Repetible-Research Generic Python Project

Manifesto

Because Human is perfectible and error-prone, because Science should be open and flow and because cogito ergo sum.

Status

Project folder structure

This project has been structured using this rr-init repository as a template. In order to keep an upstream to such project, add it as remote like this:

git remote add rr-initUPS git@github.com:massich/rr-init.git

Structure Description

    project
    |- doc/                  # documentation for the study
    |  |- paper/             # manuscript(s), whether generated or not
    |  +- source/            # sphinx source
    |
    |- data                  # raw and primary data, are not changed once created
    |  |- raw/               # raw data, will not be altered
    |  +- clean/             # cleaned data, will not be altered once created
    |
    |- results               # all output from workflows and analyses
    |  |- figures/           # graphs, likely designated for manuscript figures
    |  +- pictures/          # diagrams, images, and other non-graph graphics
    |
    |- scratch/              # temporary files that can be safely deleted or lost
    |- src/                  # any programmatic code
    |
    |- datapackage.json      # metadata for the (input and output) data files
    |- requirements.txt      # list of the required packages (see virtualenv)
    |
    |- LICENSE.md
    |- README.md             # the top level description of content

Recomendations

Use a virtual environment (Virtualenv + VirtualenvWrapper)

Virtual-environments are not virtual machines. Virtual-environments are used to avoid library classing between the libraries of a project and those fom the system. Find more information in this virtual environment post describing how to use virtual environment for a mozilla marketplace testing.

Use the following to create a myPyProject environment based on the ./requirements.txt associated with the source directory ./src:

mkvirtualenv myPyProject -a src -r ../requirements.txt

Notice that mkvirtualenv activates such environment. The command deactivate is used to exit the virtual environment. Once the virtual environment exist on the system, the command workon myPyProject is rather convenient since it jumps into the working directory and activates the virtual enviroment.

Remember to keep requirements.txt up to date. For more details regarding the usage of the virtual enviroment, please look at the command reference.

Todo

General

• Add sphinx documentation as project.io website
• Add paper submodule
• Add code modules
• Add travis
• [ ]

Coding