BranchBroxy · BranchBroxy · Sep 15, 2020 · Jun 22, 2020 · Jun 30, 2020 · Jul 27, 2020
diff --git a/.gitignore b/.gitignore
@@ -44,10 +44,9 @@ lib
 lib64
 # sphinx build directory
 doc/_build
-doc/reference/toctree/asset/elephant.asset.synchronous*
-doc/reference/toctree/parallel
-doc/reference/toctree/statistics
-doc/reference/toctree/unitary_event_analysis
+doc/reference/toctree/*
+!doc/reference/toctree/asset/elephant.asset.ASSET.rst
+!doc/reference/toctree/kernels
 *.h5
 # setup.py dist directory
 dist

diff --git a/.travis.yml b/.travis.yml
@@ -12,6 +12,7 @@ matrix:
     - name: "conda 2.7"
       python: 2.7
       env: DISTRIB="conda"
+      before_install: sed -i 's/conda-forge/conda/g' requirements/environment.yml
 
     - name: "pip 2.7"
       python: 2.7
@@ -41,6 +42,18 @@ matrix:
       python: 3.8
       env: DISTRIB="pip"
 
+    - name: "docs"
+      python: 3.6
+      env: DISTRIB="conda"
+      before_install: sudo apt install -y libopenmpi-dev openmpi-bin
+      before_script:
+        - conda install -c conda-forge pandoc
+        - pip install -r requirements/requirements-docs.txt
+        - pip install -r requirements/requirements-tutorials.txt
+        - pip install -r requirements/requirements-extras.txt
+        - sed -i -E "s/nbsphinx_execute *=.*/nbsphinx_execute = 'always'/g" doc/conf.py
+      script: cd doc && make html
+
 install:
   - if [[ "${DISTRIB}" == "conda" ]];
     then

diff --git a/CITATION.txt b/CITATION.txt
@@ -0,0 +1,4 @@
+To refer to the Elephant software package in publications, please use 
+    Elephant (RRID:SCR_003833)
+
+To cite Elephant, please see doc/citation.rst.
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -2,6 +2,7 @@ recursive-include elephant *.py
 include requirements/*
 include README.md
 include LICENSE.txt
+include CITATION.txt
 include elephant/VERSION
 include elephant/current_source_density_src/README.md
 include elephant/current_source_density_src/test_data.mat

diff --git a/README.md b/README.md
@@ -4,13 +4,14 @@
 ![](https://coveralls.io/repos/NeuralEnsemble/elephant/badge.png "Unit Test Coverage")
 ![](https://readthedocs.org/projects/elephant/badge/?version=latest "Documentation Status")
 ![](https://img.shields.io/pypi/v/elephant)
-![](https://img.shields.io/pypi/dd/elephant)
+![](https://img.shields.io/pypi/dm/elephant)
 [![Gitter](https://badges.gitter.im/python-elephant/community.svg)](https://gitter.im/python-elephant/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
 
 *Elephant* package analyses all sorts of neurophysiological data:
 spike trains, LFP, analog signals. The input-output data format is either
 [Neo](https://github.com/NeuralEnsemble/python-neo), Quantity or Numpy array.
 
+
 ### More Information
 
 * Documentation: https://elephant.readthedocs.io/en/latest/
@@ -21,10 +22,18 @@ spike trains, LFP, analog signals. The input-output data format is either
 
 Modified BSD License, see [LICENSE.txt](LICENSE.txt) for details.
 
+
 #### Copyright
 
 :copyright: 2014-2020 by the [Elephant team](doc/authors.rst).
 
+
 #### Acknowledgments
 
 See [acknowledgments](doc/acknowledgments.rst).
+
+
+#### Citation
+
+See [citations](doc/citation.rst).
+
diff --git a/doc/acknowledgments.rst b/doc/acknowledgments.rst
@@ -2,4 +2,4 @@
 Acknowledgments
 ***************
 
-This open source software code was developed in part or in whole in the Human Brain Project, funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreements No. 720270 and No. 785907 (Human Brain Project SGA1 and SGA2).
+This open source software code was developed in part or in whole in the Human Brain Project, funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreements No. 720270, No. 785907 and No. 945539 (Human Brain Project SGA1, SGA2 and SGA3).
diff --git a/doc/authors.rst b/doc/authors.rst
@@ -47,6 +47,8 @@ Do you want to contribute to Elephant? Please refer to the
 * Jan Lewen [1]
 * Alexander Kleinjohann [1]
 * Danylo Ulianych [1]
+* Anno Kurth [1]
+* Regimantas Jurkus [1]
 * Philipp Steigerwald [12]
 * Manuel Ciba [12]
 

diff --git a/doc/bib/elephant.bib b/doc/bib/elephant.bib
@@ -1,4 +1,23 @@
-@article{Gruen02_43, 
+@misc{Ding06_0608035,
+  title={Granger Causality: Basic Theory and Application to Neuroscience},
+  author={Mingzhou Ding and Yonghong Chen and Steven L. Bressler},
+  year={2006},
+  eprint={q-bio/0608035},
+  archivePrefix={arXiv},
+  primaryClass={q-bio.QM}
+}
+
+@article{Granger69_424,
+  title={Investigating causal relations by econometric models and cross-spectral methods},
+  author={Granger, Clive WJ},
+  journal={Econometrica: journal of the Econometric Society},
+  volume={37},
+  pages={424--438},
+  year={1969},
+  doi={10.2307/1912791}
+}
+
+@article{Gruen02_43,
   title = {Unitary events in multiple single-neuron spiking activity: I. Detection and significance},
   author = {Gr{\"u}n, S. and Diesmann, M. and Aertsen, A.},
   year = {2002},
@@ -49,8 +68,7 @@ @article{Gruen99_67
   volume = {94},
   number = {1},
   pages = {67--79},
-  doi = {10.1016/s0165-0270(99)00126-0}
-
+  doi = {10.1016/s0165-0270(99)00126-0} 
 }
 
 @article{Riehle97_1950,
@@ -64,13 +82,56 @@ @article{Riehle97_1950
   doi = {10.1126/science.278.5345.1950}
 }
 
-@article{torre2016asset,
+@article{Seth07_1667,
+  author = {Seth, A. },
+  title   = {Granger causality},
+  year    = {2007},
+  journal = {Scholarpedia},
+  volume  = {2},
+  number  = {7},
+  pages   = {1667},
+  doi     = {10.4249/scholarpedia.1667},
+  note    = {revision \#127333}
+}
+
+@article{Stella19_104022,
+  title = {3d-{SPADE}: {S}ignificance evaluation of spatio-temporal patterns of various temporal extents},
+  author = {Stella, A. and Quaglio, P. and Torre, E. and Gr{\"u}n, S.},
+  year = {2019},
+  journal = {Biosystems},
+  volume = {185},
+  pages = {104022},
+  doi = {10.1016/j.biosystems.2019.104022}
+}
+
+@article{Torre16_e1004939,
   title={ASSET: analysis of sequences of synchronous events in massively parallel spike trains},
-  author={Torre, Emiliano and Canova, Carlos and Denker, Michael and Gerstein, George and Helias, Moritz and Gr{\"u}n, Sonja},
+  author={Torre, E. and Canova, C. and Denker, M. and Gerstein, G. and Helias, M. and Gr{\"u}n, S.},
   year={2016},
-  journal={PLoS computational biology},
+  journal={PLoS Comp. Biol.},
   volume={12},
   number={7},
   pages={e1004939},
   doi={10.1371/journal.pcbi.1004939}
 }
+
+@article{ciba2018spike,
+  title={Spike-contrast: A novel time scale independent and multivariate measure of spike train synchrony},
+  author={Ciba, Manuel and Isomura, Takuya and Jimbo, Yasuhiko and Bahmer, Andreas and Thielemann, Christiane},
+  year={2018},
+  journal={Journal of Neuroscience Methods},
+  volume={293},
+  pages={136--143},
+  doi={10.1016/j.jneumeth.2017.09.008}
+}
+
+@article{Rostami17_3,
+  title = {[{Re}] {S}pike synchronization and rate modulation differentially involved in motor cortical function},
+  author = {Rostami, V. and Ito, J. and Denker, M. and Gr{\"u}n, S.},
+  year = {2017},
+  journal = {ReScience},
+  volume = {3},
+  number = {1},
+  pages = {3},
+  doi = {10.5281/zenodo.583814}
+}
diff --git a/doc/citation.rst b/doc/citation.rst
@@ -0,0 +1,34 @@
+***************
+Citing Elephant
+***************
+
+To refer to the Elephant software package in publications, please use: **Elephant (RRID:SCR_003833)**.
+
+
+To cite Elephant, please use:
+
+**Denker M, Yegenoglu A, Grün S (2018) Collaborative HPC-enabled workflows on the HBP Collaboratory using the Elephant framework. Neuroinformatics 2018, P19. doi: 10.12751/incf.ni2018.0019**
+
+A BibTeX entry for LaTeX users is:
+
+.. code-block:: bibtex
+
+    @conference{elephant18,
+        author = {Denker, M. and Yegenoglu, A. and Grün, S.},
+        booktitle = {Neuroinformatics 2018},
+        title = {{C}ollaborative {HPC}-enabled workflows on the {HBP} {C}ollaboratory using the {E}lephant framework},
+        pages = {P19},
+        year = {2018}
+        doi = {10.12751/incf.ni2018.0019},
+        url = {https://abstracts.g-node.org/conference/NI2018/abstracts#/uuid/023bec4e-0c35-4563-81ce-2c6fac282abd},
+    }
+
+
+Further publications directly related to Elephant development 
+:cite:`citations-Rostami17_3,citations-Stella19_104022` (see
+`doc/bib/elephant.bib` for full BibTeX entries).
+
+.. bibliography:: bib/elephant.bib
+   :labelprefix: citations-
+   :keyprefix: citations-
+   :style: unsrt    
diff --git a/doc/index.rst b/doc/index.rst
@@ -34,6 +34,7 @@ Table of Contents
     release_notes
     get_in_touch
     acknowledgments
+    citation
 
 
 

diff --git a/doc/modules.rst b/doc/modules.rst
@@ -6,6 +6,7 @@ Function Reference by Module
    :maxdepth: 1
 
    reference/asset
+   reference/causality
    reference/cell_assembly_detection
    reference/change_point_detection
    reference/conversion
@@ -20,11 +21,15 @@ Function Reference by Module
    reference/signal_processing
    reference/spade
    reference/spectral
-   reference/spike_train_correlation
-   reference/spike_train_dissimilarity
    reference/spike_train_generation
    reference/spike_train_surrogates
    reference/sta
    reference/statistics
    reference/unitary_event_analysis
    reference/waveform_features
+
+
+.. toctree::
+   :maxdepth: 2
+
+   reference/_spike_train_processing
diff --git a/doc/reference/_spike_train_processing.rst b/doc/reference/_spike_train_processing.rst
@@ -0,0 +1,11 @@
+======================
+Spike train processing
+======================
+
+
+.. toctree::
+   :maxdepth: 1
+
+   spike_train_correlation
+   spike_train_dissimilarity
+   spike_train_synchrony
diff --git a/doc/reference/causality.rst b/doc/reference/causality.rst
@@ -0,0 +1,5 @@
+==================
+Causality measures
+==================
+
+.. automodule:: elephant.causality.granger
diff --git a/doc/reference/spike_train_dissimilarity.rst b/doc/reference/spike_train_dissimilarity.rst
@@ -1,6 +1,6 @@
-=======================================
-Spike train dissimilarity and synchrony
-=======================================
+=========================
+Spike train dissimilarity
+=========================
 
 
 .. automodule:: elephant.spike_train_dissimilarity

diff --git a/doc/reference/spike_train_synchrony.rst b/doc/reference/spike_train_synchrony.rst
@@ -0,0 +1,14 @@
+=====================
+Spike train synchrony
+=====================
+
+.. automodule:: elephant.spike_train_synchrony
+
+
+References
+----------
+
+.. bibliography:: ../bib/elephant.bib
+   :labelprefix: syn
+   :keyprefix: synchrony-
+   :style: unsrt
diff --git a/doc/release_notes.rst b/doc/release_notes.rst
@@ -2,6 +2,34 @@
 Release Notes
 *************
 
+Elephant 0.8.0 release notes
+============================
+
+New features
+------------
+* The `parallel` module is a new experimental module (https://github.com/NeuralEnsemble/elephant/pull/307) to run python functions concurrently. Supports native (pythonic) ProcessPollExecutor and MPI. Not limited to Elephant functional.
+* Added an optional `refractory_period` argument, set to None by default, to `dither_spikes` function (https://github.com/NeuralEnsemble/elephant/pull/297).
+* Added `cdf` and `icdf` functions in Kernel class to correctly estimate the median index, needed for `instantaneous_rate` function in statistics.py (https://github.com/NeuralEnsemble/elephant/pull/313).
+* Added an optional `center_kernel` argument, set to True by default (to behave as in Elephant <0.8.0 versions) to `instantaneous_rate` function in statistics.py (https://github.com/NeuralEnsemble/elephant/pull/313).
+
+New tutorials
+-------------
+* Analysis of Sequences of Synchronous EvenTs (ASSET) tutorial: https://elephant.readthedocs.io/en/latest/tutorials/asset.html
+* Parallel module tutorial: https://elephant.readthedocs.io/en/latest/tutorials/parallel.html
+
+Optimization
+------------
+* Optimized ASSET runtime by a factor of 10 and more (https://github.com/NeuralEnsemble/elephant/pull/259, https://github.com/NeuralEnsemble/elephant/pull/333).
+
+Python 2.7 and 3.5 deprecation
+------------------------------
+Python 2.7 and 3.5 are deprecated and will not be maintained by the end of 2020. Switch to Python 3.6+.
+
+Breaking changes
+----------------
+* Naming convention changes (`binsize` -> `bin_size`, etc.) in almost all Elephant functions (https://github.com/NeuralEnsemble/elephant/pull/316).
+
+
 Elephant 0.7.0 release notes
 ============================
 

diff --git a/doc/style_guide.rst b/doc/style_guide.rst
@@ -42,6 +42,10 @@ throughout Elephant.
 
 .. code-block:: python
 
+    def pair_of_signals_example(spiketrain_i, spiketrain_j):
+        # Add '_i' and '_j' suffixes to a pair of signals, spiketrains or any
+        # other variables that come in pairs.
+
     def perfect_naming_of_parameters(spiketrains, spiketrain, reference_spiketrain,
                          target_spiketrain, signal, signals, max_iterations,
                          min_threshold, n_bins, n_surrogates, bin_size, max_size,
@@ -119,9 +123,8 @@ throughout Elephant.
             Therefore, do not use terms as `n` or `n_surr`, that are not
             immediately understood.
         bin_size : pq.Quantity or int
-            Separate the words by underscore. Do not use `binsize`. Old functions
-            which use `binsize` will be gradually refactored to conform to the new
-            convention.
+            Separate the words by underscore. Do not use `bin_size`. Old functions
+            which use `binsize` are deprecated.
         max_size : float
             Another example showing that words should be separated by underscores.
             This intersects with the naming convention for a maximum value.