Source code for qcdb.psiutil

#
#@BEGIN LICENSE
#
# 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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# 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()


[docs]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)
[docs]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)
[docs]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)
[docs]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)
[docs]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)
[docs]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/ }}}
[docs]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
[docs]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
[docs]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
[docs]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