TODO: Replace with the name of the repo

Note: Analysis repo names should be prefixed with the year (ie 2024-noveltree-analysis)

Purpose

TODO: Briefly describe the core analyses performed in the repository and the motivation behind them.

Installation and Setup

This repository uses conda to manage software environments and installations. You can find operating system-specific instructions for installing miniconda here. After installing conda and mamba, run the following command to create the pipeline run environment.

TODO: Replace <NAME> with the name of your environment
mamba env create -n <NAME> --file envs/dev.yml
conda activate <NAME>

Developer Notes (click to expand/collapse)

1. Install your pre-commit hooks:

   pre-commit install
   

   This installs the pre-commit hooks defined in your config (./.pre-commit-config.yaml).

2. Export your conda environment before sharing:

   As your project develops, the number of dependencies in your environment may increase. Whenever you install new dependencies (using either pip install or mamba install), you should update the environment file using the following command.

   conda env export --from-history --no-builds > envs/dev.yml
   

   --from-history only exports packages that were explicitly added by you (e.g., the packages you installed with pip or mamba) and --no-builds removes build specification from the exported packages to increase portability between different platforms.

Data

TODO: Add details about the description of input / output data and links to Zenodo depositions, if applicable.

Overview

Description of the folder structure

Methods

TODO: Include a brief, step-wise overview of analyses performed.

Example:

1. Download scripts using download.ipynb.
2. Preprocess using ./preprocessing.sh -a data/
3. Run Snakemake pipeline snakemake --snakefile Snakefile
4. Generate figures using pub/make_figures.ipynb.

Compute Specifications

TODO: Describe what compute resources were used to run the analysis. For example, you could list the operating system, number of cores, RAM, and storage space.

Contributing

See how we recognize feedback and contributions to our code.

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For Developers

This section contains information for developers who are working off of this template. Please adjust or edit this section as appropriate when you're ready to share your repo.

GitHub templates

This template uses GitHub templates to provide checklists when making new pull requests. These templates are stored in the .github/ directory.

VSCode

This template includes recommendations to VSCode users for extensions, particularly the ruff linter. These recommendations are stored in .vscode/extensions.json. When you open the repository in VSCode, you should see a prompt to install the recommended extensions.

.gitignore

This template uses a .gitignore file to prevent certain files from being committed to the repository.

pyproject.toml

pyproject.toml is a configuration file to specify your project's metadata and to set the behavior of other tools such as linters, type checkers etc. You can learn more here

Linting

This template automates linting and formatting using GitHub Actions and the ruff linter. When you push changes to your repository, GitHub will automatically run the linter and report any errors, blocking merges until they are resolved.