Merge pull request #31 from fsimkovic/master

Updates, fixes and added features

CHANGELOG.rst

@@ -2,48 +2,79 @@
 Changelog
 =========
 
-v0.8.3
-------
-- General
-    - ``requirements.txt`` file re-added for easier dependency installation
-    - Distance definitions accept floating point values
-    - ``_BandwidthCalc`` class renamed to ``BandwidthBase``
-    - Abstractified ``BandwidthBase``, and ``Parser`` with all subparser classes 
-    - Refactored ``conkit/io/__init__.py`` to avoid duplication of code
+[Unreleased]
+------------
+Added
+~~~~~
+- ``Entity.top`` property to always return the first child in the list
+- ``ContactMap.find`` function accepts ``strict`` keyword argument to find contact pairs with both residues in ``register``
+- ``PdbParser`` takes a distance cutoff of ``0`` to include all Cb-Cb contacts in the protein structure
+- ``ContactMatchState`` enumerated type for definitions of state constants for contact
+- ``SequenceAlignmentState`` enumerated type for definitions of state constants for each sequence file 
+- ``NcontParser`` added to extract contact pairs identified by NCONT (CCP4 Software Suite) 
+Changed
+~~~~~~~
+- Optimized some functions and comparisons according to the recommended Python optimization instructions 
+- ``ContactMap.match`` does __not__ modifiy ``other`` by default anymore. Specify ``match_other=True`` as kwarg!
+- ``ContactMap.calculate_kernel_density`` renamed to ``ContactMap.calculate_contact_density`` 
+- ``ContactDensityFigure`` draws domain boundary lines instead of symbols
 
-- New features
-    - ``LinearBW`` calculator added for linear bandwidth calculation in analysis
-    - ``seq_ascii`` property to ``Sequence`` for encoded sequence
-    - ``ascii_matrix`` property to ``SequenceFile`` for encoded alignment 
-    - ``SequenceFile`` and ``ContactFile`` classes have new ``empty`` properties
-    - ``flib`` format for ``ContactFile`` classes to allow easier conversions for the Flib-Coevo fragment picking library
+[0.8.3]
+-------
+Added
+~~~~~
+- ``requirements.txt`` file re-added for easier dependency installation
+- ``LinearBW`` calculator added for linear bandwidth calculation in analysis
+- ``seq_ascii`` property to ``Sequence`` for encoded sequence
+- ``ascii_matrix`` property to ``SequenceFile`` for encoded alignment 
+- ``SequenceFile`` and ``ContactFile`` classes have new ``empty`` properties
+- ``flib`` format for ``ContactFile`` classes to allow easier conversions for the Flib-Coevo fragment picking library
+Changed
+~~~~~~~
+- Distance definitions accept floating point values
+- ``_BandwidthCalc`` class renamed to ``BandwidthBase``
+- Abstractified ``BandwidthBase``, and ``Parser`` with all subparser classes 
+- Refactored ``conkit/io/__init__.py`` to avoid duplication of code
+Fixed
+~~~~~
+- ``PconsParser`` class accepts negative ``raw_score`` values
+- ``SequenceFile.neff`` returns ``float`` instead of ``int``
+- ``CCMpredParser.read()`` returns empty ``ContactFile`` when matrix file empty
 
-- Bug fix
-    - ``PconsParser`` class accepts negative ``raw_score`` values
-    - ``SequenceFile.neff`` returns ``float`` instead of ``int``
-    - ``CCMpredParser.read()`` returns empty ``ContactFile`` when matrix file empty
-
-v0.8.2
-------
-
-- Critical bug fix for automated opening of filehandle in Python2.7 
+[0.8.2]
+-------
+Added
+~~~~~
 - Test function skipping added for ``SequenceFile.filter()`` when SciPy not installed
+Changed
+~~~~~~~
 - Renamed conkit/io/tests files for filenames to agree with modules in conkit/io
 - Performance of ``write()`` in parsers improved by construction of string and single call to ``write()`` of filehandle
+Fixed
+~~~~~
+- Critical bug fix for automated opening of filehandle in Python2.7 
 
-v0.8.1
-------
-
+[0.8.1]
+-------
+Changed
+~~~~~~~
 - Revoked catching of ``SystemExit(0)`` exception in scripts when invoked with ``--help`` flag 
+Fixed
+~~~~~
 - Bug fix relating to Python3 automatic opening of file handles - Thanks to Miguel Correa for reporting this bug
 
-v0.8
-----
-
-- Default value in ``calculate_meff()`` and ``calculate_weights()`` changed from 0.7 to 0.8 [more commonly used in literature]
-- Bug fix with PyPi installation where ``requirements.txt`` not found; fix includes removal of ``requirements.txt`` and addition of ``install_requires`` to ``setup.py`` instead. - Thanks to Miguel Correa for reporting this bug
+[0.8]
+-----
+Added
+~~~~~
 - Logging message coloring according to message level
 - ``filter()`` function added for redundancy/distant homolog removal from ``SequenceFile``
+- License text added to each module
 - ``io`` sub-package caches modules and imports upon request
+Changed
+~~~~~~~
+- Default value in ``calculate_meff()`` and ``calculate_weights()`` changed from 0.7 to 0.8 [more commonly used in literature]
 - ``core`` classes extracted to individual module files
-- License text added to each module
+Fixed
+~~~~~
+- Bug fix with PyPi installation where ``requirements.txt`` not found; fix includes removal of ``requirements.txt`` and addition of ``install_requires`` to ``setup.py`` instead. - Thanks to Miguel Correa for reporting this bug

conkit/command_line/__init__.py

@@ -35,6 +35,7 @@
 
 import logging
 import os
+import sys
 
 
 def setup_logging(level='info', logfile=None):
@@ -55,26 +56,27 @@ def setup_logging(level='info', logfile=None):
        Instance of a :obj:`logger <logging.Logger>`
 
     """
-    
+
     class ColorFormatter(logging.Formatter):
         """Formatter to color console logging output"""
-    
+
         # ANSI foreground color codes
-        colors = { 
+        colors = {
             logging.DEBUG: 34,           # blue
-            logging.INFO: 0   ,          # reset to default
             logging.WARNING: 33,         # yellow
             logging.ERROR: 31,           # red
             logging.CRITICAL: 31,        # red
         }
 
         def format(self, record):
-            if record.exc_info is None:
-                # REM: get the ANSI FG color code
-                color = ColorFormatter.colors[record.levelno]
-                prefix = '\033[{}m'.format(color)
-                record.msg = os.linesep.join([prefix + l for l in str(record.msg).splitlines()])
-
+            if record.levelno in self.colors:
+                prefix = '\033[1;{}m'.format(
+                    ColorFormatter.colors[record.levelno])
+                postfix = '\033[0m'
+                record.msg = os.linesep.join(
+                    [prefix + l +
+                        postfix for l in str(record.msg).splitlines()]
+                )
             return logging.Formatter.format(self, record)
 
     # Reset any Handlers or Filters already in the logger to start from scratch
@@ -91,7 +93,7 @@ def format(self, record):
     logging.getLogger().setLevel(logging.DEBUG)
 
     # create console handler with a higher log level
-    ch = logging.StreamHandler()
+    ch = logging.StreamHandler(stream=sys.stdout)
     ch.setLevel(logging_levels.get(level, logging.INFO))
     ch.setFormatter(ColorFormatter('%(message)s'))
     logging.getLogger().addHandler(ch)
@@ -101,12 +103,13 @@ def format(self, record):
         fh = logging.FileHandler(logfile)
         fh.setLevel(logging.NOTSET)
         fh.setFormatter(
-            logging.Formatter('%(asctime)s\t%(name)s [%(lineno)d]\t%(levelname)s\t%(message)s')
+            logging.Formatter(
+                '%(asctime)s\t%(name)s [%(lineno)d]\t%(levelname)s\t%(message)s')
         )
         logging.getLogger().addHandler(fh)
 
-    logging.getLogger().debug('Console logger level: %s', logging_levels.get(level, logging.INFO))
+    logging.getLogger().debug('Console logger level: %s',
+                              logging_levels.get(level, logging.INFO))
     logging.getLogger().debug('File logger level: %s', logging.NOTSET)
 
     return logging.getLogger()
-