Note: the standardized file structure (sFSS) is also referred to as 'Project Compendium'

ENCORE setup

Five components of ENCORE. The main component comprises the sFSS template (1) that organizes all parts of the project. ‘Project’ corresponds to the root directory of the template. The blocks represent project dependent sub-directories (Figure 4). Project documentation resides in (pre-defined) files (2) that are found in all subdirectories of the sFSS template. The pre-defined files contain instructions about the minimum information that needs to be provided in terms of documentation for the different parts of a project. Each project is complemented with a GitHub repository (3) for version control of the code and documentation in the ‘Processing’ (sub-)directories. The sFSS Navigator (4) allows (end) users to browse the main contents of the project. The external ENCORE user documentation (5) provides instructions for new users on how to instantiate a new project.

standardized File System Structure

The standardized File System Structure (sFSS) and associated pre-defined files. Standardized directory structure of the sFSS containing pre-defined files (brown), which include README files (in Markdown format) that provide a documentation template and instructions. Note that the pre-defined files in the ‘Data’ directories (red) and the ‘0_SoftwareEnvironment’ subdirectories are only shown once. The names of the directories ‘NameOfDataset_1’ and ‘NameOfComputation_1’ are placeholders and should be replaced with more descriptive names. These directories can be replicated if multiple datasets are used or if different computation procedures are performed. Subdirectories shown in light blue are under version control using Git/GitHub. The ‘0’ prefix ensures that the corresponding files/directories are always on top of the file list when using lexicographic ordering. The README.md in ‘Processing’ is the default GitHub repository README file and therefore does not have the ‘0’ prefix.