[CI] Add GitHub actions

.github/workflows/pythonpackage.yml

@@ -0,0 +1,35 @@
+name: Python package
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: [3.5, 3.6, 3.7]
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+    - name: Install meegkit
+      run: |
+        pip install -e .
+    - name: Lint with flake8
+      run: |
+        make pep
+    - name: Test with pytest
+      run: |
+        pytest --cov=meegkit --cov-report=xml tests/
+    - name: Upload coverage to Codecov
+      # token: ${{secrets.CODECOV_TOKEN}}
+      run: bash <(curl -s https://codecov.io/bash)

.travis.yml

@@ -11,27 +11,9 @@ python:
   - "3.7"
 install:
   - sudo apt-get update
-  # We do this conditionally because it saves us some downloading if the
-  # version is the same.
-  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
-      wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
-    else
-      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-    fi
-  - bash miniconda.sh -b -p $HOME/miniconda
-  - export PATH="$HOME/miniconda/bin:$PATH"
-  - hash -r
-  - conda config --set always_yes yes --set changeps1 no
-  - conda update -q conda
-
-  - export DISPLAY=:99.0
-  - /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1400x900x24 -ac +extension GLX +render -noreset
-  # Useful for debugging any issues with conda
-  - conda info -a
-  - conda env create -f environment.yml
-  - source activate meegkit
-  - python setup.py develop
+  - pip install -r requirements.txt
+  - pip install -e .
 script: make pep
-script: pytest --cov=meegkit tests/
-after_success:
-  - bash <(curl -s https://codecov.io/bash)
+script: pytest tests/ --cov=meegkit --cov-report=xml
+# after_success:
+#   - bash <(curl -s https://codecov.io/bash)

meegkit/utils/sig.py

@@ -1,3 +1,4 @@
+# coding: utf-8
 """Signal processing tools."""
 from __future__ import absolute_import, division, print_function
 
@@ -53,10 +54,13 @@ def modulation_index(phase, amp, n_bins=18):
     time series can be constructed by cutting the amplitude time series at a
     random time point and reversing the order of both parts [2]_. The observed
     coupling value is standardized to the distribution of the shuffled coupling
-    values according to the following formula: MI_z = (MI_observed −
-    µ_MI_shuffled) / σ_MI_shuffled, where μ denotes the mean and σ the standard
-    deviation. Only when the observed phase-locking value is larger than 95 %
-    of shuffled values, it is defined as significant. See [2]_ for details.
+    values according to the following formula:
+
+    MI_z = (MI_observed − µ_MI_shuffled) / σ_MI_shuffled
+
+    where μ denotes the mean and σ the standard deviation. Only when the
+    observed phase-locking value is larger than 95 % of shuffled values, it is
+    defined as significant. See [2]_ for details.
 
     References
     ----------

requirements.txt

@@ -0,0 +1,14 @@
+numpy
+scipy
+matplotlib
+scikit-learn
+sphinx
+joblib
+numpydoc
+flake8
+pytest
+pytest-cov
+codecov
+codespell
+pydocstyle
+tqdm