro": IO_style.copy(), "rw": IO_style.copy(), "raw": IO_style.copy()},
+    "main": default_style.copy(),
+    "ext": default_style.copy(),
+}
 
-styles['IO']['ro']['color'] = '#20B2AA '
-styles['IO']['rw']['color'] = '#4169E1 '
-styles['IO']['raw']['color'] = '#008080 '
-styles['ext']['shape'] = 'circle'
-styles['ext']['fillcolor'] = 'red'
-styles['ext']['style'] = 'filled'
+styles["IO"]["ro"]["color"] = "#20B2AA "
+styles["IO"]["rw"]["color"] = "#4169E1 "
+styles["IO"]["raw"]["color"] = "#008080 "
+styles["ext"]["shape"] = "circle"
+styles["ext"]["fillcolor"] = "red"
+styles["ext"]["style"] = "filled"
 
 
 # styles['ext']['fixedsize'] = 'True'
 
 
 def generate_diagram(filename, plot_extensions=False):
-    dia = pygraphviz.AGraph(strict=False, splines='true')
+    dia = pygraphviz.AGraph(strict=False, splines="true")
     G = dia
-    G.node_attr['fontname'] = 'Arial'
+    G.node_attr["fontname"] = "Arial"
     # G.node_attr['shape'] = 'circle'
     # G.node_attr['fixedsize'] = 'true'
     # G.node_attr['sep'] = '-100'
-    G.node_attr['fixedsize'] = 'False'
+    G.node_attr["fixedsize"] = "False"
     # G.graph_attr['overlap'] = 'False'
-    G.graph_attr['packMode'] = 'clust'
+    G.graph_attr["packMode"] = "clust"
     # G.graph_attr['levelsgap'] = -500
-    G.node_attr['fontsize'] = '20'
-    G.edge_attr['minlen'] = '0'
+    G.node_attr["fontsize"] = "20"
+    G.edge_attr["minlen"] = "0"
     # G.node_attr['style'] = 'filled'
     # G.graph_attr['outputorder'] = 'edgesfirst'
     # G.graph_attr['splines'] = "compound"
-    G.graph_attr['label'] = "NEO {}".format(neo.__version__)
-    G.graph_attr['ratio'] = '1.0'
+    G.graph_attr["label"] = "NEO {}".format(neo.__version__)
+    G.graph_attr["ratio"] = "1.0"
     # G.edge_attr['color'] = '#1100FF'
 
-    G.edge_attr['style'] = 'setlinewidth(4)'
+    G.edge_attr["style"] = "setlinewidth(4)"
 
-    dia.add_node('NEO', shape='circle', fontsize=50)
+    dia.add_node("NEO", shape="circle", fontsize=50)
 
     for io in neo.io.iolist:
         io_name = io.name
         rawio = False
         if issubclass(io, neo.io.basefromrawio.BaseFromRaw):
             rawio = True
-            if io_name == 'BaseIO':
-                io_name = io.__name__.rstrip('RawIO')
+            if io_name == "BaseIO":
+                io_name = io.__name__.rstrip("RawIO")
         if io_name is None:
-            io_name = io.__name__.rstrip('IO')
-        if 'example' in io_name:
+            io_name = io.__name__.rstrip("IO")
+        if "example" in io_name:
             continue
 
         if io.is_writable and io.is_readable:
-            mode = 'rw'
+            mode = "rw"
         elif io.is_readable:
-            mode = 'ro'
+            mode = "ro"
         if rawio:
-            mode = 'raw'
+            mode = "raw"
 
-        dia.add_node(io_name, **styles['IO'][mode])
-        dia.add_edge('NEO', io_name)
+        dia.add_node(io_name, **styles["IO"][mode])
+        dia.add_edge("NEO", io_name)
 
         if plot_extensions:
             for ext in io.extensions:
-                dia.add_node(ext, **styles['ext'])
+                dia.add_node(ext, **styles["ext"])
                 dia.add_edge(io_name, ext, minlen=0)
 
-    dia.layout(prog='fdp')  # neato, dot, twopi, circo, fdp, nop, wc, acyclic, gvpr, gvcolor,
+    dia.layout(prog="fdp")  # neato, dot, twopi, circo, fdp, nop, wc, acyclic, gvpr, gvcolor,
     # ccomps, sccmap, tred, sfdp.
-    for ext in ['png', 'svg', 'eps']:
-        dia.draw('{}.{}'.format(filename, ext))
+    for ext in ["png", "svg", "eps"]:
+        dia.draw("{}.{}".format(filename, ext))
 
 
-if __name__ == '__main__':
-    generate_diagram('IODiagram', plot_extensions=False)
-    generate_diagram('IODiagram_ext', plot_extensions=True)
+if __name__ == "__main__":
+    generate_diagram("IODiagram", plot_extensions=False)
+    generate_diagram("IODiagram_ext", plot_extensions=True)
     # pyplot.show()

doc/source/scripts/multi_tetrode_example.py

@@ -11,23 +11,19 @@
 store_signals = False
 
 block = Block(name="probe data", tetrode_ids=["Tetrode #1", "Tetrode #2"])
-block.segments = [Segment(name="trial #1", index=0),
-                  Segment(name="trial #2", index=1),
-                  Segment(name="trial #3", index=2)]
+block.segments = [
+    Segment(name="trial #1", index=0),
+    Segment(name="trial #2", index=1),
+    Segment(name="trial #3", index=2),
+]
 
-n_units = {
-    "Tetrode #1": 2,
-    "Tetrode #2": 5
-}
+n_units = {"Tetrode #1": 2, "Tetrode #2": 5}
 
 # Create a group for each neuron, annotate each group with the tetrode from which it was recorded
 groups = []
 counter = 0
 for tetrode_id, n in n_units.items():
-    groups.extend(
-        [Group(name=f"neuron #{counter + i + 1}", tetrode_id=tetrode_id)
-         for i in range(n)]
-    )
+    groups.extend([Group(name=f"neuron #{counter + i + 1}", tetrode_id=tetrode_id) for i in range(n)])
     counter += n
 block.groups.extend(groups)
 
@@ -38,10 +34,8 @@
 
     # create two 4-channel AnalogSignals with dummy data
     signals = {
-        "Tetrode #1": AnalogSignal(np.random.rand(1000, 4) * mV,
-                                   sampling_rate=10 * kHz, tetrode_id="Tetrode #1"),
-        "Tetrode #2": AnalogSignal(np.random.rand(1000, 4) * mV,
-                                   sampling_rate=10 * kHz, tetrode_id="Tetrode #2")
+        "Tetrode #1": AnalogSignal(np.random.rand(1000, 4) * mV, sampling_rate=10 * kHz, tetrode_id="Tetrode #1"),
+        "Tetrode #2": AnalogSignal(np.random.rand(1000, 4) * mV, sampling_rate=10 * kHz, tetrode_id="Tetrode #2"),
     }
     if store_signals:
         segment.analogsignals.extend(signals.values())

doc/source/scripts/spike_sorting_example.py

@@ -9,15 +9,21 @@
 # generate some fake data
 seg = Segment()
 seg.analogsignals.append(
-    AnalogSignal([[0.1, 0.1, 0.1, 0.1],
-                  [-2.0, -2.0, -2.0, -2.0],
-                  [0.1, 0.1, 0.1, 0.1],
-                  [-0.1, -0.1, -0.1, -0.1],
-                  [-0.1, -0.1, -0.1, -0.1],
-                  [-3.0, -3.0, -3.0, -3.0],
-                  [0.1, 0.1, 0.1, 0.1],
-                  [0.1, 0.1, 0.1, 0.1]],
-                 sampling_rate=1000 * Hz, units='V'))
+    AnalogSignal(
+        [
+            [0.1, 0.1, 0.1, 0.1],
+            [-2.0, -2.0, -2.0, -2.0],
+            [0.1, 0.1, 0.1, 0.1],
+            [-0.1, -0.1, -0.1, -0.1],
+            [-0.1, -0.1, -0.1, -0.1],
+            [-3.0, -3.0, -3.0, -3.0],
+            [0.1, 0.1, 0.1, 0.1],
+            [0.1, 0.1, 0.1, 0.1],
+        ],
+        sampling_rate=1000 * Hz,
+        units="V",
+    )
+)
 
 # extract spike trains from all channels
 st_list = []
@@ -32,7 +38,7 @@
     # remember the spike waveforms
     wf_list = []
     for spike_idx in np.nonzero(spike_mask)[0]:
-        wf_list.append(signal[spike_idx - 1:spike_idx + 2, :])
+        wf_list.append(signal[spike_idx - 1 : spike_idx + 2, :])
     st.waveforms = np.array(wf_list)
 
     st_list.append(st)