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commit 19d3c7b Author: Danylo Ulianych <dizcza@gmail.com> Date: Thu Aug 1 15:09:34 2019 +0200 fixed min requirements (NeuralEnsemble#235) * fixed min requirements * travis install libopenmpi-dev * added .coveragerc omit=elephant/test* rule not to count test files as source code commit 36e6096 Author: Danylo Ulianych <dizcza@gmail.com> Date: Wed Jul 31 16:55:47 2019 +0200 Integrated GPFA (NeuralEnsemble#233) * Rename neural_trajectory to gpfa and refactor the codes accordingly * Remove codes related to the (not fully implemented) cross-validation feature * added tqdm as an extra requirement * push coverage only for requirements-extras test * gpfa verbose flag; added licence in the docs * Fixed and extended documentation, removed misleading function outputs. commit d6822d6 Author: Danylo Ulianych <dizcza@gmail.com> Date: Tue Jul 23 16:35:45 2019 +0300 Acknowledgments (NeuralEnsemble#241) * acknowledgments * removed reference file AUTHORS.txt * recursive-exclude . *~ commit 6fd3a5b Author: Danylo Ulianych <dizcza@gmail.com> Date: Mon Jul 22 23:14:36 2019 +0300 Release v0.6.3 (NeuralEnsemble#240) * Release v0.6.3 * Update doc/reference/waveform_features.rst Co-Authored-By: Michael Denker <m.denker@fz-juelich.de> commit c013e39 Author: Danylo Ulianych <dizcza@gmail.com> Date: Sun Jul 21 09:18:03 2019 +0300 elephant dir packages are back (NeuralEnsemble#239) * reverted removed imports of elephant's internal packages; download fim during the setup * download fim from tools/fim_manager.py * dummy tools/__init__.py to support py2 * include requirements in MANIFEST back * fixed spade licence typo * included waveform_features module; removed tools; don't donwload fim at setup while macking a tarball with 'sdist' command travis not fixed downloading fim * skip time consuming test_spade_cpp if not HAVE_FIM * travis pip install generated tarball * recursive-include elephant *.py commit 3c30574 Author: Danylo Ulianych <dizcza@gmail.com> Date: Wed Jul 10 18:21:37 2019 +0200 Butterworth supports sosfiltfilt filter_function (NeuralEnsemble#234) * Butterworth supports sosfiltfilt filter_function * higher order filters comment
INM-6 · Aug 1, 2019 · 2c49122 · 2c49122
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diff --git a/.coveragerc b/.coveragerc
@@ -0,0 +1,3 @@
+# .coveragerc to control coverage.py
+[report]
+omit = elephant/test/*
diff --git a/.gitignore b/.gitignore
@@ -15,7 +15,9 @@ nosetests.xml
 .pydevproject
 .settings
 *.tmp*
-.idea
+.idea/
+venv/
+env/
 .pytest_cache/
 
 # Compiled source #

diff --git a/.travis.yml b/.travis.yml
@@ -35,19 +35,20 @@ matrix:
       before_install: sudo apt install -y libopenmpi-dev openmpi-bin
       before_script: pip install -r requirements-extras.txt
       script: mpiexec -n 1 nosetests --with-coverage --cover-package=elephant
+      after_success: coveralls || echo "coveralls failed"
 
     - name: "conda 3.7"
       python: 3.7
       env: DISTRIB="conda"
 
-  exclude:
-    - name: "pip 3.6 requirements min version"
-      # excluded due to unmet dependencies in neo, quantities, and scipy
+    - name: "pip 3.6 requirements-extras min version"
       python: 3.6
       env: DISTRIB="pip"
       before_install:
-        - sudo apt install libblas-dev liblapack-dev libatlas-base-dev gfortran
-        - sed -i 's/>=/==/g' requirements.txt
+        - sudo apt install -y libopenmpi-dev openmpi-bin
+        - sudo apt install -y libblas-dev liblapack-dev libatlas-base-dev gfortran
+        - sed -i 's/>=/==/g' requirements*.txt
+      before_script: pip install -r requirements-extras.txt
 
 
 install:
@@ -73,12 +74,10 @@ install:
 
   - pip -V
   - pip install coverage coveralls nose
-  - pip install .
+  - python setup.py install
+  - python -c "from elephant.spade import HAVE_FIM; assert HAVE_FIM"
   - pip list
   - python --version
 
 script:
   nosetests --with-coverage --cover-package=elephant
-
-after_success:
-  coveralls || echo "coveralls failed"
diff --git a/AUTHORS.txt b/AUTHORS.txt
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,12 +1,14 @@
-include README.rst
+recursive-include elephant *.py
+include requirements*.txt
+include README.md
 include LICENSE.txt
-include AUTHORS.txt
 include elephant/VERSION
 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
+recursive-include elephant/spade_src *.so *.pyd
 include elephant/test/spike_extraction_test_data.txt
 recursive-include doc *
-
-# special care for the files, used in setup.py
-include elephant/spade_src/fim_manager.py
+prune doc/_build
+recursive-exclude . *~
diff --git a/README.md b/README.md
@@ -0,0 +1,22 @@
+# Elephant - Electrophysiology Analysis Toolkit
+
+Elephant is a package for the analysis of neurophysiological data, based on Neo.
+
+## Code status
+
+![](https://travis-ci.org/NeuralEnsemble/elephant.png?branch=master "Unit Test Status")
+![](https://coveralls.io/repos/NeuralEnsemble/elephant/badge.png "Unit Test Coverage")
+![](https://requires.io/github/NeuralEnsemble/elephant/requirements.png?branch=master "Requirements Status")
+![](https://readthedocs.org/projects/elephant/badge/?version=latest "Documentation Status")
+
+#### Copyright
+
+:copyright: 2014-2019 by the [Elephant team](doc/authors.rst).
+
+#### License
+
+Modified BSD License, see [LICENSE.txt](LICENSE.txt) for details.
+
+#### Acknowledgments
+
+See [acknowledgments](doc/acknowledgments.rst).
diff --git a/README.rst b/README.rst
diff --git a/doc/acknowledgments.rst b/doc/acknowledgments.rst
@@ -0,0 +1,5 @@
+***************
+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).
diff --git a/doc/developers_guide.rst b/doc/developers_guide.rst
@@ -175,17 +175,17 @@ Python 2.7 and 3.2-3.5.
 
 
 Making a release (maintainers only)
-----------------
+-----------------------------------
 
 .. TODO: discuss branching/tagging policy.
 
-.. Add a section in /doc/releases/<version>.rst for the release.
+.. Add a section in /doc/release_notes.rst for the release.
 
 1. Increment the Elephant package version in :file:`elephant/VERSION`, if necessary.
 
 2. Check that the copyright statement (in :file:`LICENCE.txt`, :file:`README.md`, and :file:`doc/conf.py`) is correct.
 
-3. If there is a new module do not forget to add the modulename to the :file:`doc/module.rst` and make a file with a short description in :file:`doc/reference/<modulename>.rst`.
+3. If there is a new module do not forget to add the modulename to the :file:`doc/modules.rst` and make a file with a short description in :file:`doc/reference/<modulename>.rst`.
 
 To build a source package::
 

diff --git a/doc/index.rst b/doc/index.rst
@@ -25,7 +25,8 @@ Table of Contents
     modules
     developers_guide
     authors
-    release_notes	       
+    release_notes
+    acknowledgements
 
 
 

diff --git a/doc/modules.rst b/doc/modules.rst
@@ -23,4 +23,4 @@ Function Reference by Module
    reference/sta
    reference/statistics
    reference/unitary_event_analysis
-
+   reference/waveform_features
diff --git a/doc/reference/waveform_features.rst b/doc/reference/waveform_features.rst
@@ -0,0 +1,6 @@
+=====================================================================================================
+`waveform_features` - Functions for computing waveform features like signal-to-noise ratio, etc.
+=====================================================================================================
+
+.. automodule:: elephant.waveform_features
+   :members:
diff --git a/doc/release_notes.rst b/doc/release_notes.rst
@@ -2,6 +2,28 @@
 Release Notes
 *************
 
+Elephant 0.6.3 release notes
+============================
+July 22nd 2019
+
+The release v0.6.3 is mostly about improving maintenance.
+
+New functions
+-------------
+* `waveform_features` module
+    * Waveform signal-to-noise ratio (https://github.com/NeuralEnsemble/elephant/pull/219).
+* Added support for Butterworth `sosfiltfilt` - numerically stable (in particular, higher order) filtering (https://github.com/NeuralEnsemble/elephant/pull/234).
+
+Buf fixes
+---------
+* Fixed neo version typo in requirements file (https://github.com/NeuralEnsemble/elephant/pull/218)
+* Fixed broken docs (https://github.com/NeuralEnsemble/elephant/pull/230, https://github.com/NeuralEnsemble/elephant/pull/232)
+* Fixed issue with 32-bit arch (https://github.com/NeuralEnsemble/elephant/pull/229)
+
+Other changes
+-------------
+* Added issue templates (https://github.com/NeuralEnsemble/elephant/pull/226)
+* Single VERSION file (https://github.com/NeuralEnsemble/elephant/pull/231)
 
 Elephant 0.6.2 release notes
 ============================

diff --git a/elephant/VERSION b/elephant/VERSION
@@ -1 +1 @@
-0.6.2
+0.6.3
diff --git a/elephant/__init__.py b/elephant/__init__.py
@@ -2,10 +2,37 @@
 """
 Elephant is a package for the analysis of neurophysiology data, based on Neo.
 
-:copyright: Copyright 2014-2019 by the Elephant team, see AUTHORS.txt.
+:copyright: Copyright 2014-2019 by the Elephant team, see `doc/authors.rst`.
 :license: Modified BSD, see LICENSE.txt for details.
 """
 
+from . import (statistics,
+               spike_train_generation,
+               spike_train_correlation,
+               unitary_event_analysis,
+               cubic,
+               spectral,
+               kernels,
+               spike_train_dissimilarity,
+               spike_train_surrogates,
+               signal_processing,
+               current_source_density,
+               change_point_detection,
+               phase_analysis,
+               sta,
+               conversion,
+               neo_tools,
+               spade,
+               cell_assembly_detection,
+               waveform_features)
+
+try:
+    from . import pandas_bridge
+    from . import asset
+except ImportError:
+    # requirements-extras are missing
+    pass
+
 
 def _get_version():
     import os

diff --git a/elephant/conversion.py b/elephant/conversion.py
@@ -6,7 +6,7 @@
 An example is the representation of a spike train as a sequence of 0-1 values
 (binned spike train).
 
-:copyright: Copyright 2014-2016 by the Elephant team, see AUTHORS.txt.
+:copyright: Copyright 2014-2016 by the Elephant team, see `doc/authors.rst`.
 :license: BSD, see LICENSE.txt for details.
 """
 

diff --git a/elephant/cubic.py b/elephant/cubic.py
@@ -14,7 +14,7 @@
        >>> alpha = 0.05  # significance level of the tests used
        >>> xi, p_val, k = cubic(data, ximax=100, alpha=0.05, errorval=4.):
 
-:copyright: Copyright 2016 by the Elephant team, see AUTHORS.txt.
+:copyright: Copyright 2016 by the Elephant team, see `doc/authors.rst`.
 :license: BSD, see LICENSE.txt for details.
 '''
 # -*- coding: utf-8 -*-
@@ -203,7 +203,7 @@ def _kstat(data):
 
     Returns
     -----
-    kappa : numpy.ndarray
+    moments : list
         The first three unbiased cumulants of the population count
     '''
     if len(data) == 0:

diff --git a/elephant/current_source_density_src/KCSD.py b/elephant/current_source_density_src/KCSD.py
@@ -48,7 +48,7 @@ def validate(self, ele_pos, pots):
         if ele_pos.shape[0] < 1+ele_pos.shape[1]: #Dim+1
             raise Exception("Number of electrodes must be at least :",
                             1+ele_pos.shape[1])
-        if utils.check_for_duplicated_electrodes(ele_pos) is False:
+        if utils.contains_duplicated_electrodes(ele_pos):
             raise Exception("Error! Duplicated electrode!")
 
     def sanity(self, true_csd, pos_csd):

diff --git a/elephant/current_source_density_src/utility_functions.py b/elephant/current_source_density_src/utility_functions.py
@@ -35,17 +35,19 @@ def patch_quantities():
         lastdefinition = definition
     return
 
-def check_for_duplicated_electrodes(elec_pos):
+
+def contains_duplicated_electrodes(elec_pos):
     """Checks for duplicate electrodes
     Parameters
     ----------
     elec_pos : np.array
+
     Returns
     -------
     has_duplicated_elec : Boolean
     """
-    unique_elec_pos = np.unique(elec_pos, axis=0)
-    has_duplicated_elec = unique_elec_pos.shape == elec_pos.shape
+    unique_elec_pos = set(map(tuple, elec_pos))
+    has_duplicated_elec = len(unique_elec_pos) < len(elec_pos)
     return has_duplicated_elec