First release candidate for Neo 0.9.0

Author: apdavison

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2010-2019, Neo authors and contributors
+Copyright (c) 2010-2020, 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

@@ -13,7 +13,7 @@ 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.
 
-Neo is used by a number of other software tools, including 
+Neo 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).
@@ -56,7 +56,7 @@ For installation instructions, see doc/source/install.rst
 
 To cite Neo in publications, see CITATION.txt
 
-:copyright: Copyright 2010-2019 by the Neo team, see doc/source/authors.rst.
+:copyright: Copyright 2010-2020 by the Neo team, see doc/source/authors.rst.
 :license: 3-Clause Revised BSD License, see LICENSE.txt for details.
 
 Funding
@@ -66,7 +66,7 @@ Development of PyNN has been partially funded by the European Union Sixth Framew
 grant agreement FETPI-015879 (FACETS), by the European Union Seventh Framework Program (FP7/2007­-2013)
 under grant agreements no. 269921 (BrainScaleS) and no. 604102 (HBP),
 and by the European Union’s Horizon 2020 Framework Programme for
-Research and Innovation under the Specific Grant Agreements No. 720270 (Human Brain Project SGA1), 
+Research and Innovation under the Specific Grant Agreements No. 720270 (Human Brain Project SGA1),
 No. 785907 (Human Brain Project SGA2) and No. 945539 (Human Brain Project SGA3).
 
 .. _OpenElectrophy: https://github.com/OpenElectrophy/OpenElectrophy

doc/source/conf.py

@@ -51,7 +51,7 @@
 
 # General information about the project.
 project = 'Neo'
-copyright = '2010-2019, ' + AUTHORS
+copyright = '2010-2020, ' + 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

doc/source/core.rst

@@ -64,6 +64,8 @@ cut across the simple container hierarchy.
     are three subclasses that link :class:`ImageSequence` objects to signals (:class:`AnalogSignal` objects)
     extracted from them.
 
+For more details, see :doc:`grouping`.
+
 
 NumPy compatibility
 ===================

doc/source/grouping.rst

@@ -3,14 +3,22 @@ Grouping and linking data
 *************************
 
 
-... to do
-
-
+Migrating from ChannelIndex/Unit to ChannelView/Group
+=====================================================
 
+While the basic hierarchical :class:`Block` - :class:`Segment` structure of Neo has remained
+unchanged since the inception of Neo, the structures used to cross-link objects
+(for example to link a signal to the spike trains derived from it) have undergone changes,
+in an effort to find an easily understandable and usable approach.
 
-Migrating from ChannelIndex/Unit to ChannelView/Group
-==============================================
+Below we give some examples of how to migrate from :class:`ChannelIndex` and :class:`Unit`,
+as used in Neo 0.8, to the new classes :class:`Group` and :class:`ChannelView`
+introduced in Neo 0.9.
+Note that Neo 0.9 supports the new and old API in parallel, to facilitate migration.
+IO classes in Neo 0.9 can read :class:`ChannelIndex` and :class:`Unit` objects,
+but do not write them.
 
+:class:`ChannelIndex` and :class:`Unit` will be removed in Neo 0.10.0.
 
 Examples
 --------

doc/source/releases/0.9.0.rst

@@ -2,13 +2,35 @@
 Neo 0.9.0 release notes
 =======================
 
-[TODO] th October 2020
+10th November 2020
 
 
 Group and ChannelView replace Unit and ChannelIndex
 ---------------------------------------------------
 
+Experience with :class:`ChannelIndex` and :class:`Unit` has shown that these classes are
+often confusing and difficult to understand.
+In particular, :class:`ChannelIndex` was trying to provide three different functionalities in a
+single object:
 
+- providing information about individual traces within :class:`AnalogSignals` like the channel id and the channel name (labelling)
+- grouping a subset of traces within an :class:`AnalogSignal` via the ``index`` attribute (masking)
+- linking between / grouping :class:`AnalogSignals` (grouping)
+
+while grouping :class:`SpikeTrains` required a different class, :class:`Unit`.
+For more pointers to the difficulties this created, and some of the limitations of this approach,
+see `this Github issue`_.
+
+With the aim of making the three functionalities of labelling, masking and grouping
+both easier to use and more flexible, we have replaced :class:`ChannelIndex` and :class:`Unit`
+with:
+
+- array annotations (*labelling*) - already available since Neo 0.8
+- :class:`~neo.core.ChannelView` (*masking*) - defines subsets of channels within an `AnalogSignal` using a mask
+- :class:`~neo.core.Group`  (*grouping*) - allows any Neo object except :class`Segment` and :class:`Block` to be grouped
+
+For some guidance on migrating from :class:`ChannelIndex`/:class:`Unit`
+to :class:`Group` and :class:`ChannelView` see :doc:`../grouping`.
 
 Python 3 only
 -------------
@@ -35,7 +57,10 @@ 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.
+    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`_.
 
@@ -46,16 +71,19 @@ Bug fixes and improvements in IO modules
   * 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
 ----------------
 
 Thanks to Julia Sprenger, Samuel Garcia, Andrew Davison, Alexander Kleinjohann, Hugo van Kemenade,
- Achilleas Koutsou, Jeffrey Gill, Corentin Fragnaud, Aitor Morales-Gregorio, Rémi Proville,
- Robin Gutzen, Marin Manuel, Simon Danner, Michael Denker, Peter N. Steinmetz, Diziet Asahi and
- Lucien Krapp for their contributions to this release.
+Achilleas Koutsou, Jeffrey Gill, Corentin Fragnaud, Aitor Morales-Gregorio, Rémi Proville,
+Robin Gutzen, Marin Manuel, Simon Danner, Michael Denker, Peter N. Steinmetz, Diziet Asahi and
+Lucien Krapp for their contributions to this release.
 
 .. _`list of closed issues`: https://github.com/NeuralEnsemble/python-neo/issues?q=is%3Aissue+milestone%3A0.9.0+is%3Aclosed
 .. _`pull requests`: https://github.com/NeuralEnsemble/python-neo/pulls?q=is%3Apr+is%3Aclosed+merged%3A%3E2019-09-30+milestone%3A0.9.0
 .. _NEP29: https://numpy.org/neps/nep-0029-deprecation_policy.html
 .. _`discussed here`: https://github.com/NeuralEnsemble/python-neo/issues/788
+.. _`this Github issue`: https://github.com/NeuralEnsemble/python-neo/issues/456

neo/core/view.py

@@ -14,7 +14,7 @@
 class ChannelView(BaseNeo):
     """
     A tool for indexing a subset of the channels within an :class:`AnalogSignal`
-    or :class:`IrregularlySampledSignal`\\s;
+    or :class:`IrregularlySampledSignal`;
 
     *Required attributes/properties*:
         :obj: (AnalogSignal or IrregularlySampledSignal) The signal being indexed.

neo/version.py

@@ -1 +1 @@
-version = '0.9.0.dev'
+version = '0.9.0.rc0'