Merge pull request #619 from neuropsychology/dev

0.2.0

.coveragerc

@@ -1,5 +1,5 @@
 [report]
-fail_under = 60
+fail_under = 50
 show_missing = True
 
 [run]

.github/workflows/checks.yml

@@ -10,14 +10,13 @@ jobs:
     - uses: actions/checkout@master
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: '3.8'
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install https://github.com/DominiqueMakowski/popularipy/zipball/master
         cd $GITHUB_WORKSPACE && pip install .[test]
 
     - name: Run README_examples.py

.github/workflows/docs-build.yml

@@ -0,0 +1,56 @@
+name: "📜 Documentation builder"
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+      with:
+        fetch-depth: 0 # To be able to push refs to destination repo
+    - name: Set up Python 🐍
+      uses: actions/setup-python@v3
+      with:
+        cache: 'pip'
+
+    - name: Install dependencies 🏭
+      run: |
+        python -m pip install --upgrade pip
+        pip install sphinx-book-theme
+        pip install sphinxemoji
+        pip install sphinx-copybutton
+        pip install ipython
+        pip install myst-parser
+        pip install myst-nb
+        pip install numpy
+        pip install pandas
+        pip install scipy
+        pip install scikit-learn
+        pip install matplotlib
+        pip install mne
+        pip install PyWavelets
+        pip install EMD-signal
+        pip install astropy
+        pip install seaborn
+        pip install EMD-signal
+        pip install cvxopt
+        pip install https://github.com/neuropsychology/neurokit/zipball/dev
+
+    - name: Build documentation 📜
+      run: |
+        cd docs
+        sphinx-build -b html . _build
+
+    - name: Deploy 🚀
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./docs/_build

.github/workflows/docs-check.yml

@@ -0,0 +1,42 @@
+name: "📜 Documentation check"
+on:
+- pull_request
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+      with:
+        fetch-depth: 0 # To be able to push refs to destination repo
+    - name: Set up Python 🐍
+      uses: actions/setup-python@v3
+      with:
+        cache: 'pip'
+
+    - name: Install dependencies 🏭
+      run: |
+        python -m pip install --upgrade pip
+        pip install sphinx-book-theme
+        pip install sphinxemoji
+        pip install sphinx-copybutton
+        pip install ipython
+        pip install myst-parser
+        pip install myst-nb
+        pip install numpy
+        pip install pandas
+        pip install scipy
+        pip install scikit-learn
+        pip install matplotlib
+        pip install mne
+        pip install PyWavelets
+        pip install astropy
+        pip install seaborn
+        pip install EMD-signal
+        pip install cvxopt
+        pip install https://github.com/neuropsychology/neurokit/zipball/dev
+
+    - name: Build documentation 📜
+      run: |
+        cd docs
+        sphinx-build -b html . _build

.github/workflows/tests.yml

@@ -1,4 +1,4 @@
-name: Tests
+name: 🏭Tests
 
 # on: [push, pull_request]
 on:
@@ -25,7 +25,7 @@ jobs:
     - uses: actions/checkout@master
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -39,5 +39,5 @@ jobs:
         cd $GITHUB_WORKSPACE && python -m tox -e py
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v2
 

.gitignore

@@ -64,6 +64,8 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/_build/
+docs/savefig/
 
 # PyBuilder
 target/
@@ -197,3 +199,9 @@ data/mit_long-term/mit-bih-long-term-ecg-database-1.0.0/SHA256SUMS.txt
 data/mit_long-term/ECGs.csv
 data/mit_long-term/ECGs.csv
 .DS_Store
+docs/readme/README_popularity.py
+paper/OHBM2022/OHBM2022_Makowski.mp4
+
+
+studies/complexity_benchmark/README_cache/
+studies/complexity_benchmark/manuscript_cache/

AUTHORS.rst

@@ -2,18 +2,27 @@ Authors
 =======
 
 .. hint::
-   Want to be a part of the project? Read how to `contribute and join us <https://neurokit2.readthedocs.io/en/latest/contributing/index.html>`_!
+   Want to be a part of the project? Read how to `contribute and join us <https://neuropsychology.github.io/NeuroKit/resources/contributing.html>`_!
 
-
-Core team
-----------------
+Maintainers
+-----------
 
 * `Dominique Makowski <https://github.com/DominiqueMakowski>`_ *(Nanyang Technological University, Singapore)*
+* `An Shu Te <https://github.com/anshu-97>`_ *(Nanyang Technological University, Singapore)*
+* `Max Ngoi Zi Liang <https://github.com/Max-ZiLiang>`_ *(Nanyang Technological University, Singapore)*
+
+
+Core contributors
+------------------
+
 * `Tam Pham <https://github.com/Tam-Pham>`_ *(Nanyang Technological University, Singapore)*
 * `Zen Juen Lau <https://github.com/zen-juen>`_ *(Nanyang Technological University, Singapore)*
 * `Jan C. Brammer <https://github.com/JanCBrammer>`_ *(Radboud University, Netherlands)*
 * `François Lespinasse <https://github.com/sangfrois>`_ *(Université de Montréal, Canada)*
 
+.. note::
+   We might sometimes update the authors page categories, order of display, etc., and we won't necessarily notify each contributor every time. However, if you are for any reasons unsatisfied with the list, or your position in it, please do let us know!
+
 
 Contributors
 -------------
@@ -23,6 +32,7 @@ Contributors
 * `Duy Le <https://github.com/duylp>`_ *(Hubble, Singapore)*
 * `Leonardo Rydin Gorjão <https://github.com/lrydin>`_ *(OsloMet, Norway)*
 * `Alexander Wong <https://github.com/awwong1>`_ *(University of Alberta, Canada)*
+* `Pierre Elias <https://twitter.com/pierreeliasmd>`_ *(Columbia University, USA)*
 * `Jukka Zitting <https://github.com/jukka>`_
 * `Stavros Avramidis <https://github.com/purpl3F0x>`_
 * `Tiago Rodrigues <https://github.com/TiagoTostas>`_ *(IST, Lisbon)*
@@ -35,33 +45,14 @@ Contributors
 * `Celal Savur <https://github.com/csavur>`_ *(Rochester Institute of Technology, USA)*
 * `Jacob Epifano <https://github.com/jrepifano>`_ *(Rowan University - Children's Hospital of Philadelphia, USA)*
 * `Patryk Wielopolski <https://github.com/pfilo8>`_ *(Wrocław University of Science and Technology, Poland)*
+* `Danielle Benesch <https://github.com/danibene>`_ *(École de technologie supérieure, Canada)*
 
 
 Thanks also to `Gansheng Tan <https://github.com/GanshengT>`_, `Chuan-Peng Hu <https://github.com/hcp4715>`_, `@ucohen <https://github.com/ucohen>`_, `Anthony Gatti <https://github.com/gattia>`_, `Julien Lamour <https://github.com/lamourj>`_, `@renatosc <https://github.com/renatosc>`_, `Nicolas Beaudoin-Gagnon <https://github.com/Fegalf>`_ and `@rubinovitz <https://github.com/rubinovitz>`_ for their contribution in `NeuroKit 1 <https://github.com/neuropsychology/NeuroKit.py>`_.
 
-How to Cite
--------------
-
-
-Makowski, D., Pham, T., Lau, Z. J., Brammer, J. C., Lespinasse, F., Pham, H.,
-Schölzel, C., & Chen, S. A. (2021). NeuroKit2: A Python toolbox for neurophysiological signal processing.
-Behavior Research Methods. https://doi.org/10.3758/s13428-020-01516-y
 
 
-Full bibtex reference:
+.. seealso::
 
-.. code-block:: tex
+   Information about **how to cite** the software in publications can be found `here <https://neuropsychology.github.io/NeuroKit/cite_us.html>`_.
 
-    @article{Makowski2021neurokit,
-      author = {Makowski, Dominique and Pham, Tam and Lau, Zen J. and Brammer, Jan C. and Lespinasse, Fran{\c{c}}ois and Pham, Hung and Sch{\"o}lzel, Christopher and Chen, S. H. Annabel},
-      title={NeuroKit2: A Python toolbox for neurophysiological signal processing},
-      journal={Behavior Research Methods},
-      year={2021},
-      month={Feb},
-      day={02},
-      abstract={NeuroKit2 is an open-source, community-driven, and user-centered Python package for neurophysiological signal processing. It provides a comprehensive suite of processing routines for a variety of bodily signals (e.g., ECG, PPG, EDA, EMG, RSP). These processing routines include high-level functions that enable data processing in a few lines of code using validated pipelines, which we illustrate in two examples covering the most typical scenarios, such as an event-related paradigm and an interval-related analysis. The package also includes tools for specific processing steps such as rate extraction and filtering methods, offering a trade-off between high-level convenience and fine-tuned control. Its goal is to improve transparency and reproducibility in neurophysiological research, as well as foster exploration and innovation. Its design philosophy is centred on user-experience and accessibility to both novice and advanced users.},
-      issn={1554-3528},
-      doi={10.3758/s13428-020-01516-y},
-      url={https://doi.org/10.3758/s13428-020-01516-y}
-    }
-..

NEWS.rst

@@ -14,6 +14,8 @@ Breaking Changes
 New Features
 +++++++++++++
 
+* Add new time-domain measures in `hrv_time()`: `Prc20NN`, `Prc80NN`, `MinNN`, and `MaxNN`
+
 Fixes
 +++++++++++++