pub const DEFAULT_CONFIG_TEXT: &str = "# This is the default configuration for `scilo`.\n# For details on each option, see the comments below or the documentation at https://scilo.jrhawley.ca/configuration\n\n# All subdirectories within the `root_dirs.code` and `root_dirs.results` directories much match this regular expression.\n# If this is not a valid regular expression, `scilo` will fail.\n# By default, the naming scheme is `YYYY-mm-dd_kebab-case-short-title`.\ncode_results_subdir_regex = \"2\\\\d{3}-(0[1-9]|1[0-2])-([0-2][0-9]|3[0-1])_[A-Za-z-]+\"\n\n# An array containing the names of the checks that should be performed when running the `lint` subcommand.\n# By default, all lints are included.\nlints = [\n \"code_results_subdir_pairing\",\n \"code_results_subdir_regex\",\n \"code_subdir_readmes\",\n \"code_subdir_workflows\",\n \"data_subdir_readmes\",\n \"root_dirs\",\n \"root_files\",\n]\n\n# An array of acceptable file names for the README in a directory.\n# By default, each subdirectory in the `root_dirs.code` and `root_dirs.data` directories should have a README.\n# You can disable this check by leaving the array empty or by removing the `code_subdir_readmes` lint from the `lints` array.\nreadme_names = [\n \"README.md\",\n \"README.org\",\n \"README.txt\",\n \"README\",\n]\n\n# An array of required files at the project root.\nroot_files = [ ]\n\n# An array of acceptable file names for the workflow file in a directory.\n# By default, each subdirectory in the `root_dirs.code` directory should have a workflow file.\n# You can disable this check by leaving the array empty or by removing the `code_subdir_workflows` lint from the `lints` array.\nworkflow_names = [\n \"Snakefile\",\n \"_targets.R\",\n \"main.cwl\",\n \"main.nf\",\n \"main.pipe\",\n \"main.w\",\n \"main.wdl\",\n \"Makefile\",\n]\n\n# The root directories that contain different types of files for the entire repository.\n[root_dirs]\n# This folder contains all the code used to process files from data, perform statistical analyses, create visualizations, and save the outputs in results.\n# Generally, this directory contains a series of subdirectories, each of which contain a set of related scripts for a single research question.\ncode = \"code\"\n# All raw and processed data should be found within this directory.\n# The datasets located here will then be sourced by code within the code directory and used to generate outputs in the results directory.\ndata = \"data\"\n# Documentation such as a manuscript, experimental descriptions from contract research organizations, or software user guides can go in this directory.\n# Interactive HTML notebooks like Jupyter, R Markdown, or Quarto that render or explain the data, but don\'t create artefacts that belong in results, could also go here.\n# Data that belongs in data or notebooks which process data that belong in code should not be placed in here.\ndocs = \"docs\"\n# In many research projects you will need a package manifest, like a Nix expression or an Anaconda recipe.\n# Alternatively, you may need to vendor a copy of some external code using a git submodule.\n# This folder can be used to house all of the relevant code so as to not populate the custom code present in code.\nexternal = \"pkgs\"\n# Code and scripts in the code directory should create outputs in this directory to ensure a separation of inputs, code, and outputs.\n# Generally, this directory contains a series of subdirectories, each of which will contain all the outputs originating from the code in the corresponding code subdirectory.\nresults = \"results\"\n";