psi4-data 1:0.3-5 / usr / share / psi / python / qcdb / psiutil.py

#
#@BEGIN LICENSE
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# PSI4: an ab initio quantum chemistry software package
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
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# (at your option) any later version.
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# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# GNU General Public License for more details.
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# with this program; if not, write to the Free Software Foundation, Inc.,
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r"""Stuff stolen from psi. Should import or not as necessary
or some better way. Apologies to the coders.

"""
import sys
import math
import re
import os
import string
from vecutil import *
from p4xcpt import *


def _success(label):
    """Function to print a '*label*...PASSED' line to screen.
    Used by :py:func:`util.compare_values` family when functions pass.

    """
    print('\t{0:.<66}PASSED'.format(label))
    sys.stdout.flush()


def compare_values(expected, computed, digits, label):
    """Function to compare two values. Prints :py:func:`util.success`
    when value *computed* matches value *expected* to number of *digits*
    (or to *digits* itself when *digits* > 1 e.g. digits=0.04). Performs
    a system exit on failure. Used in input files in the test suite.

    """
    thresh = 10 ** -digits if digits > 1 else digits
    if abs(expected - computed) > thresh:
        message = ("\t%s: computed value (%f) does not match (%f) to %f digits." % (label, computed, expected, digits))
        raise ValidationError(message)
    if math.isnan(computed):
        message = ("\t%s: computed value (%f) does not match (%f)\n\tprobably because the computed value is nan." % (label, computed, expected))
        raise ValidationError(message)
    _success(label)


def compare_integers(expected, computed, label):
    """Function to compare two integers. Prints :py:func:`util.success`
    when value *computed* matches value *expected*.
    Performs a system exit on failure. Used in input files in the test suite.

    """
    if (expected != computed):
        message = ("\t%s: computed value (%d) does not match (%d)." % (label, computed, expected))
        raise ValidationError(message)
    _success(label)


def compare_strings(expected, computed, label):
    """Function to compare two strings. Prints :py:func:`util.success`
    when string *computed* exactly matches string *expected*.
    Performs a system exit on failure. Used in input files in the test suite.

    """
    if(expected != computed):
        message = ("\t%s: computed value (%s) does not match (%s)." % (label, computed, expected))
        raise ValidationError(message)
    _success(label)


def compare_matrices(expected, computed, digits, label):
    """Function to compare two matrices. Prints :py:func:`util.success`
    when elements of matrix *computed* match elements of matrix *expected* to
    number of *digits*. Performs a system exit on failure to match symmetry
    structure, dimensions, or element values. Used in input files in the test suite.

    """
    rows = len(expected)
    cols = len(expected[0])
    failed = 0
    for row in range(rows):
        for col in range(cols):
            if abs(expected[row][col] - computed[row][col]) > 10 ** (-digits):
                print("\t%s: computed value (%s) does not match (%s)." % (label, expected[row][col], computed[row][col]))
                failed = 1
                break

    if failed:
        print("The Failed Test Matrices\n")
        show(computed)
        print('\n')
        show(expected)
        raise ValidationError("\n")
    _success(label)


def query_yes_no(question, default=True):
    """Ask a yes/no question via raw_input() and return their answer.

    *question* is a string that is presented to the user.
    *default* is the presumed answer if the user just hits <Enter>.
    It must be yes (the default), no or None (meaning
    an answer is required of the user).

    The return value is one of True or False.

    """

    yes = re.compile(r'^(y|yes|true|on|1)', re.IGNORECASE)
    no = re.compile(r'^(n|no|false|off|0)', re.IGNORECASE)

    if default == None:
        prompt = " [y/n] "
    elif default == True:
        prompt = " [Y/n] "
    elif default == False:
        prompt = " [y/N] "
    else:
        raise ValueError("invalid default answer: '%s'" % default)

    while True:
        sys.stdout.write(question + prompt)
        choice = raw_input().strip().lower()
        if default is not None and choice == "":
            return default
        elif yes.match(choice):
            return True
        elif no.match(choice):
            return False
        else:
            sys.stdout.write("    Please respond with 'yes' or 'no'.\n")


## {{{ http://code.activestate.com/recipes/52224/ (r1)
def search_file(filename, search_path):
    """Given an os.pathsep divided *search_path*, find first occurance of
    *filename*. Returns full path to file if found or None if unfound.

    """
    file_found = False
    paths = string.split(search_path, os.pathsep)
    for path in paths:
        if os.path.exists(os.path.join(path, filename)):
            file_found = True
            break
    if file_found:
        return os.path.abspath(os.path.join(path, filename))
    else:
        return None
## end of http://code.activestate.com/recipes/52224/ }}}


def drop_duplicates(seq):
    """Function that given an array *seq*, returns an array without any duplicate
    entries. There is no guarantee of which duplicate entry is dropped.

    """
    #noDupes = []
    #[noDupes.append(i) for i in seq if not noDupes.count(i)]
    #return noDupes
    noDupes = []
    seq2 = sum(seq, [])
    [noDupes.append(i) for i in seq2 if not noDupes.count(i)]
    return noDupes


def all_casings(input_string):
    """Function to return a generator of all lettercase permutations
    of *input_string*.

    """
    if not input_string:
        yield ""
    else:
        first = input_string[:1]
        if first.lower() == first.upper():
            for sub_casing in all_casings(input_string[1:]):
                yield first + sub_casing
        else:
            for sub_casing in all_casings(input_string[1:]):
                yield first.lower() + sub_casing
                yield first.upper() + sub_casing


def getattr_ignorecase(module, attr):
    """Function to extract attribute *attr* from *module* if *attr*
    is available in any possible lettercase permutation. Returns
    attribute if available, None if not.

    """
    array = None
    for per in list(all_casings(attr)):
        try:
            getattr(module, per)
        except AttributeError:
            pass
        else:
            array = getattr(module, per)
            break

    return array


def import_ignorecase(module):
    """Function to import *module* in any possible lettercase
    permutation. Returns module object if available, None if not.

    """
    modobj = None
    for per in list(all_casings(module)):
        try:
            modobj = __import__(per)
        except ImportError:
            pass
        else:
            break

    return modobj