OSS

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title
OSS Training Course
author
Lukasz Sokolowski


OSS

OSS Training Materials

Introduction/Outline

  • Code management, versioning, and licensing
  • Automation and code quality (best practices)
  • Continuous Integration (CI) on GitHub/GitLab
  • Automated testing (unit, integration, end-to-end)
  • Changelog (Keep a Changelog, Conventional Commits)
  • Issue management and roadmap
  • Best practices in issue creation (templates, labels, milestones)
  • Documentation
    • Effective README: objectives, installation, usage, contributions
    • Contributing Guide (CONTRIBUTING.md)
    • API documentation (Swagger, Sphinx, Docusaurus, etc.)

Main Keys/Concerns

From Andre's notes/suggestions (=

Open Source Software in Research: Strategy, Practice, and Impact

Open Source Software (OSS) as a strategic, technical, and scientific asset for research institutes, illustrated with real-world examples.

Slide 1 — The Strategic Role of OSS in a Research Institute

Open Source Software is foundational to modern research practice.

Benefits:

  • Visibility of research outputs
  • Increased scientific impact
  • Collaboration across institutions
  • Transparency and reproducibility
  • Long-term sustainability

OSS functions as shared research infrastructure.

Slide 2 — Real-World Example: CERN

CERN treats software as a first-class research output.

Practices:

  • Public repositories for core software (e.g., ROOT, Geant4)
  • Strong open source licensing culture
  • Long-term maintenance beyond individual projects

Impact:

  • Software reused globally in physics and beyond
  • Industrial and academic adoption
  • Software cited alongside publications

Key lesson: Large-scale research infrastructures depend on open software.

Slide 3 — OSS and Publicly Funded Research

Open software aligns with public funding principles.

Key drivers:

  • Open science mandates
  • Reproducibility requirements
  • Accountability to taxpayers

OSS ensures research results are:

  • Verifiable
  • Reusable
  • Preserved beyond project lifetimes

Slide 4 — Real-World Example: European Commission & EOSC

The European Open Science Cloud (EOSC) promotes OSS.

Practices:

  • Preference for open licenses
  • FAIR principles applied to software
  • Software recognized as a research output

Impact:

  • Policy-level support for open software
  • Alignment across national research infrastructures

Key lesson: OSS is increasingly embedded in research policy.

Slide 5 — Licensing Choices: Why They Matter

Licenses define legal reuse.

Without a license:

  • Code cannot be reused
  • Collaboration is legally blocked

Licensing must be intentional and documented.

Slide 6 — Real-World Example: NumPy & SciPy

NumPy and SciPy originated in academic research.

License choice:

  • BSD (permissive)

Outcomes:

  • Massive industrial and academic adoption
  • Integration into commercial products
  • Long-term sustainability via a broad community

Key lesson: Permissive licenses can maximize scientific reach.

Slide 7 — Permissive vs. Copyleft Licenses

Two main license families are common in research.

Permissive:

  • MIT, BSD, Apache 2.0
  • Fewer restrictions
  • High reuse potential

Copyleft:

  • GPL, LGPL
  • Ensures openness of derivatives
  • May limit industrial integration

Slide 8 — Real-World Example: GNU Scientific Software

GNU scientific tools use copyleft licenses.

License choice:

  • GPL

Outcomes:

  • Guaranteed openness of derivatives
  • Strong alignment with free software principles
  • Smaller but ideologically aligned ecosystem

Key lesson: Copyleft prioritizes openness over adoption scale.

Slide 9 — Minimum Best Practices for Publishing Research Software

Research software should meet baseline standards.

Required:

  • Public repository
  • Clear license
  • Documentation
  • Versioning
  • Citation metadata

Quality enables reuse.

Slide 10 — Real-World Example: EMBL-EBI

EMBL-EBI publishes bioinformatics software openly.

Practices:

  • Standardized repositories
  • Clear documentation
  • Explicit versioning and releases

Impact:

  • Tools reused globally in life sciences
  • Software cited in publications
  • Long-lived community tools

Key lesson: Consistency scales reuse.

Slide 11 — Documentation as a Research Output

Documentation supports reproducibility.

Minimum documentation:

  • Purpose and scope
  • Installation
  • Usage examples
  • Limitations

Good documentation is an investment, not overhead.

Slide 12 — Versioning, Releases, and Citation

Stable versions enable scientific referencing.

Best practices:

  • Semantic Versioning
  • Git tags
  • DOI assignment via Zenodo
  • CITATION.cff file

Slide 13 — Real-World Example: Zenodo + GitHub

Many institutes integrate GitHub with Zenodo.

Practices:

  • DOI minted for each release
  • Software cited like a paper
  • Version-specific references

Used by:

  • CERN
  • Universities
  • EU-funded projects

Key lesson: Infrastructure exists — use it.

Slide 14 — Governance When Opening Internal Code

Open code requires explicit governance.

Key questions:

  • Who reviews changes?
  • Who releases software?
  • Who resolves disputes?

Governance should be lightweight but explicit.

Slide 15 — Real-World Example: Apache Software Foundation

ASF provides a mature governance model.

Practices:

  • Merit-based contributor model
  • Clear maintainer roles
  • Transparent decision-making

Impact:

  • Sustainable projects
  • Low institutional dependency
  • Long-term continuity

Key lesson: Governance enables longevity.

Slide 16 — Managing External Contributions

External contributions need structure.

Best practices:

  • Pull Requests only
  • Mandatory reviews
  • CI enforcement
  • Code of Conduct

These practices protect both contributors and institutions.

Slide 17 — Positioning OSS as Scientific Impact

Software impact is measurable.

Indicators:

  • Citations (DOIs)
  • External contributors
  • Downstream reuse
  • Inclusion in workflows or infrastructures

Slide 18 — Real-World Example: Research Software as Impact

Examples:

  • R language ecosystem (originated in academia)
  • scikit-learn (academic origins, global adoption)
  • Astropy (community-governed astronomy software)

Recognized impact:

  • Thousands of citations
  • Used in publications across disciplines

Key lesson: OSS can outlive individual projects.

Slide 19 — Technical Repository Management

Engineering practices support trust.

Minimum requirements:

  • Stable main branch
  • PR-based workflow
  • Automated tests
  • CI pipelines
  • Release tagging
  • Dependency management

Slide 20 — Real-World Example: NASA Open Source

NASA publishes and maintains OSS.

Practices:

  • Mandatory open repositories
  • Automated CI
  • Clear contribution rules

Impact:

  • External reuse
  • Industry collaboration
  • Increased transparency

Key lesson: Technical discipline enables openness at scale.

Slide 21 — Key Takeaways

  • OSS is strategic research infrastructure
  • Licensing shapes reuse and impact
  • Minimum quality standards are essential
  • Governance enables safe collaboration
  • Software impact is measurable and reportable
  • Automation sustains quality over time

Extended Details

Unfold it with the Expand button on the very right side below

Modern Software Development Practices (Python & JavaScript)

Best practices for managing, testing, and documenting software projects built with Python and JavaScript.

Code Management, Versioning, and Licensing

  • Use Git for source control
  • Branching strategy:
    • main – stable production code
    • feature branches – new development
  • Use Semantic Versioning (MAJOR.MINOR.PATCH)
  • Add a LICENSE file (MIT or Apache 2.0 commonly used)
  • Protect main branches with:
    • Pull / Merge Request reviews
    • Mandatory CI checks

Automation and Code Quality (Python & JS)

Python

  • Linters: flake8, pylint
  • Formatter: black
  • Import sorting: isort
  • Type checking: mypy

JavaScript

  • Linter: ESLint
  • Formatter: Prettier
  • Type checking: TypeScript (recommended)

Best practices:

  • Run linters and formatters automatically
  • Keep functions small and readable
  • Follow PEP 8 (Python) and standard JS style guides

Continuous Integration (CI)

CI pipelines automatically validate code on each push or pull request.

Example: GitHub Actions

name: CI

on:
  pull_request:
  push:
    branches: [ main ]

jobs:
  build:
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4

      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.11"

      - name: Install Python dependencies
        run: |
          pip install -r requirements.txt

      - name: Lint Python
        run: |
          flake8 .
          black --check .

      - name: Run Python tests
        run: pytest

      - name: Set up Node.js
        uses: actions/setup-node@v4
        with:
          node-version: "20"

      - name: Install JS dependencies
        run: npm ci

      - name: Lint JS
        run: npm run lint

      - name: Run JS tests
        run: npm test

Example: GitLab CI

stages:
  - lint
  - test

python_lint:
  stage: lint
  image: python:3.11
  script:
    - pip install flake8 black
    - flake8 .
    - black --check .

python_test:
  stage: test
  image: python:3.11
  script:
    - pip install -r requirements.txt
    - pytest

js_lint:
  stage: lint
  image: node:20
  script:
    - npm ci
    - npm run lint

js_test:
  stage: test
  image: node:20
  script:
    - npm ci
    - npm test

Benefits:

  • Early detection of issues
  • Enforced quality standards
  • Reliable and repeatable builds

Automated Testing

Python

  • Frameworks: pytest, unittest
  • Tools:
    • pytest-cov (coverage)
    • requests-mock / responses (API mocking)

JavaScript

  • Unit & integration: Jest, Vitest
  • End-to-end (E2E): Cypress, Playwright

Best practices:

  • Run tests automatically in CI
  • Test behavior, not implementation details
  • Keep test execution fast

Changelog and Commit Standards

  • Maintain CHANGELOG.md
  • Follow Keep a Changelog structure:
    • Added
    • Changed
    • Fixed
    • Deprecated

Conventional Commits

  • feat: new feature
  • fix: bug fix
  • docs: documentation
  • test: tests
  • chore: maintenance

Issue Management and Roadmap

  • Use issues to track bugs, features, and technical debt
  • Organize work using milestones and boards
  • Reference issues in commits and merge requests

Best Practices in Issue Creation

  • Use issue templates (bug / feature)
  • Apply labels:
    • python
    • javascript
    • bug
    • enhancement
    • documentation
  • Always include clear reproduction steps for bugs

Documentation

Effective README

A strong README.md includes:

  • Project overview
  • Python / Node.js requirements
  • Installation steps
  • Usage examples
  • Testing instructions
  • License

Contributing Guide (CONTRIBUTING.md)

Should define:

  • Environment setup
  • Coding standards
  • Commit conventions
  • Pull Request workflow

API Documentation

Python

  • Sphinx – documentation from docstrings
  • FastAPI – automatic OpenAPI / Swagger
  • MkDocs – lightweight docs

JavaScript

  • Swagger / OpenAPI – REST APIs
  • JSDoc – inline documentation
  • Docusaurus – documentation portals

Recommended Project Structure

Example structure for a combined Python + JavaScript repository: 

project-root/
├── backend/
│   ├── app/
│   │   ├── __init__.py
│   │   ├── main.py
│   │   ├── api/
│   │   └── services/
│   ├── tests/
│   ├── requirements.txt
│   └── pyproject.toml
│
├── frontend/
│   ├── src/
│   │   ├── components/
│   │   ├── pages/
│   │   └── services/
│   ├── tests/
│   ├── package.json
│   └── package-lock.json
│
├── docs/
│   ├── api/
│   └── guides/
│
├── .github/ or .gitlab/
│   └── ci/
│
├── CHANGELOG.md
├── CONTRIBUTING.md
├── README.md
└── LICENSE

Key Takeaways

  • CI enforces quality for Python and JavaScript
  • Automated testing reduces regressions
  • Clear structure improves maintainability
  • Documentation is part of the codebase

Open Source Best Practices (Python & JavaScript)

This section extends the project guidelines with patterns commonly used in successful open source projects.

Separate CI Pipelines per Service

In multi-service or monorepo projects, each service should have an independent CI pipeline.

Benefits:

  • Faster CI execution
  • Clear ownership per service
  • Reduced coupling between frontend and backend

GitHub Actions (Per Service)

Each service has its own workflow file. 

.github/workflows/
├── backend-ci.yml
└── frontend-ci.yml

Example: Backend CI

name: Backend CI

on:
  push:
    paths:
      - "backend/**"
  pull_request:
    paths:
      - "backend/**"

jobs:
  backend:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: "3.11"
      - run: pip install -r backend/requirements.txt
      - run: flake8 backend
      - run: pytest backend/tests

Example: Frontend CI

name: Frontend CI

on:
  push:
    paths:
      - "frontend/**"
  pull_request:
    paths:
      - "frontend/**"

jobs:
  frontend:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-node@v4
        with:
          node-version: "20"
      - run: cd frontend && npm ci
      - run: cd frontend && npm run lint
      - run: cd frontend && npm test

GitLab CI (Per Service)

backend:
  stage: test
  rules:
    - changes:
        - backend/**/*
  image: python:3.11
  script:
    - pip install -r backend/requirements.txt
    - pytest backend/tests

Monorepo vs Multirepo

Choosing the right repository strategy is critical for scalability.

Aspect Monorepo Multirepo
Code location Single repository One repository per service
CI complexity Higher Lower
Dependency sharing Easy Requires versioning
Access control Unified Granular
Tooling Requires advanced CI Simpler
Open source friendliness Good for small teams Best for large ecosystems

Recommendations:

  • Monorepo – small teams, tight coupling, shared releases
  • Multirepo – independent services, different release cycles, large communities

Issue Templates (Wiki Format)

Clear issue templates improve collaboration and contributor experience.

Bug Report

== Description ==
A clear and concise description of the bug.

== Steps to Reproduce ==
# Step 1
# Step 2
# Step 3

== Expected Behavior ==
What you expected to happen.

== Actual Behavior ==
What actually happened.

== Environment ==
* OS:
* Python / Node.js version:
* Browser (if applicable):

== Additional Context ==
Logs, screenshots, or links.

Feature Request

== Summary ==
Short description of the requested feature.

== Motivation ==
Why is this feature needed?

== Proposed Solution ==
Describe the preferred solution.

== Alternatives ==
Other approaches considered.

== Additional Context ==
Links, mockups, or references.

Documentation Issue

== Documentation Section ==
Which page or file needs improvement?

== Problem ==
What is unclear, missing, or incorrect?

== Suggested Improvement ==
Proposed text or structure.

Open Source Project Best Practices

These practices help attract and retain contributors.

Governance and Transparency

  • Define maintainers and roles
  • Use public roadmaps
  • Make decisions in issues and PRs

Contribution Experience

  • Clear README and CONTRIBUTING.md
  • Friendly issue templates
  • Label beginner issues (e.g. good first issue)

Licensing and Legal

  • Always include a LICENSE file
  • Ensure dependencies are license-compatible
  • Avoid committing secrets or credentials

Community Standards

  • Add a Code of Conduct (e.g. Contributor Covenant)
  • Enforce respectful communication
  • Moderate discussions consistently

Release Management

  • Use semantic versioning
  • Maintain a changelog
  • Tag releases
  • Automate releases where possible

Security

  • Provide a SECURITY.md
  • Define responsible disclosure process
  • Keep dependencies up to date

Open Source Checklist

  • README.md
  • CONTRIBUTING.md
  • CHANGELOG.md
  • LICENSE
  • CODE_OF_CONDUCT.md
  • SECURITY.md
  • CI pipelines enabled
  • Issue and PR templates

Open Source Collaboration and Release Management

This section defines contribution workflows, security policies, community standards, and automated releases.

Pull Request Templates

Pull Request templates help reviewers and contributors align on expectations.

Pull Request Template (General)

## Description
Brief summary of the changes introduced by this PR.

## Related Issue
Closes #<issue-number>

## Type of Change
- [ ] Bug fix
- [ ] New feature
- [ ] Documentation update
- [ ] Refactoring
- [ ] CI / tooling

## How Has This Been Tested?
Describe the tests that you ran.

## Checklist
- [ ] Code follows project style guidelines
- [ ] Tests added or updated
- [ ] Documentation updated (if applicable)
- [ ] CI pipeline passes

Best practices:

  • Require PR templates for all contributions
  • Enforce reviews via branch protection
  • Keep PRs small and focused

Security Policy (SECURITY.md)

Open source projects should clearly define how to report vulnerabilities.

Example SECURITY.md

# Security Policy

## Supported Versions
Only the latest major version is actively supported with security updates.

## Reporting a Vulnerability
If you discover a security vulnerability, please do NOT open a public issue.

Instead, report it by emailing:
security@project-domain.example

Please include:
- A description of the vulnerability
- Steps to reproduce
- Potential impact
- Suggested remediation (if available)

We aim to respond within 72 hours.

Best practices:

  • Never discuss vulnerabilities publicly before a fix
  • Acknowledge reporters responsibly
  • Publish security advisories after resolution

Code of Conduct (CODE_OF_CONDUCT.md)

A Code of Conduct creates a safe and welcoming community.

Example CODE_OF_CONDUCT.md

# Code of Conduct

## Our Pledge
We are committed to providing a respectful and inclusive environment for everyone.

## Expected Behavior
- Be respectful and considerate
- Use welcoming and inclusive language
- Accept constructive criticism
- Focus on what is best for the community

## Unacceptable Behavior
- Harassment or discrimination
- Trolling or personal attacks
- Publishing private information

## Enforcement
Project maintainers are responsible for enforcing this code of conduct.

## Reporting
Report incidents to:
conduct@project-domain.example

Recommendation:

  • Use the Contributor Covenant as a base
  • Enforce consistently and transparently

Release Automation (semantic-release)

Automated releases reduce human error and ensure consistency.

What semantic-release Does

  • Determines next version from commit messages
  • Generates changelog entries
  • Creates Git tags and releases
  • Publishes artifacts automatically

Commit Requirements

semantic-release requires Conventional Commits:

  • feat: introduces a new feature (MINOR)
  • fix: bug fix (PATCH)
  • feat!: or BREAKING CHANGE (MAJOR)

Example semantic-release Configuration

{
  "branches": ["main"],
  "plugins": [
    "@semantic-release/commit-analyzer",
    "@semantic-release/release-notes-generator",
    "@semantic-release/changelog",
    "@semantic-release/github"
  ]
}

GitHub Actions: Automated Release

name: Release

on:
  push:
    branches:
      - main

jobs:
  release:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-node@v4
        with:
          node-version: "20"
      - run: npm ci
      - run: npx semantic-release
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

Python + semantic-release Notes

  • semantic-release manages versions and tags
  • Python packages should:
    • Read version from git tags
    • Or inject version during build (setuptools_scm)

Open Source Release Best Practices

  • Use automated releases
  • Never manually edit versions
  • Always release from main branch
  • Keep CHANGELOG.md generated automatically
  • Tag every release

Final Open Source Readiness Checklist

  • README.md
  • CONTRIBUTING.md
  • CHANGELOG.md
  • LICENSE
  • CODE_OF_CONDUCT.md
  • SECURITY.md
  • Issue templates
  • Pull Request templates
  • CI pipelines per service
  • Automated releases enabled

Advanced Open Source Project Setup

This section completes the open source framework with publishing automation, governance, labeling standards, and repository structure.

Automated Package Publishing

Automated publishing ensures consistent, repeatable releases.

PyPI Publishing (Python)

Best practice:

  • Publish only from tagged releases
  • Use CI for trusted publishing

GitHub Actions: Publish to PyPI

name: Publish Python Package

on:
  release:
    types: [published]

jobs:
  publish:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: "3.11"
      - run: pip install build
      - run: python -m build
      - uses: pypa/gh-action-pypi-publish@release/v1

Requirements:

  • pyproject.toml configured
  • Trusted Publishing enabled in PyPI

npm Publishing (JavaScript)

Best practice:

  • Use semantic-release
  • Publish only from main branch

GitHub Actions: Publish to npm

name: Publish npm Package

on:
  push:
    branches:
      - main

jobs:
  publish:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-node@v4
        with:
          node-version: "20"
          registry-url: https://registry.npmjs.org
      - run: npm ci
      - run: npx semantic-release
        env:
          NPM_TOKEN: ${{ secrets.NPM_TOKEN }}
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

GitHub Labels Taxonomy

A consistent label system improves triage and contributor onboarding.

Type Labels

  • bug
  • enhancement
  • documentation
  • refactor
  • security
  • question

Priority Labels

  • priority: critical
  • priority: high
  • priority: medium
  • priority: low

Status Labels

  • status: triage
  • status: blocked
  • status: in progress
  • status: ready for review

Scope / Stack Labels

  • python
  • javascript
  • frontend
  • backend
  • api
  • ci

Community Labels

  • good first issue
  • help wanted
  • breaking change

Maintainers and Governance Model

Clear governance improves trust and sustainability.

Roles

  • Maintainers
    • Own project direction
    • Review and merge PRs
    • Manage releases
  • Contributors
    • Submit issues and PRs
    • Improve code and documentation

Decision Making

  • Decisions are made publicly in issues or PRs
  • Maintainers aim for consensus
  • Maintainer vote is final when consensus cannot be reached

Becoming a Maintainer

  • Consistent high-quality contributions
  • Community engagement
  • Invitation by existing maintainers

Governance File

Recommended file:

  • GOVERNANCE.md

Complete Open Source Starter Repository Structure

Recommended structure for a Python + JavaScript open source project: 

project-root/
├── backend/
│   ├── app/
│   │   ├── __init__.py
│   │   ├── main.py
│   │   ├── api/
│   │   └── services/
│   ├── tests/
│   ├── pyproject.toml
│   └── README.md
│
├── frontend/
│   ├── src/
│   │   ├── components/
│   │   ├── pages/
│   │   └── services/
│   ├── tests/
│   ├── package.json
│   └── README.md
│
├── docs/
│   ├── api/
│   ├── guides/
│   └── README.md
│
├── .github/
│   ├── workflows/
│   │   ├── backend-ci.yml
│   │   ├── frontend-ci.yml
│   │   └── release.yml
│   ├── ISSUE_TEMPLATE/
│   └── PULL_REQUEST_TEMPLATE.md
│
├── CHANGELOG.md
├── CODE_OF_CONDUCT.md
├── CONTRIBUTING.md
├── GOVERNANCE.md
├── LICENSE
├── README.md
├── SECURITY.md
└── semantic-release.json

Open Source Maturity Checklist

  • Automated CI per service
  • Automated releases
  • PyPI and npm publishing
  • Clear contribution workflow
  • Governance defined
  • Labels and templates configured
  • Security policy documented
  • Code of conduct enforced

Final Notes

Well-maintained open source projects prioritize:

  • Automation over manual work
  • Transparency over private decisions
  • Documentation over tribal knowledge
  • Community over individual ownership
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