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commit 08e23a8
Author: pbouss <[email protected]>
Date:   Fri Dec 20 15:20:01 2019 +0100

    SPADE refactored if-else statements (NeuralEnsemble#285)

    Simplified code complexity by move if-else blocks here and there

commit fce24ad
Author: pbouss <[email protected]>
Date:   Tue Dec 17 12:23:00 2019 +0100

    Bug fixed while dealing with the units of the refr. period (NeuralEnsemble#283)

commit 8200eef
Author: pbouss <[email protected]>
Date:   Fri Dec 13 16:11:22 2019 +0100

    Feature/spade speed up (NeuralEnsemble#280)

    * Remove while loop, change mpi-use in pvalue spec

    * Use sparse representation of the BinnedSpikeTrain

    * refactored false discovery rate

    * reorganized errors for test_signature_significance

    * Implement filtering for pattern subsets

    when not performing pattern set reduction
    check for subset patterns trivially
    explained by longer patterns with the
    same n_occ due to the moving window

    * Adapt tests to new filtering proceidure

    * Always apply subset filtering

commit 160e8e2
Author: Danylo Ulianych <[email protected]>
Date:   Wed Dec 11 15:44:04 2019 +0100

    fixed bug in BinnedSpikeTrain.sparsity (NeuralEnsemble#281)

commit 0d44cd7
Author: Danylo Ulianych <[email protected]>
Date:   Thu Dec 5 10:25:48 2019 +0100

    unitary event decorate_deprecated_N refactoring (NeuralEnsemble#278)

commit b116804
Author: Danylo Ulianych <[email protected]>
Date:   Mon Nov 25 12:31:36 2019 +0100

    Fast covariance() and Pearson corrcoef() (NeuralEnsemble#274)

    clarified the difference in the implementation of CrossCorrHist.cross_corr_coef() and the reference book "Analysis of parallel spike trains", 2010

commit 59e6412
Author: pbouss <[email protected]>
Date:   Wed Nov 20 09:46:54 2019 +0100

    Feature/spade duration (NeuralEnsemble#263)

    * Corrected error message

    * Doc. for Holm-Bonferroni

    * Changed calculation of duration for output of patterns

    * fixed calculation of duration for the signature

    * Pass spectrum to concepts_to_output function

    * Bug fixed in vairable assignment: concept

commit de077d6
Author: Danylo Ulianych <[email protected]>
Date:   Tue Nov 19 16:17:52 2019 +0100

    Use fftconvolve instead of np.correlate in cross_correlation_histogram (NeuralEnsemble#273)

    * cch np.correlate -> fftconvolve

    * moved internal functions in cross_correlation_histogram to a separate class

    * added BinnedSpikeTrain.get_num_of_spikes() function

    * added BinnedSpikeTrain.binarize() function

commit 059ccf5
Author: pbouss <[email protected]>
Date:   Fri Nov 15 16:24:58 2019 +0100

    Homogeneous Poisson Process with refr. period (NeuralEnsemble#261)

commit f378f07
Author: Alexander van Meegen <[email protected]>
Date:   Tue Nov 12 10:23:29 2019 +0100

    Feature timescale (NeuralEnsemble#271)

    * Implementation of timescale calculation

    * Use cross_corr_coef of CCH function

    * Check that tau_max is an integer multiple of binsize

commit 82f307f
Author: Danylo Ulianych <[email protected]>
Date:   Mon Nov 11 11:09:44 2019 +0100

    fixed BinnedSpikeTrain.bin_edges property (NeuralEnsemble#257)

    * fixed BinnedSpikeTrain.bin_edges property

    * bin_edges: include t_stop if spiketrain duration is divisible by binsize

    * BinnedSpikeTrain: warn if binning discards the spikes in the last (excluded) bin

    * reuse is_binary func from utility.py

commit bd684f5
Author: Danylo Ulianych <[email protected]>
Date:   Mon Nov 11 10:14:34 2019 +0100

    Refactored unitary event (NeuralEnsemble#251)

    * completely removed misleading N arg - num. of neurons, which is always extracted from the data

    * fixed inverse_hash_from_pattern for long N > int64; added test_hash_inverse_longpattern

    * UE: deprecation warning

commit 2967dac
Author: Alexander van Meegen <[email protected]>
Date:   Fri Nov 8 16:38:27 2019 +0100

    Calculate spike train auto-correlation time ('timescale') (NeuralEnsemble#266)

    * Implementation of timescale calculation

commit 092d2fb
Author: Michael Denker <[email protected]>
Date:   Fri Nov 8 12:33:32 2019 +0100

    Added a simplified to correctly handle division with Compound Units (NeuralEnsemble#270)

    .magnitude -> .simplified.magnitude

commit 5dfa042
Author: Danylo Ulianych <[email protected]>
Date:   Thu Oct 31 15:54:30 2019 +0100

    elephant v0.6.4 [workshop] (NeuralEnsemble#268)

commit 5b5a023
Author: Danylo Ulianych <[email protected]>
Date:   Tue Oct 22 16:10:16 2019 +0200

    neo v0.8.0 compatible (NeuralEnsemble#256)

    * fixes for neo v0.8.0

    * upd array_annotation comment

    * added todo for neo empty array_annotations

commit eac914c
Author: PaulinaDabrowska <[email protected]>
Date:   Tue Oct 22 16:09:41 2019 +0200

    Improved doc string of covariance() and corrcoef() (NeuralEnsemble#260)

    * corrected explanation of the formula used in corrcoef and covariance (in the doc string)

    * pep8

commit 434cacd
Author: Robin Gutzen <[email protected]>
Date:   Mon Oct 21 13:56:38 2019 +0200

    keep array_annotations in the output of signal_processing functions (NeuralEnsemble#258)

    * pass array_annotations on to output of signal_processing functions

    * test keep array_annotations for zscore, butter, hilbert
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dizcza committed Jan 9, 2020
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1 change: 1 addition & 0 deletions MANIFEST.in
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Expand Up @@ -7,6 +7,7 @@ include elephant/current_source_density_src/README.md
include elephant/current_source_density_src/test_data.mat
include elephant/neural_trajectory_src/README.md
include elephant/spade_src/LICENCE
include elephant/gpfa_src/INFO.md
recursive-include elephant/spade_src *.so *.pyd
include elephant/test/spike_extraction_test_data.txt
recursive-include doc *
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2 changes: 2 additions & 0 deletions doc/authors.rst
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Expand Up @@ -37,6 +37,8 @@ contribution, and may not be the current affiliation of a contributor.
* Simon Essink [1]
* Alessandra Stella [1]
* Peter Bouss [1]
* Alexander van Meegen [1]
* Aitor Morales-Gregorio [1]

1. Institute of Neuroscience and Medicine (INM-6), Computational and Systems Neuroscience & Institute for Advanced Simulation (IAS-6), Theoretical Neuroscience, Jülich Research Centre and JARA, Jülich, Germany
2. Unité de Neurosciences, Information et Complexité, CNRS UPR 3293, Gif-sur-Yvette, France
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6 changes: 6 additions & 0 deletions doc/reference/gpfa.rst
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=========================================
`GPFA` - Gaussian-process factor analysis
=========================================

.. automodule:: elephant.gpfa
:members:
32 changes: 32 additions & 0 deletions doc/release_notes.rst
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Release Notes
*************

Elephant 0.6.4 release notes
============================

This release has been made for the "1st Elephant User Workshop" (https://www.humanbrainproject.eu/en/education/participatecollaborate/infrastructure-events-trainings/1st-elephant-user-workshop-accelerate-structured-and-reproducibl).


Main features
-------------
* neo v0.8.0 compatible


New modules
-----------
* GPFA - Gaussian-process factor analysis - dimensionality reduction method for neural trajectory visualization (https://github.com/NeuralEnsemble/elephant/pull/233). _Note: the API could change in the future._


Buf fixes
---------
* [signal processing] Keep `array_annotations` in the output of signal processing functions (https://github.com/NeuralEnsemble/elephant/pull/258).
* [SPADE] Fixed the calculation of the duration of a pattern in the output (https://github.com/NeuralEnsemble/elephant/pull/254).
* [statistics] Fixed automatic kernel selection yields incorrect values (https://github.com/NeuralEnsemble/elephant/pull/246).


Improvements
------------
* Vectorized `spike_time_tiling_coefficient()` function - got rid of a double for-loop (https://github.com/NeuralEnsemble/elephant/pull/244)
* Reduced the number of warnings during the tests (https://github.com/NeuralEnsemble/elephant/pull/238).
* Removed unused debug code in `spade/fast_fca.py` (https://github.com/NeuralEnsemble/elephant/pull/249).
* Improved doc string of `covariance()` and `corrcoef()` (https://github.com/NeuralEnsemble/elephant/pull/260).



Elephant 0.6.3 release notes
============================
July 22nd 2019
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2 changes: 1 addition & 1 deletion elephant/VERSION
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0.6.3
0.6.4
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