update chromedriver

auto check chromedriver

set specific chrome driver versioni for unit test

fix ci

ci

work around

use browser-action

add vitalDSP to the requirements

astro

update ci

fix ci again

final update

chrome-version

check coverall upload

rtd fix

update docstring

update rtd

gen rtd

update manifest

fix rtd

update rtd

update coverage

add contributing.md

update installation instruction

update readme pyproject toml file

update readthedocs

update pyproject.toml

fix pyproject

fix pyproj

update pyproject

fix rtd

use install editable in rtd

fix rtd hyphen

go go go

to the mars

.coveragerc

@@ -0,0 +1,3 @@
+[run]
+omit =
+    vital_sqi/app/*

.github/workflows/ci.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9, 3.10, 3.11]
+        python-version: [3.7, 3.8, 3.9, 3.11]
 
     env:
       COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
@@ -33,41 +33,28 @@ jobs:
           pip install --upgrade setuptools importlib-metadata
           pip install -e .
 
-      - name: Install Chrome and dependencies
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y google-chrome-stable libnss3 xvfb
-          
-      # - 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: Install Chromedriver using webdriver-manager
-      #   run: |
-      #     pip install webdriver-manager
-      #     python -c "from webdriver_manager.chrome import ChromeDriverManager; print(ChromeDriverManager().install())"
-      - name: Install Chromedriver
-        run: |
-          CHROME_VERSION=$(google-chrome --version | awk '{print $3}' | cut -d'.' -f1)
-          wget https://chromedriver.storage.googleapis.com/${CHROME_VERSION}.0.5249.61/chromedriver_linux64.zip || true
-          wget https://chromedriver.storage.googleapis.com/${CHROME_VERSION}.0/chromedriver_linux64.zip
-          unzip chromedriver_linux64.zip
-          sudo mv chromedriver /usr/local/bin/chromedriver
-          sudo chmod +x /usr/local/bin/chromedriver
+      - name: Set up Chrome and ChromeDriver
+        uses: browser-actions/setup-chrome@v1
+        with:
+          chrome-version: '131.0.6778.85'          # Use 'latest' or specify a specific version
+          install-chromedriver: true        # Install the compatible ChromeDriver
 
       - name: Run tests with coverage
         env:
           DISPLAY: :99.0
         run: |
           Xvfb :99 & sleep 3
-          pytest --cov=vital_sqi --cov-report=xml --cov-report=term-missing tests
-            
+          pytest --cov=vital_sqi --cov-config=.coveragerc --cov-report=xml --cov-report=term-missing tests
+      
+      - name: Debug coverage files
+        run: |
+          ls -la
+          cat coverage.xml
+      
       - name: Upload to Coveralls
         uses: coverallsapp/[email protected]
         with:
           github-token: ${{ secrets.COVERALLS_REPO_TOKEN }}
           coveralls-endpoint: https://coveralls.io
-          path-to-lcov: ./tests  # Adjust if necessary
+          path-to-lcov: coverage.xml
+          # path-to-lcov: ./tests 

.gitignore

@@ -7,6 +7,9 @@ environment.yml
 
 # -------------------------------------------------
 
+# Example gen by local makefile
+examples/
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -49,6 +52,11 @@ pip-delete-this-directory.txt
 # ChromeDriver
 chromedriver/
 
+# extra docstrings
+docs/source/extra/.
+docs/source/_examples/tutorials
+docs/source/sg_execution_times.rst
+
 # Unit test / coverage reports
 htmlcov/
 .tox/

.readthedocs.yaml

@@ -11,18 +11,19 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.7" 
+    python: "3.9" 
   jobs:
     post_install:
       - pip install -r docs/requirements.txt  # Documentation dependencies
       - pip install -r requirements.txt       # Project dependencies
-      - pip install git+https://github.com/Oucru-Innovations/vital-sqi.git  # Latest code from GitHub if needed
+      # - pip install git+https://github.com/Oucru-Innovations/vital-sqi.git  # Latest code from GitHub if needed
+      - pip install -e .
 
 # Sphinx configuration
 sphinx:
   builder: html
   configuration: docs/source/conf.py
-  fail_on_warning: true  # Fail build on any warnings for stricter error checking
+  fail_on_warning: false  # Fail build on any warnings for stricter error checking
 
 # Python setup
 python:

CONTRIBUTING.md

@@ -0,0 +1,123 @@
+
+# Contributing to Vital_SQI
+
+🎉 Thank you for your interest in contributing to **Vital_SQI**! 🎉  
+We’re thrilled to have you on board. Below is a step-by-step guide to help you navigate the contribution process.
+
+---
+
+## How Can You Contribute? 🤔
+
+There are several ways you can contribute to the project:
+- **Report Bugs** 🐛
+- **Request Features** ✨
+- **Submit Pull Requests** 🔧
+- **Improve Documentation** 📖
+
+---
+
+## Reporting Issues 🐞
+
+If you find a bug or want to suggest an enhancement, let us know:
+1. Go to the [Issues](https://github.com/Oucru-Innovations/vital-sqi/issues) page.
+2. Click on `New Issue`.
+3. Choose the appropriate template:
+   - **Bug Report** for bugs.
+   - **Feature Request** for enhancements.
+4. Fill out the form and submit!
+
+---
+
+## Contributing Code 🔨
+
+Ready to dive into the code? Awesome! Here’s how you can get started:
+
+### 1. Fork the Repository 🍴
+Click the **Fork** button at the top right of the [Vital_SQI GitHub page](https://github.com/Oucru-Innovations/vital-sqi).
+
+### 2. Clone Your Fork 🖥️
+```bash
+git clone https://github.com/<your-username>/vital-sqi.git
+cd vital-sqi
+```
+
+### 3. Create a New Branch 🌿
+Always create a new branch for your work:
+```bash
+git checkout -b feature/my-awesome-feature
+```
+
+### 4. Install Dependencies 📦
+We use `pip` for dependencies:
+```bash
+pip install -r requirements.txt
+```
+
+### 5. Make Your Changes ✏️
+- Write clean, modular, and well-documented code.
+- Ensure your changes align with our [Code of Conduct](#code-of-conduct).
+
+### 6. Run Tests ✅
+Before pushing your code, ensure all tests pass:
+```bash
+pytest tests/
+```
+
+### 7. Push Your Changes 🚀
+```bash
+git add .
+git commit -m "Add my awesome feature"
+git push origin feature/my-awesome-feature
+```
+
+### 8. Open a Pull Request 🔃
+1. Go to the [Pull Requests](https://github.com/Oucru-Innovations/vital-sqi/pulls) page.
+2. Click `New Pull Request`.
+3. Choose your branch and describe your changes.
+
+---
+
+## Style Guide 🖌️
+
+To keep our code consistent:
+- Follow **PEP8** guidelines.
+- Use meaningful variable and function names.
+- Document your code with docstrings.
+- Format code using `flake8`:
+```bash
+flake8 --config=.flake8 vital_sqi tests
+```
+
+---
+
+## Local Development 🛠️
+
+For development and debugging, use the `Makefile`:
+- Install the package:
+  ```bash
+  make install
+  ```
+- Run tests with coverage:
+  ```bash
+  make test
+  ```
+
+---
+
+## Code of Conduct ❤️
+
+Be respectful and kind. We are committed to fostering an inclusive community where everyone feels welcome.
+
+---
+
+## Need Help? 🤝
+
+If you’re stuck or have any questions, feel free to:
+- Open a discussion on the [Discussions](https://github.com/Oucru-Innovations/vital-sqi/discussions) page.
+- Reach out via email: **[email protected]**.
+
+---
+
+Thank you for contributing! Your efforts make **Vital_SQI** better for everyone. 🚀
+
+— The **Vital_SQI** Development Team

MANIFEST.in

@@ -1,2 +1,8 @@
 include LICENSE
-include Readme.md
+include Readme.md
+include vital_sqi/resource/sqi_dict.json
+include vital_sqi/resource/rule_dict.json
+include tests/test_data/sqi_dict.json
+include tests/test_data/rule_dict.json
+include vital_sqi/resource/peak_dectector_list.txt
+include vital_sqi/resource/citations.bib

Makefile

@@ -48,12 +48,12 @@ doc-style: ## convert documentation style to numpy style
 	pyment -o numpydoc -w $(filename)
 
 test: ## run tests with coverage report
-	pytest --cov=vital_sqi --cov-report term tests/
+	pytest --cov=vital_sqi --cov-config=.coveragerc --cov-report term tests/
 
 BROWSER ?= firefox
 
 cov: ## Run tests and show coverage report by file in the terminal
-	pytest --cov=vital_sqi --browser=$(BROWSER) tests/ 
+	pytest --cov=vital_sqi --cov-config=.coveragerc --browser=$(BROWSER) tests/ 
 	coverage report -m
 
 test-all: ## run tests on every Python version with tox