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fix: Improve PyPI package setup and CI/CD configuration
Fixed multiple issues to improve the project's appearance on PyPI and ensure CI/CD pipelines work correctly. CI/CD Improvements: - Fixed GitHub Actions test workflow to use pyproject.toml instead of missing requirements.txt - Tests now install with `pip install -e .[dev]` for proper dev setup - All test configuration now centralized in pyproject.toml Codecov Integration: - Added codecov.yml configuration for proper coverage reporting - Configured coverage precision, ranges, and ignore paths - Enabled PR comments with coverage details - Excluded tests, backend, and website from coverage README Improvements: - Updated to use dynamic GitHub Actions badges (tests status) - Added PyPI version badge and download statistics - Added Codecov badge for coverage tracking - Added "Code style: black" and Ruff badges - Removed static test/coverage badges that were misleading Package Distribution: - Updated MANIFEST.in to include LICENSE-COMMERCIAL.md, CODE_OF_CONDUCT.md - Added codecov.yml to package manifest - Removed pytest.ini and .coveragerc (now in pyproject.toml) - Properly exclude backend/ and website/ from distribution PyPI Configuration: - Updated pyproject.toml to specify README as markdown content-type - Ensures proper rendering on PyPI project page Requirements.txt: - Simplified to contain only core dependencies - Added helpful comments directing users to pyproject.toml - Maintains backward compatibility for CI systems Documentation: - Created comprehensive docs/PUBLISHING.md guide - Covers automated and manual PyPI publishing - Includes troubleshooting, best practices, and versioning guide - Documents GitHub Actions automated release workflow These changes will: ✅ Fix failing CI tests (no more missing requirements.txt) ✅ Show accurate test status and coverage badges ✅ Display properly on PyPI when published ✅ Use "Code style: black" badge instead of generic quality badge ✅ Enable Codecov integration for coverage tracking 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
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.github/workflows/tests.yml

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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -r requirements.txt
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pip install pytest pytest-cov pytest-asyncio
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pip install -e .[dev]
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- name: Run tests with coverage
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run: |
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pytest --cov --cov-report=xml --cov-report=term-missing -v
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pytest
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env:
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ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}
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MANIFEST.in

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# Include documentation
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include README.md
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include LICENSE
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include LICENSE-COMMERCIAL.md
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include CHANGELOG.md
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include CONTRIBUTING.md
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include SPONSORSHIP.md
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include CODE_OF_CONDUCT.md
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# Include configuration files
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include pyproject.toml
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include setup.py
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include requirements.txt
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include .bandit
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include pytest.ini
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include .coveragerc
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include codecov.yml
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# Include all YAML/JSON configs
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recursive-include src *.yml *.yaml *.json
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# Include examples
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recursive-include examples *.py *.md *.yml *.yaml
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# Include tests (for source distributions)
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recursive-include tests *.py
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# Exclude unnecessary files
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global-exclude *.pyc
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global-exclude *.pyo

README.md

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**A five-level maturity model for AI-human collaboration**
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[![License](https://img.shields.io/badge/License-Fair%20Source%200.9-blue.svg)](LICENSE)
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[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
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[![Tests](https://img.shields.io/badge/tests-553%20passing-success)](https://github.com/Smart-AI-Memory/empathy)
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[![Coverage](https://img.shields.io/badge/coverage-63.87%25-green)](https://github.com/Smart-AI-Memory/empathy)
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[![Security](https://img.shields.io/badge/security-0%20vulnerabilities-success)](https://github.com/Smart-AI-Memory/empathy)
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[![Quality](https://img.shields.io/badge/commercial%20ready-10%2F10-brightgreen)](https://github.com/Smart-AI-Memory/empathy)
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[![PyPI version](https://img.shields.io/pypi/v/empathy.svg)](https://pypi.org/project/empathy/)
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[![Python 3.10+](https://img.shields.io/pypi/pyversions/empathy.svg)](https://www.python.org/downloads/)
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[![Tests](https://github.com/Smart-AI-Memory/empathy/actions/workflows/tests.yml/badge.svg)](https://github.com/Smart-AI-Memory/empathy/actions/workflows/tests.yml)
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[![codecov](https://codecov.io/gh/Smart-AI-Memory/empathy/branch/main/graph/badge.svg)](https://codecov.io/gh/Smart-AI-Memory/empathy)
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[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
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[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
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[![Downloads](https://img.shields.io/pypi/dm/empathy.svg)](https://pypi.org/project/empathy/)
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---
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codecov.yml

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codecov:
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require_ci_to_pass: yes
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notify:
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wait_for_ci: yes
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coverage:
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precision: 2
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round: down
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range: "60...100"
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status:
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project:
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default:
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target: auto
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threshold: 1%
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base: auto
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patch:
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default:
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target: auto
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threshold: 1%
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base: auto
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parsers:
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gcov:
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branch_detection:
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conditional: yes
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loop: yes
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method: no
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macro: no
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comment:
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layout: "reach,diff,flags,tree,files"
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behavior: default
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require_changes: no
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require_base: no
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require_head: yes
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ignore:
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- "tests/"
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- "**/__pycache__/"
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- "**/test_*.py"
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- "**/*_test.py"
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- "setup.py"
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- "docs/"
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- "examples/"
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- "backend/"
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- "website/"

docs/PUBLISHING.md

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# Publishing to PyPI
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This guide explains how to publish the Empathy framework to PyPI.
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## Prerequisites
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1. PyPI account at https://pypi.org/
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2. PyPI API token (create at https://pypi.org/manage/account/token/)
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3. Add token to GitHub Secrets as `PYPI_API_TOKEN`
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## Automated Publishing (Recommended)
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The framework uses GitHub Actions for automated publishing:
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1. **Update version** in `pyproject.toml`:
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```toml
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version = "1.7.0" # Update this
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```
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2. **Update CHANGELOG.md** with release notes
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3. **Create and push a git tag**:
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```bash
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git tag v1.7.0
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git push origin v1.7.0
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```
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4. **GitHub Actions will automatically**:
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- Run all tests
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- Build the package
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- Create a GitHub release
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- Publish to PyPI (if token is configured)
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## Manual Publishing
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If you need to publish manually:
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### 1. Clean previous builds
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```bash
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rm -rf dist/ build/ *.egg-info
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```
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### 2. Build the package
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```bash
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python -m pip install --upgrade build twine
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python -m build
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```
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This creates two files in `dist/`:
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- `empathy-1.6.0.tar.gz` (source distribution)
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- `empathy-1.6.0-py3-none-any.whl` (wheel distribution)
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### 3. Check the package
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```bash
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twine check dist/*
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```
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### 4. Test upload to TestPyPI (optional)
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```bash
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twine upload --repository testpypi dist/*
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```
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Install from TestPyPI to verify:
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```bash
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pip install --index-url https://test.pypi.org/simple/ empathy
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```
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### 5. Upload to PyPI
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```bash
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twine upload dist/*
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```
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You'll be prompted for your PyPI username and password/token.
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## Verification
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After publishing, verify the package:
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1. **Check PyPI page**: https://pypi.org/project/empathy/
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2. **Install and test**:
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```bash
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pip install empathy
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python -c "from empathy_os import EmpathyOS; print('Success!')"
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```
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## Version Numbering
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Follow [Semantic Versioning](https://semver.org/):
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- **Major** (1.x.x): Breaking changes
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- **Minor** (x.1.x): New features, backward compatible
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- **Patch** (x.x.1): Bug fixes, backward compatible
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Examples:
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- `1.6.0``1.6.1`: Bug fix
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- `1.6.0``1.7.0`: New features
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- `1.6.0``2.0.0`: Breaking changes
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## Troubleshooting
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### "Package already exists"
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- Version already published to PyPI
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- Update version in `pyproject.toml`
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- You cannot overwrite or delete PyPI versions
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### "Invalid distribution"
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- Run `twine check dist/*` to see errors
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- Common issues:
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- Missing README.md
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- Invalid pyproject.toml
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- Missing required files in MANIFEST.in
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### "Authentication failed"
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- Check your PyPI token/password
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- Tokens must start with `pypi-`
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- Use username `__token__` with API tokens
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## Best Practices
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1. **Always test locally** before publishing
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2. **Run full test suite**: `pytest`
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3. **Check code quality**: `black . && ruff check .`
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4. **Update documentation** before release
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5. **Tag releases** in git for traceability
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6. **Never publish** with failing tests
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## Package Contents
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The published package includes:
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- Core framework code (`empathy_os/`, `empathy_llm_toolkit/`)
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- All wizards (`wizards/`, `coach_wizards/`)
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- Plugins (`empathy_healthcare_plugin/`, `empathy_software_plugin/`)
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- Documentation (`README.md`, `LICENSE`, etc.)
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- Configuration files
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Excluded from package (see MANIFEST.in):
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- Tests (`tests/`)
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- CI/CD configs (`.github/`)
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- Development files (`.gitignore`, `.pre-commit-config.yaml`)
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- Backend API (`backend/`)
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- Website (`website/`)

pyproject.toml

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name = "empathy"
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version = "1.6.0"
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description = "A five-level maturity model for AI-human collaboration with anticipatory empathy"
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readme = "README.md"
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readme = {file = "README.md", content-type = "text/markdown"}
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requires-python = ">=3.10"
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license = {file = "LICENSE"}
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authors = [

requirements.txt

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# Empathy - Python Dependencies
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# Empathy Framework - Core Dependencies
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# Fair Source License 0.9
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# Copyright 2025 Smart-AI-Memory
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# LangChain ecosystem
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langchain>=0.1.0
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langchain-core>=0.1.0
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langgraph>=0.0.20
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langchain-anthropic>=0.1.0
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langchain-openai>=0.0.5
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# AI/ML
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anthropic>=0.8.0
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openai>=1.6.0
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# Core utilities
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python-dotenv>=1.0.0
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pydantic>=2.0.0
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typing-extensions>=4.0.0
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# Logging and monitoring
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structlog>=23.0.0
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# Testing
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pytest>=7.4.0
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pytest-asyncio>=0.21.0
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pytest-cov>=4.1.0
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# Documentation
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python-docx>=1.0.0
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markdown>=3.5.0
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# Copyright 2025 Deep Study AI, LLC
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#
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# For development installation, use: pip install -e .[dev]
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# For full installation, use: pip install -e .[full]
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# See pyproject.toml for all optional dependencies
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# Core required dependencies (minimal to run framework)
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pydantic>=2.0.0,<3.0.0
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typing-extensions>=4.0.0,<5.0.0
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python-dotenv>=1.0.0,<2.0.0
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structlog>=23.0.0,<25.0.0

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