From 9a50b72e914978b360f23d0b3874488090103a5a Mon Sep 17 00:00:00 2001 From: Alessio Buccino Date: Wed, 24 Jun 2026 09:47:21 +0200 Subject: [PATCH 1/5] prepare 0.14.5 release --- codemeta.json | 13 +++++++----- doc/source/authors.rst | 4 ++++ doc/source/releases.rst | 1 + doc/source/releases/0.14.5.rst | 37 ++++++++++++++++++++++++++++++++++ pyproject.toml | 2 +- 5 files changed, 51 insertions(+), 6 deletions(-) create mode 100644 doc/source/releases/0.14.5.rst diff --git a/codemeta.json b/codemeta.json index c06edcb97..ad8b76e53 100644 --- a/codemeta.json +++ b/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": "2026-03-12", - "downloadUrl": "https://files.pythonhosted.org/packages/7f/b1/e9228d616c817098b673ab990e82acb431856559f4e0235a687854df1ef4/neo-0.14.4.tar.gz", + "dateModified": "2026-06-23", + "downloadUrl": "https://files.pythonhosted.org/packages/neo-0.14.5.tar.gz", "issueTracker": "https://github.com/NeuralEnsemble/python-neo/issues", "name": "Neo", - "version": "0.14.4", + "version": "0.14.5", "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/0.14.4.html", + "releaseNotes": "https://neo.readthedocs.io/en/latest/releases/0.14.5.html", "funding": "https://cordis.europa.eu/project/id/945539", "developmentStatus": "active", "referencePublication": "https://doi.org/10.3389/fninf.2014.00010", @@ -122,6 +122,9 @@ {"@type": "Person", "givenName": "Akshaj", "familyName": "Verma"}, {"@type": "Person", "givenName": "Letizia", "familyName": "Signorelli"}, {"@type": "Person", "givenName": "Daniel", "familyName": "Parthier"}, - {"@type": "Person", "givenName": "Kuntal", "familyName": "Kokate"} + {"@type": "Person", "givenName": "Kuntal", "familyName": "Kokate"}, + { "@type": "Person", "alternateName": "LizzyMcKay@github" }, + { "@type": "Person", "givenName": "Reema", "familyName": "Gupta" }, + { "@type": "Person", "givenName": "Sai Asish", "familyName": "Y" } ] } diff --git a/doc/source/authors.rst b/doc/source/authors.rst index 0f40f2df7..a7331e688 100644 --- a/doc/source/authors.rst +++ b/doc/source/authors.rst @@ -99,6 +99,9 @@ and may not be the current affiliation of a contributor. * Letizia Signorelli [47] * Daniel Parthier [48] * Kuntal Kokate [49] +* LizzyMcKay (github) +* Reema Gupta [50] +* Sai Asish Y 1. Centre de Recherche en Neuroscience de Lyon, CNRS UMR5292 - INSERM U1028 - Université Claude Bernard Lyon 1 2. Unité de Neuroscience, Information et Complexité, CNRS UPR 3293, Gif-sur-Yvette, France @@ -149,6 +152,7 @@ and may not be the current affiliation of a contributor. 47. Centre for Molecular Medicine Norway (NCMM), University of Oslo, Norway 48. Charité - Universitätmedizin Berlin, Freie Universität Berlin and Humboldt Universität zu Berlin 49. Swartz Center for Computational Neuroscience, University of California, San Diego +50. Ludwig-Maximilians-Universität München, Munich, Germany diff --git a/doc/source/releases.rst b/doc/source/releases.rst index a9df0c50a..3b775c50f 100644 --- a/doc/source/releases.rst +++ b/doc/source/releases.rst @@ -6,6 +6,7 @@ Release notes .. toctree:: :maxdepth: 1 + releases/0.14.5.rst releases/0.14.4.rst releases/0.14.3.rst releases/0.14.2.rst diff --git a/doc/source/releases/0.14.5.rst b/doc/source/releases/0.14.5.rst new file mode 100644 index 000000000..df31ea33d --- /dev/null +++ b/doc/source/releases/0.14.5.rst @@ -0,0 +1,37 @@ +======================== +Neo 0.14.5 release notes +======================== + +23 June 2026 + +This release of Neo includes many bug fixes across various IOs, removal of previously deprecated features, and improvements to the SpikeGLX Neuropixels probe detection infrastructure. + +See all `pull requests`_ included in this release and the `list of closed issues`_. + + +Removed deprecated features +---------------------------- + +The ``load_sync_channel`` parameter has been removed from :code:`SpikeGLXRawIO` and :code:`OpenEphysBinaryRawIO`, as it was deprecated in a prior release. + + +Bug fixes and improvements in IO modules +----------------------------------------- + +Bug fixes and/or improvements have been made to :code:`AxonaIO`, :code:`BlackrockIO`, :code:`IntanRawIO`, :code:`OpenEphysBinaryIO`, :code:`SpikeGadgetsRawIO`, :code:`SpikeGLXIO`, and :code:`TdtIO`. + + +SpikeGLX improvements +~~~~~~~~~~~~~~~~~~~~~~ + +:code:`SpikeGLXIO` now uses a ProbeTable to infer the Neuropixels probe type, replacing hardcoded probe type detection. A GitHub Action was added to automatically keep the probe features table up-to-date from the upstream ProbeTable. Additionally, a missing ``firstSample`` field in SpikeGLX meta files now defaults to 0, and the stream-collision error message has been improved. + + +Acknowledgements +---------------- + +Thanks to Alessio Buccino, Andrew Davison, Heberto Mayorquin, LizzyMcKay, Michael Denker, Reema Gupta, Sai Asish Y, and Zach McKenzie. + +.. _`pull requests` : https://github.com/NeuralEnsemble/python-neo/pulls?q=is%3Apr+is%3Aclosed+milestone%3A0.14.5 + +.. _`list of closed issues` : https://github.com/NeuralEnsemble/python-neo/issues?q=is%3Aissue%20state%3Aclosed%20milestone%3A0.14.5 diff --git a/pyproject.toml b/pyproject.toml index d2a7df309..5223256b3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "neo" -version = "0.15.0dev" +version = "0.14.5" 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" From b557fa12311cf47b7ae2a72fec2befcab17f7a1f Mon Sep 17 00:00:00 2001 From: Alessio Buccino Date: Wed, 24 Jun 2026 09:57:57 +0200 Subject: [PATCH 2/5] minor fixes --- codemeta.json | 8 ++++---- doc/source/releases/0.14.5.rst | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/codemeta.json b/codemeta.json index ad8b76e53..921e85dac 100644 --- a/codemeta.json +++ b/codemeta.json @@ -4,8 +4,8 @@ "license": "https://spdx.org/licenses/BSD-3-Clause", "codeRepository": "https://github.com/NeuralEnsemble/python-neo", "contIntegration": "https://github.com/NeuralEnsemble/python-neo/actions", - "dateModified": "2026-06-23", - "downloadUrl": "https://files.pythonhosted.org/packages/neo-0.14.5.tar.gz", + "dateModified": "2026-06-24", + "downloadUrl": "", "issueTracker": "https://github.com/NeuralEnsemble/python-neo/issues", "name": "Neo", "version": "0.14.5", @@ -123,8 +123,8 @@ {"@type": "Person", "givenName": "Letizia", "familyName": "Signorelli"}, {"@type": "Person", "givenName": "Daniel", "familyName": "Parthier"}, {"@type": "Person", "givenName": "Kuntal", "familyName": "Kokate"}, - { "@type": "Person", "alternateName": "LizzyMcKay@github" }, { "@type": "Person", "givenName": "Reema", "familyName": "Gupta" }, - { "@type": "Person", "givenName": "Sai Asish", "familyName": "Y" } + { "@type": "Person", "givenName": "Sai Asish", "familyName": "Yamani" }, + { "@type": "Person", "alternateName": "LizzyMcKay@github" } ] } diff --git a/doc/source/releases/0.14.5.rst b/doc/source/releases/0.14.5.rst index df31ea33d..76617cdb8 100644 --- a/doc/source/releases/0.14.5.rst +++ b/doc/source/releases/0.14.5.rst @@ -30,7 +30,7 @@ SpikeGLX improvements Acknowledgements ---------------- -Thanks to Alessio Buccino, Andrew Davison, Heberto Mayorquin, LizzyMcKay, Michael Denker, Reema Gupta, Sai Asish Y, and Zach McKenzie. +Thanks to Alessio Buccino, Andrew Davison, Heberto Mayorquin, LizzyMcKay, Michael Denker, Reema Gupta, Sai Asish Yamani, and Zach McKenzie. .. _`pull requests` : https://github.com/NeuralEnsemble/python-neo/pulls?q=is%3Apr+is%3Aclosed+milestone%3A0.14.5 From 99b4f60d98465afce5094726b76f9fc13f679a48 Mon Sep 17 00:00:00 2001 From: Alessio Buccino Date: Thu, 25 Jun 2026 11:00:56 +0200 Subject: [PATCH 3/5] update release ntoes --- doc/source/releases/0.14.5.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/source/releases/0.14.5.rst b/doc/source/releases/0.14.5.rst index 76617cdb8..7da656cd8 100644 --- a/doc/source/releases/0.14.5.rst +++ b/doc/source/releases/0.14.5.rst @@ -2,7 +2,7 @@ Neo 0.14.5 release notes ======================== -23 June 2026 +25 June 2026 This release of Neo includes many bug fixes across various IOs, removal of previously deprecated features, and improvements to the SpikeGLX Neuropixels probe detection infrastructure. @@ -18,7 +18,7 @@ The ``load_sync_channel`` parameter has been removed from :code:`SpikeGLXRawIO` Bug fixes and improvements in IO modules ----------------------------------------- -Bug fixes and/or improvements have been made to :code:`AxonaIO`, :code:`BlackrockIO`, :code:`IntanRawIO`, :code:`OpenEphysBinaryIO`, :code:`SpikeGadgetsRawIO`, :code:`SpikeGLXIO`, and :code:`TdtIO`. +Bug fixes and/or improvements have been made to :code:`AxonaIO`, :code:`IntanRawIO`, :code:`OpenEphysBinaryIO`, :code:`SpikeGadgetsRawIO`, and :code:`SpikeGLXIO`. SpikeGLX improvements From 6a351c81ae6904fc084cd25521a33704a68b826a Mon Sep 17 00:00:00 2001 From: Alessio Buccino Date: Thu, 25 Jun 2026 11:02:12 +0200 Subject: [PATCH 4/5] add affiliation --- doc/source/authors.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/source/authors.rst b/doc/source/authors.rst index a7331e688..c4065ac6c 100644 --- a/doc/source/authors.rst +++ b/doc/source/authors.rst @@ -101,7 +101,7 @@ and may not be the current affiliation of a contributor. * Kuntal Kokate [49] * LizzyMcKay (github) * Reema Gupta [50] -* Sai Asish Y +* Sai Asish Yamani [51] 1. Centre de Recherche en Neuroscience de Lyon, CNRS UMR5292 - INSERM U1028 - Université Claude Bernard Lyon 1 2. Unité de Neuroscience, Information et Complexité, CNRS UPR 3293, Gif-sur-Yvette, France @@ -153,6 +153,7 @@ and may not be the current affiliation of a contributor. 48. Charité - Universitätmedizin Berlin, Freie Universität Berlin and Humboldt Universität zu Berlin 49. Swartz Center for Computational Neuroscience, University of California, San Diego 50. Ludwig-Maximilians-Universität München, Munich, Germany +51. Stony Brook University, Stony Brook, NY, USA From 829f76ef27a6f493f4034ac154729e78d4fe17d0 Mon Sep 17 00:00:00 2001 From: Alessio Buccino Date: Thu, 25 Jun 2026 11:02:47 +0200 Subject: [PATCH 5/5] fix date in codemeta --- codemeta.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/codemeta.json b/codemeta.json index 921e85dac..f1340f9fb 100644 --- a/codemeta.json +++ b/codemeta.json @@ -4,7 +4,7 @@ "license": "https://spdx.org/licenses/BSD-3-Clause", "codeRepository": "https://github.com/NeuralEnsemble/python-neo", "contIntegration": "https://github.com/NeuralEnsemble/python-neo/actions", - "dateModified": "2026-06-24", + "dateModified": "2026-06-25", "downloadUrl": "", "issueTracker": "https://github.com/NeuralEnsemble/python-neo/issues", "name": "Neo",