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sherlock

Documentation Status Coverage Status

A python package and command-line tools to contextually classify astronomical transient sources. Sherlock mines a library of historical and on-going survey data to attempt to identify the source of a transient event, and predict the classification of the event based on the associated crossmatched data.

Command-Line Usage

# SHERLOCK #
: INFERING TRANSIENT-SOURCE CLASSIFICATIONS FROM SPATIALLY CROSS-MATCHED CATALOGUED SOURCES :
=============================================================================================

Documentation for sherlock can be found here: http://sherlock.readthedocs.org/en/stable

.. todo ::

    - docuument cl_utils module
    - tidy usage text

Usage:
    sherlock init
    sherlock info [-s <pathToSettingsFile>]
    sherlock [-N] dbmatch [-f --update] [-s <pathToSettingsFile>]
    sherlock [-vN] match -- <ra> <dec> [<pathToSettingsFile>]
    sherlock clean [-s <pathToSettingsFile>]
    sherlock wiki [-s <pathToSettingsFile>]
    sherlock import ned <ra> <dec> <radiusArcsec> [-s <pathToSettingsFile>]
    sherlock import cat <cat_name> <pathToDataFile> <cat_version> [-s <pathToSettingsFile>]
    sherlock import stream <stream_name> [-s <pathToSettingsFile>]

Options:
    init                    setup the sherlock settings file for the first time
    match                   XXXX
    dbmatch                 database match
    clean                   XXXX
    wiki                    XXXX
    import                  XXXX
    ned                     use the online NED database as the source catalogue
    cat                     import a static catalogue into the crossmatch catalogues database
    stream                  download/stream new data from a give source catalogue into the sherlock crossmatch catalogues database
    info                    print an overview of the current catalogues, views and streams in the sherlock database ready for crossmatching

    ra                      the right-ascension coordinate with which to perform a conesearch (sexegesimal or decimal degrees)
    dec                     the declination coordinate with which to perform a conesearch (sexegesimal or decimal degrees)
    radiusArcsec            radius in arcsec of the footprint to download from the online NED database
    cat_name                name of the catalogue being imported. The following catalogues can be imported:
                                * ``veron``: Veron AGN/QSO catalogue
                                    http://cdsarc.u-strasbg.fr/viz-bin/Cat?VII/258
                                * ``milliquas``: Million Quasars Catalog
                                    http://heasarc.gsfc.nasa.gov/w3browse/all/milliquas.html
                                * ``ned_d``: NED's Master List of Redshift-Independent Extragalactic Distances
                                    https://ned.ipac.caltech.edu/Library/Distances/
    stream_name             name of the stream to import into the crossmatch catalogues database. The following streams can be imported:
                                * ``ifs``: Multi Unit Spectroscopic Explorer (MUSE) IFS galaxy catalogue (L. Galbany)
                                    http://www.das.uchile.cl/~lgalbany/LG/research.html

    -N, --skipNedUpdate     do not update the NED database before classification
    -f, --fast              faster but errors in crossmatch table ingest my be misses
    -h, --help              show this help message
    -s, --settings          the settings file
    -v, --verbose           print more details to stdout
    -l, --transientlistId   the id of the transient list to classify
    -u, --update            update the transient database with new classifications and crossmatches

Documentation

Documentation for sherlock is hosted by Read the Docs (last stable version and latest version).

Installation

The easiest way to install sherlock is to use pip:

pip install qub-sherlock

Or you can clone the github repo and install from a local version of the code:

git clone git@github.com:thespacedoctor/sherlock.git
cd sherlock
python setup.py install

To upgrade to the latest version of sherlock use the command:

pip install qub-sherlock --upgrade
.. todo::

    - make a note about how to setup mysql login paths and have them associated with the database setting in the sherlock settings file


mysql_config_editor set --login-path=xxx --host=127.0.0.1 --user=myuser --password --port=xxx

Development

If you want to tinker with the code, then install in development mode. This means you can modify the code from your cloned repo:

git clone git@github.com:thespacedoctor/sherlock.git
cd sherlock
python setup.py develop

Pull requests are welcomed!

Sublime Snippets

If you use Sublime Text as your code editor, and you're planning to develop your own python code with sherlock, you might find my Sublime Snippets useful.

Issues

Please report any issues here.

License

Copyright (c) 2016 David Young

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.