Sumatra 0.8.0

A tool for automated tracking of computation-based scientific projects

About Sumatra

Sumatra is a tool for managing and tracking projects based on numerical simulation and/or analysis, with the aim of supporting reproducible research. It can be thought of as an automated electronic lab notebook for computational projects.

It consists of:

• a command-line interface, smt, for launching simulations/analyses with automatic recording of information about the experiment, annotating these records, linking to data files, etc.

• a web interface with a built-in web-server, smtweb, for browsing and annotating simulation/analysis results.

• a Python API, on which smt and smtweb are based, that can be used in your own scripts in place of using smt, or could be integrated into a GUI-based application.

Sumatra is currently beta code, and should be used with caution and frequent backups of your records.

For documentation, see http://neuralensemble.org/sumatra/

Functionality:

• launch simulations and analyses, and record various pieces of information, including:

  • the executable (identity, version)

  • the script (identity, version)

  • the parameters

  • the duration (execution time)

  • console output

  • links to all data (whether in files, in a database, etc.) produced by the simulation/analysis

  • the reason for doing the simulation/analysis

  • the outcome of the simulation/analysis

• allow browsing/searching/visualising the results of previous experiments

• allow the re-running of previous simulations/analyses with automatic verification that the results are unchanged

• launch single or batch experiments, serial or parallel

Requirements

Sumatra requires Python version 3.9 or later The web interface requires Django (>= 4.2). Sumatra requires that you keep your own code in a version control system (currently Subversion, Mercurial, Git and Bazaar are supported). If you are already using Bazaar there is nothing else to install. If you are using Subversion you will need to install the pysvn package. If you are using Git, you will need to install git-python bindings, and for Mercurial install hg-api.

Installation

These instructions are for Unix and Mac OS. They may work on Windows as well, but it hasn’t been thoroughly tested.

The easiest way to install is with pip:

$ pip install sumatra[default]

The “default” option installs the most commonly-used features:

• Git support

• the local web-based GUI

• support for remote record stores

Other options are available. For example, to install support for Mercurial and for using a PostgreSQL database as the record store, run:

$ pip install sumatra[default,hg,postgres]

Code status