New directory layout

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Nov 28, 2014, 11:23:38 AM11/28/14
Especially projects with the "full" layout seem very crowded to me. In a development branch I have changed this to a two-level layout. Short of `config`, now only three directories exist at the top level: `code`, `input` and `results`. See [1] for details.

Before releasing this, I'd be interested in hearing opinions: Is this too much structure, are the new names okay, perhaps the directory layout should be configurable, etc..

Please install this development branch version using


Existing projects can be migrated using `migrate.project()`, you'll be prompted to do so when you call `load.project()` on an "old-style" configuration. The actual layout is still subject to change, so please make sure you have a backup.

Your feedback is appreciated -- on this mailing list or as comment on GitHub [2]. Thanks!

Marshall Feldman

Mar 30, 2017, 10:16:57 AM3/30/17
to ProjectTemplate
This post is old, so I can only guess what happened to it. If the issue is still alive, here are 3 comments/suggestions:
  1. The idea of making projects more easily managed with better file structure is excellent.
  2. When you do make this change, please update the documentation at the same time.
  3. I'd very much like to see the current munging sequence mechanism -- proceeding through files according to the sorted sequence of their file names -- replaced by a control file (e.g., one named "munge_sequence" that lists the files in the desired order. In fact, one could leave the existing approach intact but override it if a "munge_sequence" file exists in the munge directory. The motivation for this change is ease of use. Currently, if one has, say, ten munge files and wants to insert a new file to start the process, then all of the other ten will also need to be renamed; reordering the entire sequence is an even bigger headache. But with a list of file names, one simply has to insert the name of the new file at the start of the list.
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