Merge pull request #2155 from desihub/fix-2142

remove deprecated test_suite() function from all unit tests that use it

py/desispec/database/metadata.py

@@ -16,9 +16,8 @@
 from pytz import utc
 from sqlalchemy import (create_engine, text, Table, ForeignKey, Column,
                         Integer, String, Float, DateTime)
-from sqlalchemy.ext.declarative import declarative_base
 from sqlalchemy.ext.associationproxy import association_proxy
-from sqlalchemy.orm import sessionmaker, relationship, reconstructor
+from sqlalchemy.orm import sessionmaker, relationship, reconstructor, declarative_base
 from sqlalchemy.orm.exc import NoResultFound, MultipleResultsFound
 from matplotlib.patches import Circle, Polygon, Wedge
 from matplotlib.collections import PatchCollection

py/desispec/image_model.py

@@ -23,7 +23,7 @@
 from desispec.qproc.qsky import qproc_sky_subtraction
 from desispec.qproc.qfiberflat import qproc_apply_fiberflat
 
-@numba.jit
+@numba.jit(nopython=True)
 def numba_proj(image,x,sigma,flux) :
     '''
     Add a spectrum to a model of the pixel values in a CCD image assuming a Gaussian cross-dispersion profile.

py/desispec/io/__init__.py

@@ -12,7 +12,7 @@
 import warnings
 warnings.filterwarnings('ignore', message="'.*nanomaggie.* did not parse as fits unit.*")
 warnings.filterwarnings('ignore', message="'.*nanomaggy.* did not parse as fits unit.*")
-warnings.filterwarnings('ignore', message=".*'10\*\*6 arcsec.* did not parse as fits unit.*")
+warnings.filterwarnings('ignore', message=r".*'10\*\*6 arcsec.* did not parse as fits unit.*")
 
 # from .download import download, filepath2url
 from .fiberflat import read_fiberflat, write_fiberflat

py/desispec/preproc.py

@@ -375,7 +375,7 @@ def _background(image,header,patch_width=200,stitch_width=10,stitch=False) :
     log.info("done")
     return bkg
 
-@numba.jit
+@numba.jit(nopython=True)
 def numba_mean(image_flux,image_ivar,x,hw=3) :
     """
     Returns mean of pixels vs. row about x+-hw

py/desispec/qproc/qextract.py

@@ -15,7 +15,7 @@
 from desispec.qproc.qframe import QFrame
 
 
-@numba.jit
+@numba.jit(nopython=True)
 def numba_extract(image_flux,image_var,x,hw=3) :
     n0=image_flux.shape[0]
     flux=np.zeros(n0)

py/desispec/test/test_binscripts.py

@@ -352,15 +352,3 @@ def test_compute_sky(self):
         result, success = runcmd(desispec.scripts.sky.main, args=args,
             inputs=inputs, outputs=outputs, clobber=True)
         self.assertTrue(success)
-
-def test_suite():
-    """Allows testing of only this module with the command::
-
-        python setup.py test -m <modulename>
-    """
-    return unittest.defaultTestLoader.loadTestsFromName(__name__)
-
-
-#- This runs all test* functions in any TestCase class in this file
-if __name__ == '__main__':
-    unittest.main()

py/desispec/test/test_bitmask.py

@@ -22,6 +22,4 @@ def test_names(self):
                 self.assertEqual(m.mask(name), m.mask(m.bitnum(name)), 'Failed matching mask to name for '+name)
                 self.assertEqual(m.bitname(m.bitnum(name)), name, 'Failed bit name->num->name roundtrip for '+name)
                 c = m.comment(name)
-
-if __name__ == '__main__':
-    unittest.main()
+

py/desispec/test/test_bootcalib.py

@@ -221,9 +221,3 @@ def test_main(self):
         y = psf.y(ispec=indices, wavelength=waves)
 
 
-def test_suite():
-    """Allows testing of only this module with the command::
-
-        python setup.py test -m <modulename>
-    """
-    return unittest.defaultTestLoader.loadTestsFromName(__name__)

py/desispec/test/test_calibfinder.py

@@ -44,7 +44,3 @@ def test_init(self):
         print(cfinder.value("DETECTOR"))
         if cfinder.haskey("BIAS") :
             print(cfinder.findfile("BIAS"))
-
-
-if __name__ == '__main__':
-    unittest.main()

py/desispec/test/test_ccdcalib.py

@@ -110,15 +110,3 @@ def test_select_zero_expids(self):
             del os.environ['DESI_LOGLEVEL']
         else:
             os.environ['DESI_LOGLEVEL'] = original_log_level
-
-
-def test_suite():
-    """Allows testing of only this module with the command::
-
-        python setup.py test -m desispec.test.test_ccdcalib
-    """
-    return unittest.defaultTestLoader.loadTestsFromName(__name__)
-
-
-if __name__ == '__main__':
-    unittest.main()           

py/desispec/test/test_coadd.py

@@ -891,15 +891,3 @@ def test_coadd_cameras(self):
         spec.R = None
         spec.mask = None
         coadd = coadd_cameras(spec)
-
-
-def test_suite():
-    """Allows testing of only this module with the command::
-
-        python setup.py test -m desispec.test.test_coadd
-    """
-    return unittest.defaultTestLoader.loadTestsFromName(__name__)
-
-
-if __name__ == '__main__':
-    unittest.main()           

py/desispec/test/test_cosmics.py

@@ -86,7 +86,3 @@ def test_reject_cosmics(self):
         reject_cosmic_rays(image)
         cosmic = (image.pix > 0)
         self.assertTrue(np.all(image.mask[cosmic] & ccdmask.COSMIC))
-
-#- This runs all test* functions in any TestCase class in this file
-if __name__ == '__main__':
-    unittest.main()

py/desispec/test/test_database.py

@@ -123,9 +123,3 @@ def test_frameid(self):
         self.assertEqual(frameid(9876543, 'z9'), 987654329)
 
 
-def test_suite():
-    """Allows testing of only this module with the command::
-
-        python setup.py test -m <modulename>
-    """
-    return unittest.defaultTestLoader.loadTestsFromName(__name__)

py/desispec/test/test_emlinefit.py

@@ -52,13 +52,3 @@ def test_get_emlines(self):
         #- but OIII should have NaN for second since it is off wavelength grid
         self.assertFalse(np.isnan(results['OIII']['FLUX'][0]))
         self.assertTrue(np.isnan(results['OIII']['FLUX'][1]))
-
-def test_suite():
-    """Allows testing of only this module with the command::
-
-        python setup.py test -m desispec.test.test_emlinefit
-    """
-    return unittest.defaultTestLoader.loadTestsFromName(__name__)
-
-if __name__ == '__main__':
-    unittest.main()

py/desispec/test/test_extract.py

@@ -171,6 +171,3 @@ def test_bundles2(self):
 
     def test_bundles3(self):
         self._test_bundles("desi_extract_spectra -i {} -p {} -w 7500,7530,0.75 --nwavestep 10 -f {} --bundlesize 5 -o {} -m {} -s {} -n {}", 20, 5)
-
-if __name__ == '__main__':
-    unittest.main()

py/desispec/test/test_fiberbitmask.py

@@ -38,7 +38,3 @@ def test_framebitmask(self):
 
         ivar2 = get_fiberbitmasked_frame_arrays(self.frame, bitmask=1)
         self.assertTrue( np.all(ivar1 == ivar2) )
-
-#- This runs all test* functions in any TestCase class in this file
-if __name__ == '__main__':
-    unittest.main()

py/desispec/test/test_fibercrosstalk.py

@@ -74,6 +74,3 @@ def test_fiber_crosstalk(self):
 
         xyset = read_xytraceset(self.psffile)
         correct_fiber_crosstalk(spectra,xyset=xyset)
-
-if __name__ == '__main__':
-    unittest.main()

py/desispec/test/test_fiberflat.py

@@ -404,8 +404,3 @@ def test_slice(self):
         x = self.ff[1:2]
         x = self.ff[[1,2,3]]
         x = self.ff[self.ff.fibers<3]
-
-
-#- This runs all test* functions in any TestCase class in this file
-if __name__ == '__main__':
-    unittest.main()

py/desispec/test/test_fibermap.py

@@ -131,14 +131,3 @@ def test_update_survey_keywords(self):
         update_survey_keywords(hdr)
         self.assertEqual(hdr['SURVEY'], 'sv2')
         self.assertEqual(hdr['FAPRGRM'], 'dark')
-
-
-def test_suite():
-    """Allows testing of only this module with the command::
-
-        python setup.py test -m <modulename>
-    """
-    return unittest.defaultTestLoader.loadTestsFromName(__name__)
-
-if __name__ == '__main__':
-    unittest.main()

py/desispec/test/test_flux_calibration.py

@@ -232,9 +232,3 @@ def test_isStdStar(self):
 
     def test_main(self):
         pass
-
-
-
-#- This runs all test* functions in any TestCase class in this file
-if __name__ == '__main__':
-    unittest.main()

py/desispec/test/test_frame.py

@@ -112,7 +112,3 @@ def test_vet(self):
         # Mess with shape
         frame.nspec = 5
         self.assertEqual(frame.vet(), 1)
-
-#- This runs all test* functions in any TestCase class in this file
-if __name__ == '__main__':
-    unittest.main()           

py/desispec/test/test_gpu.py

@@ -50,10 +50,3 @@ def gather(self, value, root):
 
         desispec.gpu.redistribute_gpu_ranks(comm=FakeComm(0,16))
         desispec.gpu.redistribute_gpu_ranks(comm=FakeComm(1,16))
-
-
-
-
-#- This runs all test* functions in any TestCase class in this file
-if __name__ == '__main__':
-    unittest.main()           

py/desispec/test/test_image.py

@@ -122,7 +122,3 @@ def test_slicing(self):
             img1[1:2, 'blat']
         with self.assertRaises(ValueError):
             img1[None, 1:2]
-
-#- This runs all test* functions in any TestCase class in this file
-if __name__ == '__main__':
-    unittest.main()           

py/desispec/test/test_io.py

@@ -4,12 +4,6 @@
 """
 
 import sys
-if __name__ == '__main__':
-    print('Run this instead:')
-    # print('python setup.py test -m desispec.test.test_io')
-    print('pytest py/desispec/test/test_io.py')
-    sys.exit(1)
-
 import unittest
 from unittest.mock import patch, MagicMock
 import os
@@ -83,16 +77,19 @@ def tearDownClass(cls):
         for testfile in [cls.testfile, cls.testyfile, cls.testbrfile, cls.testlog]:
             if os.path.exists(testfile):
                 os.remove(testfile)
-
         for e in cls.origEnv:
             if cls.origEnv[e] is None:
                 del os.environ[e]
             else:
                 os.environ[e] = cls.origEnv[e]
 
-        if os.path.exists(cls.testDir):
+        if os.path.isdir(cls.testDir):
             rmtree(cls.testDir)
 
+        # reset the readonly cache
+        from ..io import meta
+        meta._desi_root_readonly = None
+
     def test_write_bintable(self):
         """Test writing binary tables to FITS.
         """
@@ -975,7 +972,8 @@ def test_desi_root_readonly(self):
         meta._desi_root_readonly = None
 
         #- Case 1: $DESI_ROOT_READONLY is set and exists -> use it
-        os.environ['DESI_ROOT_READONLY'] = tempfile.mkdtemp()
+        tmpdir = tempfile.mkdtemp()
+        os.environ['DESI_ROOT_READONLY'] = tmpdir
         blat = meta.get_desi_root_readonly()
         self.assertEqual(blat, os.environ['DESI_ROOT_READONLY'])
 
@@ -1636,9 +1634,3 @@ def test_camword_spectros(self):
         self.assertEqual(spectros_to_camword([5,6,0]), 'a056')
 
 
-def test_suite():
-    """Allows testing of only this module with the command::
-
-        python setup.py test -m <modulename>
-    """
-    return unittest.defaultTestLoader.loadTestsFromName(__name__)

py/desispec/test/test_linalg.py

@@ -85,6 +85,3 @@ def test_cholesky_invert(self):
 
     def runTest(self):
         pass
-
-if __name__ == '__main__':
-    unittest.main()

py/desispec/test/test_parallel.py

@@ -161,14 +161,3 @@ def check_weight_distribution(weights, groups, num_nodes, groups_per_node):
 
         groups = weighted_partition(weights, num_groups-3, groups_per_node=groups_per_node)
         check_weight_distribution(weights, groups, num_nodes, groups_per_node)
-
-def test_suite():
-    """Allows testing of only this module with the command::
-
-        python setup.py test -m <modulename>
-    """
-    return unittest.defaultTestLoader.loadTestsFromName(__name__)
-
-#- This runs all test* functions in any TestCase class in this file
-if __name__ == '__main__':
-    unittest.main()

py/desispec/test/test_params.py

@@ -52,9 +52,3 @@ def test_read(self):
             self.assertIsNot(p3, p4)
             self.assertIsNot(p2, p4)
 
-def test_suite():
-    """Allows testing of only this module with the command::
-
-        python setup.py test -m <modulename>
-    """
-    return unittest.defaultTestLoader.loadTestsFromName(__name__)

py/desispec/test/test_photo.py

@@ -11,11 +11,11 @@
 
 class TestPhoto(unittest.TestCase):
 
-    def setUp(self):
+    @classmethod
+    def setUpClass(self):
         from astropy.table import Table
-
         # for testing gather_targetphot and gather_tractorphot
-        
+
         # sv3-dark (secondary), sv1-bright (primary), main-dark (secondary), main-dark (primary, south), main-dark (primary, north), sv3-bright (TOO)
         input_cat = Table()
         input_cat['TARGETID'] = [929413348720641, 39627061832191195, 2253225356951552, 39627565329026280, 39633086782113662, 43977491483722156]
@@ -54,6 +54,10 @@ def setUp(self):
         tractorphot['LS_ID'] = np.array([10995128657712508, 10995128743167117, 10995128743105186]).astype(np.int64)
         self.tractorphot_dr10 = tractorphot
 
+    @classmethod
+    def tearDownClass(self):
+        pass
+
     @unittest.skipUnless('NERSC_HOST' in os.environ, "not at NERSC")
     def test_gather_targetdirs(self):
         """Test that we get the correct targeting directories given a tile."""
@@ -102,6 +106,3 @@ def test_gather_tractorphot_dr10(self):
         tractorphot = gather_tractorphot(self.input_cat_dr10, legacysurveydir=legacysurveydir)
         for col in self.tractorphot_dr10.colnames:
             self.assertTrue(np.all(tractorphot[col] == self.tractorphot_dr10[col]))
-
-if __name__ == '__main__':
-    unittest.main()

py/desispec/test/test_pipeline_plan.py

@@ -68,15 +68,3 @@ def test_create_load_prod(self):
         # fullgrph = load_prod()
         # self.assertTrue(grph == fullgrph)
         pass
-
-
-def test_suite():
-    """Allows testing of only this module with the command::
-
-        python setup.py test -m <modulename>
-    """
-    return unittest.defaultTestLoader.loadTestsFromName(__name__)
-
-#- This runs all test* functions in any TestCase class in this file
-if __name__ == '__main__':
-    unittest.main()

py/desispec/test/test_pipeline_run.py

@@ -82,8 +82,3 @@ def test_run(self):
         pass
 
 
-def test_suite():
-    """Allows testing of only this module with the command::
-        python setup.py test -m <modulename>
-    """
-    return unittest.defaultTestLoader.loadTestsFromName(__name__)