wtv 0.1.0

A library and CLI for ion selection in mass spectrometry data.

wtv

An implementation of ion selection based on WTV-2.0

Project setup:

1: Clone the code from wtv

2: Create an empty miniconda environment miniconda

3: Manage dependencies with poetry

Running tests:

Using unittest:

To run all tests using unittest, use the following command:

python -m unittest discover -s tests

Using pytest:

1. Ensure pytest is installed:

   poetry install --with dev
   

2. Run tests with pytest:

   poetry run pytest
   

3. Debug test failures: Run pytest with verbose output:

   poetry run pytest -v
   

4. Generate a test coverage report: Install pytest-cov:

   poetry add pytest-cov --group dev
   

   Run tests with coverage:

   poetry run pytest --cov=wtv
   

Testing Documentation Locally

To test the documentation locally, follow these steps:

1. Install MkDocs: Ensure MkDocs and its dependencies are installed. run:

   poetry install --with docs
   

2. Serve the Documentation: Use the following command to serve the documentation locally:

   poetry run mkdocs serve
   

3. Access the Documentation: Open your browser and navigate to http://127.0.0.1:8000 to view the documentation.

Running GitHub Actions Locally with act

To run all GitHub Actions workflows locally using act, follow these steps:

1. Install act: Download and install act from its GitHub repository.

2. Set Up Secrets: Create a .secrets file in the root of your repository and define the required secrets. For example:

   PYPI_API_TOKEN=your-real-or-mock-token-for-testing
   

3. Run All Workflows: Use the following command to run all workflows:

   act
   

4. Run a Specific Workflow: To run a specific workflow, use the -W flag followed by the path to the workflow file:

   act -W .github/workflows/package.yaml
   act -W .github/workflows/publish.yml
   

5. Specify an Event: If you want to simulate a specific event (e.g., push, pull_request, or release), use the -e flag:

   act -e push
   

6. Use a Specific Runner: By default, act uses a lightweight Docker image. To use a full-featured image (e.g., ubuntu-latest), specify it:

   act -P ubuntu-latest=ghcr.io/catthehacker/ubuntu:act-latest
   

Example act Commands

• Run all workflows:

  act
  

• Run the package.yaml workflow:

  act -W .github/workflows/package.yaml
  

• Run the publish.yml workflow:

  act -W .github/workflows/publish.yml
  

• Simulate a release event:

  act -e release
  

Documentation Deployment

This project uses GitHub Actions to auto-generate and deploy documentation to GitHub Pages. To enable this workflow, ensure the following secret is configured in your repository:

• GITHUB_TOKEN: This is automatically provided by GitHub for workflows. No additional setup is required unless you are using a custom token.

Known Issues

• It seems to generate slightly different results based on the OS version and/or Python version.

Acknowledgements

This project is based on the original work by Honglun Yuan, Yiding Jiangfang, Zhenhua Liu, Rong Rong Su, Qiao Li, Chuanying Fang, Sishu Huang, Xianqing Liu, Alisdair Robert Fernie, and Jie Luo, as published in WTV_2.0 and their associated publication.