https://github.com/open-research/sumatra

https://github.com/open-research/sumatra

Last synced: 3 months ago
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• Host: GitHub
• URL: https://github.com/open-research/sumatra
• Owner: open-research
• License: bsd-2-clause
• Created: 2015-01-28T21:23:43.000Z (almost 10 years ago)
• Default Branch: master
• Last Pushed: 2024-04-21T17:20:48.000Z (7 months ago)
• Last Synced: 2024-07-04T01:00:33.508Z (4 months ago)
• Language: Python
• Homepage: http://neuralensemble.org/sumatra/
• Size: 11.7 MB
• Stars: 127
• Watchers: 20
• Forks: 49
• Open Issues: 102
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

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README

        
=============

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://packages.python.org/Sumatra/ and 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 versions 2.7, 3.4, 3.5 or 3.6. The web interface requires

Django (>= 1.8) and the django-tagging package.

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 using

Git, you will need to install git-python bindings, and for Mercurial install hg-api.

============

Installation

============

These instructions are for Unix, Mac OS X. They may work on Windows as well, but

it hasn't been thoroughly tested.

If you have downloaded the source package, Sumatra-0.7.0.tar.gz::

    $ tar xzf Sumatra-0.7.0.tar.gz

    $ cd Sumatra-0.7.0

    # python setup.py install

The last step may have to be done as root.

Alternatively, you can install directly from the Python Package Index::

    $ pip install sumatra

or::

    $ easy_install sumatra

You will also need to install Python bindings for the version control system(s) you use, e.g.::

    $ pip install gitpython

    $ pip install mercurial hgapi

===========

Code status

===========

.. image:: https://travis-ci.org/open-research/sumatra.png?branch=master

   :target: https://travis-ci.org/open-research/sumatra

   :alt: Unit Test Status

.. image:: https://coveralls.io/repos/open-research/sumatra/badge.svg

   :target: https://coveralls.io/repos/open-research/r/sumatra

   :alt: Code coverage