merge conflicts

Author: alejoe91

.github/workflows/black-formatting.yml

@@ -12,13 +12,20 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: Check and apply black formatting
+      - name: Check black formatting
         id: black-check
         uses: psf/black@stable
         with:
             options: "--check --verbose"
         continue-on-error: true
 
+      - name: Apply black formatting
+        id: black-apply
+        uses: psf/black@stable
+        if : ${{ steps.black-check.outcome == 'failure' }}
+        with:
+            options: "--verbose"
+
       - name: Create PR
         uses: peter-evans/create-pull-request@v5
         if : ${{ steps.black-check.outcome == 'failure' }}

.gitignore

@@ -15,6 +15,8 @@
 .idea
 *.swp
 *.swo
+.vscode
+
 
 # Compiled source #
 ###################
@@ -56,6 +58,7 @@ cover
 .directory
 .gdb_history
 .DS_Store?
+.DS_Store
 ehthumbs.db
 Icon?
 Thumbs.db
@@ -73,4 +76,8 @@ doc/*.plx
 doc/*.nev
 doc/*.ns5
 doc/*.nix
-doc/*.nwb
+doc/*.nwb
+*.plx
+*.smr
+B95.zip
+grouped_ephys

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2010-2022, Neo authors and contributors
+Copyright (c) 2010-2024, Neo authors and contributors
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

README.rst

@@ -53,7 +53,7 @@ For installation instructions, see doc/source/install.rst
 
 To cite Neo in publications, see CITATION.txt
 
-:copyright: Copyright 2010-2022 by the Neo team, see doc/source/authors.rst.
+:copyright: Copyright 2010-2024 by the Neo team, see doc/source/authors.rst.
 :license: 3-Clause Revised BSD License, see LICENSE.txt for details.
 
 Funding

codemeta.json

@@ -4,15 +4,15 @@
   "license": "https://spdx.org/licenses/BSD-3-Clause",
   "codeRepository": "https://github.com/NeuralEnsemble/python-neo",
   "contIntegration": "https://github.com/NeuralEnsemble/python-neo/actions",
-  "dateModified": "2023-04-04",
-  "downloadUrl": "https://files.pythonhosted.org/packages/4d/95/e79e05c9bc8ef61d89a8a6b949db03adb2046b9fca38422d570c7add543d/neo-0.12.0.tar.gz",
+  "dateModified": "2024-02-02",
+  "downloadUrl": "https://files.pythonhosted.org/packages/b2/07/b8653dd235919dc13671fc31bd8bcbb57571e72d75e4cb04dc1347416357/neo-0.13.0.tar.gz",
   "issueTracker": "https://github.com/NeuralEnsemble/python-neo/issues",
   "name": "Neo",
-  "version": "0.12.0",
+  "version": "0.13.0",
   "identifier": "RRID:SCR_000634",
   "description": "Neo is a Python package for working with electrophysiology data in Python, together with support for reading a wide range of neurophysiology file formats, including Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt, and support for writing to a subset of these formats plus non-proprietary formats including HDF5.\n\nThe goal of Neo is to improve interoperability between Python tools for analyzing, visualizing and generating electrophysiology data by providing a common, shared object model. In order to be as lightweight a dependency as possible, Neo is deliberately limited to represention of data, with no functions for data analysis or visualization.\n\nNeo is used by a number of other software tools, including SpykeViewer (data analysis and visualization), Elephant (data analysis), the G-node suite (databasing), PyNN (simulations), tridesclous_ (spike sorting) and ephyviewer (data visualization).\n\nNeo implements a hierarchical data model well adapted to intracellular and extracellular electrophysiology and EEG data with support for multi-electrodes (for example tetrodes). Neo's data objects build on the quantities package, which in turn builds on NumPy by adding support for physical dimensions. Thus Neo objects behave just like normal NumPy arrays, but with additional metadata, checks for dimensional consistency and automatic unit conversion.",
   "applicationCategory": "neuroscience",
-  "releaseNotes": "https://neo.readthedocs.io/en/stable/releases/0.12.0.html",
+  "releaseNotes": "https://neo.readthedocs.io/en/stable/releases/0.13.0.html",
   "funding": "https://cordis.europa.eu/project/id/945539",
   "developmentStatus": "active",
   "referencePublication": "https://doi.org/10.3389/fninf.2014.00010",
@@ -26,10 +26,7 @@
     "Python (version 3.8+)",
     "see https://github.com/NeuralEnsemble/python-neo/blob/master/pyproject.toml"
   ],
-  "relatedLink": [
-    "https://neo.readthedocs.io",
-    "https://neuralensemble.org/community"
-  ],
+  "relatedLink": ["https://neo.readthedocs.io", "https://neuralensemble.org/community"],
   "author": [
     { "@type": "Person", "givenName": "Samuel", "familyName": "Garcia" },
     {
@@ -71,34 +68,17 @@
     { "@type": "Person", "givenName": "William", "familyName": "Hart" },
     { "@type": "Person", "alternateName": "erikli(github)" },
     { "@type": "Person", "givenName": "Jeffrey", "familyName": "Gill" },
-    {
-      "@type": "Person",
-      "givenName": "Lucas",
-      "alternateName": "lkoelman@github"
-    },
+    { "@type": "Person", "givenName": "Lucas", "alternateName": "lkoelman@github" },
     { "@type": "Person", "givenName": "Mark", "familyName": "Histed" },
     { "@type": "Person", "givenName": "Mike", "familyName": "Sintsov" },
     { "@type": "Person", "givenName": "Scott W", "familyName": "Harden" },
-    {
-      "@type": "Person",
-      "givenName": "Chek Yin",
-      "familyName": "Choi",
-      "alternateName": "hkchekc@github"
-    },
+    { "@type": "Person", "givenName": "Chek Yin", "familyName": "Choi", "alternateName": "hkchekc@github" },
     { "@type": "Person", "givenName": "Corentin", "familyName": "Fragnaud" },
-    {
-      "@type": "Person",
-      "givenName": "Alexander",
-      "familyName": "Kleinjohann"
-    },
+    { "@type": "Person", "givenName": "Alexander", "familyName": "Kleinjohann" },
     { "@type": "Person", "givenName": "Christian", "familyName": "Kothe" },
     { "@type": "Person", "alternateName": "rishidhingra@github" },
     { "@type": "Person", "givenName": "Hugo", "familyName": "van Kemenade" },
-    {
-      "@type": "Person",
-      "givenName": "Aitor",
-      "familyName": "Morales-Gregorio"
-    },
+    { "@type": "Person", "givenName": "Aitor", "familyName": "Morales-Gregorio" },
     { "@type": "Person", "givenName": "Peter N", "familyName": "Steinmetz" },
     { "@type": "Person", "givenName": "Shashwat", "familyName": "Sridhar" },
     { "@type": "Person", "givenName": "Alessio", "familyName": "Buccino" },
@@ -108,6 +88,21 @@
     { "@type": "Person", "givenName": "Ben", "familyName": "Dichter" },
     { "@type": "Person", "givenName": "Elodie", "familyName": "Legouée" },
     { "@type": "Person", "givenName": "Heberto", "familyName": "Mayorquin" },
-    { "@type": "Person", "givenName": "Thomas", "familyName": "Perret" }
+    { "@type": "Person", "givenName": "Thomas", "familyName": "Perret" },
+    { "@type": "Person", "givenName": "Zach", "familyName": "McKenzie" },
+    { "@type": "Person", "givenName": "Moritz Alexander", "familyName": "Kern" },
+    { "@type": "Person", "givenName": "Joscha", "familyName": "Schmiedt" },
+    { "@type": "Person", "givenName": "Daniel P.", "familyName": "Crepeau" },
+    { "@type": "Person", "givenName": "Divyansh", "familyName": "Gupta" },
+    { "@type": "Person", "givenName": "Nate", "familyName": "Dolensek" },
+    { "@type": "Person", "givenName": "Philipp", "familyName": "Hornauer" },
+    { "@type": "Person", "givenName": "Robert", "familyName": "Wolff" },
+    { "@type": "Person", "givenName": "Jules", "familyName": "Lebert" },
+    { "@type": "Person", "givenName": "Benjamin", "familyName": "Heasly" },
+    { "@type": "Person", "givenName": "Baptiste", "familyName": "Grimaud" },
+    { "@type": "Person", "givenName": "Cody", "familyName": "Baker" },
+    { "@type": "Person", "givenName": "Fernando J.", "familyName": "Chaure" },
+    { "@type": "Person", "alternateName": "Filipe@github" },
+    { "@type": "Person", "givenName": "Matthias Klumpp" }
   ]
 }

doc/old_stuffs/developers_guide.rst

@@ -248,7 +248,6 @@ The :doc:`governance` document describes how decisions about the project are tak
 
 
 .. _Python: https://www.python.org
-.. _nose: https://nose.readthedocs.io/
 .. _Setuptools: https://pypi.python.org/pypi/setuptools/
 .. _tox: http://codespeak.net/tox/
 .. _coverage: https://coverage.readthedocs.io/

doc/source/authors.rst

@@ -60,9 +60,25 @@ and may not be the current affiliation of a contributor.
 * Etienne Combrisson [6]
 * Ben Dichter [24]
 * Elodie Legouée [21]
+* Oliver Kloss [13]
 * Heberto Mayorquin [24]
 * Thomas Perret [25]
 * Kyle Johnsen [26, 27]
+* Zach McKenzie [28]
+* Moritz Alexander Kern
+* Joscha Schmiedt
+* Daniel P. Crepeau
+* Divyansh Gupta
+* Nate Dolensek
+* Philipp Hornauer
+* Robert Wolff
+* Jules Lebert
+* Benjamin Heasly
+* Baptiste Grimaud
+* Cody Baker
+* Fernando J. Chaure
+* Filipe*github
+* Matthias Klumpp
 
 1. Centre de Recherche en Neuroscience de Lyon, CNRS UMR5292 - INSERM U1028 - Universite Claude Bernard Lyon 1
 2. Unité de Neuroscience, Information et Complexité, CNRS UPR 3293, Gif-sur-Yvette, France
@@ -91,6 +107,7 @@ and may not be the current affiliation of a contributor.
 25. Institut des Sciences Cognitives Marc Jeannerod, CNRS UMR5229, Lyon, France
 26. Georgia Institute of Technology
 27. Emory University
+28. Harvard Medical School
 
 If we've somehow missed you off the list we're very sorry - please let us know.
 

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 = '2010-2023, ' + 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 +247,12 @@
 
 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
+    # 'only_warn_on_example_error': True, # helps with debugging broken examples
+    "examples_dirs": "../../examples",  # path to your example scripts
+    "gallery_dirs": "examples",  # path to where to save gallery generated output
 }