Development environment setup

Skill HolobiomicsLab/asb-skill-collections/collections/metabolomics/v1/skills/development-environment-setup

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Install

npx -y skills add HolobiomicsLab/asb-skill-collections --skill development-environment-setup

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Use when when you have cloned a Python package repository and need to prepare a working environment for development, debugging, or contribution. Specifically when the package declares dev dependencies in setup.py or pyproject.toml and maintains a pytest test suite in a tests/ directory.

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SKILL.md

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development-environment-setup

Summary

Install a Python package in development mode with optional dev dependencies, then execute the full test suite to verify functional integrity. This skill is essential for contributors and maintainers who need to validate package behavior before committing changes or releasing updates.

When to use

When you have cloned a Python package repository and need to prepare a working environment for development, debugging, or contribution. Specifically when the package declares dev dependencies in setup.py or pyproject.toml and maintains a pytest test suite in a tests/ directory.

When NOT to use

Package has no pytest test suite or tests/ directory is absent
You are installing the package for end-user consumption (use pip install biosynfoni without -e flag instead)
The package does not declare dev dependencies and you only need to run the main package code

Inputs

Python package source repository (cloned locally)
setup.py or pyproject.toml with [dev] extras defined
tests/ directory containing pytest test suite

Outputs

Editable package installation in the Python environment
pytest test report (stdout/stderr with test counts and pass/fail status)
Verified functional package suitable for development or contribution

How to apply

From the repository root directory, use pip to install the package in editable (development) mode with dev dependencies via pip install -e .[dev]. This preserves the source code in place and installs additional testing and formatting tools. Then execute the complete test suite using pytest tests/ to verify all unit and integration tests pass. Success is indicated by all tests passing without errors or failures, confirming the package is properly installed and all declared functionality works as expected. The pytest output will display test counts and any failures; zero failures indicates correct application.

Related tools

pip (Package manager for editable installation of package with dev dependencies) — https://pip.pypa.io
pytest (Test runner for executing complete test suite to verify package functionality) — https://docs.pytest.org
biosynfoni (Example package being installed and tested in development mode) — https://github.com/lucinamay/biosynfoni
black (Code formatter optionally installed as dev dependency for code style compliance) — https://github.com/psf/black

Examples

pip install -e .[dev] && pytest tests/

Evaluation signals

pip install command completes without errors and reports successful editable installation
pytest discovers and collects all test files in tests/ directory (test count > 0)
All pytest tests pass with exit code 0 and no FAILED or ERROR markers in output
Package can be imported and used in Python REPL after installation: from biosynfoni import Biosynfoni succeeds
Running tests multiple times produces consistent pass/fail results (no flakiness)

Limitations

Development installation requires writable file system access to the repository root
Tests may have external dependencies (network, databases, RDKit) that could cause failures unrelated to the package installation itself
No changelog or version history is formally documented in the biosynfoni repository, making it difficult to track breaking changes across development sessions

Evidence

[other] Install the package in development mode using pip with dev dependencies via pip install -e .[dev].: "Install the package in development mode using pip with dev dependencies via pip install -e .[dev]"
[other] Execute the complete test suite using pytest on the tests/ directory with pytest tests/.: "Execute the complete test suite using pytest on the tests/ directory with pytest tests/"
[other] Run the following command from the root of the project to install the project for development: "Run the following command from the root of the project to install the project for development"
[other] You can also run the tests locally with the following command: "You can also run the tests locally with the following command"
[other] The biosynfoni package has a GitHub Actions CI workflow that runs tests, as indicated by the Tests badge displayed in the repository.: "The biosynfoni package has a GitHub Actions CI workflow that runs tests, as indicated by the Tests badge displayed in the repository"