TST: --open-files did not catch ResourceWarning

@drdavella

Is this is not really an issue, feel free to close, as I am not familiar with the internals of open files check. Example log: https://travis-ci.org/astropy/astropy/jobs/442639768

It seems weird to me that --open-files option still reported passing despite the presence of following warning:

sys:1: ResourceWarning: unclosed file <_io.BufferedWriter name=13>

cc @drdavella

Maybe this issue should be at https://github.com/astropy/pytest-openfiles?

After some digging... could this be #6942 ? (Or maybe not since I don't see this warning in the log linked to that other issue.)

Moved to astropy/pytest-openfiles#14

I have some reason to believe this warning is being caused by this particular test, although I'm not sure why, and it doesn't really help much yet. (Is anyone surprised that it comes from io.fits 😝?)

astropy/astropy/io/fits/tests/test_fitsheader.py

Lines 16 to 21 in 66c7967

    
           def test_file_exists(self, capsys): 
        
               fitsheader.main([self.data('arange.fits')]) 
        
               out, err = capsys.readouterr() 
        
               assert out.splitlines()[1].startswith( 
        
                   'SIMPLE  =                    T / conforms to FITS standard') 
        
               assert err == ''

It's also entirely possible that this is just a red herring.

So the ResourceWarning is definitely being caused by an oversight in astropy/io/fits/scripts/fitsheader.py. I can make it go away by adding a close() in the right place.

The real question still is why isn't getting picked up by pytest-openfiles?

I think this is not a problem with pytest-openfiles, but there's something really strange going on, and I'm running out of ideas. I think this distills the problem nicely:

#!/usr/bin/env python -W error::ResourceWarning

import psutil
from astropy.io.fits.scripts import fitsheader

p = psutil.Process()

print('before', p.open_files())
fitsheader.main(['astropy/io/fits/tests/data/arange.fits'])
print('after', p.open_files())

And here's the output:

before []
# HDU 0 in astropy/io/fits/tests/data/arange.fits:
SIMPLE  =                    T / conforms to FITS standard
BITPIX  =                   32 / array data type
NAXIS   =                    3 / number of array dimensions
NAXIS1  =                   11
NAXIS2  =                   10
NAXIS3  =                    7
EXTEND  =                    T
Exception ignored in: <_io.FileIO name='astropy/io/fits/tests/data/arange.fits' mode='rb' closefd=True>
ResourceWarning: unclosed file <_io.FileIO name='astropy/io/fits/tests/data/arange.fits' mode='rb' closefd=True>
after []

The key takeaway is that even though we get a resource warning for the file being open at the end of the process, it does not show up in the list of open files for this process using psutil (which, incidentally, is the what pytest-openfiles uses to detect open files).

I guess it's possible that the file handle is owned by another process (???) and so looking at the open files for just this process is not sufficient. However, assuming this is actually the problem (and I really don't know), I'm not sure we can handle this in a systematic way in pytest-openfiles (due to permissions issues, etc.).

It's fairly easy to fix this particular issue in fitsheader. But I'm not sure how we could have detected it automatically.

EDIT: Actually, after all of that, I guess the obvious thing would be to make pytest-openfiles look for ResourceWarnings and report them as errors.

Thanks for the detail investigation! I have re-opened this issue.

@eteq

While looking into #7928, I might have found one of the cause:

astropy/coordinates/tests/test_solar_system.py::TestPositionsGeocentric::()::test_de432s_planet[mercury]
  .../astropy/coordinates/solar_system.py:364: ResourceWarning: unclosed file <_io.BufferedReader name='...cache/astropy/download/py3/d66c2153188958472fec67016b4b4e7a'>
    get_velocity=False)

astropy/coordinates/tests/test_solar_system.py::TestPositionsGeocentric::()::test_de432s_planet[jupiter]
  .../astropy/coordinates/solar_system.py:364: ResourceWarning: unclosed file <_io.BufferedReader name='...cache/astropy/download/py3/d66c2153188958472fec67016b4b4e7a'>
    get_velocity=False)

astropy/coordinates/tests/test_solar_system.py::TestPositionsGeocentric::()::test_de432s_planet[sun]
  .../astropy/coordinates/solar_system.py:364: ResourceWarning: unclosed file <_io.BufferedReader name='...cache/astropy/download/py3/d66c2153188958472fec67016b4b4e7a'>
    get_velocity=False)

astropy/coordinates/tests/test_solar_system.py::TestPositionsGeocentric::()::test_de432s_moon
  .../astropy/coordinates/solar_system.py:364: ResourceWarning: unclosed file <_io.BufferedReader name='...cache/astropy/download/py3/d66c2153188958472fec67016b4b4e7a'>
    get_velocity=False)

astropy/coordinates/tests/test_solar_system.py::TestPositionKittPeak::()::test_de432s_planet[mercury]
  .../astropy/coordinates/solar_system.py:364: ResourceWarning: unclosed file <_io.BufferedReader name='...cache/astropy/download/py3/d66c2153188958472fec67016b4b4e7a'>
    get_velocity=False)

astropy/coordinates/tests/test_solar_system.py::TestPositionKittPeak::()::test_de432s_planet[jupiter]
  .../astropy/coordinates/solar_system.py:364: ResourceWarning: unclosed file <_io.BufferedReader name='...cache/astropy/download/py3/d66c2153188958472fec67016b4b4e7a'>
    get_velocity=False)

astropy/coordinates/tests/test_solar_system.py::TestPositionKittPeak::()::test_de432s_moon
  .../astropy/coordinates/solar_system.py:364: ResourceWarning: unclosed file <_io.BufferedReader name='...cache/astropy/download/py3/d66c2153188958472fec67016b4b4e7a'>
    get_velocity=False)

astropy/coordinates/tests/test_solar_system.py::TestPositionKittPeak::()::test_custom_kernel_spec_body[mercury]
  .../astropy/coordinates/solar_system.py:364: ResourceWarning: unclosed file <_io.BufferedReader name='...cache/astropy/download/py3/d66c2153188958472fec67016b4b4e7a'>
    get_velocity=False)

astropy/coordinates/tests/test_solar_system.py::TestPositionKittPeak::()::test_custom_kernel_spec_body[jupiter]
  .../astropy/coordinates/solar_system.py:364: ResourceWarning: unclosed file <_io.BufferedReader name='...cache/astropy/download/py3/d66c2153188958472fec67016b4b4e7a'>
    get_velocity=False)

astropy/coordinates/tests/test_solar_system.py::test_get_sun_consistency[time0]
  .../astropy/coordinates/solar_system.py:364: ResourceWarning: unclosed file <_io.BufferedReader name='...cache/astropy/download/py3/d66c2153188958472fec67016b4b4e7a'>
    get_velocity=False)

astropy/coordinates/tests/test_solar_system.py::test_get_sun_consistency[time1]
  .../astropy/coordinates/solar_system.py:364: ResourceWarning: unclosed file <_io.BufferedReader name='...cache/astropy/download/py3/d66c2153188958472fec67016b4b4e7a'>
    get_velocity=False)

astropy/coordinates/tests/test_solar_system.py::test_get_sun_consistency[time2]
  .../astropy/coordinates/solar_system.py:364: ResourceWarning: unclosed file <_io.BufferedReader name='...cache/astropy/download/py3/d66c2153188958472fec67016b4b4e7a'>
    get_velocity=False)

astropy/coordinates/tests/test_solar_system.py::test_barycentric_velocity_consistency[mercury-pos_tol0-vel_tol0]
  .../astropy/coordinates/solar_system.py:330: ResourceWarning: unclosed file <_io.BufferedReader name='...cache/astropy/download/py3/d66c2153188958472fec67016b4b4e7a'>
    return _get_body_barycentric_posvel(body, time, ephemeris)

astropy/coordinates/tests/test_solar_system.py::test_barycentric_velocity_consistency[jupiter-pos_tol1-vel_tol1]
  .../astropy/coordinates/solar_system.py:330: ResourceWarning: unclosed file <_io.BufferedReader name='...cache/astropy/download/py3/d66c2153188958472fec67016b4b4e7a'>
    return _get_body_barycentric_posvel(body, time, ephemeris)

astropy/coordinates/tests/test_solar_system.py::test_barycentric_velocity_consistency[earth-pos_tol2-vel_tol2]
  .../astropy/coordinates/solar_system.py:330: ResourceWarning: unclosed file <_io.BufferedReader name='...cache/astropy/download/py3/d66c2153188958472fec67016b4b4e7a'>
    return _get_body_barycentric_posvel(body, time, ephemeris)

@eteq or @adrn , any suggestion on how to fix?

Wait, maybe this particular one reported originally is from io.fits...

After looking at the FITS tests, which produced hundreds of such warnings, I am not sure if we want to catch 'em all.

IIRC, I think the problem is that many of them come from other libraries. If that's the case, we would want to somehow filter to get only the ones that come from astropy, but I'm not sure there's a straightforward way to do that in Python.

That's one of the reasons I haven't really made any progress on implementing this functionality in pytest-openfiles, although it would still be really useful.

@vstinner

Actually there is a way to show a traceback for ResourceWarning, with tracemalloc: python3 -Wd -X tracemalloc=5. From https://pythondev.readthedocs.io/debug_tools.html#resourcewarning, and thanks to @vstinner !

Re #7913 (comment) above, when you get a ResourceWarning for an open file from python, it's because the garbage collector detected the unclosed file, closed it and printed that warning, so it is not surprising that p.open_files() is empty before and after.

addressed by #8439

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TST: --open-files did not catch ResourceWarning #7913

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	def test_file_exists(self, capsys):
	fitsheader.main([self.data('arange.fits')])
	out, err = capsys.readouterr()
	assert out.splitlines()[1].startswith(
	'SIMPLE = T / conforms to FITS standard')
	assert err == ''

TST: --open-files did not catch ResourceWarning #7913

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astrofrog commented on Oct 18, 2018

pllim commented on Oct 18, 2018

pllim commented on Oct 18, 2018

drdavella commented on Oct 19, 2018

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