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DM-12061: Eliminate test warnings in test_methods.py #279

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merged 5 commits into from
Sep 29, 2017
Merged

DM-12061: Eliminate test warnings in test_methods.py #279

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c06e219
Replace pyfits with astropy.io.fits
r-owen Sep 29, 2017
89b7e3b
Fix warnings in test_methods.py
r-owen Sep 29, 2017
2a096ba
Fix warnings in test_skyWcs.py
r-owen Sep 29, 2017
7182ee6
Remove unneded import in test_skyWcs.py
r-owen Sep 29, 2017
de3749c
Fix pep8 warning in skyWcs.py
r-owen Sep 29, 2017
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8 changes: 4 additions & 4 deletions tests/test_maskedImageIO.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@

from builtins import object
import numpy as np
import pyfits
import astropy.io
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Many people do this as import astropy.io.fits as pyfits to minimize code impact but that is probably more confusing in the long term since it leaves the pyfits string in the code.

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Agreed. I considered from astropy.io import fits but felt it was too ambiguous, and in at least one case fits was already used as a variable.

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Looking at other AFW code this should be plain import astropy.io.fits (we don't want to import all the other astropy IO plugins).


import lsst.utils
import lsst.utils.tests
Expand Down Expand Up @@ -204,9 +204,9 @@ def testReadWriteXY0(self):
def tmpFits(*hdus):
# Given a list of numpy arrays, create a temporary FITS file that
# contains them as consecutive HDUs. Yield it, then remove it.
hdus = [pyfits.PrimaryHDU(hdus[0])] + [pyfits.ImageHDU(hdu)
for hdu in hdus[1:]]
hdulist = pyfits.HDUList(hdus)
hdus = [astropy.io.fits.PrimaryHDU(hdus[0])] + \
[astropy.io.fits.ImageHDU(hdu) for hdu in hdus[1:]]
hdulist = astropy.io.fits.HDUList(hdus)
tempdir = tempfile.mkdtemp()
try:
filename = os.path.join(tempdir, 'test.fits')
Expand Down
50 changes: 36 additions & 14 deletions tests/test_methods.py
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Expand Up @@ -20,6 +20,7 @@
# see <http://www.lsstcorp.org/LegalNotices/>.
#
from __future__ import absolute_import, division, print_function
import contextlib
import math
import unittest
import re
Expand All @@ -39,6 +40,20 @@
class TestTestUtils(lsst.utils.tests.TestCase):
"""Test test methods added to lsst.utils.tests.TestCase
"""
def setUp(self):
# unittest did not get `assertWarns` until Python 3.2
self._addedAssertWarns = False
if not hasattr(self, "assertWarns"):
self._addedAssertWarns = True

@contextlib.contextmanager
def nullContextManger(dummy):
yield
self.assertWarns = nullContextManger

def tearDown(self):
if self._addedAssertWarns:
del self.assertWarns

def testAssertAnglesAlmostEqual(self):
"""Test assertAnglesAlmostEqual"""
Expand All @@ -50,11 +65,12 @@ def testAssertAnglesAlmostEqual(self):
maxDiff=0.010001*afwGeom.arcseconds,
)
# sanity-check deprecated version
self.assertAnglesNearlyEqual(
ang0,
ang0 + 0.01*afwGeom.arcseconds,
maxDiff=0.010001*afwGeom.arcseconds,
)
with self.assertWarns(DeprecationWarning):
self.assertAnglesNearlyEqual(
ang0,
ang0 + 0.01*afwGeom.arcseconds,
maxDiff=0.010001*afwGeom.arcseconds,
)
with self.assertRaises(AssertionError):
self.assertAnglesAlmostEqual(
ang0,
Expand Down Expand Up @@ -128,8 +144,9 @@ def testAssertBoxesAlmostEqual(self):
self.assertBoxesAlmostEqual(
box0, box1, maxDiff=radDiff*1.00001)
# sanity-check deprecated version
self.assertBoxesNearlyEqual(
box0, box1, maxDiff=radDiff*1.00001)
with self.assertWarns(DeprecationWarning):
self.assertBoxesNearlyEqual(
box0, box1, maxDiff=radDiff*1.00001)
with self.assertRaises(AssertionError):
self.assertBoxesAlmostEqual(
box0, box1, maxDiff=radDiff*0.99999)
Expand Down Expand Up @@ -158,8 +175,9 @@ def testAssertCoordsAlmostEqual(self):
self.assertCoordsAlmostEqual(
coord0, coord0, maxDiff=1e-7*afwGeom.arcseconds)
# sanity-check deprecated version
self.assertCoordsNearlyEqual(
coord0, coord0, maxDiff=1e-7*afwGeom.arcseconds)
with self.assertWarns(DeprecationWarning):
self.assertCoordsNearlyEqual(
coord0, coord0, maxDiff=1e-7*afwGeom.arcseconds)

for offAng in (0, 45, 90):
offAng = offAng*afwGeom.degrees
Expand Down Expand Up @@ -246,7 +264,8 @@ def testAssertPairsAlmostEqual(self):
for pair0 in ((-5, 4), (-5, 0.001), (0, 0), (49, 0.1)):
self.assertPairsAlmostEqual(pair0, pair0, maxDiff=1e-7)
# sanity-check deprecated version
self.assertPairsNearlyEqual(pair0, pair0, maxDiff=1e-7)
with self.assertWarns(DeprecationWarning):
self.assertPairsNearlyEqual(pair0, pair0, maxDiff=1e-7)
self.assertPairsAlmostEqual(afwGeom.Point2D(*pair0),
afwGeom.Extent2D(*pair0), maxDiff=1e-7)
for diff in ((0.001, 0), (-0.01, 0.03)):
Expand Down Expand Up @@ -285,8 +304,9 @@ def testAssertWcssAlmostEqualOverBBox(self):
self.assertWcsAlmostEqualOverBBox(wcs0, wcs0, bbox,
maxDiffSky=1e-7*afwGeom.arcseconds, maxDiffPix=1e-7)
# sanity-check deprecated version
self.assertWcsNearlyEqualOverBBox(wcs0, wcs0, bbox,
maxDiffSky=1e-7*afwGeom.arcseconds, maxDiffPix=1e-7)
with self.assertWarns(DeprecationWarning):
self.assertWcsNearlyEqualOverBBox(wcs0, wcs0, bbox,
maxDiffSky=1e-7*afwGeom.arcseconds, maxDiffPix=1e-7)
self.assertTrue(afwImage.wcsAlmostEqualOverBBox(wcs0, wcs0, bbox,
maxDiffSky=1e-7*afwGeom.arcseconds, maxDiffPix=1e-7))

Expand Down Expand Up @@ -335,7 +355,8 @@ def checkMaskedImage(self, mi):
self.assertMaskedImagesAlmostEqual(mi0, mi1, atol=0, rtol=0)
self.assertMaskedImagesAlmostEqual(mi0, mi1, atol=0, rtol=0)
# sanity-check deprecated version
self.assertMaskedImagesNearlyEqual(mi1, mi0, atol=0, rtol=0)
with self.assertWarns(DeprecationWarning):
self.assertMaskedImagesNearlyEqual(mi1, mi0, atol=0, rtol=0)
self.assertMaskedImagesAlmostEqual(
mi0.getArrays(), mi1, atol=0, rtol=0)
self.assertMaskedImagesAlmostEqual(
Expand All @@ -349,7 +370,8 @@ def checkMaskedImage(self, mi):
self.assertImagesEqual(plane1, plane0)
self.assertImagesAlmostEqual(plane0, plane1, atol=0, rtol=0)
# sanity-check deprecated version
self.assertImagesNearlyEqual(plane0, plane1, atol=0, rtol=0)
with self.assertWarns(DeprecationWarning):
self.assertImagesNearlyEqual(plane0, plane1, atol=0, rtol=0)
self.assertImagesAlmostEqual(plane1, plane0, atol=0, rtol=0)
self.assertImagesAlmostEqual(
plane0.getArray(), plane1, atol=0, rtol=0)
Expand Down
6 changes: 0 additions & 6 deletions tests/test_simpleTable.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,12 +37,6 @@
from builtins import range
import numpy as np

try:
import pyfits
except ImportError:
pyfits = None
print("WARNING: pyfits not available; some tests will not be run")

import lsst.utils.tests
import lsst.pex.exceptions
import lsst.daf.base
Expand Down
11 changes: 5 additions & 6 deletions tests/test_skyWcs.py
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Expand Up @@ -3,7 +3,6 @@
import sys
import unittest

import lsst.afw.coord # needed for assertCoordsNearlyEqual
import lsst.utils.tests
from lsst.afw.coord import IcrsCoord
from lsst.afw.geom import SkyWcs, Extent2D, Point2D, degrees, \
Expand Down Expand Up @@ -151,7 +150,7 @@ def setUp(self):
IcrsCoord(0.00001 * degrees, 45 * degrees),
IcrsCoord(359.99999 * degrees, 45 * degrees),
IcrsCoord(30 * degrees, 89.99999 * degrees),
]
]
orientationList = [
0 * degrees,
0.00001 * degrees,
Expand Down Expand Up @@ -185,10 +184,10 @@ def testGenericWcs(self):
transform = makeWcsPairTransform(wcs1, wcs2)
for point1 in self.points():
point2 = transform.applyForward(point1)
self.assertPairsNearlyEqual(
self.assertPairsAlmostEqual(
transform.applyInverse(point2),
point1)
self.assertCoordsNearlyEqual(
self.assertCoordsAlmostEqual(
wcs1.pixelToSky(point1),
wcs2.pixelToSky(point2))

Expand All @@ -200,8 +199,8 @@ def testSameWcs(self):
for point in self.points():
outPoint1 = transform.applyForward(point)
outPoint2 = transform.applyInverse(outPoint1)
self.assertPairsNearlyEqual(point, outPoint1)
self.assertPairsNearlyEqual(outPoint1, outPoint2)
self.assertPairsAlmostEqual(point, outPoint1)
self.assertPairsAlmostEqual(outPoint1, outPoint2)


class TestMemory(lsst.utils.tests.MemoryTestCase):
Expand Down
4 changes: 2 additions & 2 deletions tests/test_wcsFitsTable.py
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Expand Up @@ -23,7 +23,7 @@
from __future__ import absolute_import, division, print_function
import unittest

import pyfits
import astropy.io

import lsst.afw.image
import lsst.afw.geom
Expand Down Expand Up @@ -167,7 +167,7 @@ def testExposure(self):
# Manually mess up the headers, so we'd know if we were loading the Wcs from that;
# when there is a WCS in the header and a WCS in the FITS table, we should use the
# latter, because the former might just be an approximation.
fits = pyfits.open(fileName)
fits = astropy.io.fits.open(fileName)
fits[1].header.remove("CTYPE1")
fits[1].header.remove("CTYPE2")
fits.writeto(fileName, clobber=True)
Expand Down
2 changes: 1 addition & 1 deletion ups/afw.table
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Expand Up @@ -16,7 +16,7 @@ setupRequired(python_future)
setupRequired(log)
setupRequired(pybind11)
setupRequired(astshim)
setupOptional(pyfits)
setupOptional(astropy)
setupOptional(matplotlib)

setupOptional(afwdata)
Expand Down