Create template repositories for packages

[apulsipher]

Templates to Create (see comments for language-specific details)

• Template for R packages
• Template for Python packages
• Template for C++ packages

Things to Include in General (not exhaustive)

• README.md
• Code of Conduct
• Best Practices (some general like Semantic Versioning, some language-specific like package naming conventions for that langauge)
• .gitignore
• Consistent file structures (e.g., docs/, build/, src/, etc.)
• GitHub Actions for building a website and running tests
• Github Action workflow (likely to trigger on creation of a new release, but maybe manually) to publish package to PyPI/CRAN/etc.
  • The trigger for manually running a workflow is on: workflow_dispatch

On using Existing Templates/Templating Tools

There exist many templates and templating tools. These can be used directly or taken as inspiration. If we want to use one directly, instead of forking it, create a new project under EpiForeSITE so contributions are tracked properly and so we aren't constantly asked to merge with the original repo. See Detaching a fork.

One tool of particular note is Cookiecutter, which is primarily used for Python projects but also supports C projects. It takes a fill-in-the-blank approach to project creation, asking the user to fill in information like "Project Title" and so on. We could create our own cookiecutter (see comments below for examples) to help the researcher/developer set up their template.

Insight Net Support

These templates will likely be useful beyond just EpiForeSITE. As such, it may be worthwhile to get input from other developers in the Insight Net.

[apulsipher]

R-Specific Details

Things to Include in the EpiForeSITE Template Repo

• roxygen2 and instructions for running it
• .Rbuildignore

Resources

• RStudio Package Development Cheatsheet
• R Packages (2e) book
  • Suggest using the command create_package("<package_path")

Templating Packages

• package.skeleton function
• https://www.rdocumentation.org/packages/template/versions/0.5.3
• https://cran.r-project.org/web/packages/templates/index.html

[apulsipher]

Python-Specific Details

Things to Include in the EpiForeSITE Template Repo

• pyproject.toml
• Poetry (including poetry files, structures, and details on running it)

Resources

• PEP 8 Style Guide especially PEP 8 Naming Conventions.
  • Naming conventions for packages and modules are a nightmare in Python, but the most common for a package name on PyPI is all-lowercase with hyphens, while the most common for module names within a package are all-lowercase with underscores.

Templating Packages

• python-package-template
  • This one includes key information that is often used in a Python project (good for inspiration)
• cookiecutter-pypackage
  • This cookiecutter also links to other relevant cookiecutters that might be a better fit

[apulsipher]

C++-Specific Details

Things to Include in the EpiForeSITE Template Repo

• Makefile

Resources

• It's Time To Do CMake Right

Templating Packages

• ModernCppStarter

[apulsipher]

@WillyRay @gvegayon Here's the issue for the template repo task. I've included comments with the results of my research and brainstorm on how to do this for each of R, Python, C++. They are definitely not exhaustive and I'm sure you will know more than I do about them, but they might be a good starting point. Especially the example templates. I don't know all of what we will want to include in our templates, but they give some good ideas of the kinds of files that are commonly used.

[gvegayon]

This is awesome, @apulsipher! Did you join the Slack channel I invited you to? I will reach out to folks across Insight Net so they can chip in!

[apulsipher]

This is awesome, @apulsipher! Did you join the Slack channel I invited you to? I will reach out to folks across Insight Net so they can chip in!

Thanks for the reminder! I've now joined on Slack