Merge pull request #3 from JanCBrammer/dev

Version bump

.github/workflows/publish.yml

@@ -0,0 +1,35 @@
+name: publish
+on:
+  release:
+    types: [published]
+
+
+jobs:
+
+  build_publish:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.7
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade setuptools pip wheel twine
+      - name: Build source and wheel
+        run: |
+          python setup.py sdist bdist_wheel
+      - name: Publish
+        # env:
+        #   TWINE_USERNAME: ${{ secrets.TESTPYPI_USERNAME }}
+        #   TWINE_PASSWORD: ${{ secrets.TESTPYPI_PASSWORD }}
+        # run: |
+        #   twine upload --repository-url https://test.pypi.org/legacy/ dist/*
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: |
+          twine upload dist/*

.github/workflows/test.yml

@@ -0,0 +1,147 @@
+name: test
+on:
+  push:
+    branches:
+      - master
+      - dev
+  pull_request:
+    branches:
+      - master
+      - dev
+
+jobs:
+
+  lint:
+
+    runs-on: ubuntu-latest
+
+    steps:    # every step is marked with a leading hyphen (-)
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.7
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade setuptools pip wheel
+          python -m pip install flake8
+      - name: Linting
+        run: |
+          flake8 biopeaks --exclude biopeaks/images,biopeaks/tests/testdata,biopeaks/resources.py --max-complexity=10 --ignore E303,C901,E203,W503,E501,W504,E129,W605,E371,E731
+
+
+  build:
+
+    needs: lint    # only run if lint finishes
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.7
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade setuptools pip wheel
+      - name: Build source and wheel
+        run: |
+          python setup.py sdist bdist_wheel
+      - name: Upload source
+        uses: actions/upload-artifact@v2
+        with:
+          name: source
+          path: dist/*.tar.gz
+      - name: Upload wheel
+        uses: actions/upload-artifact@v2
+        with:
+          name: wheel
+          path: dist/*.whl
+
+
+  test_source:
+
+    needs: build    # only run if build finishes
+    runs-on: ${{ matrix.os }}
+    continue-on-error: false
+    strategy:
+      matrix:    # all steps of this job will run using this matrix (matrix not accessible to other jobs)
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: [3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up miniconda
+      uses: goanpeca/setup-miniconda@v1
+      with:
+        auto-update-conda: true
+        channels: conda-forge
+        channel-priority: strict
+        activate-environment: ci_env    # includes pytest and pip
+        environment-file: environment.yml
+        python-version: ${{ matrix.python-version }}
+        auto-activate-base: false
+    - name: Download source
+      uses: actions/download-artifact@v2
+      with:
+        name: source
+    - name: Install source
+      shell: bash -l {0}
+      run: |
+        ls
+        pip install --no-index --find-links=. biopeaks    # --no-index: do not install from PyPI, --find-links=.:search local dir for wheels or source
+    - name: Test with pytest on Ubuntu
+      if: matrix.os == 'ubuntu-latest'
+      shell: bash -l {0}
+      run: |
+        sudo apt-get install -y xvfb x11-utils libxkbcommon-x11-0
+        xvfb-run pytest -v
+    - name: Test with pytest on Windows and MacOS
+      if: matrix.os == 'windows-latest' || matrix.os == 'macos-latest'
+      shell: bash -l {0}
+      run: |
+        pytest -v
+
+
+  test_wheel:
+
+    needs: build    # only run if build finishes
+    runs-on: ${{ matrix.os }}
+    continue-on-error: false
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: [3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up miniconda
+      uses: goanpeca/setup-miniconda@v1
+      with:
+        auto-update-conda: true
+        channels: conda-forge
+        channel-priority: strict
+        activate-environment: ci_env
+        environment-file: environment.yml
+        python-version: ${{ matrix.python-version }}
+        auto-activate-base: false
+    - name: Download wheel
+      uses: actions/download-artifact@v2
+      with:
+        name: wheel
+    - name: Install wheel
+      shell: bash -l {0}
+      run: |
+        ls
+        pip install --no-index --find-links=. biopeaks
+    - name: Test with pytest on Ubuntu
+      if: matrix.os == 'ubuntu-latest'
+      shell: bash -l {0}
+      run: |
+        sudo apt-get install -y xvfb x11-utils libxkbcommon-x11-0
+        xvfb-run pytest -v
+    - name: Test with pytest on Windows and MacOS
+      if: matrix.os == 'windows-latest' || matrix.os == 'macos-latest'
+      shell: bash -l {0}
+      run: |
+        pytest -v

.gitignore

@@ -5,4 +5,5 @@ build/
 dist/
 __pycache__/
 biopeaks/__pycache__/
-biopeaks.egg-info/
+biopeaks.egg-info/
+.vscode/

README.md

@@ -1,6 +1,6 @@
 ![logo](docs/images/logo.png)
 
-![](https://github.com/JanCBrammer/biopeaks/workflows/build/badge.svg?branch=dev)
+![](https://github.com/JanCBrammer/biopeaks/workflows/test/badge.svg?branch=dev)
 
 # Citation
 Click on the badge below to cite `biopeaks` in a format of your choice.
@@ -13,17 +13,17 @@ Click on the badge below to cite `biopeaks` in a format of your choice.
 `biopeaks` is a straightforward graphical user interface for feature extraction from electrocardiogram (ECG), photoplethysmogram (PPG) and breathing biosignals.
 It processes these biosignals semi-automatically with sensible defaults and offers the following functionality:
 
-* processes files in the open biosignal formats [EDF](https://en.wikipedia.org/wiki/European_Data_Format)
-as well as [OpenSignals (Bitalino)](https://bitalino.com/en/software)
-* interactive biosignal visualization
-* biosignal segmentation
-* benchmarked, automatic extrema detection (R-peaks in ECG, systolic peaks in PPG, exhalation troughs and inhalation
-peaks in breathing signals)
-* automatic state-of-the-art [artifact correction](https://www.tandfonline.com/doi/full/10.1080/03091902.2019.1640306)
++ processes files in the open biosignal formats [EDF](https://en.wikipedia.org/wiki/European_Data_Format), [OpenSignals (Bitalino)](https://bitalino.com/en/software)
+as well as plain text files (.txt, .csv, .tsv)
++ interactive biosignal visualization
++ biosignal segmentation
++ benchmarked, automatic extrema detection (R-peaks in ECG, systolic peaks in PPG, exhalation troughs and inhalation
+peaks in breathing signals) with signal-specific, sensible defaults
++ automatic state-of-the-art [artifact correction](https://www.tandfonline.com/doi/full/10.1080/03091902.2019.1640306)
  for ECG and PPG extrema
-* manual editing of extrema (useful in case of poor biosignal quality)
-* calculation of instantaneous (heart- or breathing-) rate and period, as well as
-breathing amplitude
-* batch processing
++ manual editing of extrema
++ extraction of instantaneous features: (heart- or breathing-) rate and period, as well as breathing amplitude
++ .csv export of extrema and instantaneous features for further analysis (e.g., heart rate variability)
++ automatic analysis of multiple files (batch processing)
 
 Visit the [documentation](https://jancbrammer.github.io/biopeaks/) for additional information.

biopeaks.qrc

@@ -2,6 +2,6 @@
 <qresource>
     <file alias="python_icon.png">biopeaks/images/python_icon.png</file>
     <file alias="mouse_icon.png">biopeaks/images/mouse_icon.png</file>
-    <file alias="logo.png">biopeaks/images/logo.png</file>
+    <file alias="file_icon.png">biopeaks/images/file_icon.png</file>
 </qresource>
 </RCC>

biopeaks/__main__.py

@@ -23,4 +23,3 @@ def main():
 
 if __name__ == '__main__':
     main()
-

biopeaks/tests/benchmark_ECG.py → biopeaks/benchmarks/benchmark_ECG_local.py

@@ -2,14 +2,13 @@
 
 import glob
 import os
-import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
 from biopeaks.heart import ecg_peaks
 from wfdb.processing import compare_annotations
 
 
-GUDB_dir = r"directory\containing\GUDB\subjects"
+GUDB_dir = r"...\experiment_data"
 
 os.chdir(GUDB_dir)
 

biopeaks/benchmarks/benchmark_ECG_stream.py

@@ -0,0 +1,6 @@
+from biopeaks.heart import ecg_peaks
+from benchmark_utils import BenchmarkDetectorGUDB
+
+
+pipeline = BenchmarkDetectorGUDB(ecg_peaks, 1)
+pipeline.benchmark_records("jogging", channel="cs_V2_V1", annotation="annotation_cs")