Merge branch 'master' into neuronexus

Author: zm711

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": "2024-05-07",
-  "downloadUrl": "https://files.pythonhosted.org/packages/8b/75/a9a841dc8f5a4198fe3f7174f096726a8b71444670be3abd6ac168de44d8/neo-0.13.1.tar.gz",
+  "dateModified": "2024-08-01",
+  "downloadUrl": "https://files.pythonhosted.org/packages/0f/16/4e22eb38621183d56acde0abbe591f15e79c6332e9ec360fc5db171b39ab/neo-0.13.2.tar.gz",
   "issueTracker": "https://github.com/NeuralEnsemble/python-neo/issues",
   "name": "Neo",
-  "version": "0.13.1",
+  "version": "0.13.2",
   "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/0.13.1.html",
+  "releaseNotes": "https://neo.readthedocs.io/en/stable/releases/0.13.2.html",
   "funding": "https://cordis.europa.eu/project/id/945539",
   "developmentStatus": "active",
   "referencePublication": "https://doi.org/10.3389/fninf.2014.00010",
@@ -107,6 +107,11 @@
     { "@type": "Person", "givenName": "Matthias", "familyName": "Klumpp" },
     { "@type": "Person", "givenName": "Greg", "familyName": "Knoll" },
     { "@type": "Person", "givenName": "Chris", "familyName": "Halcrow" },
-    { "@type": "Person", "givenName": "Szonja", "familyName": "Weigl" }
+    { "@type": "Person", "givenName": "Szonja", "familyName": "Weigl" },
+    { "@type": "Person", "givenName": "Teo", "familyName": "Lohrer"},
+    { "@type": "Person", "givenName": "Kyu Hun", "familyName": "Lee"},
+    { "@type": "Person", "givenName": "Xin", "familyName": "Niu"},
+    { "@type": "Person", "givenName": "Anthony", "familyName": "Pinto"},
+    { "@type": "Person", "givenName": "Chris", "familyName": "Heydrick"}
   ]
 }

doc/source/authors.rst

@@ -65,7 +65,7 @@ and may not be the current affiliation of a contributor.
 * Heberto Mayorquin [24]
 * Thomas Perret [25]
 * Kyle Johnsen [26, 27]
-* Zach McKenzie [28]
+* Zach McKenzie [28,39]
 * Moritz Alexander Kern [29]
 * Joscha Schmiedt
 * Daniel P. Crepeau [30]
@@ -83,6 +83,11 @@ and may not be the current affiliation of a contributor.
 * Greg Knoll [36]
 * Chris Halcrow [37]
 * Szonja Weigl [24]
+* Chris Heydrick [40]
+* Kyu Hun Lee
+* Téo Lohrer
+* Anthony Pinto [41]
+* Xin Niu
 
 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
@@ -122,6 +127,10 @@ and may not be the current affiliation of a contributor.
 36. Bernstein Center for Computational Neuroscience, Berlin, Germany
 37. University of Edinburgh
 38. Allen Institute for Neural Dynamics, Seattle, WA, United States
+39. Massachusetts General Hospital, Department of Molecular Biology
+40. Plexon Inc.
+41. Paris Brain Institute
+
 
 
 If we've somehow missed you off the list we're very sorry - please let us know.

doc/source/releases.rst

@@ -6,6 +6,7 @@ Release notes
 .. toctree::
    :maxdepth: 1
 
+   releases/0.13.2.rst
    releases/0.13.1.rst
    releases/0.13.0.rst
    releases/0.12.0.rst

doc/source/releases/0.13.2.rst

@@ -0,0 +1,45 @@
+========================
+Neo 0.13.2 release notes
+========================
+
+1st August 2024
+
+This release of Neo contains bug fixes, still with a focus on the planned 1.0 release,
+along with some performance improvements in IO modules and updates to the CI.
+
+See all `pull requests`_ included in this release and the `list of closed issues`_.
+
+
+Continuous Integration
+----------------------
+
+Core tests now run on python 3.12.
+
+IO tests now run on python 3.9 and python 3.11.
+
+
+Performance Improvements & Code quality
+---------------------------------------
+
+The imports across the code base were standardized to standard library, 3rd party,
+and then 1st party for top level imports.
+
+Additionally, :code:`neo` import time was improved.
+
+
+Bug fixes and improvements in IO modules
+----------------------------------------
+
+Bug fixes and/or improvements have been made to :class:`IntanIO`, :class:`PlexonIO`, :class:`SpikeGadgetsIO`,
+:class:`NeuralynxIO`, :class:`SpikeGLXIO`, :class:`BlackrockIO`, and :class:`RawBinarySignalRawIO`.
+
+Acknowledgements
+----------------
+
+Thanks to Heberto Mayorquin, Zach McKenzie, Alessio Buccino, Andrew Davison, Chris Heydrick, 
+Anthony Pinto, Kyu Hun Lee, Téo Lohrer, Tom Donoghue, Xin Niu, and Samuel Garcia for their
+contributions to this release.
+
+.. _`pull requests`: https://github.com/NeuralEnsemble/python-neo/pulls?q=is%3Apr+is%3Aclosed+milestone%3A0.13.2
+
+.. _`list of closed issues`: https://github.com/NeuralEnsemble/python-neo/issues?q=is%3Aissue+is%3Aclosed+milestone%3A0.13.2

neo/rawio/spikeglxrawio.py

@@ -440,7 +440,7 @@ def parse_spikeglx_fname(fname):
         re_else = re.findall(r"(\S*)\.(\S*).(ap|lf)", fname)
         re_else_nidq = re.findall(r"(\S*)\.(\S*)", fname)
         if len(re_else) == 1:
-            run_name, device, stream_kind = re_else_nidq[0]
+            run_name, device, stream_kind = re_else[0]
             gate_num, trigger_num = None, None
         elif len(re_else_nidq) == 1:
             # easy case for nidaq, example: sglx_xxx.nidq

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "neo"
-version = "0.13.2.dev"
+version = "0.14.0dev"
 authors = [{name = "Neo authors and contributors"}]
 description = "Neo is a package for representing electrophysiology data in Python, together with support for reading a wide range of neurophysiology file formats"
 readme = "README.rst"