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README.md

CSciBox

CSciBox is a project to aid geologists and other scientists working with ice and sediment cores in collating, manipulating, and interpreting data derived from those cores.

The project webpage is here: CSciBox Webpage, and includes more detailed information about the project and a simple tutorial.

There are two options for those who want to use the software.

Before running cscibox you need to start a MongoDB sever. To start a server on the terminal use:

sudo mongod

If this is your first time running CSciBox you will also need to load our database:

mongorestore /usr/local/lib/python2.7/site-packages/CSciBox-0.11.1-py2.7.egg/database_dump

Dependencies

In development, this project depends on the following packages. Installing them in this order will likely reduce your unhappiness:

  1. Python 2.7

  2. wxPython -- currently tested against version 3.0.0.0, Used for the GUI

  3. scipy/numpy/matplotlib -- follow link for instructions on installation, Used for calculations and plotting. 1.4.x is required; although it will work with some older versions, not all features will work with older versions.

  4. pymongo 2.8 (install using: pip install pymongo==2.8) -- Database for storage of all data

  5. quantities -- Used for handling engineering units

  6. bagit -- Used for exporting data

There is a Windows installer (OSX and Windows) available here: CSciBox Releases (slightly out of date).

Currently CSciBox has been tested on OSX 10.11 (El Capitan).

Please send your email address to lizb@colorado.edu so that we can keep you informed of future updates and get any feedback you may have.

Windows executable is 32-bits, and can be run as a stand-alone executable, no installation is necessary.

Note that you will also need access to a running mongodb server. After you have started up your local mongodb server, you should populate it with initial data by using the mongorestore command (see mongodb manual -- mongorestorre) and the data stored in this repository at database_dump/dump/repository. This will give you a set of initial (public) data to work from.

CSciBox contains a number of code modules that were written by others:

If you want to use Bacon, you need the compiled version. You may need to run the appropriate makefile in the src/plugins/bacon directory of this distribution to produce that file. This will create a directory in src/plugins/bacon called pluginfiles. Move the contents of that directory to src/cscience/components/cfiles.

If you want to use StratiCounter, you'll need to download the Matlab 2014b runtime available here

Although the installation instructions above focus on using a local mongodb server for data storage, it is possible to use CScience with a remote mongodb installation or with hbase. To use a remote mongodb server, edit the db_location and db_port variables in the src/config.py file to point to your remote database. To run against an hbase server, you will also need to install the happybase python package and change the db_type variable to hbase.