--- a/common/__init__.py	Thu Jul 03 18:48:32 2008 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-import file
-import floateq
-#import gzipstring
-import memory
-import misc
-import mytime
-import str

--- a/common/file.py	Thu Jul 03 18:48:32 2008 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-import gzip, bz2
-import os, os.path, sys
-
-def myopen(filename, mode="r", bufsize=-1):
-    """
-    open(), detecting .gz and .bz2 file suffixes
-    """
-    if filename[-3:] == ".gz":
-        return gzip.open(filename, mode, bufsize)
-    elif filename[-4:] == ".bz2":
-        return bz2.open(filename, mode, bufsize)
-    else:
-        return open(filename, mode, bufsize)
-
-def find_files(dir, shuffle=False):
-    """
-    Find all files in dir by recursively directory walking.
-    @param shuffle: Randomly shuffle the files before returning them.
-    """
-    all = []
-    assert os.path.isdir(dir)
-    for root, dirs, files in os.walk(dir):
-        #sys.stderr.write("Walking %s...\n" % root)
-        for f in files:
-            all.append(os.path.join(root, f))
-    if shuffle:
-        import random
-        random.shuffle(all)
-    return all 
-
-def ensuredir(dir):
-    """
-    Create dir if it does not exist (including all parents).
-    Do nothing if it does.
-    """
-    if not os.path.exists(dir):
-       sys.stderr.write("Creating directory: %s\n" % dir)
-       os.makedirs(dir)
-    assert os.path.isdir(dir)

--- a/common/floateq.py	Thu Jul 03 18:48:32 2008 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-#
-# Determine if floating point numbers are very close
-###########
-
-import math
-
-DEFAULT_SANITY_CHECK_EPSILON = 1e-6
-
-def floateq(a, b, epsilon=DEFAULT_SANITY_CHECK_EPSILON):
-    """
-    Compare two floats, with some epsilon tolerance.
-    """
-    return absolute_relative_error(a, b) < epsilon
-
-def absolute_relative_error(a, b, epsilon=DEFAULT_SANITY_CHECK_EPSILON):
-    return abs(a - b) / (abs(a) + abs(b) + epsilon)
-
-def double_epsilon_multiplicative_eq(a, b, epsilon=DEFAULT_SANITY_CHECK_EPSILON):
-    """
-    Determine if doubles are equal to within a multiplicative factor of
-    L{epsilon}.
-    @note: This function should be preferred over
-    L{double_epsilon_additive_eq}, unless the values to be compared may
-    have differing signs.
-    @precondition: sign(a) == sign(b)
-    @rtype: bool
-    """
-    if a == b: return True
-    if a == 0 and b == 0: return True
-    assert a != 0
-    assert b != 0
-    assert sign(a) == sign(b)
-    if a > b: d = a / b
-    else: d = b / a
-    assert d >= 1
-    return True if d <= 1 + SANITY_CHECK_EPSILON else False
-
-def double_epsilon_additive_eq(a, b):
-    """
-    Determine if doubles are equal to within an additive factor of
-    L{SANITY_CHECK_EPSILON}.
-    @note: Prefer L{double_epsilon_multiplicative_eq} to this function
-    unless the values to be compared may have differing signs.
-    """
-    if a == b: return True
-    if a == 0 and b == 0: return True
-    assert sign(a) != sign(b)   # Should use SANITY_CHECK_EPSILON
-    d = math.fabs(a - b)
-    return d <= SANITY_CHECK_EPSILON

--- a/common/memory.py	Thu Jul 03 18:48:32 2008 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,52 +0,0 @@
-"""
-Determine memory usage of a program::
-    m0 = memory()
-    ...
-    m1 = memory(m0)
-@note: From U{http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/286222/index_txt}
-@warning: Not portable.
-"""
-
-import os
-
-_proc_status = '/proc/%d/status' % os.getpid()
-
-_scale = {'kB': 1024.0, 'mB': 1024.0*1024.0,
-          'KB': 1024.0, 'MB': 1024.0*1024.0}
-
-def _VmB(VmKey):
-    '''Private.
-    '''
-    global _proc_status, _scale
-     # get pseudo file  /proc/<pid>/status
-    try:
-        t = open(_proc_status)
-        v = t.read()
-        t.close()
-    except:
-        return 0.0  # non-Linux?
-     # get VmKey line e.g. 'VmRSS:  9999  kB\n ...'
-    i = v.index(VmKey)
-    v = v[i:].split(None, 3)  # whitespace
-    if len(v) < 3:
-        return 0.0  # invalid format?
-     # convert Vm value to bytes
-    return float(v[1]) * _scale[v[2]]
-
-
-def memory(since=0.0):
-    '''Return memory usage in bytes.
-    '''
-    return _VmB('VmSize:') - since
-
-
-def resident(since=0.0):
-    '''Return resident memory usage in bytes.
-    '''
-    return _VmB('VmRSS:') - since
-
-
-def stacksize(since=0.0):
-    '''Return stack size in bytes.
-    '''
-    return _VmB('VmStk:') - since

--- a/common/misc.py	Thu Jul 03 18:48:32 2008 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-def runcmd(args, input=None):
-    """
-    Split args into a list, run this command, and return its output.
-    Raise RuntimeError if the command does not return 0.
-    @note: This function will not work if args contains pipes |
-    @param input: If this exists, it will be fed as stdin
-    """
-    import subprocess
-#    print args
-    import string
-    if input == None: stdin = None
-    else: stdin = subprocess.PIPE
-    proc = subprocess.Popen(string.split(args), stdout=subprocess.PIPE, stdin=stdin)
-#    proc = subprocess.Popen(string.split(args), stdout=subprocess.PIPE)
-    output = proc.communicate(input=input)[0]
-    if proc.returncode != 0:
-        import exceptions
-        raise exceptions.RuntimeError
-    return output
-
-def homedir():
-    import os
-    return os.environ["HOME"]
-def utilsdir():
-    import os
-    return os.environ["UTILS"]
-
-def sign(i, assertions=True):
-    """
-    + or - 1
-    @precondition: i != 0
-    """
-    if assertions:
-        assert i != 0
-    else:
-        if i == 0: return 0
-
-    return +1 if i > 0 else -1
-
-def unique_elements_list_intersection(list1,list2):
-    """
-    Return the unique elements that are in both list1 and list2
-    (repeated elements in listi will not be duplicated in the result).
-    This should run in O(n1+n2) where n1=|list1|, n2=|list2|.
-    """
-    return list(set.intersection(set(list1),set(list2)))

--- a/common/mytime.py	Thu Jul 03 18:48:32 2008 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-
-import time
-#http://www.daniweb.com/code/snippet368.html
-def print_timing(func):
-    def wrapper(*arg):
-        t1 = time.time()
-        res = func(*arg)
-        t2 = time.time()
-        print '%s took %0.3f ms' % (func.func_name, (t2-t1)*1000.0)
-        return res
-    return wrapper
-

--- a/common/str.py	Thu Jul 03 18:48:32 2008 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-def percent(a, b):
-    """
-    Return percentage string of a and b, e.g.:
-        "1 of 10 (10%)"
-    """
-    assert a <= b
-    assert a >= 0
-    assert b > 0
-    return "%s of %s (%.2f%%)" % (a, b, 100.*a/b)