import os import functools import operator from distutils.version import LooseVersion import numpy as np from numpy.testing import assert_ import pytest import scipy.special as sc __all__ = ['with_special_errors', 'assert_func_equal', 'FuncData'] #------------------------------------------------------------------------------ # Check if a module is present to be used in tests #------------------------------------------------------------------------------ class MissingModule(object): def __init__(self, name): self.name = name def check_version(module, min_ver): if type(module) == MissingModule: return pytest.mark.skip(reason="{} is not installed".format(module.name)) return pytest.mark.skipif(LooseVersion(module.__version__) < LooseVersion(min_ver), reason="{} version >= {} required".format(module.__name__, min_ver)) #------------------------------------------------------------------------------ # Enable convergence and loss of precision warnings -- turn off one by one #------------------------------------------------------------------------------ def with_special_errors(func): """ Enable special function errors (such as underflow, overflow, loss of precision, etc.) """ @functools.wraps(func) def wrapper(*a, **kw): with sc.errstate(all='raise'): res = func(*a, **kw) return res return wrapper #------------------------------------------------------------------------------ # Comparing function values at many data points at once, with helpful # error reports #------------------------------------------------------------------------------ def assert_func_equal(func, results, points, rtol=None, atol=None, param_filter=None, knownfailure=None, vectorized=True, dtype=None, nan_ok=False, ignore_inf_sign=False, distinguish_nan_and_inf=True): if hasattr(points, 'next'): # it's a generator points = list(points) points = np.asarray(points) if points.ndim == 1: points = points[:,None] nparams = points.shape[1] if hasattr(results, '__name__'): # function data = points result_columns = None result_func = results else: # dataset data = np.c_[points, results] result_columns = list(range(nparams, data.shape[1])) result_func = None fdata = FuncData(func, data, list(range(nparams)), result_columns=result_columns, result_func=result_func, rtol=rtol, atol=atol, param_filter=param_filter, knownfailure=knownfailure, nan_ok=nan_ok, vectorized=vectorized, ignore_inf_sign=ignore_inf_sign, distinguish_nan_and_inf=distinguish_nan_and_inf) fdata.check() class FuncData(object): """ Data set for checking a special function. Parameters ---------- func : function Function to test data : numpy array columnar data to use for testing param_columns : int or tuple of ints Columns indices in which the parameters to `func` lie. Can be imaginary integers to indicate that the parameter should be cast to complex. result_columns : int or tuple of ints, optional Column indices for expected results from `func`. result_func : callable, optional Function to call to obtain results. rtol : float, optional Required relative tolerance. Default is 5*eps. atol : float, optional Required absolute tolerance. Default is 5*tiny. param_filter : function, or tuple of functions/Nones, optional Filter functions to exclude some parameter ranges. If omitted, no filtering is done. knownfailure : str, optional Known failure error message to raise when the test is run. If omitted, no exception is raised. nan_ok : bool, optional If nan is always an accepted result. vectorized : bool, optional Whether all functions passed in are vectorized. ignore_inf_sign : bool, optional Whether to ignore signs of infinities. (Doesn't matter for complex-valued functions.) distinguish_nan_and_inf : bool, optional If True, treat numbers which contain nans or infs as as equal. Sets ignore_inf_sign to be True. """ def __init__(self, func, data, param_columns, result_columns=None, result_func=None, rtol=None, atol=None, param_filter=None, knownfailure=None, dataname=None, nan_ok=False, vectorized=True, ignore_inf_sign=False, distinguish_nan_and_inf=True): self.func = func self.data = data self.dataname = dataname if not hasattr(param_columns, '__len__'): param_columns = (param_columns,) self.param_columns = tuple(param_columns) if result_columns is not None: if not hasattr(result_columns, '__len__'): result_columns = (result_columns,) self.result_columns = tuple(result_columns) if result_func is not None: raise ValueError("Only result_func or result_columns should be provided") elif result_func is not None: self.result_columns = None else: raise ValueError("Either result_func or result_columns should be provided") self.result_func = result_func self.rtol = rtol self.atol = atol if not hasattr(param_filter, '__len__'): param_filter = (param_filter,) self.param_filter = param_filter self.knownfailure = knownfailure self.nan_ok = nan_ok self.vectorized = vectorized self.ignore_inf_sign = ignore_inf_sign self.distinguish_nan_and_inf = distinguish_nan_and_inf if not self.distinguish_nan_and_inf: self.ignore_inf_sign = True def get_tolerances(self, dtype): if not np.issubdtype(dtype, np.inexact): dtype = np.dtype(float) info = np.finfo(dtype) rtol, atol = self.rtol, self.atol if rtol is None: rtol = 5*info.eps if atol is None: atol = 5*info.tiny return rtol, atol def check(self, data=None, dtype=None, dtypes=None): """Check the special function against the data.""" __tracebackhide__ = operator.methodcaller( 'errisinstance', AssertionError ) if self.knownfailure: pytest.xfail(reason=self.knownfailure) if data is None: data = self.data if dtype is None: dtype = data.dtype else: data = data.astype(dtype) rtol, atol = self.get_tolerances(dtype) # Apply given filter functions if self.param_filter: param_mask = np.ones((data.shape[0],), np.bool_) for j, filter in zip(self.param_columns, self.param_filter): if filter: param_mask &= list(filter(data[:,j])) data = data[param_mask] # Pick parameters from the correct columns params = [] for idx, j in enumerate(self.param_columns): if np.iscomplexobj(j): j = int(j.imag) params.append(data[:,j].astype(complex)) elif dtypes and idx < len(dtypes): params.append(data[:, j].astype(dtypes[idx])) else: params.append(data[:,j]) # Helper for evaluating results def eval_func_at_params(func, skip_mask=None): if self.vectorized: got = func(*params) else: got = [] for j in range(len(params[0])): if skip_mask is not None and skip_mask[j]: got.append(np.nan) continue got.append(func(*tuple([params[i][j] for i in range(len(params))]))) got = np.asarray(got) if not isinstance(got, tuple): got = (got,) return got # Evaluate function to be tested got = eval_func_at_params(self.func) # Grab the correct results if self.result_columns is not None: # Correct results passed in with the data wanted = tuple([data[:,icol] for icol in self.result_columns]) else: # Function producing correct results passed in skip_mask = None if self.nan_ok and len(got) == 1: # Don't spend time evaluating what doesn't need to be evaluated skip_mask = np.isnan(got[0]) wanted = eval_func_at_params(self.result_func, skip_mask=skip_mask) # Check the validity of each output returned assert_(len(got) == len(wanted)) for output_num, (x, y) in enumerate(zip(got, wanted)): if np.issubdtype(x.dtype, np.complexfloating) or self.ignore_inf_sign: pinf_x = np.isinf(x) pinf_y = np.isinf(y) minf_x = np.isinf(x) minf_y = np.isinf(y) else: pinf_x = np.isposinf(x) pinf_y = np.isposinf(y) minf_x = np.isneginf(x) minf_y = np.isneginf(y) nan_x = np.isnan(x) nan_y = np.isnan(y) with np.errstate(all='ignore'): abs_y = np.absolute(y) abs_y[~np.isfinite(abs_y)] = 0 diff = np.absolute(x - y) diff[~np.isfinite(diff)] = 0 rdiff = diff / np.absolute(y) rdiff[~np.isfinite(rdiff)] = 0 tol_mask = (diff <= atol + rtol*abs_y) pinf_mask = (pinf_x == pinf_y) minf_mask = (minf_x == minf_y) nan_mask = (nan_x == nan_y) bad_j = ~(tol_mask & pinf_mask & minf_mask & nan_mask) point_count = bad_j.size if self.nan_ok: bad_j &= ~nan_x bad_j &= ~nan_y point_count -= (nan_x | nan_y).sum() if not self.distinguish_nan_and_inf and not self.nan_ok: # If nan's are okay we've already covered all these cases inf_x = np.isinf(x) inf_y = np.isinf(y) both_nonfinite = (inf_x & nan_y) | (nan_x & inf_y) bad_j &= ~both_nonfinite point_count -= both_nonfinite.sum() if np.any(bad_j): # Some bad results: inform what, where, and how bad msg = [""] msg.append("Max |adiff|: %g" % diff[bad_j].max()) msg.append("Max |rdiff|: %g" % rdiff[bad_j].max()) msg.append("Bad results (%d out of %d) for the following points (in output %d):" % (np.sum(bad_j), point_count, output_num,)) for j in np.nonzero(bad_j)[0]: j = int(j) fmt = lambda x: "%30s" % np.array2string(x[j], precision=18) a = " ".join(map(fmt, params)) b = " ".join(map(fmt, got)) c = " ".join(map(fmt, wanted)) d = fmt(rdiff) msg.append("%s => %s != %s (rdiff %s)" % (a, b, c, d)) assert_(False, "\n".join(msg)) def __repr__(self): """Pretty-printing, esp. for Nose output""" if np.any(list(map(np.iscomplexobj, self.param_columns))): is_complex = " (complex)" else: is_complex = "" if self.dataname: return "" % (self.func.__name__, is_complex, os.path.basename(self.dataname)) else: return "" % (self.func.__name__, is_complex)