import os
import sys
import pandas.io.parsers
# Monkey patch for pygraphviz.agraph.AGraph._which
# noinspection PyUnusedLocal
def _which(self, name):
return which(name)
# Code from shutil.which - python 3.3+
# https://github.com/python/cpython/blob/master/Lib/shutil.py#L1096
# PYTHON SOFTWARE FOUNDATION LICENSE VERSION 2
# noinspection PyShadowingBuiltins
[docs]def shutil_which(cmd, mode=os.F_OK | os.X_OK, path=None):
"""Given a command, mode, and a PATH string, return the path which
conforms to the given mode on the PATH, or None if there is no such
file.
`mode` defaults to os.F_OK | os.X_OK. `path` defaults to the result
of os.environ.get("PATH"), or can be overridden with a custom search
path.
"""
# Check that a given file can be accessed with the correct mode.
# Additionally check that `file` is not a directory, as on Windows
# directories pass the os.access check.
# noinspection PyShadowingNames
def _access_check(fn, mode):
return (os.path.exists(fn) and os.access(fn, mode)
and not os.path.isdir(fn))
# If we're given a path with a directory part, look it up directly rather
# than referring to PATH directories. This includes checking relative to the
# current directory, e.g. ./script
if os.path.dirname(cmd):
if _access_check(cmd, mode):
return cmd
return None
if path is None:
path = os.environ.get("PATH", os.defpath)
if not path:
return None
path = path.split(os.pathsep)
if sys.platform == "win32":
# The current directory takes precedence on Windows.
if os.curdir not in path:
path.insert(0, os.curdir)
# PATHEXT is necessary to check on Windows.
pathext = os.environ.get("PATHEXT", "").split(os.pathsep)
# See if the given file matches any of the expected path extensions.
# This will allow us to short circuit when given "python.exe".
# If it does match, only test that one, otherwise we have to try
# others.
if any(cmd.lower().endswith(ext.lower()) for ext in pathext):
files = [cmd]
else:
files = [cmd + ext for ext in pathext]
else:
# On other platforms you don't have things like PATHEXT to tell you
# what file suffixes are executable, so just pass on cmd as-is.
files = [cmd]
seen = set()
for dir in path:
normdir = os.path.normcase(dir)
if normdir not in seen:
seen.add(normdir)
for thefile in files:
name = os.path.join(dir, thefile)
if _access_check(name, mode):
return name
return None
def _isclose(a, b, rel_tol=1e-09, abs_tol=0.0):
# https://www.python.org/dev/peps/pep-0485
return abs(a-b) <= max(rel_tol * max(abs(a), abs(b)), abs_tol)
# Monkey patch for pygraphviz.agraph.AGraph._which
try:
from shutil import which
except ImportError:
which = shutil_which
# Backport py 3.5+ isclose
try:
from cmath import isclose
except ImportError:
isclose = _isclose
# Monkey patch for read_* to not interpret 'NULL', 'N/A' & 'NA' as NaN
# This is an ugly hack and really *should* be implemented by library users by passing by passing
# `na_values=[], keep_default_na=False` to their pandas.read_* calls
pandas.io.parsers._NA_VALUES = {
'-1.#QNAN', '-nan', '', '-NaN', '#NA', 'N/A', 'NaN', '#N/A', '1.#QNAN', '1.#IND', 'nan', '-1.#IND', '#N/A N/A'}