Merge branch 'master' into remove-setup.py

Author: zm711

.github/workflows/core-test.yml

@@ -26,13 +26,17 @@ jobs:
       matrix:
         os: ["ubuntu-latest", "windows-latest", "macos-latest"]
         python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
-        numpy-version: ['1.24.4', '1.25.1', '1.26.4', '2.0.2','2.1.3', '2.2.4']
+        numpy-version: ['1.24.4', '1.25.1', '1.26.4', '2.0.2','2.1.3', '2.2.4', '2.3.1']
         # 1.24: 3.11, 1.25: 3.11, 1.26: 3.12
         exclude:
            - python-version: '3.9'
              numpy-version: '2.1.3'
            - python-version: '3.9'
              numpy-version: '2.2.4'
+           - python-version: '3.9'
+             numpy-version: '2.3.1'
+           - python-version: '3.10'
+             numpy-version: '2.3.1'
            - python-version: '3.12'
              numpy-version: '1.24.4'
            - python-version: '3.12'

.github/workflows/io-test.yml

@@ -18,8 +18,13 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ['3.9', '3.12']
-        numpy-version: ['1.26', '2.0']
+        python-version: ['3.9', '3.13']
+        numpy-version: ['1.26', '2.3.1']
+        exclude:
+           - python-version: '3.9'
+             numpy-version: '2.3.1'
+           - python-version: '3.13'
+             numpy-version: '1.26'
     defaults:
       # by default run in bash mode (required for conda usage)
       run:

.github/workflows/plexon2-testing.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        os: [windows-latest, ubuntu-latest]
+        os:  [ubuntu-latest]
         python-version: ['3.9', '3.12']
         numpy-version: ['1.26', '2.0']
     defaults:

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": "2025-04-14",
-  "downloadUrl": "https://files.pythonhosted.org/packages/f1/81/618538a70b0a7db16a174da9a7b5e8aec65462ebcd8f1120cd41b583a8dd/neo-0.14.1.tar.gz",
+  "dateModified": "2025-07-08",
+  "downloadUrl": "https://files.pythonhosted.org/packages/0e/47/ebc266619ea7f1e8025ba057ab446c14423b1265ec9c6810fa3a3fb02de4/neo-0.14.2.tar.gz",
   "issueTracker": "https://github.com/NeuralEnsemble/python-neo/issues",
   "name": "Neo",
-  "version": "0.14.1",
+  "version": "0.14.2",
   "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/latest/releases/0.14.1.html",
+  "releaseNotes": "https://neo.readthedocs.io/en/latest/releases/0.14.2.html",
   "funding": "https://cordis.europa.eu/project/id/945539",
   "developmentStatus": "active",
   "referencePublication": "https://doi.org/10.3389/fninf.2014.00010",
@@ -118,6 +118,9 @@
     {"@type": "Person", "givenName": "Tommaso", "familyName": "Lambresa"},
     {"@type": "Person", "givenName": "Rémi", "familyName": "Proville"},
     {"@type": "Person", "givenName": "Nina", "familyName": "Kudryashova"},
-    {"@type": "Person", "givenName": "Paul", "familyName": "Adkisson"}
+    {"@type": "Person", "givenName": "Paul", "familyName": "Adkisson"},
+    {"@type": "Person", "givenName": "Akshaj", "familyName": "Verma"},
+    {"@type": "Person", "givenName": "Letizia", "familyName": "Signorelli"},
+    {"@type": "Person", "givenName": "Daniel", "familyName": "Parthier"}
   ]
 }

doc/source/releases/0.14.1.rst

@@ -38,7 +38,7 @@ Bug fixes and improvements in IO modules
 ----------------------------------------
 
 Bug fixes and/or improvements have been made to :code:`BlackRockIO`, :code:`SpikeGLXIO`, :code:`MaxwellIO`, :code:`IntanIO`, :code:`TdtIO`,
-:code:`OpenEphysBinaryIO`, :code:`NeoMatlabIO`, :code:`EdfIO`, :code:`Neuralynx`, and :code:`SpikeGadgetsIO`.
+:code:`OpenEphysBinaryIO`, :code:`NeoMatlabIO`, :code:`EdfIO`, :code:`NeuralynxIO`, and :code:`SpikeGadgetsIO`.
 
 
 Acknowledgements

doc/source/releases/0.14.2.rst

@@ -0,0 +1,51 @@
+========================
+Neo 0.14.2 release notes
+========================
+
+08 July 25
+
+This release of Neo includes many bug fixes in various IOs, continued work on our CI, and official adoption of the NumFocus Code of Conduct with an eye to a 1.0 release.
+
+See all `pull requests`_ included in this release and the `list of closed issues`_.
+
+
+Code of Conduct 
+---------------
+
+As a NumFocus affiliated project, Neo has officially adopted the `NumFocus Code of Conduct`_. Please see `CODE_OF_CONDUCT.md`_ for 
+more information.
+
+
+CI Changes
+----------
+
+We have transitioned IO testing to Python 3.9 and Python 3.13.
+
+We have also added NumPy 2.3.1 to our core testing matrix.
+
+We fixed our installation of datalad and git-annex.
+
+We changed our :code:`Plexon2IO` tests to be a cron job as conda-wine-plexon2 behavior was leading to flaky test results.
+We hope to track the root of these issues and eventually transition :code:`Plexon2IO` back to main testing.
+
+
+Bug fixes and improvements in IO modules
+----------------------------------------
+
+Bug fixes and/or improvements have been made to :code:`BlackRockIO`, :code:`SpikeGLXIO`, :code:`MaxwellIO`, :code:`NeuralynxIO`, :code:`WinwcprIO`, and :code:`AxonaIO`.
+
+
+Acknowledgements
+----------------
+
+Thanks to Zach McKenzie, Andrew Davison, Luiz Tauffer, Heberto Mayorquin, Julia Sprenger, Daniel Parthier, Philipp Hornauer, Letizia Signorelli, and Akshaj Verma.
+
+
+
+.. _`NumFocus Code of Conduct`: https://numfocus.org/code-of-conduct
+
+.. _`CODE_OF_CONDUCT.md` : https://github.com/NeuralEnsemble/python-neo/blob/master/CODE_OF_CONDUCT.md
+
+.. _`pull requests` : https://github.com/NeuralEnsemble/python-neo/pulls?q=is%3Apr+is%3Aclosed+milestone%3A0.14.2
+
+.. _`list of closed issues` : https://github.com/NeuralEnsemble/python-neo/issues?q=is%3Aissue%20state%3Aclosed%20milestone%3A0.14.2