Merge pull request #784 from pllim/deprecation-deprecated

MNT: Stop using deprecated astropy.tests stuff

ccdproc/conftest.py

@@ -14,28 +14,9 @@
     def pytest_configure(config):
         config.option.astropy_header = True
 except ImportError:
-    # TODO: Remove this when astropy 2.x and 3.x support is dropped.
-    # Probably an old pytest-astropy package where the pytest_astropy_header
-    # is not a dependency.
-    try:
-        from astropy.tests.plugins.display import (pytest_report_header,
-                                                   PYTEST_HEADER_MODULES,
-                                                   TESTED_VERSIONS)
-    except ImportError:
-        # TODO: Remove this when astropy 2.x support is dropped.
-        # If that also did not work we're probably using astropy 2.0
-        from astropy.tests.pytest_plugins import (pytest_report_header,
-                                                  PYTEST_HEADER_MODULES,
-                                                  TESTED_VERSIONS)
+    PYTEST_HEADER_MODULES = {}
+    TESTED_VERSIONS = {}
 
-try:
-    # TODO: Remove this when astropy 2.x support is dropped.
-    # This is the way to get plugins in astropy 2.x
-    from astropy.tests.pytest_plugins import *
-except ImportError:
-    # Otherwise they are installed as separate packages that pytest
-    # automagically finds.
-    pass
 
 from .tests.pytest_fixtures import *
 
@@ -48,10 +29,6 @@ def pytest_configure(config):
 packagename = os.path.basename(os.path.dirname(__file__))
 TESTED_VERSIONS[packagename] = version
 
-# Uncomment the following line to treat all DeprecationWarnings as
-# exceptions
-# enable_deprecations_as_exceptions()
-
 # Add astropy to test header information and remove unused packages.
 
 try:

ccdproc/core.py

@@ -875,7 +875,7 @@ def transform_image(ccd, transform_func, **kwargs):
 
     if nccd.wcs is not None:
         warn = 'WCS information may be incorrect as no transformation was applied to it'
-        logging.warning(warn)
+        warnings.warn(warn, UserWarning)
 
     return nccd
 

ccdproc/tests/pytest_fixtures.py

@@ -1,16 +1,12 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 
-import gzip
-from tempfile import mkdtemp
-import os
 from shutil import rmtree
 
 import numpy as np
 
 import pytest
 from astropy import units as u
 from astropy.utils import NumpyRNGContext
-from astropy.io import fits
 from astropy.nddata import CCDData
 
 from ..utils.sample_directory import directory_for_testing

ccdproc/tests/run_for_memory_profile.py

@@ -1,3 +1,6 @@
+import pytest
+pytest.importorskip('memory_profiler')
+
 from argparse import ArgumentParser
 from tempfile import TemporaryDirectory
 from pathlib import Path

ccdproc/tests/test_bitfield.py

@@ -3,8 +3,6 @@
 import numpy as np
 import pytest
 
-from astropy.tests.helper import catch_warnings
-
 from ccdproc.core import bitfield_to_boolean_mask
 
 
@@ -69,9 +67,8 @@ def test_bitfield_flag_non_integer():
 
 def test_bitfield_duplicate_flag_throws_warning():
     bm = np.random.randint(0, 10, (10, 10))
-    with catch_warnings(UserWarning) as w:
+    with pytest.warns(UserWarning):
         bitfield_to_boolean_mask(bm, [1, 1])
-    assert len(w)
 
 
 def test_bitfield_none_identical_to_strNone():

ccdproc/tests/test_ccdproc.py

@@ -6,7 +6,6 @@
 from astropy.units.quantity import Quantity
 import astropy.units as u
 from astropy.wcs import WCS
-from astropy.tests.helper import catch_warnings
 from astropy.utils.exceptions import AstropyUserWarning
 
 from astropy.nddata import StdDevUncertainty, CCDData
@@ -80,7 +79,7 @@ def test_create_deviation_from_negative():
                                   np.isnan(ccd_var.uncertainty.array))
 
 
-def test_create_deviation_from_negative():
+def test_create_deviation_from_negative_2():
     ccd_data = ccd_data_func(data_mean=0, data_scale=10)
     ccd_data.unit = u.electron
     readnoise = 5 * u.electron
@@ -619,8 +618,13 @@ def test_catch_transform_wcs_warning():
     def tran(arr):
         return 10 * arr
 
-    with catch_warnings() as w:
-        tran = transform_image(ccd_data, tran)
+    # No warning.
+    transform_image(ccd_data, tran)
+
+    # Issue warning when data has WCS.
+    ccd_data.wcs = wcs_for_testing(ccd_data.shape)
+    with pytest.warns(UserWarning, match='WCS information may be incorrect'):
+        transform_image(ccd_data, tran)
 
 
 @pytest.mark.parametrize('mask_data, uncertainty', [
@@ -661,7 +665,7 @@ def test_block_reduce():
                   mask=np.zeros((4, 4), dtype=bool),
                   uncertainty=StdDevUncertainty(np.ones((4, 4)))
                   )
-    with catch_warnings(AstropyUserWarning) as w:
+    with pytest.warns(AstropyUserWarning) as w:
         ccd_summed = block_reduce(ccd, (2, 2))
     assert len(w) == 1
     assert 'following attributes were set' in str(w[0].message)
@@ -690,7 +694,7 @@ def test_block_average():
                   mask=np.zeros((4, 4), dtype=bool),
                   uncertainty=StdDevUncertainty(np.ones((4, 4))))
     ccd.data[::2, ::2] = 2
-    with catch_warnings(AstropyUserWarning) as w:
+    with pytest.warns(AstropyUserWarning) as w:
         ccd_avgd = block_average(ccd, (2, 2))
     assert len(w) == 1
     assert 'following attributes were set' in str(w[0].message)
@@ -716,7 +720,7 @@ def test_block_replicate():
     ccd = CCDData(np.ones((4, 4)), unit='adu', meta={'testkw': 1},
                   mask=np.zeros((4, 4), dtype=bool),
                   uncertainty=StdDevUncertainty(np.ones((4, 4))))
-    with catch_warnings(AstropyUserWarning) as w:
+    with pytest.warns(AstropyUserWarning) as w:
         ccd_repl = block_replicate(ccd, (2, 2))
     assert len(w) == 1
     assert 'following attributes were set' in str(w[0].message)
@@ -772,7 +776,7 @@ def test__overscan_schange():
 def test_create_deviation_does_not_change_input():
     ccd_data = ccd_data_func()
     original = ccd_data.copy()
-    ccd = create_deviation(ccd_data, gain=5 * u.electron / u.adu, readnoise=10 * u.electron)
+    _ = create_deviation(ccd_data, gain=5 * u.electron / u.adu, readnoise=10 * u.electron)
     np.testing.assert_array_equal(original.data, ccd_data.data)
     assert original.unit == ccd_data.unit
 
@@ -790,8 +794,7 @@ def test_cosmicray_median_does_not_change_input():
 def test_cosmicray_lacosmic_does_not_change_input():
     ccd_data = ccd_data_func()
     original = ccd_data.copy()
-    error = np.zeros_like(ccd_data)
-    ccd = cosmicray_lacosmic(ccd_data)
+    _ = cosmicray_lacosmic(ccd_data)
     np.testing.assert_array_equal(original.data, ccd_data.data)
     assert original.unit == ccd_data.unit
 
@@ -809,7 +812,7 @@ def test_flat_correct_does_not_change_input():
 def test_gain_correct_does_not_change_input():
     ccd_data = ccd_data_func()
     original = ccd_data.copy()
-    ccd = gain_correct(ccd_data, gain=1, gain_unit=ccd_data.unit)
+    _ = gain_correct(ccd_data, gain=1, gain_unit=ccd_data.unit)
     np.testing.assert_array_equal(original.data, ccd_data.data)
     assert original.unit == ccd_data.unit
 
@@ -818,15 +821,15 @@ def test_subtract_bias_does_not_change_input():
     ccd_data = ccd_data_func()
     original = ccd_data.copy()
     master_frame = CCDData(np.zeros_like(ccd_data), unit=ccd_data.unit)
-    ccd = subtract_bias(ccd_data, master=master_frame)
+    _ = subtract_bias(ccd_data, master=master_frame)
     np.testing.assert_array_equal(original.data, ccd_data.data)
     assert original.unit == ccd_data.unit
 
 
 def test_trim_image_does_not_change_input():
     ccd_data = ccd_data_func()
     original = ccd_data.copy()
-    ccd = trim_image(ccd_data, fits_section=None)
+    _ = trim_image(ccd_data, fits_section=None)
     np.testing.assert_array_equal(original.data, ccd_data.data)
     assert original.unit == ccd_data.unit
 
@@ -879,7 +882,6 @@ def test_wcs_project_onto_same_wcs_remove_headers():
     # Remove an example WCS keyword from the header
     target_wcs = wcs_for_testing(ccd_data.shape)
     ccd_data.wcs = wcs_for_testing(ccd_data.shape)
-    print(ccd_data.header)
     ccd_data.header = ccd_data.wcs.to_header()
 
     new_ccd = wcs_project(ccd_data, target_wcs)
@@ -988,8 +990,8 @@ def test_wcs_project_onto_scale_wcs():
 def test_ccd_process_does_not_change_input():
     ccd_data = ccd_data_func()
     original = ccd_data.copy()
-    ccd = ccd_process(ccd_data, gain=5 * u.electron / u.adu,
-                      readnoise=10 * u.electron)
+    _ = ccd_process(ccd_data, gain=5 * u.electron / u.adu,
+                    readnoise=10 * u.electron)
     np.testing.assert_array_equal(original.data, ccd_data.data)
     assert original.unit == ccd_data.unit
 

ccdproc/tests/test_image_collection.py

@@ -12,9 +12,7 @@
 from astropy.table import Table
 import numpy as np
 
-from astropy.tests.helper import catch_warnings
 from astropy.utils.data import get_pkg_data_filename
-from astropy.utils import minversion
 from astropy.utils.exceptions import AstropyUserWarning
 from astropy.io.fits.verify import VerifyWarning
 
@@ -25,8 +23,6 @@
 _filters = []
 _original_dir = ''
 
-_ASTROPY_LT_1_3 = not minversion("astropy", "1.3")
-
 
 def test_fits_summary(triage_setup):
     keywords = ['imagetyp', 'filter']
@@ -361,7 +357,7 @@ def test_generator_ccds_without_unit(self, triage_setup):
                 location=triage_setup.test_dir, keywords=['imagetyp'])
 
         with pytest.raises(ValueError):
-            ccd = next(collection.ccds())
+            _ = next(collection.ccds())
 
     def test_generator_ccds(self, triage_setup):
         collection = ImageFileCollection(
@@ -433,7 +429,7 @@ def test_dir_with_no_fits_files(self, tmpdir):
         empty_dir = tmpdir.mkdtemp()
         some_file = empty_dir.join('some_file.txt')
         some_file.dump('words')
-        with catch_warnings() as w:
+        with pytest.warns(Warning) as w:
             collection = ImageFileCollection(location=empty_dir.strpath,
                                              keywords=['imagetyp'])
         assert len(w) == 1
@@ -571,10 +567,6 @@ def test_setting_write_location_to_bad_dest_raises_error(self, tmpdir,
             for hdr in ic.headers(save_location=bad_directory.strpath):
                 pass
 
-    def test_no_fits_files_in_collection(self):
-        with catch_warnings(AstropyUserWarning) as warning_lines:
-            assert "no FITS files in the collection."
-
     def test_initialization_with_no_keywords(self, triage_setup):
         # This test is primarily historical -- the old default for
         # keywords was an empty list (it is now the wildcard '*').
@@ -707,10 +699,6 @@ def test_sorting(self, triage_setup):
         for i in range(len(collection.summary)):
             assert(collection.summary['file'][i] == collection.files[i])
 
-    @pytest.mark.skipif(
-        _ASTROPY_LT_1_3,
-        reason="It seems to fail with a TypeError there but because of "
-               "different reasons (something to do with NumPy).")
     def test_sorting_without_key_fails(self, triage_setup):
         ic = ImageFileCollection(location=triage_setup.test_dir)
         with pytest.raises(ValueError):
@@ -726,7 +714,7 @@ def test_duplicate_keywords(self, triage_setup):
 
         hdu.writeto(os.path.join(triage_setup.test_dir, 'duplicated.fits'))
 
-        with catch_warnings(UserWarning) as w:
+        with pytest.warns(UserWarning) as w:
             ic = ImageFileCollection(triage_setup.test_dir, keywords='*')
         assert len(w) == 1
         assert 'stupid' in str(w[0].message)
@@ -977,9 +965,8 @@ def test_less_strict_verify_option(self, triage_setup):
             TESTVERI= '2017/02/13-16:51:38 / Test VerifyWarning
         """
 
-        with catch_warnings(VerifyWarning) as warning_lines:
+        with pytest.warns(VerifyWarning):
             testh = fits.Header.fromstring(bad_header)
-            print(testh)
 
             testfits = fits.PrimaryHDU(data=np.ones((10, 10)), header=testh)
 
@@ -990,7 +977,6 @@ def test_less_strict_verify_option(self, triage_setup):
                              overwrite=True)
 
             ic = ImageFileCollection(location=str(path))
-            print(ic.summary.colnames)
 
         assert bad_fits_name in ic.files
 
@@ -1002,8 +988,8 @@ def test_less_strict_verify_option(self, triage_setup):
         assert '17/02/13' in ic.summary.colnames
 
         # Try making the summary as in the original bug report
-        ic = ImageFileCollection(location=str(path),
-                                 glob_include='*warnA*')
+        with pytest.warns(AstropyUserWarning, match='The following header keyword is invalid'):
+            ic = ImageFileCollection(location=str(path), glob_include='*warnA*')
 
     def test_type_of_empty_collection(self, triage_setup):
         # Test for implementation of the suggestion in
@@ -1015,9 +1001,7 @@ def test_type_of_empty_collection(self, triage_setup):
         # with no keys and no files returns None.
 
         # Make a dummy keyword that we then delete.
-        with catch_warnings(AstropyUserWarning) as warning_lines:
-            ic = ImageFileCollection(triage_setup.test_dir, keywords=['fafa'])
-        assert "no FITS files in the collection."
+        ic = ImageFileCollection(triage_setup.test_dir, keywords=['fafa'])
         ic.keywords = []
         assert set(ic.summary.colnames) == set(['file'])
 
@@ -1027,7 +1011,8 @@ def test_type_of_empty_collection(self, triage_setup):
             p.unlink()
 
         # Now the summary should be none
-        ic = ImageFileCollection(triage_setup.test_dir)
+        with pytest.warns(AstropyUserWarning, match='no FITS files in the collection'):
+            ic = ImageFileCollection(triage_setup.test_dir)
         assert ic.summary is None
         assert ic.keywords == []
 
@@ -1114,7 +1099,7 @@ def test_filter_on_regex_escape_characters(self, triage_setup):
         # keyword containing these
 
         special_kwds = ['CO+', 'GG420 (1)', 'V|R|I', 'O[III]', 'NaD^2']
-        for i,kw in enumerate(special_kwds,1):
+        for i, kw in enumerate(special_kwds, 1):
             hdu = fits.PrimaryHDU()
             hdu.data = np.zeros((5, 5))
             hdu.header['REGEX_FL'] = kw