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Paper organization

All Madagascar papers expect a specific organization to your directories. In particular, you are expected to have a paper-level directory where your tex files and main SConstruct will exist. These files will tell Madagascar how to build your documents for a particular project. You can have multiple documents built from the same location, using the same SConstruct as we will demonstrate later.

Below the paper directory, are the individual ``chapters" that contain the processing flows used to generate the plots or process the data that you wish to use in your reproducible documents. Ideally, each ``chapter" directory correlates to the processing flows or examples in each chapter or section for your paper. Additionally, each ``chapter" contains its own SConstruct that operates independently of the paper SConstruct one level above it. Furthermore, inside the ``chapter" folder, Madagascar needs to have a Fig folder that contains all of the VPLOT files that were created using Result commands during processing. This folder is automatically created during processing using SCons, so you don't need to manually create it. It is important to note that Madagascar can only locate VPLOT files that are in this file hierarchy for use in your papers. Figure 1 illustrates the folder hierarchy as well.

Note: ``chapter" folders may be symbolic links that point to folders elsewhere on the file system. This trick can be useful to reuse figures without copying files and folders around to various folders. If you use symlinks, make sure to avoid editing files that are symbolically linked, as your changes may propagate in unintended ways to other projects and papers.

Figure 1: The organizational hierarchy for Madagascar paper directories.

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