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Python

How to select a Python project to contribute to?

• For now I’ll pick some of the scientific libraries. e.g. Biology-related libraries.
• Search on GitHub: A semi-popular, recently updated Python project stars:100..1000 pushed:>2025-10-01 language:Python
• I can also ask ChatGPT to suggest other science-related libraries.
• PyDigger - once it is fixed.
• TBD

What and how to contribute to a Python project?

• Testing
  • Python testing demo
  • Python testing
  • Generate test coverage report
• Add type annotation
  • Python types
  • Python types at PyWeb 2025.05
• Linting
• code formatting
  • black
• Fuzz testing
• Mutation testing
• code complexity analyzis
• refactoring
• Setting up CI (GitHub Actions or GitLab pipelines)
• Updating the GitHub actions if necessary
• Add dependabot for GitHub Actions.
• Add dependabot for the code-base.
• Code reading

Projects

• MoreBeautifulPython
  • 2022.12.01
  • Article: Test and CI for MoreBeautifulPython
  • PR: Add a simple test and set up GitHub action to run it one every push - Merged ✅
• farmworld
  • 2022.12.03
  • Article: CI for farmworld, a Python package - a failed attempt
  • I sent a PR, but I don’t know what happened to it as the project was removed from GitHub. ❓
  • I still have my fork 🍴 (there is no stand-alone fork emoji)
• wsblib - Web Server Base Library.
  • 2022.12.03
  • Article: GitHub Action CI for wsblib Python
  • PR: Add GitHub Actions - Merged ✅
• col-spanish - A collection of tools to work with text write in Spanish (Colombia)
  • 2022.12.04
  • Article: GitHub Actions for Colombian Spanish
  • PR: Add GitHub Actions - Rejected ❌ without explanation.
• pcr_optimizer - A Python package to aid researchers in optimizing pcr protocols (Polymerase chain reaction)
  • 2022.12.06
  • Article: GitHub Actions CI for the pcr_optimizer Python package
  • PR: Add GitHub Actions - Merged ✅
• sdk-py - Decentralized Instant Messaging (Python SDK)
  • 2022.12.12
  • Article: CI for sdk-py Python packages
  • PR: Add GitHub Action - Waiting 🕰️
• core_curate_app - Curation functionalities for the curator core project.
  • 2022.12.13
  • Article: CI for a Python project of the National Institute of Standards and Technology
  • PR: Add GitHub Actions - Rejected ❌ without explanation.
• vfxpaths - A system analysis framework related to VFX common file operations.
  • 2022.12.15
  • Article: Failing CI to help fixing filesystem issues in a Python package
  • PR: Add GitHub Action - Merged ✅

Some python projects

(Not fully categorized yet)

Generic

• requests
• jupyter
• flask
• pandas
• pytest

• numpy

• allensdk
• box2d
• cv2
• deeplabcut
• functools
• glob
• gseapy
• h5py
• itertools
• joblib
• keras
• matplot
• matplotlib
• mayavi
• openpyxl
• PIL
• pygame
• pyppt
• ray
• redirect
• scipy
• seaborn
• skimage
• statsmodels
• tifffile
• voila

ML

• scikit-fmm
• sklearn
• tensorflow

Generic visualization

• plotly
• bokeh

Semi specialized

• Biopython

Specialized

• pcr_optimizer
• GalSim is open-source software for simulating images of astronomical objects

• farmworld

• logomaker
• BCAWT Automated tool for codon usage bias analysis for molecular evolution
• An-Open-Source-Computational-Tool-for-Measuring-Bacterial-Biofilm-Morphology-and-Growth-Kinetics
• MaLiAmPi Maximum Likelihood Amplicon Pipeline: An amplicon (PCR / 16S) microbiome pipeline.

These 3 try to solve the same problem:

• Bio.SeqUtils.CodonUsage module
• CAI Python Codon Adaptation Index
• Codon-Usage-in-Python