Merge branch 'master' into ap-end

.github/workflows/main.yml

@@ -0,0 +1,119 @@
+name: Build
+
+on:
+  schedule:
+    # Runs every sunday at 3 a.m.
+    - cron: '0 3 * * SUN'
+  push:
+    branches:
+      - master
+    tags:
+      - '[0-9]+.[0-9]+.[0-9]+'
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [2.7, 3.6, 3.7, 3.8, 3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        pip install tox tox-gh-actions
+    - name: Run tox
+      run: tox
+
+  wheels:
+    if: github.ref == 'refs/heads/master' && github.event_name == 'push'
+    needs: test
+    name: Build wheels for ${{ matrix.python }} ${{ matrix.os }} ${{ matrix.arch }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python: [cp27, cp36, cp37, cp38, cp39]
+        arch: [x86_64, i686]
+        exclude:
+          - os: macos-latest
+            arch: i686
+    env:
+      CIBW_BUILD: ${{ matrix.python }}*${{ matrix.arch }}
+      CIBW_TEST_REQUIRES: nose neo[neomatlabio]>=0.5.1
+      CIBW_TEST_COMMAND: nosetests -s -v -x -w {project}/efel/tests
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - name: Set up Python 3.6
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.6
+      - name: Install cibuildwheel
+        run: pip install cibuildwheel
+      - name: Build wheels
+        run: cibuildwheel --output-dir wheelhouse
+      - uses: actions/upload-artifact@v2
+        with:
+          name: wheels-${{ matrix.os }}-${{ matrix.python }}-${{ matrix.arch }}
+          path: ./wheelhouse/*.whl
+
+  tarball:
+    if: github.ref == 'refs/heads/master' && github.event_name == 'push'
+    name: Build tarball
+    runs-on: ubuntu-latest
+    needs: test
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - name: Set up Python 3.6
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.6
+      - name: Build a source tarball
+        run:
+            python setup.py sdist
+      - uses: actions/upload-artifact@v2
+        with:
+          name: tarball
+          path: dist
+
+
+  publish:
+    if: github.ref == 'refs/heads/master' && github.event_name == 'push'
+    name: Publish on PyPI
+    runs-on: ubuntu-latest
+    needs: [test, wheels, tarball]
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - name: Set up Python 3.6
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.6
+
+      - name: Download all artifacts
+        uses: actions/download-artifact@v2
+        with:
+          path: artifacts
+
+      - name: Put artifacts into dist directory
+        run: |
+          mkdir -p dist
+          find artifacts -type f \( -iname \*.whl -o -iname \*.tar.gz \) -exec mv {} dist \;
+
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

.jenkins.sh

@@ -0,0 +1,38 @@
+#!/bin/bash
+
+set -e
+set -x
+
+git config --global http.proxy http://bbpproxy.epfl.ch:80/
+git config --global https.proxy http://bbpproxy.epfl.ch:80/
+
+tox_args='-v --recreate'
+tox_args="${tox_args} -e py3-test"
+
+if [ "${os}" = "bb5" ]
+then
+	. /opt/rh/rh-python36/enable
+fi
+
+cd $WORKSPACE
+
+#########
+# Virtualenv
+#########
+
+if [ ! -d "${WORKSPACE}/env" ]; then
+  python -m venv env
+fi
+
+. ${WORKSPACE}/env/bin/activate
+pip install pip --upgrade
+pip install tox --upgrade   
+
+
+#####
+# Tests
+#####
+
+cd  ${WORKSPACE}/eFEL
+
+tox ${tox_args}

.travis.yml

@@ -21,13 +21,6 @@ git:
 cache:
   directories:
   - $HOME/.cache/pip
-deploy:
-  provider: pypi
-  user: wvangeit
-  password:
-    secure: c9fJz1IliA0Scg4MS1HBAFbyGHnTOViYbF0I0WhrspqeNyyF4WKBx2kQzvMguc6JVm8MrcqdrM2P/me7WiD9vO4geqO/kXsjeg8kE2JnlGtAgX8PpOaR0P/IFdVcmfIc//05QS8PyovVZMxqlOrya1CN9cO4NMDRM9LS2dAaih0=
-  distributions: sdist
-  skip_existing: true
 before_install:
 - pip install pip --upgrade
 - pip install tox --upgrade

README.md

@@ -28,8 +28,8 @@
 <tr>
   <td>Build Status</td>
   <td>
-    <a href="https://travis-ci.com/BlueBrain/eFEL">
-    <img src="https://travis-ci.com/BlueBrain/eFEL.svg?branch=master" alt="travis build status" />
+    <a href="https://github.com/BlueBrain/eFEL/actions">
+    <img src="https://github.com/BlueBrain/eFEL/workflows/Build/badge.svg?branch=master" alt="actions build status" />
     </a>
   </td>
 </tr>

docs/source/eFeatures.rst

@@ -419,6 +419,29 @@ The voltage deflection between voltage base and steady-state voltage at stimend
 
     voltage_deflection_vb_ssse = steady_state_voltage_stimend - voltage_base
 
+LibV1: minimum_voltage
+~~~~~~~~~~~~~~~~~~~~~~
+
+The minimum of the voltage during the stimulus
+
+- **Required features**: t, V, stim_start, stim_end
+- **Units**: mV
+- **Pseudocode**: ::
+
+    minimum_voltage = min(voltage[numpy.where((t >= stim_start) & (t <= stim_end))])
+
+LibV1: maximum_voltage
+~~~~~~~~~~~~~~~~~~~~~~
+
+The maximum of the voltage during the stimulus
+
+- **Required features**: t, V, stim_start, stim_end
+- **Units**: mV
+- **Pseudocode**: ::
+
+    maximum_voltage = max(voltage[numpy.where((t >= stim_start) & (t <= stim_end))])
+
+
 
 Requested eFeatures
 ===================
@@ -458,34 +481,14 @@ The average voltage during the last 90% of the stimulus duration realtive to vol
     steady_state_voltage_stimend_from_voltage_base = steady_state_voltage_stimend - voltage_base
 
 
-**LibV5 : min_duringstim**
-The minimum voltage during stimulus
-
-- **Required features**:
-- **Units**: mV
-- **Pseudocode**: ::
-
-    min_duringstim = [numpy.min(voltage[numpy.where((t <= stim_end[0]) & (t >= stim_start[0]))])]
-
-
 **LibV5 : min_duringstim_from_voltage_base**
 The minimum voltage during stimulus
 
 - **Required features**: LibV5: min_duringstim (mV), LibV5: voltage_base (mV)
 - **Units**: mV
 - **Pseudocode**: ::
 
-    min_duringstim_from_voltage_base = min_duringstim - voltage_base
-
-
-**LibV5 : max_duringstim**
-The minimum voltage during stimulus
-
-- **Required features**:
-- **Units**: mV
-- **Pseudocode**: ::
-
-    min_duringstim = [numpy.max(voltage[numpy.where((t <= stim_end[0]) & (t >= stim_start[0]))])]
+    min_duringstim_from_voltage_base = minimum_voltage - voltage_base
 
 
 **LibV5 : max_duringstim_from_voltage_base**
@@ -495,7 +498,7 @@ The minimum voltage during stimulus
 - **Units**: mV
 - **Pseudocode**: ::
 
-    max_duringstim_from_voltage_base = max_duringstim - voltage_base
+    max_duringstim_from_voltage_base = maximum_voltage - voltage_base
 
 **LibV5 : diff_max_duringstim**
 Difference between maximum and steady state during stimulation

tox.ini

@@ -1,19 +1,16 @@
 [tox]
-envlist = py{27,35,36,37,38}-{style, test}
+envlist = py{27,3}-{style,test}
 [gh-actions]
 python =
-    2.7: py27{,-style}
-    3.5: py35{,-style}
-    3.6: py36{,-style}
-    3.7: py37{,-style}
-    3.8: py38{,-style}
+    2.7: py27
+    3.6: py3
+    3.7: py3
+    3.8: py3
+    3.9: py3
 [testenv]
 envdir =
-    py27{,-style}: {toxworkdir}/py27
-    py35{,-style}: {toxworkdir}/py35
-    py36{,-style}: {toxworkdir}/py36
-    py37{,-style}: {toxworkdir}/py37
-    py38{,-style}: {toxworkdir}/py38
+    py27{,-style,-test}: {toxworkdir}/py27
+    py3{6,7,8,9,}{,-style,-test}: {toxworkdir}/py3
 deps =
     nose
     coverage