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# Copyright (c) 2016, Thomas P. Robitaille
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
#
# This package was derived from pytest-mpl, which is released under a BSD
# license and can be found here:
#
# https://github.com/astrofrog/pytest-mpl
import os
import abc
import shutil
import tempfile
import warnings
from urllib.request import urlopen
import pytest
import numpy as np
abstractstaticmethod = abc.abstractstaticmethod
abstractclassmethod = abc.abstractclassmethod
class BaseDiff(object, metaclass=abc.ABCMeta):
@abstractstaticmethod
def read(filename):
"""
Given a filename, return a data object.
"""
raise NotImplementedError()
@abstractstaticmethod
def write(filename, data, **kwargs):
"""
Given a filename and a data object (and optional keyword arguments),
write the data to a file.
"""
raise NotImplementedError()
@abstractclassmethod
def compare(self, reference_file, test_file, atol=None, rtol=None):
"""
Given a reference and test filename, compare the data to the specified
absolute (``atol``) and relative (``rtol``) tolerances.
Should return two arguments: a boolean indicating whether the data are
identical, and a string giving the full error message if not.
"""
raise NotImplementedError()
class SimpleArrayDiff(BaseDiff):
@classmethod
def compare(cls, reference_file, test_file, atol=None, rtol=None):
array_ref = cls.read(reference_file)
array_new = cls.read(test_file)
try:
np.testing.assert_allclose(array_ref, array_new, atol=atol, rtol=rtol)
except AssertionError as exc:
message = "\n\na: {0}".format(test_file) + '\n'
message += "b: {0}".format(reference_file) + '\n'
message += exc.args[0]
return False, message
else:
return True, ""
class FITSDiff(BaseDiff):
extension = 'fits'
@staticmethod
def read(filename):
from astropy.io import fits
return fits.getdata(filename)
@staticmethod
def write(filename, data, **kwargs):
from astropy.io import fits
if isinstance(data, np.ndarray):
data = fits.PrimaryHDU(data)
return data.writeto(filename, **kwargs)
@classmethod
def compare(cls, reference_file, test_file, atol=None, rtol=None):
import astropy
from astropy.io.fits.diff import FITSDiff
from astropy.utils.introspection import minversion
if minversion(astropy, '2.0'):
diff = FITSDiff(reference_file, test_file, rtol=rtol, atol=atol)
else:
# `atol` is not supported prior to Astropy 2.0
diff = FITSDiff(reference_file, test_file, tolerance=rtol)
return diff.identical, diff.report()
class TextDiff(SimpleArrayDiff):
extension = 'txt'
@staticmethod
def read(filename):
return np.loadtxt(filename)
@staticmethod
def write(filename, data, **kwargs):
fmt = kwargs.get('fmt', '%g')
kwargs['fmt'] = fmt
return np.savetxt(filename, data, **kwargs)
class PDHDFDiff(BaseDiff):
extension = 'h5'
@staticmethod
def read(filename):
import pandas as pd
return pd.read_hdf(filename)
@staticmethod
def write(filename, data, **kwargs):
import pandas as pd # noqa: F401
key = os.path.basename(filename).replace('.h5', '')
return data.to_hdf(filename, key=key, **kwargs)
@classmethod
def compare(cls, reference_file, test_file, atol=None, rtol=None):
import pandas.testing as pdt
import pandas as pd
ref_data = pd.read_hdf(reference_file)
test_data = pd.read_hdf(test_file)
try:
pdt.assert_frame_equal(ref_data, test_data)
except AssertionError as exc:
message = "\n\na: {0}".format(test_file) + '\n'
message += "b: {0}".format(reference_file) + '\n'
message += exc.args[0]
return False, message
else:
return True, ""
FORMATS = {}
FORMATS['fits'] = FITSDiff
FORMATS['text'] = TextDiff
FORMATS['pd_hdf'] = PDHDFDiff
def _download_file(url):
u = urlopen(url)
result_dir = tempfile.mkdtemp()
filename = os.path.join(result_dir, 'downloaded')
with open(filename, 'wb') as tmpfile:
tmpfile.write(u.read())
return filename
def pytest_addoption(parser):
group = parser.getgroup("general")
group.addoption('--arraydiff', action='store_true',
help="Enable comparison of arrays to reference arrays stored in files")
group.addoption('--arraydiff-generate-path',
help="directory to generate reference files in, relative to location where py.test is run", action='store')
group.addoption('--arraydiff-reference-path',
help="directory containing reference files, relative to location where py.test is run", action='store')
group.addoption('--arraydiff-default-format',
help="Default format for the reference arrays (can be 'fits' or 'text' currently)")
def pytest_configure(config):
config.getini('markers').append(
'array_compare: for functions using array comparison')
if config.getoption("--arraydiff") or config.getoption("--arraydiff-generate-path") is not None:
reference_dir = config.getoption("--arraydiff-reference-path")
generate_dir = config.getoption("--arraydiff-generate-path")
if reference_dir is not None and generate_dir is not None:
warnings.warn("Ignoring --arraydiff-reference-path since --arraydiff-generate-path is set")
if reference_dir is not None:
reference_dir = os.path.abspath(reference_dir)
if generate_dir is not None:
reference_dir = os.path.abspath(generate_dir)
default_format = config.getoption("--arraydiff-default-format") or 'text'
config.pluginmanager.register(ArrayComparison(config,
reference_dir=reference_dir,
generate_dir=generate_dir,
default_format=default_format))
else:
config.pluginmanager.register(ArrayInterceptor(config))
def generate_test_name(item):
"""
Generate a unique name for this test.
"""
if item.cls is not None:
name = f"{item.module.__name__}.{item.cls.__name__}.{item.name}"
else:
name = f"{item.module.__name__}.{item.name}"
return name
def wrap_array_interceptor(plugin, item):
"""
Intercept and store arrays returned by test functions.
"""
# Only intercept array on marked array tests
if item.get_closest_marker('array_compare') is not None:
# Use the full test name as a key to ensure correct array is being retrieved
test_name = generate_test_name(item)
def array_interceptor(store, obj):
def wrapper(*args, **kwargs):
store.return_value[test_name] = obj(*args, **kwargs)
return wrapper
item.obj = array_interceptor(plugin, item.obj)
class ArrayComparison(object):
def __init__(self, config, reference_dir=None, generate_dir=None, default_format='text'):
self.config = config
self.reference_dir = reference_dir
self.generate_dir = generate_dir
self.default_format = default_format
self.return_value = {}
@pytest.hookimpl(hookwrapper=True)
def pytest_runtest_call(self, item):
compare = item.get_closest_marker('array_compare')
if compare is None:
yield
return
file_format = compare.kwargs.get('file_format', self.default_format)
if file_format not in FORMATS:
raise ValueError("Unknown format: {0}".format(file_format))
if 'extension' in compare.kwargs:
extension = compare.kwargs['extension']
else:
extension = FORMATS[file_format].extension
atol = compare.kwargs.get('atol', 0.)
rtol = compare.kwargs.get('rtol', 1e-7)
single_reference = compare.kwargs.get('single_reference', False)
write_kwargs = compare.kwargs.get('write_kwargs', {})
reference_dir = compare.kwargs.get('reference_dir', None)
if reference_dir is None:
if self.reference_dir is None:
reference_dir = os.path.join(os.path.dirname(item.fspath.strpath), 'reference')
else:
reference_dir = self.reference_dir
else:
if not reference_dir.startswith(('http://', 'https://')):
reference_dir = os.path.join(os.path.dirname(item.fspath.strpath), reference_dir)
baseline_remote = reference_dir.startswith('http')
# Run test and get array object
wrap_array_interceptor(self, item)
yield
test_name = generate_test_name(item)
if test_name not in self.return_value:
# Test function did not complete successfully
return
array = self.return_value[test_name]
# Find test name to use as plot name
filename = compare.kwargs.get('filename', None)
if filename is None:
if single_reference:
filename = item.originalname + '.' + extension
else:
filename = item.name + '.' + extension
filename = filename.replace('[', '_').replace(']', '_')
filename = filename.replace('_.' + extension, '.' + extension)
# What we do now depends on whether we are generating the reference
# files or simply running the test.
if self.generate_dir is None:
# Save the figure
result_dir = tempfile.mkdtemp()
test_array = os.path.abspath(os.path.join(result_dir, filename))
FORMATS[file_format].write(test_array, array, **write_kwargs)
# Find path to baseline array
if baseline_remote:
baseline_file_ref = _download_file(reference_dir + filename)
else:
baseline_file_ref = os.path.abspath(os.path.join(os.path.dirname(item.fspath.strpath), reference_dir, filename))
if not os.path.exists(baseline_file_ref):
raise Exception("""File not found for comparison test
Generated file:
\t{test}
This is expected for new tests.""".format(
test=test_array))
# setuptools may put the baseline arrays in non-accessible places,
# copy to our tmpdir to be sure to keep them in case of failure
baseline_file = os.path.abspath(os.path.join(result_dir, 'reference-' + filename))
shutil.copyfile(baseline_file_ref, baseline_file)
identical, msg = FORMATS[file_format].compare(baseline_file, test_array, atol=atol, rtol=rtol)
if identical:
shutil.rmtree(result_dir)
else:
raise Exception(msg)
else:
if not os.path.exists(self.generate_dir):
os.makedirs(self.generate_dir)
FORMATS[file_format].write(os.path.abspath(os.path.join(self.generate_dir, filename)), array, **write_kwargs)
pytest.skip("Skipping test, since generating data")
class ArrayInterceptor:
"""
This is used in place of ArrayComparison when the array comparison option is not used,
to make sure that we still intercept arrays returned by tests.
"""
def __init__(self, config):
self.config = config
self.return_value = {}
@pytest.hookimpl(hookwrapper=True)
def pytest_runtest_call(self, item):
if item.get_closest_marker('array_compare') is not None:
wrap_array_interceptor(self, item)
yield
return
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