analysis/

A python package containing code used for data analysis. By virtue of being a package, this code can be run from anywhere in the project. If this is your first time working with the project, you'll need to install the analysis package before you can use it

$ pip install -e analysis

The -e flag installs the package in such a way that any changes you make to the source files are automatically reflected in the installation (i.e. you don't need to reinstall the package for changes to take effect).

data/

A single directory for any data file you collect. Data files that are relevant to a particular experiment can be symlinked into the notebook directory using exmemo data link. By default, this directory is ignored by git. Some relevant commands:

• exmemo data sync: Import any new data available.

documents/

A directory for presentations, papers, and the like. By default, this directory is ignored by git.

notebook/

A Sphinx directory with separate directories for each experiment you carry out. An experiment is defined by asking and answering a single question, which may take a single day or several months. Some relevant commands:

• exmemo expt new: Start a new experiment
• exmemo expt edit: Edit an existing experiment

protocols/

A directory for protocols, which can be text files, python script, Excel files, Word documents, whatever. Some relevant commands:

• exmemo protocol print: Print out a particular protocol