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TST: Get rid of time test warnings#8754

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bsipocz merged 4 commits intoastropy:masterfrom
pllim:tests-warn-time
Jun 20, 2019
Merged

TST: Get rid of time test warnings#8754
bsipocz merged 4 commits intoastropy:masterfrom
pllim:tests-warn-time

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@pllim
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@pllim pllim commented May 24, 2019

As part of work for #7928 . The warnings were captured by removing the line in setup.cfg to suppress pytest warnings and then add this in the same section:

[pytest]
filterwarnings =
    error

And then run tests with python setup.py -P time. Most of the changes are to handle ErfaWarning and tests accessing IERS tables (which require download) but not marked as remote_data.

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codecov bot commented May 24, 2019

Codecov Report

Merging #8754 into master will decrease coverage by 0.06%.
The diff coverage is n/a.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #8754      +/-   ##
==========================================
- Coverage   86.97%   86.91%   -0.07%     
==========================================
  Files         399      399              
  Lines       59384    59384              
  Branches     1100     1100              
==========================================
- Hits        51652    51612      -40     
- Misses       7091     7131      +40     
  Partials      641      641
Impacted Files Coverage Δ
...builtin_frames/intermediate_rotation_transforms.py 66.03% <0%> (-16.99%) ⬇️
astropy/utils/state.py 82.6% <0%> (-8.7%) ⬇️
astropy/time/core.py 92.38% <0%> (-2.58%) ⬇️
astropy/coordinates/earth.py 74.33% <0%> (-1.51%) ⬇️
astropy/coordinates/solar_system.py 69.42% <0%> (-0.64%) ⬇️
astropy/utils/data.py 80.93% <0%> (-0.45%) ⬇️

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Nice work, though I think we can reduce the impact, both by changing time scale to TAI where needed (see inline), and more specifically by ensuring that the IERS download doesn't happen unless it is really needed (for the tests that do not explicitly require it, at least, we should turn it off!). I think we may need @taldcroft for the latter...

t.write(fn)
t2 = Table.read(fn, astropy_native=True)
with pytest.warns(VerifyWarning):
t2 = Table.read(fn, astropy_native=True)
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@taldcroft - is the VerifyWarning expected?

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Looks wrong to me, see #8773

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@pllim pllim May 29, 2019

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While having the warning is a bug, I think we should still catch it for now until the bug is fixed. So that when it is fixed, this will cause the test to fail, and then we can remove the pytest.warns line?

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These changes look fine to me, with agreement on all of the comments from @mhvk (in particular using TAI to sidestep warnings when possible).

t.write(fn)
t2 = Table.read(fn, astropy_native=True)
with pytest.warns(VerifyWarning):
t2 = Table.read(fn, astropy_native=True)
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Looks wrong to me, see #8773

@pllim pllim force-pushed the tests-warn-time branch from 8653b8b to 6cabacf Compare May 29, 2019 16:29
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So, you would see that in some modules, I set the auto_download at function level, some at class level, and some at module level. My reasoning is that I should impact the tests as little as possible, hence the slightly different treatments.

Time.FORMATS.update(func.FORMATS_ORIG)


class TestBasic():
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I think this is leftover from incomplete PY2 removal? Sorry, I can't help myself and had to clean it up. 😂

t.write(fn)
t2 = Table.read(fn, astropy_native=True)

# Warning is a bug; https://github.com/astropy/astropy/issues/8773
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Added a comment here about #8773, if that helps.



class TestTimeUT1():
@pytest.mark.remote_data
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Here, I did the opposite but marking the whole test class as remote_data. This is becase its test_utc_to_utc1 was already marked as remote_data, so I am guessing the other two not being marked as remote_data was an oversight? Or is there a reason why the other two methods in this test class need local IERS table, but not the first one?

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Here, all the tests should work with the built-in table, so I'd go for your do-not-download setting.

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Actually, the test that is already marked remote_data fails when using local file because extrapolation is not allowed. I'll think of something...

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OK done.

'2008-12-31T17:27:17.193' '2010-01-01T00:00:00.000']>

>>> t.sidereal_time('apparent', 'greenwich') # doctest: +FLOAT_CMP
>>> t.sidereal_time('apparent', 'greenwich') # doctest: +FLOAT_CMP +REMOTE_DATA
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I thought about setting iers.conf.auto_download = False in the doc here too, but decided against it. I think it is cleaner this way unless you strongly oppose this approach.

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Agreed; docs should be kept clean.

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@pllim - this looks great! Only one instance where I think we can also set no-download instead of remote_data.



class TestTimeUT1():
@pytest.mark.remote_data
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Here, all the tests should work with the built-in table, so I'd go for your do-not-download setting.

'2008-12-31T17:27:17.193' '2010-01-01T00:00:00.000']>

>>> t.sidereal_time('apparent', 'greenwich') # doctest: +FLOAT_CMP
>>> t.sidereal_time('apparent', 'greenwich') # doctest: +FLOAT_CMP +REMOTE_DATA
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Agreed; docs should be kept clean.

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pllim commented May 29, 2019

@mhvk, I think I have addressed all your comments. @taldcroft , are you okay with catching that bug warning for now?

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bsipocz commented Jun 19, 2019

@pllim - could you rebase to make sure it's still all green? Let's get this in to have fewer warnings all around.

@pllim pllim force-pushed the tests-warn-time branch from 87819fa to 23783b9 Compare June 20, 2019 00:52
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pllim commented Jun 20, 2019

@bsipocz , it is rebased.

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bsipocz commented Jun 20, 2019

OK. I suggest to merge when all CI is happy. Then #8784 can remove the catching of the warning.

@bsipocz bsipocz added the zzz 💤 merge-when-ci-passes Do not use: We have auto-merge option now. label Jun 20, 2019
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Approving for now, there is a clear way for the only one remaining issue of how to be resolved.

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bsipocz commented Jun 20, 2019

@pllim - running this locally (with the changes to setup.cfg), I still see 5 failures. Can you comment on them?

======================================================= FAILURES =======================================================
______________________________________________ test_serialize_fits_masked ______________________________________________

tmpdir = local('/private/var/folders/dc/hsm7tqpx2d57n7vb3k1l81xw0000gq/T/pytest-of-bsipocz/pytest-195/test_serialize_fits_masked0')

    def test_serialize_fits_masked(tmpdir):
        tm = Time([1, 2, 3], format='cxcsec')
        tm[1] = np.ma.masked
    
        fn = str(tmpdir.join('tempfile.fits'))
        t = Table([tm])
>       t.write(fn)

astropy/time/tests/test_mask.py:165: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
astropy/table/connect.py:114: in __call__
    registry.write(instance, *args, **kwargs)
astropy/io/registry.py:563: in write
    'write', data.__class__, path, fileobj, args, kwargs)
astropy/io/registry.py:595: in _get_valid_format
    valid_formats = identify_format(mode, cls, path, fileobj, args, kwargs)
astropy/io/registry.py:417: in identify_format
    origin, path, fileobj, *args, **kwargs):
astropy/io/misc/asdf/connect.py:106: in asdf_identify
    import asdf
/usr/local/lib/python3.7/site-packages/asdf/__init__.py:27: in <module>
    import jsonschema as _
/usr/local/lib/python3.7/site-packages/jsonschema/__init__.py:12: in <module>
    from jsonschema.exceptions import (
/usr/local/lib/python3.7/site-packages/jsonschema/exceptions.py:6: in <module>
    from jsonschema import _utils
/usr/local/lib/python3.7/site-packages/jsonschema/_utils.py:6: in <module>
    from jsonschema.compat import str_types, MutableMapping, urlsplit
/usr/local/lib/python3.7/site-packages/jsonschema/compat.py:6: in <module>
    from collections import MutableMapping, Sequence  # noqa
<frozen importlib._bootstrap>:1032: in _handle_fromlist
    ???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

name = 'Sequence'

    def __getattr__(name):
        # For backwards compatibility, continue to make the collections ABCs
        # through Python 3.6 available through the collections module.
        # Note, no new collections ABCs were added in Python 3.7
        if name in _collections_abc.__all__:
            obj = getattr(_collections_abc, name)
            import warnings
            warnings.warn("Using or importing the ABCs from 'collections' instead "
                          "of from 'collections.abc' is deprecated, "
                          "and in 3.8 it will stop working",
>                         DeprecationWarning, stacklevel=2)
E           DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working

/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/collections/__init__.py:52: DeprecationWarning
______________________________________________ test_serialize_hdf5_masked ______________________________________________

tmpdir = local('/private/var/folders/dc/hsm7tqpx2d57n7vb3k1l81xw0000gq/T/pytest-of-bsipocz/pytest-195/test_serialize_hdf5_masked0')

    @pytest.mark.skipif(not HAS_YAML or not HAS_H5PY,
                        reason='Need both h5py and yaml')
    def test_serialize_hdf5_masked(tmpdir):
        tm = Time([1, 2, 3], format='cxcsec')
        tm[1] = np.ma.masked
    
        fn = str(tmpdir.join('tempfile.hdf5'))
        t = Table([tm])
>       t.write(fn, path='root', serialize_meta=True)

astropy/time/tests/test_mask.py:187: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
astropy/table/connect.py:114: in __call__
    registry.write(instance, *args, **kwargs)
astropy/io/registry.py:563: in write
    'write', data.__class__, path, fileobj, args, kwargs)
astropy/io/registry.py:595: in _get_valid_format
    valid_formats = identify_format(mode, cls, path, fileobj, args, kwargs)
astropy/io/registry.py:417: in identify_format
    origin, path, fileobj, *args, **kwargs):
astropy/io/misc/asdf/connect.py:106: in asdf_identify
    import asdf
/usr/local/lib/python3.7/site-packages/asdf/__init__.py:27: in <module>
    import jsonschema as _
/usr/local/lib/python3.7/site-packages/jsonschema/__init__.py:12: in <module>
    from jsonschema.exceptions import (
/usr/local/lib/python3.7/site-packages/jsonschema/exceptions.py:6: in <module>
    from jsonschema import _utils
/usr/local/lib/python3.7/site-packages/jsonschema/_utils.py:6: in <module>
    from jsonschema.compat import str_types, MutableMapping, urlsplit
/usr/local/lib/python3.7/site-packages/jsonschema/compat.py:6: in <module>
    from collections import MutableMapping, Sequence  # noqa
<frozen importlib._bootstrap>:1032: in _handle_fromlist
    ???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

name = 'Sequence'

    def __getattr__(name):
        # For backwards compatibility, continue to make the collections ABCs
        # through Python 3.6 available through the collections module.
        # Note, no new collections ABCs were added in Python 3.7
        if name in _collections_abc.__all__:
            obj = getattr(_collections_abc, name)
            import warnings
            warnings.warn("Using or importing the ABCs from 'collections' instead "
                          "of from 'collections.abc' is deprecated, "
                          "and in 3.8 it will stop working",
>                         DeprecationWarning, stacklevel=2)
E           DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working

/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/collections/__init__.py:52: DeprecationWarning
______________________________________________ test_serialize_ecsv_masked ______________________________________________

tmpdir = local('/private/var/folders/dc/hsm7tqpx2d57n7vb3k1l81xw0000gq/T/pytest-of-bsipocz/pytest-195/test_serialize_ecsv_masked0')

    @pytest.mark.skipif('not HAS_YAML')
    def test_serialize_ecsv_masked(tmpdir):
        tm = Time([1, 2, 3], format='cxcsec')
        tm[1] = np.ma.masked
    
        # Serializing in the default way for ECSV fails to round-trip
        # because it writes out a "nan" instead of "".  But for jd1/jd2
        # this works OK.
        tm.info.serialize_method['ecsv'] = 'jd1_jd2'
    
        fn = str(tmpdir.join('tempfile.ecsv'))
        t = Table([tm])
>       t.write(fn)

astropy/time/tests/test_mask.py:207: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
astropy/table/connect.py:114: in __call__
    registry.write(instance, *args, **kwargs)
astropy/io/registry.py:563: in write
    'write', data.__class__, path, fileobj, args, kwargs)
astropy/io/registry.py:595: in _get_valid_format
    valid_formats = identify_format(mode, cls, path, fileobj, args, kwargs)
astropy/io/registry.py:417: in identify_format
    origin, path, fileobj, *args, **kwargs):
astropy/io/misc/asdf/connect.py:106: in asdf_identify
    import asdf
/usr/local/lib/python3.7/site-packages/asdf/__init__.py:27: in <module>
    import jsonschema as _
/usr/local/lib/python3.7/site-packages/jsonschema/__init__.py:12: in <module>
    from jsonschema.exceptions import (
/usr/local/lib/python3.7/site-packages/jsonschema/exceptions.py:6: in <module>
    from jsonschema import _utils
/usr/local/lib/python3.7/site-packages/jsonschema/_utils.py:6: in <module>
    from jsonschema.compat import str_types, MutableMapping, urlsplit
/usr/local/lib/python3.7/site-packages/jsonschema/compat.py:6: in <module>
    from collections import MutableMapping, Sequence  # noqa
<frozen importlib._bootstrap>:1032: in _handle_fromlist
    ???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

name = 'Sequence'

    def __getattr__(name):
        # For backwards compatibility, continue to make the collections ABCs
        # through Python 3.6 available through the collections module.
        # Note, no new collections ABCs were added in Python 3.7
        if name in _collections_abc.__all__:
            obj = getattr(_collections_abc, name)
            import warnings
            warnings.warn("Using or importing the ABCs from 'collections' instead "
                          "of from 'collections.abc' is deprecated, "
                          "and in 3.8 it will stop working",
>                         DeprecationWarning, stacklevel=2)
E           DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working

/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/collections/__init__.py:52: DeprecationWarning
____________________________________________ [doctest] docs/time/index.rst _____________________________________________
/usr/local/lib/python3.7/site-packages/pluggy/hooks.py:289: in __call__
    return self._hookexec(self, self.get_hookimpls(), kwargs)
/usr/local/lib/python3.7/site-packages/pluggy/manager.py:87: in _hookexec
    return self._inner_hookexec(hook, methods, kwargs)
/usr/local/lib/python3.7/site-packages/pluggy/manager.py:81: in <lambda>
    firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
/usr/local/lib/python3.7/site-packages/_pytest/runner.py:123: in pytest_runtest_call
    item.runtest()
/usr/local/lib/python3.7/site-packages/pytest_doctestplus/plugin.py:164: in runtest
    raise_on_error=True, verbose=False, encoding='utf-8')
/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/doctest.py:2070: in testfile
    test = parser.get_doctest(text, globs, name, filename, 0)
/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/doctest.py:668: in get_doctest
    return DocTest(self.get_examples(string, name), globs,
/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/doctest.py:682: in get_examples
    return [x for x in self.parse(string, name)
/usr/local/lib/python3.7/site-packages/pytest_doctestplus/plugin.py:213: in parse
    .format(file_format, comment_characters['rst']))
E   UserWarning: file format '' is not recognized, assuming '\.\.' as the comment character.
_______________________________________ [doctest] docs/time/performance.inc.rst ________________________________________
/usr/local/lib/python3.7/site-packages/pluggy/hooks.py:289: in __call__
    return self._hookexec(self, self.get_hookimpls(), kwargs)
/usr/local/lib/python3.7/site-packages/pluggy/manager.py:87: in _hookexec
    return self._inner_hookexec(hook, methods, kwargs)
/usr/local/lib/python3.7/site-packages/pluggy/manager.py:81: in <lambda>
    firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
/usr/local/lib/python3.7/site-packages/_pytest/runner.py:123: in pytest_runtest_call
    item.runtest()
/usr/local/lib/python3.7/site-packages/pytest_doctestplus/plugin.py:164: in runtest
    raise_on_error=True, verbose=False, encoding='utf-8')
/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/doctest.py:2070: in testfile
    test = parser.get_doctest(text, globs, name, filename, 0)
/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/doctest.py:668: in get_doctest
    return DocTest(self.get_examples(string, name), globs,
/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/doctest.py:682: in get_examples
    return [x for x in self.parse(string, name)
/usr/local/lib/python3.7/site-packages/pytest_doctestplus/plugin.py:213: in parse
    .format(file_format, comment_characters['rst']))
E   UserWarning: file format '' is not recognized, assuming '\.\.' as the comment character.
============================== 5 failed, 353 passed, 5 skipped, 1 xfailed in 9.25 seconds ==============================

@pllim
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pllim commented Jun 20, 2019

@bsipocz , those look so familiar! Where have I seen them before! Can you please post your pytest header?

@bsipocz
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bsipocz commented Jun 20, 2019

Sure:

================================================= test session starts ==================================================
platform darwin -- Python 3.7.3, pytest-4.6.3, py-1.8.0, pluggy-0.12.0

Running tests with Astropy version 4.0.dev24982.
Running tests in astropy/time docs/time.

Date: 2019-06-19T18:24:52

Platform: Darwin-17.7.0-x86_64-i386-64bit

Executable: /usr/local/opt/python/bin/python3.7

Full Python Version: 
3.7.3 (default, Mar 27 2019, 09:23:39) 
[Clang 10.0.0 (clang-1000.11.45.5)]

encodings: sys: utf-8, locale: UTF-8, filesystem: utf-8
byteorder: little
float info: dig: 15, mant_dig: 15

Numpy: 1.16.4
Scipy: 1.3.0
Matplotlib: 3.1.0.post1209+g6ba265188
h5py: 2.8.0
Pandas: 0.24.2
Cython: 0.29.10
Scikit-image: 0.15.0
astropy_helpers: 3.2.1
Using Astropy options: remote_data: none.

rootdir: /private/var/folders/dc/hsm7tqpx2d57n7vb3k1l81xw0000gq/T/astropy-test-h1r6cd0p/lib/python3.7/site-packages, inifile: setup.cfg
plugins: openfiles-0.3.2, forked-1.0.2, arraydiff-0.3, cov-2.6.0, xonsh-0.8.3, dependency-0.4.0, doctestplus-0.3.0, remotedata-0.3.1, requests-mock-1.6.0
collected 364 items                                                                                                    

astropy/time/core.py .....                                                                                       [  1%]
astropy/time/formats.py ..                                                                                       [  1%]
astropy/time/tests/test_basic.py .............................................s................................. [ 23%]
.........                                                                                                        [ 26%]
astropy/time/tests/test_comparisons.py ...                                                                       [ 26%]
astropy/time/tests/test_corrs.py ...s                                                                            [ 28%]
astropy/time/tests/test_delta.py ............................................................................... [ 49%]
..............                                                                                                   [ 53%]
astropy/time/tests/test_guess.py ....                                                                            [ 54%]
astropy/time/tests/test_mask.py ......FFF                                                                        [ 57%]
astropy/time/tests/test_methods.py ............................................................................. [ 78%]
....................                                                                                             [ 83%]
astropy/time/tests/test_pickle.py .                                                                              [ 84%]
astropy/time/tests/test_precision.py ........x..                                                                 [ 87%]
astropy/time/tests/test_quantity_interaction.py .....................                                            [ 92%]
astropy/time/tests/test_sidereal.py ...................                                                          [ 98%]
astropy/time/tests/test_ut1.py s..ss                                                                             [ 99%]
docs/time/index.rst F                                                                                            [ 99%]
docs/time/performance.inc.rst F                                                                                  [100%]

======================================================= FAILURES =======================================================

@pllim
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pllim commented Jun 20, 2019

What are your asdf and jsonschema version?

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pllim commented Jun 20, 2019

For the "file format not recognized" one, there is an issue at scientific-python/pytest-doctestplus#59 . For the asdf one, I am guessing that either your asdf version is too old, or your asdf + jsonschema combo is incompatible (see asdf-format/asdf#530) pretty sure it is upstream at jsonschema and has been fixed in python-jsonschema/jsonschema#465.

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bsipocz commented Jun 20, 2019

asdf 2.3.3
jsonschema 2.6.0

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pllim commented Jun 20, 2019

@bsipocz , you might need to upgrade to jsonschema>=3 to get rid of the deprecation warning, even though jsonschema>=3 is incompatible with asdf, which is a different problem altogether.

Overall, all the warnings you reported can be explained and fixing them is out of scope for this PR.

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bsipocz commented Jun 20, 2019

you might need to upgrade to jsonschema>=3 to get rid of the deprecation warning, even though jsonschema>3 is incompatible with asdf, which is a different problem altogether.

tried to, it has no effect, still 5 failures.

Overall, all the warnings you reported can be explained and fixing them is out of scope for this PR.

that is perfectly reasonable. This PR clears up a significant amount of stuff, and we still have a few to go until we can turn off ignoring the warnings.

@bsipocz bsipocz merged commit a22c724 into astropy:master Jun 20, 2019
@pllim pllim deleted the tests-warn-time branch June 20, 2019 02:07
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4 participants