def ipython_break(frame, depth, #pylint: disable-msg=W0613
color_scheme='Linux'):
'''Start an interactive debugger session based on the IPython
debugger'''
#This code is a pretty dirty hack to get around some obscure
#IPython issue
global IPYTHON_TRACER
if not IPYTHON_TRACER:
# This is the first time this procedure is called
# Due to some funky IPython 0.10 internals, we need the following:
import IPython
if map(int, IPython.__version__.split('.'))[:2] == [0, 10]:
from IPython.Shell import IPShellEmbed
IPShellEmbed(argv=[])
old_colors = ExceptionColors.active_scheme_name
ExceptionColors.active_scheme_name = color_scheme
if not IPYTHON_TRACER:
IPYTHON_TRACER = Tracer(color_scheme)
IPYTHON_TRACER.debugger.set_trace(frame)
ExceptionColors.active_scheme_name = old_colors
def debug():
"""
Invokes a debugger at the point where it is called, but only if
the Ipython-shell is available.
"""
if HaveIpython:
Tracer()
else:
return
def breakpoint():
"""BREAKPOINT - Set breakpoint. Opens an IPDB window when the next
exception is raised.
Usage: breakpoint()
NOTE: In order for the breakpoints to do anything, you need to
execute your script with 'ipython -pdb YOUR_SCRIPT.py'.
"""
from IPython.Debugger import Tracer
Tracer()
def breaknow():
"""BREAKNOW - Set unconditional breakpoint. Raises an exception and
opens the IPDB shell.
Usage: breaknow()
NOTE: In order for the breakpoints to do anything, you need to
execute your script with 'ipython -pdb YOUR_SCRIPT.py'.
"""
from IPython.Debugger import Tracer
Tracer()
raise KeyError, "You set an unconditional breakpoint here, so we stop."
"""
Program for running bwa on nuclear reads from 5 different cell lines
"""
from IPython.Debugger import Tracer
debug = Tracer()
from subprocess import Popen, call
import os
import glob
# You tested having on read pair in the index and another not -- that works
# fine. You must also try the funny faste file output by bedtools.
def get_dsets(dset_dir, cell_lines):
"""
Return the paths to the datsets for nuclear rna-seq
"""
dsets = {}
for line in glob.glob(dset_dir + '/*'):
# I'm cheating for now!
#for line in open('those_files', 'rb'):
if 'NucleusPap' not in line or 'fastq' not in line:
continue
dname, fname = os.path.split(line.rstrip())
class mymagic:
if sys.platform.lower().startswith('win'):
if hasattr(__IPYTHON__, 'rc'): __IPYTHON__.rc.editor = 'scite'
else: __IPYTHON__.editor = 'scite'
############################################################################
try: from IPython.Debugger import Tracer # IPython v 0.10 and earlier
except ImportError: from IPython.core.debugger import Tracer # IPython v 0.11 and later
__IPYTHON__.dbstop = Tracer()
# calling __IPYTHON__.dbstop() is easier than having to remember and type
# "from IPython.Debugger import Tracer; Tracer()()" just to invoke the debugger
# (and *much* easier than having to remember the version-specific variants of that)
############################################################################
@makemagic
def magic_edit(fn):
"""\
A more Matlab-like replacement for IPython's default editing behaviour:
search the path for possible matches; edit them in the background; don't
execute the result. Set your editor with the line 'editor WHATEVER' in
ipythonrc, or by otherwise setting __IPYTHON__.rc.editor = 'WHATEVER'
Examples:
edit site.py # edits existing file on path with .py extension $BLAH/Lib/site.py
edit ipythonrc # edits existing file on path without .py extension $HOME/.ipython/ipythonrc
edit site # adds .py extension and edits existing file on path $BLAH/Lib/site.py
edit IPython/iplib.py # edits existing file in subdirectory on path $BLAH/IPython/iplib.py
edit IPython/iplib # edits existing file in subdirectory on path $BLAH/IPython/iplib.py
edit IPython.iplib # edits existing file in package on path $BLAH/IPython/iplib.py
edit xml # edits __init__.py file in existing package on path $BLAH/xml/__init__.py
edit foo.py # edits new file with .py extension ./foo.py
edit foo.txt # edits new file with non-.py extension ./foo.txt
edit foo # adds .py extension and edits new file ./foo.py
edit IPython/foo.py # edits new file in existing subdirectory on path $BLAH/IPython/foo.py
edit IPython/foo # edits new file in existing subdirectory on path $BLAH/IPython/foo.py
edit IPython.foo # edits new file in existing subdirectory on path $BLAH/IPython/foo.py
"""###
# NB: one (unlikely) case is not handled: a new file with a non-.py extension
# in an existing subdirectory on the path, e.g. edit IPython/foo.txt
if hasattr(__IPYTHON__, 'rc'): editor = __IPYTHON__.rc.editor
else: editor = __IPYTHON__.editor
if sys.platform.lower().startswith('win'): editor = 'start ' + editor
ed = lambda x: os.system(editor + ' "' + os.path.abspath(x) + '"')
got = lambda x: os.path.isfile(os.path.abspath(x)) and (ed(x) or True)
if got(fn): return
# this allows for spaces in the path, e.g. edit C:\Documents and Settings\me\Desktop\blah.py
# but if the whole thing isn't an existing file, assume a space-delimited list of filenames:
for original in fn.split():
stem = original
if stem.lower().endswith('.py'): stem = stem[:-3]
original_withpy = stem + '.py'
path_withoutpy = os.path.join(*stem.split('.'))
path_withpy = path_withoutpy + '.py'
potential_location = ''
for p in sys.path:
if got(os.path.join(p, original)): break
elif got(os.path.join(p, original_withpy)): break
elif got(os.path.join(p, path_withpy)): break
elif got(os.path.join(p, path_withoutpy)): break
elif stem == original and got(os.path.join(p, path_withoutpy, '__init__.py')): break
elif potential_location == '':
pp = os.path.join(p, path_withoutpy)
dd = os.path.realpath(os.path.dirname(pp))
d = os.path.realpath(p)
if len(dd) > len(d) and os.path.isdir(dd): potential_location = pp
else: # not found anywhere else, so edit as new
if potential_location == '': potential_location = original
fn, xtn = os.path.splitext(potential_location)
if xtn == '': xtn = '.py'
ed(fn + xtn)
############################################################################
@makemagic
def magic_addpath(d=None):
"""\
Make absolute paths out of the input(s) and append them to sys.path if they are
not already there. Supply a space-delimited list of arguments, or one argument
enclosed in quotes (which may, in that case, contain a space).
"""###
if d == None: dd = (os.getcwd(),)
else:
if (d.startswith('"') and d.endswith('"')) or (d.startswith("'") and d.endswith("'")):
dd = (d[1:-1],)
else:
dd = d.split()
for d in dd:
d = os.path.realpath(d)
if os.path.isdir(d):
if not d in sys.path: sys.path.append(d)
else:
print 'no such directory "%s"' % d
############################################################################
@makemagic
def magic_desk(subdir=''):
"""\
cd to the Desktop, but keep a global record of where we were (stored in
__IPYTHON__.undeskdir) so that we can snap back with %undesk
"""###
if sys.platform.lower().startswith('win'):
homedrive = os.environ.get('HOMEDRIVE')
homepath = os.environ.get('HOMEPATH')
userprofile = os.environ.get('USERPROFILE')
if userprofile == None:
d = os.path.join(homedrive, homepath, 'Desktop')
else:
d = os.path.join(userprofile, 'Desktop')
else:
d = os.path.join(os.environ.get('HOME'), 'Desktop')
if subdir != '':
return os.path.realpath(os.path.join(d, subdir))
here = os.path.realpath(os.curdir)
if os.path.realpath(d) == here:
print "already at desktop"
else:
__IPYTHON__.undeskdir = here
print 'changing directory from ' + here
print ' to ' + d
print 'type %undesk to change back'
os.chdir(d)
############################################################################
@makemagic
def magic_undesk(arg):
"""\
Undo a previous call to %desk
"""###
d = getattr(__IPYTHON__, 'undeskdir', None)
if d == None:
print 'no global record of previous call to %desk'
else:
print 'changing directory from ' + os.path.realpath(os.curdir)
print ' back to ' + d
os.chdir(d)
############################################################################
@makemagic
def magic_pip(d=''):
try:
import pip
except ImportError:
import sys; sys.stderr.write("""
The pip module is not installed. See the instructions
at http://www.pip-installer.org/en/latest/installing.html
In short:
(1) Ensure setuptools (i.e. easy_install) is installed first
(download and run ez_setup.py if not).
(2) Download and run get-pip.py
(3) Quit and relaunch Python
(4) Then the first thing you should do with pip is:
pip install --upgrade setuptools
""")
return
try:
return pip.main(d.split())
except SystemExit:
pass
############################################################################
@makemagic
def magic_easy_install(d=None):
"""\
Run the easy_install command from IPython, invoking the setuptools script
Scripts/easy_install-script.py (on Windows) or easy_install (on anything else).
Particularly useful on Windows, where IPython may well be the best command-line
you have.
"""###
def readpth(pth):
sitedir = os.path.split(pth)[0] # assume easy-install.pth is directly in the site-packages dir
lines = [x.strip() for x in open(pth, 'rt').readlines()]
return [os.path.realpath(os.path.join(sitedir, x)) for x in lines if not x.startswith('import') and not x.startswith('#')]
# assume a line is a relative path unless it begins with # or import
def isbelow(x, p):
x,p = os.path.realpath(x), os.path.realpath(p)
return x == p or x.startswith(os.path.join(p, ''))
pth = [os.path.join(os.path.realpath(x), 'easy-install.pth') for x in sys.path] # assume 'easy-install.pth' is on the path
pth = ([x for x in pth if os.path.isfile(x)]+[None])[0]
if pth != None: oldpaths = readpth(pth)
############ This is the part that actually runs easy_install.
############ The rest, before and after, is to attempt to keep the session going with intelligent updates to
############ sys.path and sys.modules (still won't work for upgrades to IPython and some messy others like simplejson).
home = os.environ.get('PYTHONHOME')
if sys.platform.lower().startswith('win'):
if home == None: home = os.path.dirname(sys.executable)
getmagic('run')('"' + os.path.join(home, 'Scripts', 'easy_install-script.py') + '" ' + d)
else:
# TODO: need to set $PYTHONHOME for system call using env? If so, how to fill it in if home==None?
os.system('"' + sys.executable + '" "`which easy_install`" ' + d)
############
if pth == None:
print "restart this python session to take advantage of the new package"
return
newpaths = readpth(pth)
addpaths = [x for x in newpaths if x not in oldpaths]
gone = [x for x in oldpaths if x not in newpaths]
rmpaths = []
for x in sys.path:
if not len(x): continue
for stem in gone:
if isbelow(x,stem):
rmpaths.append(x)
break
stripped = [x for x in sys.path if x not in rmpaths]
for i in range(len(stripped)):
if len(stripped[i]): stripped[i] = os.path.realpath(stripped[i])
sys.path[:] = stripped + addpaths
if len(addpaths): print('\n '.join(['Added to sys.path:'] + map(repr, addpaths)))
if len(rmpaths): print('\n '.join(['Removed from sys.path:'] + map(repr, rmpaths)))
rmmod = []
for k,v in sys.modules.items():
v = getattr(v, '__file__', None)
if not isinstance(v, basestring): continue
for p in rmpaths:
if isbelow(v, p): rmmod.append(k); break
rmmod = [sys.modules.pop(k) for k in sorted(rmmod)]
if len(rmmod): print('\n '.join(['Removed from sys.modules:'] + map(repr, rmmod)))
############################################################################
@makemagic
def magic_reimport(dd):
"""\
The syntax
%reimport foo, bar.*
is a shortcut for the following:
import foo; foo = reload(foo)
import bar; bar = reload(bar); from bar import *
"""###
ipython = getworkspace()
for d in dd.replace(',', ' ').split(' '):
if len(d):
bare = d.endswith('.*')
if bare: d = d[:-2]
exec 'import xx; xx = reload(xx)'.replace('xx', d) in ipython
if bare: exec 'from xx import *'.replace('xx', d) in ipython
############################################################################
@makemagic
def magic_loadpylab(d=''):
"""\
The syntax
%loadpylab
imports matplotlib and pylab into the IPython workspace, ensuring that, if matplotlib
has not previously been loaded, it is loaded in interactive mode.
%loadpylab *
is the same, but additionally imports the requested symbols from pylab, directly into
the workspace.
"""###
import sys
ipython = getworkspace()
try: import matplotlib
except ImportError: print "WARNING: failed to import matplotlib"
else:
#!/usr/bin/python
# -*- coding: utf-8 -*-
from __future__ import division
import os
import sys
import numpy as np
import numpy.lib.recfunctions as rec
import pymc as pm
from copy import copy
from scipy.stats import norm
from scipy.integrate import quad
try:
from IPython.Debugger import Tracer
debug_here = Tracer()
except:
def debug_here():
pass
#for import settings file
from kabuki import Hierarchical, Knode
from kabuki.utils import load_csv
import stop_likelihoods_wtf
from collections import OrderedDict
#settings file
path__analysisDescription = sys.argv[3]
#make dict for input arguments
vars = dict()
class MyMagics(Magics):
if sys.platform.lower().startswith('win'):
if hasattr(__IPYTHON__, 'rc'): __IPYTHON__.rc.editor = 'scite'
else: __IPYTHON__.editor = 'scite'
############################################################################
dbstop = None
try:
if not dbstop:
from IPython.Debugger import Tracer
dbstop = Tracer() # IPython v 0.10 and earlier
except:
pass
try:
if not dbstop:
from IPython.core.debugger import Tracer
dbstop = Tracer() # IPython v 0.11 and later
except:
pass
try:
if not dbstop:
from IPython.core import debugger
dbstop = debugger.Pdb(
).set_trace # Some other f***ing version of IWishYoudStopMovingTheGoalposts
except:
pass
sys.dbstop = __IPYTHON__.dbstop = dbstop
# because calling sys.dbstop() is easier than having to remember and type
# "from IPython.Debugger import Tracer; Tracer()()" just to invoke the debugger
# (and *much* easier than having to remember the version-specific variants of that)
# Note however that you can also run in debug mode and set breakpoints with:
# %run -d -b LINENUMBER file.py
# %run -d -b OTHERFILENAME:LINENUMBER file.py
############################################################################
@line_magic
def edit(self, arg):
"""\
A more Matlab-like replacement for IPython's default editing behaviour:
search the path for possible matches; edit them in the background; don't
execute the result (NB: the latter can also be achieved in IPython with
%edit -x). Set your editor with the line 'editor WHATEVER' in
ipythonrc, or by otherwise setting __IPYTHON__.rc.editor = 'WHATEVER'
Examples:
edit site.py # edits existing file on path with .py extension $BLAH/Lib/site.py
edit ipythonrc # edits existing file on path without .py extension $HOME/.ipython/ipythonrc
edit site # adds .py extension and edits existing file on path $BLAH/Lib/site.py
edit IPython/iplib.py # edits existing file in subdirectory on path $BLAH/IPython/iplib.py
edit IPython/iplib # edits existing file in subdirectory on path $BLAH/IPython/iplib.py
edit IPython.iplib # edits existing file in package on path $BLAH/IPython/iplib.py
edit xml # edits __init__.py file in existing package on path $BLAH/xml/__init__.py
edit foo.py # edits new file with .py extension ./foo.py
edit foo.txt # edits new file with non-.py extension ./foo.txt
edit foo # adds .py extension and edits new file ./foo.py
edit IPython/foo.py # edits new file in existing subdirectory on path $BLAH/IPython/foo.py
edit IPython/foo # edits new file in existing subdirectory on path $BLAH/IPython/foo.py
edit IPython.foo # edits new file in existing subdirectory on path $BLAH/IPython/foo.py
Most Windows or Unixoid editors will behave well if you give them the name of a not-yet-
existing file to edit. On OSX, however, if you're using an editor script that redirects
to `open -a Some.app file.txt`, this will fail if file.txt doesn't exist. For this reason,
you can use `edit -t ....` where the -t stands for "touch": the file will be created if it
doesn't already exist, before being opened in the editor. (Typos will then sometimes mean
that you're left with unwanted 0-byte files hanging around, needing to be deleted by hand.)
"""###
# NB: one (unlikely) case is not handled: a new file with a non-.py extension
# in an existing subdirectory on the path, e.g. edit IPython/foo.txt
if hasattr(__IPYTHON__, 'rc'): editor = __IPYTHON__.rc.editor
else: editor = __IPYTHON__.editor
windows = sys.platform.lower().startswith('win')
if windows: editor = 'start ' + editor
def edit(x, mode='existing'):
if not x: return os.system(editor) or True
x = os.path.abspath(x)
if mode == 'existing' and not os.path.isfile(x): return False
if os.path.isdir(x):
return sys.stderr.write(
'cannot edit directory %s\n' % x) and False
if mode == '-t' and not os.path.isfile(x): open(x, 'a').close()
os.system(editor + ' "' + x.strip('"') + '"')
return True
if edit(arg): return
# that allows for spaces in the path, e.g. edit C:\Documents and Settings\me\Desktop\blah.py
# but if the whole thing isn't an existing file, we'll assume a space-delimited list of filenames.
arg = arg.strip()
if arg.startswith('(') and arg.endswith(')'):
arg = eval('[' + arg[1:-1] + ']', getworkspace())
else:
if windows:
arg = arg.replace(
'\\', '\\\\'
) # otherwise shlex.split will decode/eat backslashes that might be important as file separators
import shlex
arg = shlex.split(arg) # shlex.split copes with quoted substrings
creation_policy = arg.pop(0) if (arg and arg[0] == '-t') else 'auto'
for original in arg:
stem = original
if stem.lower().endswith('.py'): stem = stem[:-3]
original_withpy = stem + '.py'
path_withoutpy = os.path.join(*stem.split('.'))
path_withpy = path_withoutpy + '.py'
potential_location = ''
for p in sys.path:
if edit(os.path.join(p, original)): break
elif edit(os.path.join(p, original_withpy)): break
elif edit(os.path.join(p, path_withpy)): break
elif edit(os.path.join(p, path_withoutpy)): break
elif stem == original and edit(
os.path.join(p, path_withoutpy, '__init__.py')):
break
elif potential_location == '':
pp = os.path.join(p, path_withoutpy)
dd = os.path.realpath(os.path.dirname(pp))
d = os.path.realpath(p)
if len(dd) > len(d) and os.path.isdir(dd):
potential_location = pp
else: # not found anywhere else, so edit as new
if potential_location == '': potential_location = original
fn, xtn = os.path.splitext(potential_location)
if xtn == '': xtn = '.py'
edit(fn + xtn, creation_policy)
############################################################################
@line_magic
def addpath(self, d=None):
"""\
Make absolute paths out of the input(s) and append them to sys.path if they are
not already there. Supply a space-delimited list of arguments, or one argument
enclosed in quotes (which may, in that case, contain a space).
"""###
if d == None: dd = (os.getcwd(), )
else:
d = d.replace('\\ ', ' ').strip()
if (d.startswith('"')
and d.endswith('"')) or (d.startswith("'")
and d.endswith("'")):
dd = (d[1:-1], )
else:
dd = d.split()
for d in dd:
d = os.path.realpath(d)
if os.path.isdir(d):
if not d in sys.path: sys.path.append(d)
else:
print(('no such directory "%s"' % d))
############################################################################
@line_magic
def desk(self, subdir=''):
"""\
cd to the Desktop, but keep a global record of where we were (stored in
__IPYTHON__.undeskdir) so that we can snap back with %undesk
"""###
if sys.platform.lower().startswith('win'):
homedrive = os.environ.get('HOMEDRIVE')
homepath = os.environ.get('HOMEPATH')
userprofile = os.environ.get('USERPROFILE')
if userprofile == None:
d = os.path.join(homedrive, homepath, 'Desktop')
else:
d = os.path.join(userprofile, 'Desktop')
else:
d = os.path.join(os.environ.get('HOME'), 'Desktop')
if subdir != '':
return os.path.realpath(os.path.join(d, subdir))
here = os.path.realpath(os.curdir)
if os.path.realpath(d) == here:
print("already at desktop")
else:
__IPYTHON__.undeskdir = here
print(('changing directory from ' + here))
print((' to ' + d))
print('type %undesk to change back')
os.chdir(d)
############################################################################
@line_magic
def undesk(self, arg):
"""\
Undo a previous call to %desk
"""
###
d = getattr(__IPYTHON__, 'undeskdir', None)
if d == None:
print('no global record of previous call to %desk')
else:
print(('changing directory from ' + os.path.realpath(os.curdir)))
print((' back to ' + d))
os.chdir(d)
############################################################################
@line_magic
def pip(self, d=''):
try:
import pip
except ImportError:
import sys
sys.stderr.write("""
The pip module is not installed. See the instructions
at http://www.pip-installer.org/en/latest/installing.html
In short:
(1) Ensure setuptools (i.e. easy_install) is installed first
(download and run ez_setup.py if not).
(2) Download and run get-pip.py
(3) Quit and relaunch Python
(4) Then the first thing you should do with pip is:
pip install --upgrade setuptools
""")
return
try:
return pip.main(d.split())
except SystemExit:
pass
############################################################################
@line_magic
def easy_install(self, d=None):
"""\
Run the easy_install command from IPython, invoking the setuptools script
Scripts/easy_install-script.py (on Windows) or easy_install (on anything else).
Particularly useful on Windows, where IPython may well be the best command-line
you have.
"""###
def readpth(pth):
sitedir = os.path.split(
pth
)[0] # assume easy-install.pth is directly in the site-packages dir
lines = [x.strip() for x in open(pth, 'rt').readlines()]
return [
os.path.realpath(os.path.join(sitedir, x)) for x in lines
if not x.startswith('import') and not x.startswith('#')
]
# assume a line is a relative path unless it begins with # or import
def isbelow(x, p):
x, p = os.path.realpath(x), os.path.realpath(p)
return x == p or x.startswith(os.path.join(p, ''))
pth = [
os.path.join(os.path.realpath(x), 'easy-install.pth')
for x in sys.path
] # assume 'easy-install.pth' is on the path
pth = ([x for x in pth if os.path.isfile(x)] + [None])[0]
if pth != None: oldpaths = readpth(pth)
############ This is the part that actually runs easy_install.
############ The rest, before and after, is to attempt to keep the session going with intelligent updates to
############ sys.path and sys.modules (still won't work for upgrades to IPython and some messy others like simplejson).
home = os.environ.get('PYTHONHOME')
if sys.platform.lower().startswith('win'):
if home == None: home = os.path.dirname(sys.executable)
getmagic('run')(
'"' + os.path.join(home, 'Scripts', 'easy_install-script.py') +
'" ' + d)
else:
# TODO: need to set $PYTHONHOME for system call using env? If so, how to fill it in if home==None?
bang('"' + sys.executable + '" "`which easy_install`" ' + d)
############
if pth == None:
print(
"restart this python session to take advantage of the new package"
)
return
newpaths = readpth(pth)
addpaths = [x for x in newpaths if x not in oldpaths]
gone = [x for x in oldpaths if x not in newpaths]
rmpaths = []
for x in sys.path:
if not len(x): continue
for stem in gone:
if isbelow(x, stem):
rmpaths.append(x)
break
stripped = [x for x in sys.path if x not in rmpaths]
for i in range(len(stripped)):
if len(stripped[i]): stripped[i] = os.path.realpath(stripped[i])
sys.path[:] = stripped + addpaths
if len(addpaths):
print(('\n '.join(['Added to sys.path:'] +
list(map(repr, addpaths)))))
if len(rmpaths):
print(('\n '.join(['Removed from sys.path:'] +
list(map(repr, rmpaths)))))
rmmod = []
for k, v in list(sys.modules.items()):
v = getattr(v, '__file__', None)
if not isinstance(v, str): continue
for p in rmpaths:
if isbelow(v, p):
rmmod.append(k)
break
rmmod = [sys.modules.pop(k) for k in sorted(rmmod)]
if len(rmmod):
print(('\n '.join(['Removed from sys.modules:'] +
list(map(repr, rmmod)))))
############################################################################
@line_magic
def search(self, dd):
"""\
search TERM
search TERM TOP_LEVEL_DIR
search TERM TOP_LEVEL_DIR FILE_PATTERN
Searches case-insensitively for TERM through all files matching FILE_PATTERN (default: '*')
in the directory tree starting at TOP_LEVEL_DIR (default: '.') and prints the filename, line
number and line content for any matches.
Because, on Windows, native file content searches are not reliable and IPython is going to
be the best command-line you have.
Also, for convenience, the following syntax does the simpler job of matching file names
rather than file content: search --filename ...
"""###
import os, sys, fnmatch, re, getopt
args = [
''.join(matches) for matches in re.findall(
'|'.join([r'"([^"]*)"', r"'([^']*)'", r'(\S+)']), dd)
]
opts, args = getopt.getopt(args, '', ['filename'])
opts = dict(opts)
if not 1 <= len(args) <= 3:
sys.stderr.write(
'arguments: SEARCH_STRING [TOP_DIR] [FILE_PATTERN]\n')
sys.stderr.flush()
return
search_string, root_dir, file_pattern = (args + ['', '', ''])[:3]
sys.stdout.write('\n')
sys.stdout.flush()
if not root_dir: root_dir = '.'
matches = []
if not os.path.isdir(root_dir):
sys.stderr.write(str(root_dir) + ' is not a directory\n')
sys.stderr.flush()
return
search_string = str(search_string).lower()
limit = 200
for root, dirnames, filenames in os.walk(root_dir):
if file_pattern:
filenames = fnmatch.filter(filenames, file_pattern)
for filename in filenames:
file_path = os.path.join(root, filename)
if '--filename' in opts:
if search_string in str(
os.path.split(filename)[1]).lower():
sys.stdout.write('%s\n' % (file_path))
sys.stdout.flush()
matches.append(file_path)
continue
matches.append(file_path)
try:
file_handle = open(file_path)
except IOError:
sys.stderr.write('/!\\ failed to open %s\n\n' %
file_path)
sys.stderr.flush()
for line_number, line in enumerate(file_handle):
hit = search_string in str(line).lower()
if hit:
try:
sys.stdout.write(
'%s:%d:\n %s\n\n' %
(file_path.replace('\\', '/'), line_number + 1,
str(line).strip()[:limit]))
except UnicodeDecodeError:
sys.stdout.write(
'%s:%d matches (no preview available)\n\n' %
(file_path, line_number + 1))
sys.stdout.flush()
if len(matches) == 0:
sys.stderr.write('/!\\ no files matched the input pattern\n')
sys.stderr.flush()
else:
sys.stdout.write('\n')
############################################################################
@line_magic
def reimport(self, dd):
"""\
The syntax
%reimport foo, bar.*
is a shortcut for the following:
import foo; foo = reload(foo)
import bar; bar = reload(bar); from bar import *
"""###
ipython = getworkspace()
for d in dd.replace(',', ' ').split(' '):
if len(d):
bare = d.endswith('.*')
if bare: d = d[:-2]
exec('import xx; xx = reload(xx)'.replace('xx', d), ipython)
if bare: exec('from xx import *'.replace('xx', d), ipython)
############################################################################
@line_magic
def loadpylab(self, d=''):
"""\
The syntax
%loadpylab
imports matplotlib and pylab into the IPython workspace, ensuring that, if matplotlib
has not previously been loaded, it is loaded in interactive mode.
%loadpylab *
is the same, but additionally imports the requested symbols from pylab, directly into
the workspace.
"""###
import sys
ipython = getworkspace()
try:
import matplotlib
except ImportError:
print("WARNING: failed to import matplotlib")
else:
if not 'matplotlib.backends' in sys.modules:
matplotlib.interactive(True)
try:
exec('import matplotlib, pylab', ipython)
except ImportError:
print("WARNING: failed to import pylab")
#if __OLDER_IPYTHON__:
if len(d): exec('from pylab import ' + d, ipython)
############################################################################
@line_magic
def njh(self, *pargs):
"""\
Imports a number of packages, including the BCPy2000 sub-packages WavTools and
SigTools, but also copy, struct, ctypes, numpy, scipy and matplotlib and pylab
(the latter in interactive mode).
"""###
ipython = getworkspace()
exec('import copy,struct,ctypes,time,numpy,scipy', ipython)
try:
exec('import WavTools,SigTools', ipython)
except ImportError:
exec('import BCPy2000.Paths', ipython)
exec('import WavTools,SigTools', ipython)
getmagic('loadpylab')()
############################################################################
@line_magic
def pp(self, name=''):
"""\
An ipython command-line shortcut to SigTools.summarize, to give a quick look at
object attributes--- especially useful for numpy arrays.
"""###
if name == None: return
ipython = getworkspace()
val = eval(name, ipython)
from . import SigTools
print((SigTools.summarize(val)))
############################################################################
@line_magic
def l(self, dd='.'):
if dd in [None, '']: dd = '.'
dd = dd.replace('\\ ', ' ').strip().strip('"\'')
if sys.platform.lower().startswith('win'):
cmd = 'dir "%s"' % dd.replace('/', '\\')
else:
cmd = 'ls -AFlh %s' % dd
bang(cmd, shell=True)
############################################################################
@line_magic
def bootstrap_shortcuts(self, *pargs):
"""\
import BCPy2000.Shortcuts allows you access to these useful shortcuts (edit,
search, desk, addpath, easy_install...). This shortcut writes the import
command into an .ipy file in the default ipython profile directory of your
home directory, so that the shortcuts will be loaded automatically whenever
you start IPython (versions 0.13 and later) in future.
"""###
code = """\
try: import BCPy2000.Shortcuts
except ImportError: print ("Failed to import BCPy2000.Shortcuts")
"""
import os, sys
if __OLDER_IPYTHON__:
sys.stderr.write(
"\nFAILED: this bootstrapper only works for newer versions of IPython.\nYou'll have to add the following lines manually to ipy_user_conf.py\nin the _ipython or .ipython subdirectory of your home directory:\n\n%s\n"
% code)
return
if sys.platform.lower().startswith('win'):
home = os.environ['USERPROFILE']
else:
home = os.environ['HOME']
startup_dir = os.path.join(home, '.ipython', 'profile_default',
'startup')
startup_file = os.path.join(
startup_dir, 'BCPy2000Shortcuts.ipy'
) # cannot be a .py file, must be an .ipy - the latter seem to be executed later, when ipython is running and its instance can be accessed with get_ipython()
if not os.path.isdir(startup_dir): os.makedirs(startup_dir)
open(startup_file, 'wt').write(code)
sys.stderr.write(
'\nSUCCESS: the file\n %s\nhas been created containing the following lines:\n\n%s\n'
% (startup_file, code))
#!/usr/bin/python
# -*- coding: utf-8 -*-
from __future__ import division
import numpy as np
import numpy.lib.recfunctions as rec
import pymc as pm
from copy import copy
from scipy.stats import norm
from scipy.integrate import quad
try:
from IPython.Debugger import Tracer; debug_here = Tracer()
except:
def debug_here(): pass
from kabuki import Hierarchical, Knode
import stop_likelihoods
from collections import OrderedDict
def cython_Go(value, imu_go, isigma_go, itau_go):
"""Ex-Gaussian log-likelihood of GoRTs"""
return stop_likelihoods.Go(value, imu_go, isigma_go, itau_go)
def cython_SRRT(value, issd, imu_go, isigma_go, itau_go, imu_stop, isigma_stop, itau_stop):
"""Censored ExGaussian log-likelihood of SRRTs"""
return stop_likelihoods.SRRT(value, issd, imu_go, isigma_go, itau_go, imu_stop, isigma_stop, itau_stop)
def cython_Inhibitions(value, imu_go, isigma_go, itau_go, imu_stop, isigma_stop, itau_stop):
"""Censored ExGaussian log-likelihood of inhibitions"""
return stop_likelihoods.Inhibitions(value, imu_go, isigma_go, itau_go, imu_stop, isigma_stop, itau_stop)
Go_like = pm.stochastic_from_dist(name="Ex-Gauss GoRT",
import pyyaks.context as pyc
from .files import files as xija_files
from . import clogging
# HDF5 version of commanded states table
H5FILE = '/proj/sot/ska/data/cmd_states/cmd_states.h5'
src = pyc.CONTEXT['src'] if 'src' in pyc.CONTEXT else pyc.ContextDict('src')
files = (pyc.CONTEXT['file'] if 'file' in pyc.CONTEXT else pyc.ContextDict(
'files', basedir=os.getcwd()))
files.update(xija_files)
if 'debug' in globals():
from IPython.Debugger import Tracer
pdb_settrace = Tracer()
logger = clogging.config_logger('xija', level=clogging.INFO)
DEFAULT_DT = 328.0
dt_factors = np.array([1.0, 0.5, 0.25, 0.2, 0.125, 0.1, 0.05, 0.025])
#int calc_model(int n_times, int n_preds, int n_tmals, double dt,
# double **mvals, int **tmal_ints, double **tmal_floats)
def convert_type_star_star(array, ctype_type):
f4ptr = ctypes.POINTER(ctype_type)
return (f4ptr * len(array))(*[row.ctypes.data_as(f4ptr) for row in array])
descent1 - func - gradient descent
proj - func - project given point onto constraint manifold
tgt - func - approximate tangent space to manifold
armijoproj - func - Armijo stepsize rule, projected onto manifold
descent1proj - func - gradient descent, projected onto manifold
by Sam Burden, Humberto Gonzalez, Ram Vasudevan, Berkeley 2011
"""
import numpy as np
import pylab as plt
import scipy as sp
import scipy.optimize as op
try:
from IPython.Debugger import Tracer; dbg = Tracer()
except:
dbg = lambda : 1/0
import sys
class Struct(object):
"""
Struct struct-like class
Acts like a dict, but keys are members of the object.
Also, its string representation is Python code which
yields the object when executed.
>>> a = Struct(foo='bar', goo=7)
>>> b = a.copy()
def theexecpthook(type, value, traceback):
fnc()
ip_excepthook(type, value, traceback)
# write this to a File without Colors
if not filename == None:
outFile = open(filename, "a")
outFile.write("--" + time.ctime() + " --\n")
outFile.write(fileTraceback.text(type, value, traceback))
outFile.write("\n-- --\n")
outFile.close()
# assign it
sys.excepthook = theexecpthook
from IPython.Debugger import Tracer
ST = Tracer() # "ST" = "start trace"
except ImportError:
# IPython seems not to be installed
# create dummy functions
def IPS():
print "(EE): IPython is not available"
pass
def ip_syshook(*args, **kwargs):
pass
def ST():
pass
// and its documentation for any purpose is hereby granted without fee, // provided that the above copyright notice appear in all copies and // that both that copyright notice and this permission notice appear // in supporting documentation. The authors make no representations // about the suitability of this software for any purpose. // It is provided "as is" without express or implied warranty. // import pylab import scipy, time, sys import matplotlib.pyplot as plt import pyublas, _debugMsg, _maximizer as mx import lininterp2 as linterp from IPython.Debugger import Tracer; BREAKPOINT = Tracer() def maximizer1d(controlGridList, bellmanParams, parallel): def objFn(x): return bellmanParams.objectiveFunction([x]) fArray = scipy.array(map(objFn, controlGridList[0])) argmax = scipy.argmax(fArray) return (1, [controlGridList[0][argmax]], fArray[argmax]) # wArray is a multidimensional array on a grid # stateGridList is a list of 1d arrays representing the grid coordinates # bellmanParams is an object containing the problem-specific information # objectiveFunction() is implemented in C++ # should implement these member functions: setStateVars, setPrevIteration, getControlGridList, getNControls # parallel is a bool, if true, use the parallel grid search algorithm def grid_bellman(stateGridList, wArray, bellmanParams, parallel=True):
from pylab import *
from IPython.Debugger import Tracer; keyboard = Tracer()
#------------------------------------------------------------------------------
# Experimental code for generating samples positions which are well-distributed
# in time and space, and appropriate for use with interleaved sampling.
#
# Demo of some of the experimental code:
'''
tileWidth = 21
t = jitteredSamp(tileWidth**2)
ts = makeTileSet(t, r=2)
h = SpatialHash()
showFiltered(t[applyTileSet(30, ts, h)], lambda x,y:x, gaussKer(8), 4)
show()
'''
def scatter3D(*args, **kwargs):
'''Convenience function to plot 3D scatter diagrams'''
from mpl_toolkits.mplot3d import Axes3D
ax = Axes3D(gcf())
ax.scatter(*args, **kwargs)
def centred_figimage(image, *args, **kwargs):
'''
Show an image in the centre of a figure at natural (unscaled) resolution.
'''
bound = gcf().get_window_extent()
xo = (bound.width - image.shape[0])//2
yo = (bound.height - image.shape[1])//2