diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 59622b4..0000000 --- a/.travis.yml +++ /dev/null @@ -1,34 +0,0 @@ -dist: xenial -language: python -sudo: false - -addons: - apt: - update: false - - -matrix: - include: - - - name: "pip 3.6" - python: 3.6 - - - name: "pip 3.7" - python: 3.7 - - - name: "pip 3.8" - python: 3.8 - - -install: - - pip install -r requirements/requirements.txt - - pip install -r requirements/requirements-docs.txt - - pip -V - - python -c "from elephant.spade import HAVE_FIM; assert HAVE_FIM" - - pip install . - - pip list - - python --version - - -script: - cd doc && make html SPHINXOPTS="-W --keep-going -n" diff --git a/LICENSE.txt b/LICENSE.txt index d8ab8aa..828bad0 100644 --- a/LICENSE.txt +++ b/LICENSE.txt @@ -1,4 +1,4 @@ -Copyright (c) 2017-2020, Institute of Neuroscience and Medicine (INM-6), Forschungszentrum Jülich +Copyright (c) 2017-2022, Institute of Neuroscience and Medicine (INM-6), Forschungszentrum Jülich All rights reserved. Redistribution and use in source and binary forms, with or without diff --git a/README.md b/README.md index 97cfcfe..4201db5 100644 --- a/README.md +++ b/README.md @@ -1,36 +1,29 @@ # Viziphant -[![Build Status](https://travis-ci.org/INM-6/viziphant.svg?branch=master)](https://travis-ci.org/INM-6/viziphant) [![Documentation Status](https://readthedocs.org/projects/viziphant/badge/?version=latest)](https://viziphant.readthedocs.io/en/latest/?badge=latest) [![![PyPi]](https://img.shields.io/pypi/v/viziphant)](https://pypi.org/project/viziphant/) [![Viziphant-tests](https://github.com/INM-6/viziphant/actions/workflows/CI_actions.yml/badge.svg)](https://github.com/INM-6/viziphant/actions/workflows/CI_actions.yml) -A Python module for easy visualization of [Neo](https://github.com/NeuralEnsemble/python-neo) objects and [Elephant](https://github.com/NeuralEnsemble/elephant) results. +A Python module for easy visualization of [Neo](https://github.com/NeuralEnsemble/python-neo) objects and +[Elephant](https://github.com/NeuralEnsemble/elephant) results. -Viziphant provides a high-level API to easily generate plots and interactive visualizations of neuroscientific data and analysis results. This API uses and extends the same structure as in Elephant to ensure intuitive usage for scientists that are used to Elephant. +Viziphant provides a high-level API to easily generate plots and interactive visualizations of neuroscientific data and +analysis results. This API uses and extends the same structure as in Elephant to ensure intuitive usage for scientists +that are used to Elephant. #### Documentation - https://viziphant.readthedocs.io/en/latest/ #### Getting in touch - * Mailing list: https://groups.google.com/group/neuralensemble -* Gitter chat: https://gitter.im/python-elephant/community #### Installation - -Viziphant works with Python 3.6+ only. For a development install follow these instructions: - -``` -pip install git+https://github.com/INM-6/viziphant.git#egg=viziphant -``` - +For instructions on installing Viziphant, please see https://viziphant.readthedocs.io/en/latest/install.html #### Copyright -:copyright: 2015-2020 by the [Viziphant team](doc/authors.rst). +:copyright: 2017-2022 by the [Viziphant team](doc/authors.rst). #### License BSD 3-Clause License, see [LICENSE.txt](LICENSE.txt) for details. diff --git a/doc/conf.py b/doc/conf.py index 48a4b19..d1b162e 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -94,7 +94,6 @@ # The name of an image file (relative to this directory) to place at the top # of the sidebar. -# TODO: create logo and favicon html_logo = 'images/viziphant_logo_sidebar.png' # The name of an image file (within the static path) to use as favicon of the diff --git a/doc/index.rst b/doc/index.rst index 73a0d6f..65b7c4d 100644 --- a/doc/index.rst +++ b/doc/index.rst @@ -14,6 +14,7 @@ scientists that are used to Elephant. install modules + release_notes authors acknowledgments diff --git a/doc/release_notes.rst b/doc/release_notes.rst new file mode 100644 index 0000000..8ae6593 --- /dev/null +++ b/doc/release_notes.rst @@ -0,0 +1,34 @@ +============= +Release Notes +============= + +Viziphant 0.2.0 release notes +***************************** + +Documentation +------------- +* Documentation revised in style, logo was added + +New functionality and features +------------------------------ +* New `patterns` module to display spike patterns by elephant modules, such as SPADE or CAD (https://github.com/INM-6/viziphant/pull/35) +* New function to display the spike contrast measure (https://github.com/INM-6/viziphant/pull/34) +* Added function to display rate trajectories plotted by the GPFA module (https://github.com/INM-6/viziphant/pull/37) + +Bug fixes +--------- +* Bug fixes for the ISI and Unitary Event plots (https://github.com/INM-6/viziphant/pull/31) and (https://github.com/INM-6/viziphant/pull/32). + +Miscellaneous +------------- +* Continuous Integration (CI) was moved to github actions (https://github.com/INM-6/viziphant/pull/41) + +Selected dependency changes +--------------------------- +* `elephant>=0.9.0` + + +Viziphant 0.1.0 release notes +***************************** + +This release constitutes the initial Viziphant release. diff --git a/requirements/environment.yml b/requirements/environment.yml deleted file mode 100644 index 5e97b79..0000000 --- a/requirements/environment.yml +++ /dev/null @@ -1,10 +0,0 @@ -name: viziphant - -dependencies: - - python>=3.6 - - pip - - numpy - - matplotlib - - seaborn - - pip: - - -r file:requirements.txt diff --git a/requirements/requirements.txt b/requirements/requirements.txt index 77d24fa..9d1ea66 100644 --- a/requirements/requirements.txt +++ b/requirements/requirements.txt @@ -1,10 +1,10 @@ neo>=0.9.0 elephant>=0.9.0 -# elephant @ git+https://github.com/NeuralEnsemble/elephant.git#egg=elephant[extras] numpy>=1.18.1 quantities>=0.12.1 -six>=1.10.0 matplotlib>=3.3.2 seaborn>=0.9.0 -scikit-learn>=0.23.2 -statsmodels>=0.12.1 +# six>=1.10.0 +# scikit-learn>=0.23.2 +# statsmodels>=0.12.1 +# elephant @ git+https://github.com/NeuralEnsemble/elephant.git#egg=elephant[extras] diff --git a/viziphant/VERSION b/viziphant/VERSION index 6c6aa7c..341cf11 100644 --- a/viziphant/VERSION +++ b/viziphant/VERSION @@ -1 +1 @@ -0.1.0 \ No newline at end of file +0.2.0 \ No newline at end of file diff --git a/viziphant/__init__.py b/viziphant/__init__.py index 665fa68..4423d0c 100644 --- a/viziphant/__init__.py +++ b/viziphant/__init__.py @@ -3,7 +3,7 @@ Elephant, which is a package for the analysis of neurophysiological data, based on Neo. """ -# Copyright 2017-2020 by the Viziphant team, see `doc/authors.rst`. +# Copyright 2017-2022 by the Viziphant team, see `doc/authors.rst`. # License: Modified BSD, see LICENSE.txt for details. from . import (asset, events, gpfa, patterns, rasterplot, diff --git a/viziphant/asset.py b/viziphant/asset.py index df2ceee..4761a35 100644 --- a/viziphant/asset.py +++ b/viziphant/asset.py @@ -9,7 +9,7 @@ plot_synchronous_events """ -# Copyright 2017-2020 by the Viziphant team, see `doc/authors.rst`. +# Copyright 2017-2022 by the Viziphant team, see `doc/authors.rst`. # License: Modified BSD, see LICENSE.txt for details. diff --git a/viziphant/events.py b/viziphant/events.py index 2f6e233..2360556 100644 --- a/viziphant/events.py +++ b/viziphant/events.py @@ -8,7 +8,7 @@ add_event """ -# Copyright 2017-2020 by the Viziphant team, see `doc/authors.rst`. +# Copyright 2017-2022 by the Viziphant team, see `doc/authors.rst`. # License: Modified BSD, see LICENSE.txt.txt for details. diff --git a/viziphant/gpfa.py b/viziphant/gpfa.py index 2600173..b31c8aa 100644 --- a/viziphant/gpfa.py +++ b/viziphant/gpfa.py @@ -14,6 +14,8 @@ plot_cumulative_shared_covariance plot_transform_matrix """ +# Copyright 2017-2022 by the Viziphant team, see `doc/authors.rst`. +# License: Modified BSD, see LICENSE.txt for details. import itertools import math diff --git a/viziphant/patterns.py b/viziphant/patterns.py index d00e1af..0a27833 100644 --- a/viziphant/patterns.py +++ b/viziphant/patterns.py @@ -24,7 +24,7 @@ plot_patterns_statistics_lags """ -# Copyright 2017-2020 by the Viziphant team, see `doc/authors.rst`. +# Copyright 2017-2022 by the Viziphant team, see `doc/authors.rst`. # License: Modified BSD, see LICENSE.txt for details. from collections import defaultdict diff --git a/viziphant/rasterplot.py b/viziphant/rasterplot.py index 59a0aec..b248cc2 100644 --- a/viziphant/rasterplot.py +++ b/viziphant/rasterplot.py @@ -10,7 +10,7 @@ rasterplot_rates """ -# Copyright 2017-2020 by the Viziphant team, see `doc/authors.rst`. +# Copyright 2017-2022 by the Viziphant team, see `doc/authors.rst`. # License: Modified BSD, see LICENSE.txt for details. import matplotlib.axes diff --git a/viziphant/spike_train_correlation.py b/viziphant/spike_train_correlation.py index b338380..5e801d5 100644 --- a/viziphant/spike_train_correlation.py +++ b/viziphant/spike_train_correlation.py @@ -9,7 +9,7 @@ plot_cross_correlation_histogram """ -# Copyright 2017-2020 by the Viziphant team, see `doc/authors.rst`. +# Copyright 2017-2022 by the Viziphant team, see `doc/authors.rst`. # License: Modified BSD, see LICENSE.txt.txt for details. diff --git a/viziphant/spike_train_synchrony.py b/viziphant/spike_train_synchrony.py index ebe8908..5efc71c 100644 --- a/viziphant/spike_train_synchrony.py +++ b/viziphant/spike_train_synchrony.py @@ -8,6 +8,8 @@ plot_spike_contrast """ +# Copyright 2017-2022 by the Viziphant team, see `doc/authors.rst`. +# License: Modified BSD, see LICENSE.txt for details. import matplotlib.pyplot as plt import numpy as np diff --git a/viziphant/statistics.py b/viziphant/statistics.py index 7c7d633..487195a 100644 --- a/viziphant/statistics.py +++ b/viziphant/statistics.py @@ -10,7 +10,7 @@ plot_instantaneous_rates_colormesh """ -# Copyright 2017-2020 by the Viziphant team, see `doc/authors.rst`. +# Copyright 2017-2022 by the Viziphant team, see `doc/authors.rst`. # License: Modified BSD, see LICENSE.txt.txt for details. import matplotlib.pyplot as plt diff --git a/viziphant/unitary_event_analysis.py b/viziphant/unitary_event_analysis.py index d584589..faf99e7 100644 --- a/viziphant/unitary_event_analysis.py +++ b/viziphant/unitary_event_analysis.py @@ -12,7 +12,7 @@ plot_ue """ -# Copyright 2017-2020 by the Viziphant team, see `doc/authors.rst`. +# Copyright 2017-2022 by the Viziphant team, see `doc/authors.rst`. # License: Modified BSD, see LICENSE.txt.txt for details. import numpy as np diff --git a/viziphant/utils.py b/viziphant/utils.py index d6eec38..ffd84f9 100644 --- a/viziphant/utils.py +++ b/viziphant/utils.py @@ -1,4 +1,4 @@ -# Copyright 2017-2020 by the Viziphant team, see `doc/authors.rst`. +# Copyright 2017-2022 by the Viziphant team, see `doc/authors.rst`. # License: Modified BSD, see LICENSE.txt for details. from elephant.utils import check_same_units as check_same_units_single