qub-sherlock 1.3.0

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

sherlock
=========================

.. image:: https://readthedocs.org/projects/qub-sherlock/badge/
:target: http://qub-sherlock.readthedocs.io/en/latest/?badge
:alt: Documentation Status

.. image:: https://cdn.rawgit.com/thespacedoctor/sherlock/master/coverage.svg
:target: https://cdn.rawgit.com/thespacedoctor/sherlock/master/htmlcov/index.html
:alt: 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
==================

.. code-block:: bash


# 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 <http://sherlock.readthedocs.org/en/stable/>`__ (last `stable version <http://sherlock.readthedocs.org/en/stable/>`__ and `latest version <http://sherlock.readthedocs.org/en/latest/>`__).

Installation
============

The easiest way to install sherlock is to use ``pip``:

.. code:: bash

pip install qub-sherlock

Or you can clone the `github repo <https://github.com/thespacedoctor/sherlock>`__ and install from a local version of the code:

.. code:: bash

git clone [e-mail]:thespacedoctor/sherlock.git
cd sherlock
python setup.py install

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

.. code:: bash

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

.. code:: bash

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:

.. code:: bash

git clone [e-mail]:thespacedoctor/sherlock.git
cd sherlock
python setup.py develop

`Pull requests <https://github.com/thespacedoctor/sherlock/pulls>`__
are welcomed!

Sublime Snippets
~~~~~~~~~~~~~~~~

If you use `Sublime Text <https://www.sublimetext.com/>`_ as your code editor, and you're planning to develop your own python code with sherlock, you might find `my Sublime Snippets <https://github.com/thespacedoctor/sherlock-Sublime-Snippets>`_ useful.

Issues
------

Please report any issues
`here <https://github.com/thespacedoctor/sherlock/issues>`__.

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.