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Python User Group

The Python User Group meets weekly to discuss programming, data analysis, and troubleshooting in python as well as dedicate one meeting a month to general software development; topics will be announced ahead of time. Bring your lunch, code, questions, and thoughts! Python coders of all levels of expertise are welcome. Contact the Coop (coophelp at fredhutch.org) for more information. Additionally, check out the #python-user-comm channel on the Coop Communities Slack and our other training and community resources at Training, Community and Finding Help . Current meeting schedules and locations are available on the Google calendar.

Please see this issue to add ideas for these meetings.

The fredpyapplication repository is a collaborative, community-developed package of useful python functions being developed by the Python community at Fred Hutch.

Developing Python packages

Templates

  • Fred Hutch maintains a template for Python package development. The README for that directory contains an explanation of all required and recommended files. Please see the README for the templates repository for usage instructions.
  • The templates maintained by Fred Hutch represent core, essential components for software development. For projects that require more complexity, cookiecutter may be a reasonable template alternative. eScience also maintains a template called shablona.

Recommended development practices

  • The Data Science Wiki includes recommendations for software development practices.
  • The following practices may also assist in increasing the robustness of software developed, by avoiding common pitfalls and oversights in academic research software development:
    • including GitHub releases
    • specifying requirements (e.g., other people's software and databases) and using environment variables to locate

Examples

  • fredpyapplication: a collaborative, community-developed package of useful python functions being developed by the Python community at Fred Hutch.
  • phydms: from Jesse Bloom's lab; phylogenetic analyses informed by deep mutational scanning data
  • sci-pkg: from FH Scientific Computing; a collection of convenience and wrapper functions for common science research tasks
  • proxmox-tools: from FH SciComp; prox command line interface for proxmox and other tools and customizations
  • laminar: from Dane Gellerup FH Informatics Analyst Geraghty lab; High-level parallelization for easy multi-processing. Laminar seeks to take most of the effort out of parallel processing in Python by providing user-friendly parallelization functionality.
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