From a5b01802037df1c61eb41d0a9eb62ab3c0d31684 Mon Sep 17 00:00:00 2001
From: Nicolas Barascud <10333715+nbara@users.noreply.github.com>
Date: Mon, 2 Sep 2019 10:13:00 +0200
Subject: [PATCH 01/13] test GitHub actions

---
 .github/workflows/pythonpackage.yml | 31 +++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 .github/workflows/pythonpackage.yml

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
new file mode 100644
index 00000000..bb9d9775
--- /dev/null
+++ b/.github/workflows/pythonpackage.yml
@@ -0,0 +1,31 @@
+name: Python package
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: [2.7, 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: Lint with flake8
+      run: |
+        pip install flake8 pytest pytest-cov codecov codespell pydocstyle
+        make pep
+    - name: Test with pytest
+      run: |
+        pip install pytest
+        pytest

From 91b90d1bf179c62a8c9c6cde009af97142078b42 Mon Sep 17 00:00:00 2001
From: nbara <10333715+nbara@users.noreply.github.com>
Date: Mon, 2 Sep 2019 10:18:06 +0200
Subject: [PATCH 02/13] add requirements

---
 .github/workflows/pythonpackage.yml |  5 ++---
 requirements.txt                    | 14 ++++++++++++++
 2 files changed, 16 insertions(+), 3 deletions(-)
 create mode 100644 requirements.txt

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index bb9d9775..210eca1b 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -9,7 +9,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [2.7, 3.5, 3.6, 3.7]
+        python-version: [3.5, 3.6, 3.7]
 
     steps:
     - uses: actions/checkout@v1
@@ -23,9 +23,8 @@ jobs:
         pip install -r requirements.txt
     - name: Lint with flake8
       run: |
-        pip install flake8 pytest pytest-cov codecov codespell pydocstyle
         make pep
     - name: Test with pytest
       run: |
         pip install pytest
-        pytest
+        pytest --cov=meegkit tests/
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 00000000..9ffbbc83
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,14 @@
+numpy
+scipy
+matplotlib
+scikit-learn
+sphinx
+joblib
+numpydoc
+flake8
+pytest
+pytest-cov
+codecov
+codespell
+pydocstyle
+tqdm

From a6e827a8835cba904209be5ef9def88f63ad92d4 Mon Sep 17 00:00:00 2001
From: nbara <10333715+nbara@users.noreply.github.com>
Date: Mon, 2 Sep 2019 10:20:46 +0200
Subject: [PATCH 03/13] Update pythonpackage.yml

---
 .github/workflows/pythonpackage.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index 210eca1b..b0518aea 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -21,6 +21,9 @@ jobs:
       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

From ec997bcf4a34b2700c4f6e41450e893cef0efbd7 Mon Sep 17 00:00:00 2001
From: nbara <10333715+nbara@users.noreply.github.com>
Date: Mon, 2 Sep 2019 10:33:32 +0200
Subject: [PATCH 04/13] Update pythonpackage.yml

---
 .github/workflows/pythonpackage.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index b0518aea..d863dbcc 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -31,3 +31,10 @@ jobs:
       run: |
         pip install pytest
         pytest --cov=meegkit tests/
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action
+      with:
+        token: ${{secrets.CODECOV_TOKEN}}
+        file: ./coverage.xml
+        flags: unittests
+        name: codecov-umbrella

From c588ec35de7b8bdc2e05626c7581ceee7f04483a Mon Sep 17 00:00:00 2001
From: nbara <10333715+nbara@users.noreply.github.com>
Date: Mon, 2 Sep 2019 10:33:59 +0200
Subject: [PATCH 05/13] remove coverage from travis

---
 .travis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index b712e266..59a7a0bc 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -33,5 +33,5 @@ install:
   - python setup.py develop
 script: make pep
 script: pytest --cov=meegkit tests/
-after_success:
-  - bash <(curl -s https://codecov.io/bash)
+# after_success:
+#   - bash <(curl -s https://codecov.io/bash)

From b3a20b85675495e1b24c85e166a77735bbc8d700 Mon Sep 17 00:00:00 2001
From: nbara <10333715+nbara@users.noreply.github.com>
Date: Mon, 2 Sep 2019 10:35:43 +0200
Subject: [PATCH 06/13] Update pythonpackage.yml

---
 .github/workflows/pythonpackage.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index d863dbcc..d6a2c1c9 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -32,7 +32,7 @@ jobs:
         pip install pytest
         pytest --cov=meegkit tests/
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action
+      uses: codecov/codecov-action@v1.0.2
       with:
         token: ${{secrets.CODECOV_TOKEN}}
         file: ./coverage.xml

From 5d27c731e0d5673abe957428dd7409eee7b4e0d1 Mon Sep 17 00:00:00 2001
From: nbara <10333715+nbara@users.noreply.github.com>
Date: Mon, 2 Sep 2019 10:55:35 +0200
Subject: [PATCH 07/13] Update .travis.yml

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 59a7a0bc..4e683e4b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -32,6 +32,6 @@ install:
   - source activate meegkit
   - python setup.py develop
 script: make pep
-script: pytest --cov=meegkit tests/
+script: pytest tests/ --cov=meegkit --cov-report=xml
 # after_success:
 #   - bash <(curl -s https://codecov.io/bash)

From 072333837b71eaf3159ec3e713adb4b09625c88e Mon Sep 17 00:00:00 2001
From: nbara <10333715+nbara@users.noreply.github.com>
Date: Mon, 2 Sep 2019 10:56:35 +0200
Subject: [PATCH 08/13] Update pythonpackage.yml

---
 .github/workflows/pythonpackage.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index d6a2c1c9..646bfa76 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -30,7 +30,7 @@ jobs:
     - name: Test with pytest
       run: |
         pip install pytest
-        pytest --cov=meegkit tests/
+        pytest --cov=meegkit --cov-report=xml tests/
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v1.0.2
       with:

From 5d6b026ff7e702a7570ed9c54e96a8f4d5a1b3b6 Mon Sep 17 00:00:00 2001
From: nbara <10333715+nbara@users.noreply.github.com>
Date: Mon, 2 Sep 2019 11:40:00 +0200
Subject: [PATCH 09/13] Update pythonpackage.yml

---
 .github/workflows/pythonpackage.yml | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index 646bfa76..ed422f42 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -29,12 +29,11 @@ jobs:
         make pep
     - name: Test with pytest
       run: |
-        pip install pytest
         pytest --cov=meegkit --cov-report=xml tests/
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v1.0.2
       with:
         token: ${{secrets.CODECOV_TOKEN}}
-        file: ./coverage.xml
-        flags: unittests
-        name: codecov-umbrella
+        # file: ./coverage.xml
+        # flags: unittests
+        # name: codecov-umbrella

From a6f34148c81a9e2987449eb2d76d8447fb430f0b Mon Sep 17 00:00:00 2001
From: nbara <10333715+nbara@users.noreply.github.com>
Date: Mon, 2 Sep 2019 11:49:41 +0200
Subject: [PATCH 10/13] remove conda

---
 .github/workflows/pythonpackage.yml |  5 +----
 .travis.yml                         | 22 ++--------------------
 environment.yml                     | 21 ---------------------
 3 files changed, 3 insertions(+), 45 deletions(-)
 delete mode 100644 environment.yml

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index ed422f42..af0874e2 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -31,9 +31,6 @@ jobs:
       run: |
         pytest --cov=meegkit --cov-report=xml tests/
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v1.0.2
       with:
         token: ${{secrets.CODECOV_TOKEN}}
-        # file: ./coverage.xml
-        # flags: unittests
-        # name: codecov-umbrella
+      run: bash <(curl -s https://codecov.io/bash)
diff --git a/.travis.yml b/.travis.yml
index 4e683e4b..7dfb33ea 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -11,26 +11,8 @@ python:
   - "3.7"
 install:
   - sudo apt-get update
-  # We do this conditionally because it saves us some downloading if the
-  # version is the same.
-  - if [[ "$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 tests/ --cov=meegkit --cov-report=xml
 # after_success:
diff --git a/environment.yml b/environment.yml
deleted file mode 100644
index 3c48147d..00000000
--- a/environment.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-# run: conda env create --file environment.yml
-name: meegkit
-dependencies:
-- python>=3.5
-- pip
-- numpy
-- scipy
-- matplotlib
-- scikit-learn
-- sphinx
-- joblib
-- numpydoc
-- flake8
-- pip:
-  - pytest
-  - pytest-cov
-  - codecov
-  - codespell
-  - pydocstyle
-  - sphinx-gallery
-  - tqdm

From 8b75ff53388dd6dcf64224397a36eb4d4c18e7bc Mon Sep 17 00:00:00 2001
From: nbara <10333715+nbara@users.noreply.github.com>
Date: Mon, 2 Sep 2019 11:50:13 +0200
Subject: [PATCH 11/13] Update pythonpackage.yml

---
 .github/workflows/pythonpackage.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml
index af0874e2..038c20cd 100644
--- a/.github/workflows/pythonpackage.yml
+++ b/.github/workflows/pythonpackage.yml
@@ -31,6 +31,5 @@ jobs:
       run: |
         pytest --cov=meegkit --cov-report=xml tests/
     - name: Upload coverage to Codecov
-      with:
-        token: ${{secrets.CODECOV_TOKEN}}
+      # token: ${{secrets.CODECOV_TOKEN}}
       run: bash <(curl -s https://codecov.io/bash)

From 3f1d45264b0954125fc5d4f7261ebe0285dddb25 Mon Sep 17 00:00:00 2001
From: nbara <10333715+nbara@users.noreply.github.com>
Date: Mon, 2 Sep 2019 12:00:15 +0200
Subject: [PATCH 12/13] Update sig.py

---
 meegkit/utils/sig.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/meegkit/utils/sig.py b/meegkit/utils/sig.py
index 20cec6a8..26e197b3 100644
--- a/meegkit/utils/sig.py
+++ b/meegkit/utils/sig.py
@@ -1,4 +1,5 @@
 """Signal processing tools."""
+# coding: utf-8
 from __future__ import absolute_import, division, print_function
 
 import numpy as np
@@ -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
     ----------

From 60e1914f61ce91b0d53757daa6b23e6e44aa7136 Mon Sep 17 00:00:00 2001
From: nbara <10333715+nbara@users.noreply.github.com>
Date: Mon, 2 Sep 2019 12:02:50 +0200
Subject: [PATCH 13/13] Update sig.py

---
 meegkit/utils/sig.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/meegkit/utils/sig.py b/meegkit/utils/sig.py
index 26e197b3..4182ee33 100644
--- a/meegkit/utils/sig.py
+++ b/meegkit/utils/sig.py
@@ -1,5 +1,5 @@
-"""Signal processing tools."""
 # coding: utf-8
+"""Signal processing tools."""
 from __future__ import absolute_import, division, print_function
 
 import numpy as np