Update my fork of the package

INFO.url

@@ -1 +1 @@
-URL=http://bbcf.epfl.ch/track
+http://xapple.github.com/track/

README.md

@@ -2,6 +2,7 @@ track 1.1.0
 ===========
 
 Copyright 2011 EPFL BBCF <[email protected]>
+Written by <[email protected]>
 
 track is a python module for reading and writing genomic data.
 
@@ -14,4 +15,4 @@ of this license is in the LICENSE.txt file.
 Full documentation
 ==================
 
-The full documentation can be found [on our website](http://bbcf.epfl.ch/track).
+The full documentation can be found [on the website](http://xapple.github.com/track/).

doc/conf.py

@@ -22,7 +22,7 @@
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.pngmath', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode', 'sphinxcontrib.googleanalytics']
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.pngmath', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['templates']
@@ -128,7 +128,7 @@
 #html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-html_sidebars = {'**': 'bbcflinks.html'}
+#html_sidebars = {'**': 'bbcflinks.html'}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
@@ -150,7 +150,7 @@
 html_show_sphinx = False
 
 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
+html_show_copyright = False
 
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the
@@ -163,9 +163,6 @@
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'trackdoc'
 
-# Google analytics
-googleanalytics_id = "UA-24167610-22"
-
 # -- Options for LaTeX output --------------------------------------------------
 
 # The paper size ('letter' or 'a4').

doc/content/bugs.rst

@@ -1,4 +1,4 @@
 ##############
 Reporting bugs
 ##############
-Our `issue tracking system <https://github.com/bbcf/track/issues>`_ is found in the github repository. You are welcome to open a new ticket in it if you think you have found a bug. You will however need to create a github account if you don't already have one to open a new issue, sorry.
+Our `issue tracking system <https://github.com/xapple/track/issues>`_  is found in the github repository. You are welcome to open a new ticket in it if you think you have found a bug. You will however need to create a github account if you don't already have one to open a new issue, sorry.

doc/content/installation.rst

@@ -2,19 +2,11 @@
 Installation
 ############
 
-To install you should download the latest source code from GitHub, either by going to::
+To install you can simply type::
 
-    http://github.com/bbcf/track
+    $ sudo easy_install empty
 
-and clicking on "Downloads", or by cloning the git repository with::
+That's it. However, if that doesn't work because you don't have sufficient permissions, you can simply install it somewhere else (for instance in your home)::
 
-    $ git clone https://github.com/bbcf/track.git
-
-Once you have the source code, run::
-
-    $ cd track
-    $ sudo python setup.py install
-
-to install it. If you don't have permission to install it in the default directory, you can simply build the source in-place and use the package from the git repository::
-
-    $  python setup.py build_ext --inplace
+    $ cd ~
+    $ pip install -e git+https://github.com/xapple/track

doc/content/licensing.rst

@@ -3,4 +3,4 @@ Licensing
 #########
 The code is free and open source, licensed under the GNU General Public License version 3. You can download, copy or fork the source code on github:
 
-    https://github.com/bbcf/track/
+    https://github.com/xapple/track

samples/build.py

@@ -32,6 +32,6 @@ def create_tracks():
         for track_name, track_info in sorted(samples[collection].items()):
             print Color.ylw + "Creating track '" + track_info['name'] + "'" + Color.end
             from_path = track_info[conversion_info['from']]
-            to_path =   track_info[conversion_info['to']]
+            to_path   = track_info[conversion_info['to']]
             if os.path.exists(to_path): os.remove(to_path)
             track.convert(from_path, to_path, assembly = conversion_info['assembly'])

setup.py

@@ -6,17 +6,17 @@
         description      =   'Python package for reading and writing genomic data',
         long_description =   open('README.md').read(),
         license          =   'GNU General Public License 3.0',
-        url              =   'http://bbcf.epfl.ch/track',
-        author           =   'EPFL BBCF',
-        author_email     =   '[email protected]',
+        url              =   'http://xapple.github.com/track/',
+        author           =   'Lucas Sinclair',
+        author_email     =   '[email protected]',
         classifiers      =   ['Topic :: Scientific/Engineering :: Bio-Informatics'],
         packages         =   ['track',
                               'track.parse',
                               'track.serialize',
                               'track.test',
                               'track.manips',
                              ],
-        package_data     = {'track': ['genomes.db']},
         ext_modules      = [Extension('track.pyrow', ['src/pyrow.c'])],
         scripts          = ['track/track'],
+        install_requires = ['genomes'],
     )

track/__init__.py

@@ -21,11 +21,13 @@
 from track.common import JournaledDict, natural_sort, int_to_roman, roman_to_int
 from track.common import Color, pick_iterator_elements, get_next_item, is_gzip
 from track.common import if_url_then_get_url
-from track.genomes import Assembly
 
 # Compiled modules #
 from track.pyrow import SuperRow
 
+# Extra modules #
+from genomes import Assembly
+
 # Constants #
 special_tables = ('attributes', 'chrNames', 'types')
 minimum_fields = ('start', 'end')
@@ -790,7 +792,7 @@ def find_column_name(self, synonyms, table_name=None):
         if table_name is not None: fields = self.fields
         else:                      fields = self._get_fields_of_table(table_name)
         for name in synonyms:
-            if name in self.fields: return name
+            if name in fields: return name
         return ''
 
     #-----------------------------------------------------------------------------#

track/serialize/__init__.py

@@ -6,7 +6,7 @@
 import sys
 
 # Other modules #
-from track.genomes import Assembly
+from genomes import Assembly
 
 # Variables #
 serializers = {