Modernize testing to pytest

.github/workflows/ci.yml

@@ -156,7 +156,7 @@ jobs:
 
                 # Extra packages needed for testing
                 pip install -U -r test_requirements.txt
-                pip install -U nose coverage
+                pip install -U coverage
 
                 pip install -U matplotlib
 
@@ -208,7 +208,7 @@ jobs:
             - name: Check shared library
               if: matrix.py == 3.8
               run: |
-                # On a few systems (arbitrarily py3.8, where we also chec mac and clang),
+                # On a few systems (arbitrarily py3.8, where we also check mac and clang),
                 # check the shared library creation and link.
                 GALSIM_BUILD_SHARED=1 python setup.py install
 

docs/install.rst

@@ -73,10 +73,6 @@ You can also run them with multiple jobs (e.g. for 4 jobs) by typing::
 
 You need the ``pytest-xdist`` and ``pytest-timeout`` plugins for this to work.
 
-If you prefer to use nosetests, the equivalent command is::
-
-    nosetests --processes=4 --process-timeout=60 test*.py
-
 .. note::
 
     If your system does not have ``pytest`` installed, and you do not want

setup.py

@@ -244,7 +244,7 @@ def supports_gpu(compiler, cc_type):
     extra_cflags = copt[cc_type]
     extra_lflags = lopt[cc_type]
     return try_compile(cpp_code, compiler, extra_cflags, extra_lflags)
-    
+
 # Check for the fftw3 library in some likely places
 def find_fftw_lib(output=False):
     import distutils.sysconfig
@@ -434,29 +434,29 @@ def find_eigen_dir(output=False):
         if output:
             print("Downloaded %s.  Unpacking tarball."%fname)
         with tarfile.open(fname) as tar:
-            
+
             def is_within_directory(directory, target):
-                
+
                 abs_directory = os.path.abspath(directory)
                 abs_target = os.path.abspath(target)
-            
+
                 prefix = os.path.commonprefix([abs_directory, abs_target])
-                
+
                 return prefix == abs_directory
-            
+
             def safe_extract(tar, path=".", members=None, *, numeric_owner=False):
                 # Avoid security vulnerability in tar.extractall function.
                 # This bit of code was added by the Advanced Research Center at Trellix in PR #1188.
                 # For more information about the security vulnerability, see
                 # https://github.com/advisories/GHSA-gw9q-c7gh-j9vm
-            
+
                 for member in tar.getmembers():
                     member_path = os.path.join(path, member.name)
                     if not is_within_directory(path, member_path):
                         raise Exception("Attempted Path Traversal in Tar File")
-            
-                tar.extractall(path, members, numeric_owner=numeric_owner) 
-            
+
+                tar.extractall(path, members, numeric_owner=numeric_owner)
+
             safe_extract(tar, dir)
         os.remove(fname)
         # This actually extracts into a subdirectory with a name eigen-eigen-5a0156e40feb/
@@ -1345,9 +1345,7 @@ def run_tests(self):
 
 build_dep = ['setuptools>=38,<72', 'pybind11>=2.2', 'numpy>=1.17']
 run_dep = ['astropy', 'LSSTDESC.Coord']
-test_dep = ['pytest', 'pytest-xdist', 'pytest-timeout', 'nose', 'scipy', 'pyyaml']
-# Note: Even though we don't use nosetests, nose is required for some tests to work.
-#       cf. https://gist.github.com/dannygoldstein/e18866ebb9c39a2739f7b9f16440e2f5
+test_dep = ['pytest', 'pytest-xdist', 'pytest-timeout', 'scipy', 'pyyaml']
 
 # If Eigen doesn't exist in the normal places, download it.
 find_eigen_dir(output=True)

test_requirements.txt

@@ -1,7 +1,6 @@
 pyyaml>=3.12
-pytest>=3.4, <8
+pytest>=3.4
 pytest-xdist>=1.19
 pytest-timeout>=1.2
 scipy>=1.0
-nose>=1.3
 matplotlib

tests/conftest.py

@@ -0,0 +1,4 @@
+def pytest_addoption(parser):
+    parser.addoption(
+        "--run_slow", action="store_true", default=False, help="Run slow tests"
+    )

tests/galsim_test_helpers.py

@@ -16,6 +16,7 @@
 #    and/or other materials provided with the distribution.
 #
 
+import pytest
 import numpy as np
 import galsim
 
@@ -389,24 +390,26 @@ def drawNoise(noise):
     return im.array.astype(np.float32).tolist()
 
 
-def runtests(testfns, parser=None):
+# Define a fixture to check if the tests were run via python script
+@pytest.fixture
+def run_slow(pytestconfig):
+    return pytestconfig.getoption("--run_slow", default=False)
+
+
+def runtests(filename, parser=None):
     if parser is None:
         from argparse import ArgumentParser
         parser = ArgumentParser()
-    parser.add_argument('-k', type=str, help='Run only the tests that match the given substring expression.')
     parser.add_argument('--profile', action='store_true', help='Profile tests')
     parser.add_argument('--prof_out', default=None, help="Profiler output file")
-    args = parser.parse_args()
+    args, unknown_args = parser.parse_known_args()
+    pytest_args = [filename] + unknown_args + ["--run_slow", "--tb=short", "-s"]
 
     if args.profile:
         import cProfile, pstats
         pr = cProfile.Profile()
         pr.enable()
-
-    for testfn in testfns:
-        if args.k is None or args.k in testfn.__name__:
-            testfn()
-
+    pytest.main(pytest_args)
     if args.profile:
         pr.disable()
         ps = pstats.Stats(pr).sort_stats('tottime')

tests/test_airy.py

@@ -280,5 +280,4 @@ def test_ne():
 
 
 if __name__ == "__main__":
-    testfns = [v for k, v in vars().items() if k[:5] == 'test_' and callable(v)]
-    runtests(testfns)
+    runtests(__file__)

tests/test_bandpass.py

@@ -398,5 +398,4 @@ def test_truncate_inputs():
 
 
 if __name__ == "__main__":
-    testfns = [v for k, v in vars().items() if k[:5] == 'test_' and callable(v)]
-    runtests(testfns)
+    runtests(__file__)

tests/test_bessel.py

@@ -503,5 +503,4 @@ def test_ci():
 
 
 if __name__ == "__main__":
-    testfns = [v for k, v in vars().items() if k[:5] == 'test_' and callable(v)]
-    runtests(testfns)
+    runtests(__file__)

tests/test_box.py

@@ -27,7 +27,7 @@
                                                            # images.
 
 @timer
-def test_box():
+def test_box(run_slow):
     """Test the generation of a specific box profile against a known result.
     """
     savedImg = galsim.fits.read(os.path.join(imgdir, "box_1.fits"))
@@ -81,7 +81,7 @@ def test_box():
         box = galsim.Box(width=width, height=height, flux=test_flux, gsparams=gsp)
         check_basic(box, "Box with width,height = %f,%f"%(width,height))
         do_shoot(box,im,"Box with width,height = %f,%f"%(width,height))
-        if __name__ == '__main__':
+        if run_slow:
             # These are slow because they require a pretty huge fft.
             # So only do them if running as main.
             do_kvalue(box,im,"Box with width,height = %f,%f"%(width,height))
@@ -118,7 +118,7 @@ def test_box():
     box = box.shear(galsim.Shear(g1=0.2, g2=-0.3))
     check_basic(box, "Sheared Box", approx_maxsb=True)
     do_shoot(box,im, "Sheared Box")
-    if __name__ == '__main__':
+    if run_slow:
         do_kvalue(box,im, "Sheared Box")
         check_pickle(box, lambda x: x.drawImage(method='no_pixel'))
         check_pickle(box)
@@ -129,7 +129,7 @@ def test_box():
     np.testing.assert_almost_equal(box.xValue(cen), box.max_sb)
 
     # This is also a profile that may be convolved using real space convolution, so test that.
-    if __name__ == '__main__':
+    if run_slow:
         conv = galsim.Convolve(box, galsim.Pixel(scale=scale), real_space=True)
         check_basic(conv, "Sheared Box convolved with pixel in real space",
                     approx_maxsb=True, scale=0.2)
@@ -317,6 +317,6 @@ def test_ne():
             galsim.TopHat(radius=1.0, gsparams=gsp)]
     check_all_diff(gals)
 
+
 if __name__ == "__main__":
-    testfns = [v for k, v in vars().items() if k[:5] == 'test_' and callable(v)]
-    runtests(testfns)
+    runtests(__file__)

tests/test_calc.py

@@ -370,5 +370,4 @@ def test_fwhm():
 
 
 if __name__ == "__main__":
-    testfns = [v for k, v in vars().items() if k[:5] == 'test_' and callable(v)]
-    runtests(testfns)
+    runtests(__file__)

tests/test_catalog.py

@@ -330,5 +330,4 @@ def test_output_catalog():
 
 
 if __name__ == "__main__":
-    testfns = [v for k, v in vars().items() if k[:5] == 'test_' and callable(v)]
-    runtests(testfns)
+    runtests(__file__)

tests/test_cdmodel.py

@@ -360,5 +360,4 @@ def test_exampleimage():
 
 
 if __name__ == "__main__":
-    testfns = [v for k, v in vars().items() if k[:5] == 'test_' and callable(v)]
-    runtests(testfns)
+    runtests(__file__)

tests/test_celestial.py

@@ -747,5 +747,4 @@ def test_ecliptic():
 
 
 if __name__ == '__main__':
-    testfns = [v for k, v in vars().items() if k[:5] == 'test_' and callable(v)]
-    runtests(testfns)
+    runtests(__file__)

tests/test_chromatic.py

@@ -500,7 +500,7 @@ def test_monochromatic_filter():
                         "GSObject.drawImage()")
 
 @timer
-def test_monochromatic_sed():
+def test_monochromatic_sed(run_slow):
     # Similar to the above test, but this time with a broad bandpass and a narrow sed.
 
     bandpass = galsim.Bandpass(galsim.LookupTable([500,1000], [1,1], 'linear'), wave_type='nm')
@@ -515,7 +515,7 @@ def test_monochromatic_sed():
     nstruts = 5
     aberrations = np.array([0,0,0,0, 0.02, -0.05, -0.15, -0.02, 0.13, 0.06, -0.09, 0.11])
 
-    if __name__ == '__main__':
+    if run_slow:
         wave_list = [515, 690, 900]
     else:
         wave_list = [515]
@@ -2089,7 +2089,7 @@ def __repr__(self):
 
 
 @timer
-def test_ChromaticOpticalPSF():
+def test_ChromaticOpticalPSF(run_slow):
     """Test the ChromaticOpticalPSF functionality."""
     import time
 
@@ -2174,7 +2174,7 @@ def test_ChromaticOpticalPSF():
     print("Time to initialize InterpolatedChromaticObject: {0}s".format(t5-t4))
     obj = galsim.Convolve(star, psf)
 
-    if __name__ == '__main__':
+    if run_slow:
         # This is slow, but it is worth testing the pickling of InterpolatedChromaticObjects.
         check_pickle(psf)
     else:
@@ -2304,7 +2304,7 @@ def test_ChromaticAiry():
         err_msg='ChromaticObject flux is wrong when convolved with ChromaticAiry')
 
 @timer
-def test_phot():
+def test_phot(run_slow):
     """Test photon shooting with various chromatic PSFs.
     """
     import time
@@ -2391,7 +2391,7 @@ def test_phot():
         print('fft time = ',t1-t0)
         print('im1.max,sum = ', im1.array.max(), im1.array.sum())
 
-        if __name__ == '__main__':
+        if run_slow:
             # Now the direct photon shooting method
             t0 = time.time()
             # This is the old way that photon shooting used to work.  The new way will be tested
@@ -3388,5 +3388,4 @@ def test_save_photons():
 
 
 if __name__ == "__main__":
-    testfns = [v for k, v in vars().items() if k[:5] == 'test_' and callable(v)]
-    runtests(testfns)
+    runtests(__file__)

tests/test_config_gsobject.py

@@ -2167,5 +2167,4 @@ def test_sed():
 
 
 if __name__ == "__main__":
-    testfns = [v for k, v in vars().items() if k[:5] == 'test_' and callable(v)]
-    runtests(testfns)
+    runtests(__file__)