setup ci

Oucru-Innovations · Nov 14, 2024 · a1839de · a1839de
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,60 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7, 3.8]
+
+    env:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox-travis flake8 tox pytest matplotlib==3.3.4 pytest-cov codecov
+          pip install dash-bootstrap-components dash[testing] webdriver_manager selenium
+          pip install --upgrade setuptools importlib-metadata
+          pip install -e .
+
+      - name: Install Chrome
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y google-chrome-stable libnss3
+          
+      - name: Install Chromedriver
+        run: |
+          wget http://chromedriver.storage.googleapis.com/106.0.5249.61/chromedriver_linux64.zip
+          unzip chromedriver_linux64.zip
+          sudo mv chromedriver /usr/local/bin/chromedriver
+          sudo chmod +x /usr/local/bin/chromedriver
+
+      - name: Run tests with coverage
+        env:
+          DISPLAY: :99.0
+        run: |
+          Xvfb :99 & sleep 3
+          pytest --cov=vital_sqi tests
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v2
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true
+          flags: unittests
diff --git a/.gitignore b/.gitignore
@@ -136,3 +136,148 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+.pytest_cache
+*.py[cod]
+*.pyo
+*.pyd
+
+# C extensions
+*.so
+
+# Notes
+Features.txt
+markdowns/
+visualizations/
+health_analysis_report.html
+report.html
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# Virtual environment
+venv/
+env/
+ENV/
+.venv/
+.env/
+
+# Jupyter Notebook
+.ipynb_checkpoints/
+
+# PyCharm
+.idea/
+*.iml
+
+# VSCode
+.vscode/
+*.code-workspace
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+cov_html/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+
+# Sample data
+sample_data/private
+sample_data/analysis
+sample_data/Event_Data
+
+
+# Notebook
+# src/notebooks/
+
+# pytest
+.cache/
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pylint
+.pylint.d/
+
+# Environments
+.env
+.env.*
+.envrc
+venv.bak/
+.pip/
+
+# macOS
+.DS_Store
+
+# Windows
+Thumbs.db
+ehthumbs.db
+Desktop.ini
+$RECYCLE.BIN/
+*.lnk
+
+docs/source/_static/_images/
+docs/source/notebooks/docs/_static/_images/*
+
+# Logs and databases
+*.log
+*.sqlite3
+*.db
+
+# Temporary files
+*.tmp
+*.temp
+
+# CI/CD
+# .github/workflows/
+
+# Sphinx documentation
+docs/_build/
+
+# Executive Makefile
+make.bat
+
+# Coverage reports
+.coverage
+coverage.xml
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Other
+*.DS_Store
+*.swp
diff --git a/README.md b/README.md
@@ -1,11 +1,21 @@
 # Vital_sqi: Signal quality control of physiological signals
 
-[![Build Status](https://travis-ci.com/meta00/vital_sqi.svg?token=CDjcmJqzLe7opuWagsPJ&branch=main)](https://travis-ci.com/meta00/vital_sqi)
+<!-- [![Build Status](https://travis-ci.com/meta00/vital_sqi.svg?token=CDjcmJqzLe7opuWagsPJ&branch=main)](https://travis-ci.com/meta00/vital_sqi)
 [![codecov](https://codecov.io/gh/meta00/vital_sqi/branch/main/graph/badge.svg?token=6RV5BUK340)](https://codecov.io/gh/meta00/vital_sqi)
 [![Documentation Status](https://readthedocs.org/projects/vitalsqi/badge/?version=latest)](https://vitalsqi.readthedocs.io/en/latest/?badge=latest)
 [![PyPI version](https://badge.fury.io/py/vital-sqi.svg)](https://badge.fury.io/py/vital-sqi)
-[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
-
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) -->
+
+![GitHub stars](https://img.shields.io/github/stars/Oucru-Innovations/vital-sqi?style=social)
+![Build Status](https://github.com/Oucru-Innovations/vital-sqi/actions/workflows/ci.yml/badge.svg)
+[![Coverage Status](https://coveralls.io/repos/github/Oucru-Innovations/vital-sqi/badge.svg)](https://coveralls.io/github/Oucru-Innovations/vital-sqi)
+<!-- [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) -->
+![GitHub License](https://img.shields.io/github/license/Oucru-Innovations/vital-sqi)
+![Python Versions](https://img.shields.io/badge/python-3.7%2B-blue)
+[![Documentation Status](https://readthedocs.org/projects/vital-sqi/badge/?version=latest)](https://vital-sqi.readthedocs.io/en/latest/?badge=latest)
+<!-- ![PyPI Downloads](https://img.shields.io/pypi/dm/vitalsqi)
+[![PyPI version](https://badge.fury.io/py/vitalsqi.svg)](https://badge.fury.io/py/vitalsqi)
+[![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Oucru-Innovations/vital-sqi/blob/main/docs/source/notebooks/synthesize_data.ipynb) -->
 
 # Description
 Vital_sqi is a Python package for signal quality index (SQI) extraction and quality assignment