Merge pull request #1015 from NeuralEnsemble/release-notes-0.10

Release notes for v0.10.0
NeuralEnsemble · Jul 27, 2021 · aec6832 · aec6832
2 parents a807ce8 + ec7fc1d
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diff --git a/.travis.yml b/.travis.yml
@@ -4,26 +4,34 @@ sudo: false
 
 matrix:
   include:
-    - python: "3.6"
-      env: NUMPY_VERSION="1.14.6"
-    - python: "3.6"
-      env: NUMPY_VERSION="1.18.3"
     - python: "3.7"
-      env: NUMPY_VERSION="1.14.6"
+      env: NUMPY_VERSION="1.16.6"
     - python: "3.7"
-      env: NUMPY_VERSION="1.19.2"
-    - python: "3.8"
-      env: NUMPY_VERSION="1.14.6"
-    - python: "3.8"
-      env: NUMPY_VERSION="1.15.4"
+      env: NUMPY_VERSION="1.21.0"
     - python: "3.8"
       env: NUMPY_VERSION="1.16.6"
     - python: "3.8"
       env: NUMPY_VERSION="1.17.5"
     - python: "3.8"
       env: NUMPY_VERSION="1.18.5"
     - python: "3.8"
-      env: NUMPY_VERSION="1.19.2"
+      env: NUMPY_VERSION="1.19.5"
+    - python: "3.8"
+      env: NUMPY_VERSION="1.20.3"
+    - python: "3.8"
+      env: NUMPY_VERSION="1.21.0"
+    - python: "3.9"
+      env: NUMPY_VERSION="1.16.6"
+    - python: "3.9"
+      env: NUMPY_VERSION="1.17.5"
+    - python: "3.9"
+      env: NUMPY_VERSION="1.18.5"
+    - python: "3.9"
+      env: NUMPY_VERSION="1.19.5"
+    - python: "3.9"
+      env: NUMPY_VERSION="1.20.3"
+    - python: "3.9"
+      env: NUMPY_VERSION="1.21.0"
 
 # command to install dependencies
 before_install:

diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,4 +1,4 @@
-Copyright (c) 2010-2020, Neo authors and contributors
+Copyright (c) 2010-2021, 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:

diff --git a/README.rst b/README.rst
@@ -53,7 +53,7 @@ For installation instructions, see doc/source/install.rst
 
 To cite Neo in publications, see CITATION.txt
 
-:copyright: Copyright 2010-2020 by the Neo team, see doc/source/authors.rst.
+:copyright: Copyright 2010-2021 by the Neo team, see doc/source/authors.rst.
 :license: 3-Clause Revised BSD License, see LICENSE.txt for details.
 
 Funding

diff --git a/doc/source/authors.rst b/doc/source/authors.rst
@@ -24,10 +24,10 @@ and may not be the current affiliation of a contributor.
 * Erik Li [9]
 * Georg Raiser [10]
 * Joffrey Gonin [2]
-* Kyler Brown [?]
+* Kyler Brown
 * Mikkel Elle Lepperød [11]
 * C Daniel Meliza [12]
-* Julia Sprenger [13]
+* Julia Sprenger [13, 6]
 * Maximilian Schmidt [13]
 * Johanna Senk [13]
 * Carlos Canova [13]
@@ -57,6 +57,9 @@ and may not be the current affiliation of a contributor.
 * Alessio Buccino [23]
 * Regimantas Jurkus [13]
 * Steffen Buergers [24]
+* Etienne Combrisson [6]
+* Ben Dichter [24]
+* Elodie Legouée [21]
 
 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

diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -51,7 +51,7 @@
 
 # General information about the project.
 project = 'Neo'
-copyright = '2010-2020, ' + AUTHORS
+copyright = '2010-2021, ' + 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

diff --git a/doc/source/install.rst b/doc/source/install.rst
@@ -11,8 +11,8 @@ Installing from the Python Package Index
 Dependencies
 ------------
 
-    * Python_ >= 3.6
-    * numpy_ >= 1.13.0
+    * Python_ >= 3.7
+    * numpy_ >= 1.16.1
     * quantities_ >= 0.12.1
 
 You can install the latest published version of Neo and its dependencies using::

diff --git a/doc/source/releases/0.10.0.rst b/doc/source/releases/0.10.0.rst
@@ -0,0 +1,72 @@
+========================
+Neo 0.10.0 release notes
+========================
+
+27th July 2021
+
+
+New IO modules
+--------------
+
+.. currentmodule:: neo.io
+
+* :class:`CedIO` - an alternative to :class:`Spike2IO`
+* :class:`AxonaIO`
+* :class:`OpenEphysIO` - handle the binary format
+* :class:`PhyIO`
+* :class:`SpikeGLXIO`
+* :class:`NWBIO` - support for a subset of the `NWB:N`_ format
+* :class:`MaxwellIO`
+
+
+Bug fixes and improvements in IO modules
+----------------------------------------
+
+* :class:`NeuralynxIO` was refactored and now supports new file versions (neuraview) and single file loading.
+* Legacy versions of old IOs were removed for NeuralynxIO (neuralynxio_v1), BlackrockIO, NeoHdf5IO.
+* :class:`NixIOfr` now supports array annotations of :class:`AnalogSignal` objects.
+* :class:`NSDFIO` was removed because we can no longer maintain it.
+* all IOs now accept :class:`pathlib.Path` objects.
+* The IO modules of this release have been tested with version 0.1.0 of the `ephy_testing_data`_.
+
+
+Removal of Unit and ChannelIndex
+--------------------------------
+
+.. currentmodule:: neo.core
+
+In version 0.9.0 :class:`Group` and :class:`ChannelView` were introduced, replacing :class:`Unit` and :class:`ChannelIndex`, which were deprecated.
+In this version the deprecated :class:`Unit` and :class:`ChannelIndex` are removed and only the new :class:`Group` and :class:`ChannelView` objects are available.
+
+Supported Python and NumPy versions
+-----------------------------------
+
+We no longer support Python 3.6, nor versions of NumPy older than 1.16.
+
+Other new or modified features
+------------------------------
+
+* Lists of :class:`SpikeTrain` objects can now also be created from two arrays: one containing spike times
+  and the other unit identities of the times (:class:`SpikeTrainList`).
+* Object identity is now preserved when using utility :func:`time_slice()` methods.
+
+See all `pull requests`_ included in this release and the `list of closed issues`_.
+
+RawIO modules
+-------------
+
+Internal refactoring of the neo.rawio module regarding channel grouping.
+Now the concept of a signal stream is used to handle channel groups for signals.
+This enhances the way the :attr:`annotation` and :attr:`array_annotation` attributes are rendered at neo.io level.
+
+Acknowledgements
+----------------
+
+Thanks to Samuel Garcia, Julia Sprenger, Peter N. Steinmetz, Andrew Davison, Steffen Bürgers,
+Regimantas Jurkus, Alessio Buccino,  Shashwat Sridhar, Jeffrey Gill, Etienne Combrisson,
+Ben Dichter and Elodie Legouée for their contributions to this release.
+
+.. _`list of closed issues`: https://github.com/NeuralEnsemble/python-neo/issues?q=is%3Aissue+milestone%3A0.10.0+is%3Aclosed
+.. _`pull requests`: https://github.com/NeuralEnsemble/python-neo/pulls?q=is%3Apr+is%3Aclosed+merged%3A%3E2020-11-10+milestone%3A0.10.0
+.. _`ephy_testing_data`: https://gin.g-node.org/NeuralEnsemble/ephy_testing_data/src/v0.1.0
+.. _`NWB:N`: https://www.nwb.org/nwb-neurophysiology/
diff --git a/doc/source/releases/0.8.0.rst b/doc/source/releases/0.8.0.rst
@@ -70,25 +70,25 @@ returning an :class:`AnalogSignal` object::
 Other new features
 ------------------
 
-  * new neo.utils module
-  * Numpy 1.16+ compatibility
-  * :meth:`time_shift()` method for :class:`Epoch`/:class:`Event`/:class:`AnalogSignal`
-  * :meth:`time_slice()` method is now more robust
-  * dropped support for Python 3.4
+* new neo.utils module
+* Numpy 1.16+ compatibility
+* :meth:`time_shift()` method for :class:`Epoch`/:class:`Event`/:class:`AnalogSignal`
+* :meth:`time_slice()` method is now more robust
+* dropped support for Python 3.4
 
 See all `pull requests`_ included in this release and the `list of closed issues`_.
 
 Bug fixes and improvements in IO modules
 ----------------------------------------
 
-  * Blackrock
-  * Neuroshare
-  * NixIOFr
-  * NixIO (array annotation + 1d coordinates)
-  * AsciiSignal (fix + json metadata + IrregularlySampledSignals + write proxy)
-  * Spike2 (group same sampling rate)
-  * Brainvision
-  * NeuralynxIO
+* Blackrock
+* Neuroshare
+* NixIOFr
+* NixIO (array annotation + 1d coordinates)
+* AsciiSignal (fix + json metadata + IrregularlySampledSignals + write proxy)
+* Spike2 (group same sampling rate)
+* Brainvision
+* NeuralynxIO
 
 .. Warning:: Some IOs (based on rawio) when loading can choose to split each
     channel into its own 1-channel :class:`AnalogSignal` or to group them

diff --git a/doc/source/releases/0.9.0.rst b/doc/source/releases/0.9.0.rst
@@ -54,24 +54,24 @@ To get the "multiple single-channel signals" behaviour, use::
 Other new or modified features
 ------------------------------
 
-  * added methods :func:`rectify()`, :func:`downsample` and :func:`resample` to :class:`AnalogSignal`
-  * :func:`SpikeTrain.merge()` can now merge multiple spiketrains
-  * the utility function :func:`cut_block_by_epochs()` gives a new :class:`Block` now
-    rather than modifying the block in place
-  * some missing properties such as ``t_start`` were added to :class:`ImageSequence`,
-    and ``sampling_period`` was renamed to ``frame_duration``
-  * :func:`AnalogSignal.time_index()` now accepts arrays of times, not just a scalar.
+* added methods :func:`rectify()`, :func:`downsample` and :func:`resample` to :class:`AnalogSignal`
+* :func:`SpikeTrain.merge()` can now merge multiple spiketrains
+* the utility function :func:`cut_block_by_epochs()` gives a new :class:`Block` now
+  rather than modifying the block in place
+* some missing properties such as ``t_start`` were added to :class:`ImageSequence`,
+  and ``sampling_period`` was renamed to ``frame_duration``
+* :func:`AnalogSignal.time_index()` now accepts arrays of times, not just a scalar.
 
 See all `pull requests`_ included in this release and the `list of closed issues`_.
 
 Bug fixes and improvements in IO modules
 ----------------------------------------
 
-  * NeoMatlabIO (support for signal annotations)
-  * NeuralynxIO (fix handling of empty .nev files)
-  * AxonIO (support EDR3 header, fix channel events bug)
-  * Spike2IO (fix rounding problem, fix for v9 SON files)
-  * MicromedIO (fix label encoding)
+* NeoMatlabIO (support for signal annotations)
+* NeuralynxIO (fix handling of empty .nev files)
+* AxonIO (support EDR3 header, fix channel events bug)
+* Spike2IO (fix rounding problem, fix for v9 SON files)
+* MicromedIO (fix label encoding)
 
 
 Acknowledgements

diff --git a/doc/source/whatisnew.rst b/doc/source/whatisnew.rst
@@ -6,6 +6,7 @@ Release notes
 .. toctree::
    :maxdepth: 1
 
+   releases/0.10.0.rst
    releases/0.9.0.rst
    releases/0.8.0.rst
    releases/0.7.2.rst

diff --git a/neo/version.py b/neo/version.py
@@ -1 +1 @@
-version = '0.9.0'
+version = '0.10.0'
diff --git a/requirements.txt b/requirements.txt
@@ -1,2 +1,2 @@
-numpy>=1.13.0,!=1.16.0
+numpy>=1.16.1
 quantities>=0.12.1
diff --git a/setup.py b/setup.py
@@ -4,13 +4,13 @@
 import os
 
 long_description = open("README.rst").read()
-install_requires = ['numpy>=1.13.0,!=1.16.0',
+install_requires = ['numpy>=1.16.1',
                     'quantities>=0.12.1']
 extras_require = {
     'igorproio': ['igor'],
     'kwikio': ['scipy', 'klusta'],
     'neomatlabio': ['scipy>=1.0.0'],
-    'nixio': ['nixio>=1.5.0b2'],
+    'nixio': ['nixio>=1.5.0'],
     'stimfitio': ['stfio'],
     'tiffio': ['pillow']
 }
@@ -34,17 +34,17 @@
     long_description=long_description,
     license="BSD-3-Clause",
     url='https://neuralensemble.org/neo',
-    python_requires=">=3.6",
+    python_requires=">=3.7",
     classifiers=[
         'Development Status :: 4 - Beta',
         'Intended Audience :: Science/Research',
         'License :: OSI Approved :: BSD License',
         'Natural Language :: English',
         'Operating System :: OS Independent',
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3 :: Only',
         'Topic :: Scientific/Engineering']
 )