medcheck 0.1.0__tar.gz

medcheck-0.1.0/.dockerignore

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+.git
+.venv
+__pycache__
+*.pyc
+.env
+.pytest_cache
+.mypy_cache
+.ruff_cache
+tests/
+docs/
+*.md
+!README.md

medcheck-0.1.0/.env.example

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+# AI Provider API Keys
+ANTHROPIC_API_KEY=your_anthropic_api_key_here
+OPENAI_API_KEY=your_openai_api_key_here
+GOOGLE_API_KEY=your_google_api_key_here
+
+# Server Configuration
+MEDCHECK_HOST=127.0.0.1
+MEDCHECK_PORT=8000
+
+# LLM Provider Selection (anthropic | openai | google)
+MEDCHECK_LLM_PROVIDER=anthropic
+
+# Language / Locale
+MEDCHECK_LANGUAGE=en

medcheck-0.1.0/.github/CODEOWNERS

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+* @Liohtml

medcheck-0.1.0/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug Report
+description: Report a bug or unexpected behavior in MedCheck
+title: "[Bug]: "
+labels: ["bug", "triage"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to fill out this bug report! Please provide as much detail as possible.
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description
+      description: A clear and concise description of what the bug is.
+      placeholder: What happened? What did you expect to happen?
+    validations:
+      required: true
+
+  - type: textarea
+    id: steps
+    attributes:
+      label: Steps to Reproduce
+      description: Step-by-step instructions to reproduce the issue.
+      placeholder: |
+        1. Run `medcheck ...`
+        2. Provide input `...`
+        3. Observe error `...`
+    validations:
+      required: true
+
+  - type: input
+    id: version
+    attributes:
+      label: Version
+      description: What version of MedCheck are you using? Run `medcheck --version` or check `pyproject.toml`.
+      placeholder: "e.g., 0.1.0"
+    validations:
+      required: true
+
+  - type: dropdown
+    id: installation
+    attributes:
+      label: Installation Method
+      description: How did you install MedCheck?
+      options:
+        - pip install medcheck
+        - uv add medcheck
+        - uv sync (from source)
+        - poetry add medcheck
+        - Other (describe in logs section)
+    validations:
+      required: true
+
+  - type: textarea
+    id: logs
+    attributes:
+      label: Relevant Logs / Stack Trace
+      description: Paste any error messages, stack traces, or log output here.
+      render: shell
+      placeholder: |
+        Traceback (most recent call last):
+          ...

medcheck-0.1.0/.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature Request
+description: Suggest a new feature or enhancement for MedCheck
+title: "[Feature]: "
+labels: ["enhancement"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for suggesting an improvement! Please describe your idea clearly so we can evaluate it.
+
+  - type: textarea
+    id: problem
+    attributes:
+      label: Problem Statement
+      description: What problem does this feature solve? Is your request related to a specific frustration?
+      placeholder: "I'm always frustrated when... / I can't currently do..."
+    validations:
+      required: true
+
+  - type: textarea
+    id: solution
+    attributes:
+      label: Proposed Solution
+      description: Describe the feature you'd like to see. Include any relevant API design ideas or examples.
+      placeholder: |
+        I would like MedCheck to support...
+
+        Example usage:
+        ```python
+        medcheck.add_provider(...)
+        ```
+    validations:
+      required: true
+
+  - type: dropdown
+    id: area
+    attributes:
+      label: Area
+      description: Which part of MedCheck does this feature relate to?
+      options:
+        - Data Provider (new source integration)
+        - LLM Provider (new model integration)
+        - Pipeline / Orchestration
+        - CLI / Interface
+        - Output / Formatting
+        - Configuration
+        - Documentation
+        - Testing / CI
+        - Other
+    validations:
+      required: true
+
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternatives Considered
+      description: Have you considered any workarounds or alternative approaches?
+      placeholder: I tried... but it doesn't work because...
+
+  - type: textarea
+    id: context
+    attributes:
+      label: Additional Context
+      description: Any other context, screenshots, or references that might be helpful.

medcheck-0.1.0/.github/dependabot.yml

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+version: 2
+updates:
+  - package-ecosystem: pip
+    directory: "/"
+    schedule:
+      interval: weekly
+  - package-ecosystem: github-actions
+    directory: "/"
+    schedule:
+      interval: weekly

medcheck-0.1.0/.github/pull_request_template.md

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+## Summary
+
+<!-- Briefly describe what this PR does and why. Link the related issue: "Fixes #123" or "Closes #456" -->
+
+Fixes #
+
+## Changes
+
+<!-- List the key changes made in this PR -->
+
+-
+-
+-
+
+## Testing
+
+<!-- Describe how you tested your changes -->
+
+- [ ] Existing tests pass (`uv run pytest`)
+- [ ] New tests added for new functionality
+- [ ] Coverage does not decrease (`uv run pytest --cov-fail-under=85`)
+- [ ] Linting passes (`uv run ruff check .`)
+- [ ] Type checking passes (`uv run mypy src/medcheck --strict`)
+- [ ] Pre-commit hooks pass (`pre-commit run --all-files`)
+
+## Additional Notes
+
+<!-- Anything else reviewers should know? Breaking changes? Deployment considerations? -->

medcheck-0.1.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - uses: astral-sh/setup-uv@v7
+      - run: uv sync --all-extras
+      - run: uv run ruff check src/ tests/
+      - run: uv run ruff format --check src/ tests/
+
+  type-check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - uses: astral-sh/setup-uv@v7
+      - run: uv sync --all-extras
+      - run: uv run mypy src/medcheck
+
+  security:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - uses: astral-sh/setup-uv@v7
+      - run: uv sync --all-extras
+      - run: uv run bandit -r src/medcheck -ll -q
+
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.10", "3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v6
+      - uses: astral-sh/setup-uv@v7
+        with:
+          python-version: ${{ matrix.python-version }}
+      - run: uv sync --all-extras
+      - run: uv run pytest tests/ --cov=medcheck --cov-report=xml --cov-fail-under=55
+      - uses: codecov/codecov-action@v6
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.13'
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ./coverage.xml

medcheck-0.1.0/.github/workflows/codeql.yml

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+name: CodeQL
+
+on:
+  push:
+    branches: [main]
+  schedule:
+    - cron: "0 2 * * 1"
+
+jobs:
+  analyze:
+    runs-on: ubuntu-latest
+    permissions:
+      security-events: write
+    steps:
+      - uses: actions/checkout@v6
+      - uses: github/codeql-action/init@v4
+        with:
+          languages: python
+      - uses: github/codeql-action/analyze@v4

medcheck-0.1.0/.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+*.egg
+*.egg-info/
+dist/
+build/
+eggs/
+.eggs/
+
+# Virtual environments
+.venv/
+venv/
+env/
+ENV/
+
+# Environment variables
+.env
+.env.*
+!.env.example
+
+# Type checking
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Testing
+.pytest_cache/
+.coverage
+coverage.xml
+htmlcov/
+.tox/
+
+# DICOM and medical imaging files
+*.dcm
+*.dicom
+*.zip
+*.npy
+*.pt
+*.pth
+
+# Model cache
+models_cache/
+.cache/
+
+# Distribution / packaging
+*.tar.gz
+*.whl
+MANIFEST
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+.DS_Store
+Thumbs.db
+
+# Logs
+*.log
+logs/
+
+# uv
+.uv/
+uv.lock

medcheck-0.1.0/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-yaml
+      - id: check-toml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: no-commit-to-branch
+        args: [--branch, main]
+      - id: check-added-large-files
+        args: [--maxkb=500]
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.4.1
+    hooks:
+      - id: codespell
+        exclude: "(uv.lock)"
+
+  - repo: local
+    hooks:
+      - id: ruff-format
+        name: ruff format
+        language: system
+        entry: uv run ruff format
+        types: [python]
+
+      - id: ruff-lint
+        name: ruff lint
+        language: system
+        entry: uv run ruff check --fix
+        types: [python]

medcheck-0.1.0/.python-version

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+3.13

medcheck-0.1.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+### Added
+- Initial project scaffold with `src/medcheck` package structure
+- Core provider abstraction (`DataProvider` base class)
+- Core LLM provider abstraction (`LLMProvider` base class)
+- `pyproject.toml` with uv-managed dependencies
+- Pre-commit hooks (ruff, mypy)
+- GitHub Actions CI workflow
+- Community files: CONTRIBUTING.md, CODE_OF_CONDUCT.md, SECURITY.md, issue templates
+
+### Changed
+
+### Deprecated
+
+### Removed
+
+### Fixed
+
+### Security
+
+[Unreleased]: https://github.com/Liohtml/MedCheck/compare/HEAD...HEAD

medcheck-0.1.0/CODE_OF_CONDUCT.md

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+# Code of Conduct
+
+This project follows the [Contributor Covenant v2.1](https://www.contributor-covenant.org/version/2/1/code_of_conduct/).
+
+## Our Pledge
+
+We are committed to providing a friendly, safe and welcoming environment for all contributors regardless of background or identity.
+
+## Enforcement
+
+Instances of unacceptable behavior may be reported via [GitHub Issues](https://github.com/Liohtml/MedCheck/issues) or by contacting the maintainers directly.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org).

medcheck-0.1.0/CONTRIBUTING.md

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+# Contributing to MedCheck
+
+Thank you for your interest in contributing to MedCheck! We welcome contributions of all kinds, from bug reports and feature requests to code changes and documentation improvements.
+
+## Ways to Contribute
+
+### Reporting Bugs
+Found a bug? We appreciate detailed bug reports. Please use our bug report template when opening an issue.
+
+### Requesting Features
+Have an idea for a new feature? Share it with us using the feature request template. We especially encourage:
+- Requests for new data providers
+- Suggestions for new LLM providers
+- Pipeline improvements and enhancements
+
+### Submitting Pull Requests
+Code contributions are welcome! Whether it's a bug fix, feature implementation, or documentation update, we're happy to review your work.
+
+### Improving Documentation
+Help us make MedCheck better documented. You can:
+- Fix typos or clarify existing documentation
+- Add examples and usage guides
+- Improve API documentation
+
+## Before You Start
+
+**Please open an issue first** to discuss your proposed changes with the maintainers. This helps us avoid duplicate work and ensures your changes align with the project's direction.
+
+For small changes (typo fixes, minor documentation updates), you can skip this and go straight to a PR.
+
+## Development Setup
+
+### Prerequisites
+- Python 3.11+
+- Git
+- [uv](https://github.com/astral-sh/uv) package manager
+
+### Getting Started
+
+1. Fork the repository on GitHub
+2. Clone your fork:
+   ```bash
+   git clone https://github.com/YOUR_USERNAME/MedCheck.git
+   cd MedCheck
+   ```
+3. Install dependencies:
+   ```bash
+   uv sync --all-extras
+   ```
+4. Install pre-commit hooks:
+   ```bash
+   pre-commit install
+   ```
+
+## Code Standards
+
+We maintain high code quality standards to ensure maintainability and reliability.
+
+### Line Length
+- Maximum 120 characters per line (enforced by Ruff)
+
+### Type Hints
+- Type hints are **required** for all public functions and methods
+- Use `from typing import ...` or `from collections.abc import ...` for type annotations
+- Return types must be specified
+
+### Docstrings
+- Google-style docstrings are required for all public functions, classes, and modules
+- Include brief description, Args, Returns, and Raises sections
+- Example:
+  ```python
+  def fetch_data(provider: str, query: str) -> dict:
+      """Fetch medical data from the specified provider.
+
+      Args:
+          provider: Name of the data provider
+          query: Search query for the data
+
+      Returns:
+          Dictionary containing the fetched data
+
+      Raises:
+          ValueError: If provider is not supported
+      """
+  ```
+
+### Linting and Type Checking
+- Ruff is used for code formatting and linting:
+  ```bash
+  uv run ruff check .
+  uv run ruff format .
+  ```
+- MyPy is used for static type checking in strict mode:
+  ```bash
+  uv run mypy src/medcheck --strict
+  ```
+
+## Testing
+
+Tests are required for all new features and bug fixes.
+
+### Running Tests
+```bash
+# Run all tests
+uv run pytest
+
+# Run with coverage
+uv run pytest --cov=src/medcheck --cov-report=html
+
+# Run specific test file
+uv run pytest tests/test_providers.py
+
+# Run tests matching a pattern
+uv run pytest -k "test_llm"
+```
+
+### Coverage Requirements
+- Minimum coverage is 85% (`--cov-fail-under=85`)
+- All new code must be covered by tests
+- Aim for meaningful tests, not just coverage targets
+
+## PR Process
+
+### Before Submitting
+1. Create a feature branch from `main`:
+   ```bash
+   git checkout -b feat/my-feature
+   ```
+2. Make your changes and commit them (see commit message format below)
+3. Ensure all tests pass:
+   ```bash
+   uv run pytest
+   ```
+4. Ensure linting passes:
+   ```bash
+   uv run ruff check .
+   ```
+5. Ensure type checking passes:
+   ```bash
+   uv run mypy src/medcheck --strict
+   ```
+6. Push to your fork and open a pull request
+
+### Commit Message Format
+Use conventional commit format:
+- `feat:` - A new feature
+- `fix:` - A bug fix
+- `docs:` - Documentation changes
+- `refactor:` - Code refactoring without behavior changes
+- `test:` - Adding or updating tests
+- `chore:` - Build, CI, or dependency updates
+
+Example: `feat: add support for FHIR data provider`
+
+### Pull Request Requirements
+- Link related issues: "Fixes #123" or "Closes #456"
+- Clear description of changes
+- At least one maintainer review is required
+- All CI checks must pass
+- Code coverage must not decrease
+
+## Adding a New Data Provider
+
+To add a new data provider for medical data sources:
+
+1. Create a new file in `src/medcheck/providers/`:
+   ```python
+   # src/medcheck/providers/my_provider.py
+   from medcheck.providers.base import DataProvider
+
+   class MyDataProvider(DataProvider):
+       """Provider for my medical data source."""
+
+       name = "my_provider"
+
+       async def fetch(self, query: str) -> dict:
+           """Fetch data from the provider."""
+           pass
+   ```
+
+2. Implement the `DataProvider` interface:
+   - Implement required abstract methods
+   - Add proper error handling
+   - Include rate limiting if needed
+
+3. Register URL patterns in the router:
+   ```python
+   # src/medcheck/providers/__init__.py
+   url_patterns = [
+       # ... existing patterns
+       ("my-provider", MyDataProvider),
+   ]
+   ```
+
+4. Add comprehensive tests:
+   ```python
+   # tests/test_providers/test_my_provider.py
+   import pytest
+   from medcheck.providers.my_provider import MyDataProvider
+
+   @pytest.mark.asyncio
+   async def test_fetch():
+       provider = MyDataProvider()
+       result = await provider.fetch("test query")
+       assert result is not None
+   ```
+
+## Adding a New LLM Provider
+
+To add a new LLM provider for language model integration:
+
+1. Create a new file in `src/medcheck/llm/`:
+   ```python
+   # src/medcheck/llm/my_llm.py
+   from medcheck.llm.base import LLMProvider
+
+   class MyLLMProvider(LLMProvider):
+       """LLM provider for my model."""
+
+       name = "my_llm"
+
+       async def generate(self, prompt: str) -> str:
+           """Generate response from the LLM."""
+           pass
+   ```
+
+2. Implement the `LLMProvider` interface:
+   - Implement required abstract methods
+   - Add proper error handling and retries
+   - Implement streaming if supported
+
+3. Add environment variable for API key:
+   ```python
+   import os
+   api_key = os.getenv("MY_LLM_API_KEY")
+   ```
+
+4. Register the provider:
+   ```python
+   # src/medcheck/llm/__init__.py
+   from medcheck.llm.my_llm import MyLLMProvider
+   ```
+
+5. Add comprehensive tests:
+   ```python
+   # tests/test_llm/test_my_llm.py
+   import pytest
+   from medcheck.llm.my_llm import MyLLMProvider
+
+   @pytest.mark.asyncio
+   async def test_generate():
+       provider = MyLLMProvider()
+       response = await provider.generate("test prompt")
+       assert response is not None
+   ```
+
+## License
+
+By contributing to MedCheck, you agree that your contributions will be licensed under the Apache License 2.0. See the LICENSE file for details.
+
+## Questions?
+
+If you have questions about contributing, feel free to open an issue or reach out to the maintainers. We're here to help!
+
+Happy coding!