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Post-Copy Checklist

After running copier copy, see .copier-answers/post-copier-todos/package.md for next steps on implementing your project. You can copy-paste the contents of that file into a GitHub issue or a project management tool to track the implementation of the project.

Post Copier To-Do's for {{ project_name }}

This issue is for tracking the development of the {{ project_name }} project copied from the able-workflow-copier template.

Next steps

Environment Setup

  1. Install minimal dependencies: See README.md for adding the {{ package_name }}-py312-workflow Conda environment.

  2. Localize Conda environments: Run the conda_localize rule to set up the Snakemake environment files:

snakemake conda_localize
  1. Build the documentation: If the documentation is not hosted, you can build it locally using Snakemake. This will require the minimal workflow requirements.
snakemake docs_serve
  1. Open the documentation in your browser and follow the instructions for setting up the development environment on the Contributing page.

Development Environment

Initialize git

If you haven't already, initialize a git repository in the project directory:

git init

Then, add the remote repository URL if you have one:

git remote add origin <your-repo-url>

Then, commit the initial files:

git add .
git commit -m "Initial commit from able-workflow-copier template"
Create conda development environment

Use the conda_update Snakemake rule to create all the development conda ennvironments.

snakemake --cores 1 conda_update

Then activate the main development environment:

conda activate {{ package_name }}-py312-dev-runner

Project Development

Add a module: Use the able-workflow-module template to create a new module for your project.

Aspirational to-do's

These might be converted to issues to address throughout the life of the project.

Functionality
Online tools
  • Configure codecov for the repository.
  • TODO explain how to do this.
  • Update the codecov badge in README.md with the correct URL.
  • Update the codecov badge in docs/docs/index.md with the correct URL.
  • Host the documentation on a public server (e.g. github pages)
  • TODO explain how to do this.
Documentation
  • Add citation to the README.md with a public GitHub repository and/or DOI.
    • TODO explain how to get a DOI for a GitHub repo.
  • Update docs/docs/_images/logo.png with your project logo in [README.md].