drive tests with run-tests. #18

rainwoodman · 2018-01-18T18:41:58Z

This is a demonstration.

Unfortunately I couldn't test this because pip install healpy failed
on my box with anaconda-5.0 cross compilation tools chain -- It couldn't link with cfitsio.

We need a good binary package of healpy.

#17

Unfortunately I couldn't test this because pip install healpy failed on my box with anaconda-5.0 cross compilation tools chain. It couldn't find cfitsio. We need a good binary package of healpy on conda.

rainwoodman · 2018-01-18T18:45:33Z

The data files needs to be moved too for the tests to run due to the rename into pysm.test.

I am not sure about the best way of doing this.

(base) [yfeng1@waterfall PySM_public]$ python run-mpitests.py 
Purging /home/yfeng1/source/PySM_public/build/testenv ...
Purging /home/yfeng1/source/PySM_public/build/test ...
Building, see build.log...
Build OK
============================= test session starts ==============================
platform linux -- Python 3.6.3, pytest-3.3.0, py-1.5.2, pluggy-0.6.0
rootdir: /home/yfeng1/source/PySM_public, inifile:
plugins: hypothesis-3.38.5
collected 24 items

../testenv/lib/python3.6/site-packages/pysm/test/test_components.py .    [  4%]
../testenv/lib/python3.6/site-packages/pysm/test/test_common.py .        [  8%]
../testenv/lib/python3.6/site-packages/pysm/test/test_components.py .    [ 12%]
../testenv/lib/python3.6/site-packages/pysm/test/test_common.py .        [ 16%]
../testenv/lib/python3.6/site-packages/pysm/test/test_components.py F

=================================== FAILURES ===================================
__________________________ test_AME.test_AME_model_1 ___________________________

self = <pysm.test.test_components.test_AME testMethod=test_AME_model_1>

    def setUp(self):
        data_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', 'pysm', 'template'))
        test_data_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), 'test_data', 'benchmark'))
    
        a1_config = models("a1", 64)
        AME1 = components.AME(a1_config[0])
        AME2 = components.AME(a1_config[1])
    
        signal = lambda nu: AME1.signal()(nu) + AME2.signal()(nu)
    
>       ame_1_30GHz = read_map(os.path.join(test_data_dir, 'check3spinn_30p0_64.fits'), 64, field = (0, 1, 2))

../testenv/lib/python3.6/site-packages/pysm/test/test_components.py:148: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
../testenv/lib/python3.6/site-packages/pysm/common.py:83: in read_map
    output_map = hp.ud_grade(hp.read_map(fname, field = field, verbose = verbose), nside_out = nside)
../../../../anaconda3/install/lib/python3.6/site-packages/healpy/fitsfunc.py:283: in read_map
    fits_hdu = _get_hdu(filename, hdu=hdu, memmap=memmap)
../../../../anaconda3/install/lib/python3.6/site-packages/healpy/fitsfunc.py:547: in _get_hdu
    hdulist = pf.open(input_data, memmap=memmap)
../../../../anaconda3/install/lib/python3.6/site-packages/astropy/io/fits/hdu/hdulist.py:160: in fitsopen
    lazy_load_hdus, **kwargs)
../../../../anaconda3/install/lib/python3.6/site-packages/astropy/io/fits/hdu/hdulist.py:413: in fromfile
    lazy_load_hdus=lazy_load_hdus, **kwargs)
../../../../anaconda3/install/lib/python3.6/site-packages/astropy/io/fits/hdu/hdulist.py:998: in _readfrom
    fileobj = _File(fileobj, mode=mode, memmap=memmap, cache=cache)
../../../../anaconda3/install/lib/python3.6/site-packages/astropy/utils/decorators.py:507: in wrapper
    return function(*args, **kwargs)
../../../../anaconda3/install/lib/python3.6/site-packages/astropy/io/fits/file.py:150: in __init__
    self._open_filename(fileobj, mode, overwrite)
../../../../anaconda3/install/lib/python3.6/site-packages/astropy/io/fits/file.py:506: in _open_filename
    self._file = fileobj_open(self.name, IO_FITS_MODES[mode])
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

filename = '/home/yfeng1/source/PySM_public/build/testenv/lib/python3.6/site-packages/pysm/test/test_data/benchmark/check3spinn_30p0_64.fits'
mode = 'rb'

    def fileobj_open(filename, mode):
        """
            A wrapper around the `open()` builtin.
    
            This exists because in Python 3, `open()` returns an
            `io.BufferedReader` by default.  This is bad, because
            `io.BufferedReader` doesn't support random access, which we need in
            some cases.  In the Python 3 case (implemented in the py3compat module)
            we must call open with buffering=0 to get a raw random-access file
            reader.
            """
    
>       return open(filename, mode, buffering=0)
E       FileNotFoundError: [Errno 2] No such file or directory: '/home/yfeng1/source/PySM_public/build/testenv/lib/python3.6/site-packages/pysm/test/test_data/benchmark/check3spinn_30p0_64.fits'

../../../../anaconda3/install/lib/python3.6/site-packages/astropy/io/fits/util.py:409: FileNotFoundError
=============================== warnings summary ===============================
build/testenv/lib/python3.6/site-packages/pysm/test/test_components.py::ComponentsTests::testBlack_Body
  /home/yfeng1/source/PySM_public/build/testenv/lib/python3.6/site-packages/pysm/test/test_components.py:20: AstropyDeprecationWarning: The blackbody_nu function is deprecated and may be removed in a future version.
          Use astropy.modeling.blackbody.blackbody_nu instead.
    astropy = blackbody_nu(90.e9, 100.) / blackbody_nu(30.e9, 100.)

-- Docs: http://doc.pytest.org/en/latest/warnings.html

zonca · 2018-01-19T17:45:20Z

the healpy conda package doesn't work?

rainwoodman · 2018-01-19T19:17:54Z

You mean the one from conda-forge? Yes -- that's the one I tried, and it worked! Though it pulled in replacements a few unrelated packages (that's what I mean 'not clean').

I can fix the file not found error -- but it does seem the package contains some relatively big data files -- are they for testing only or are they necessary for the application to function? If they are for testing only perhaps a smaller version of file is preferred.

templates looked like an asset of PYSM, so the path shall be calculated in the root package.

For in-tree testing, PYSM_TESTDATA_DIR is not set, so we guess a relpath to the test data for out-tree testing (run-tests.py), PYSM_TESTDATA_DIR is set to the in-tree position. This is to avoid installing the 64 MB and growing size of the test data set. It appears that trimming it down requires subsential work that's beyond my judgement.

The test case appears to be broken -- no one produce the file (but it is removed after test) It's likely better to use a temporary file (but must be aware that if MPI is used the filename needs to be broadcasted).

Since the intention is not to distribute them with the package.

This avoids '/', which was also avoided in the old code.

zonca · 2018-01-23T15:00:06Z

you can probably install mpi on travis with apt

zonca · 2018-01-23T15:02:20Z

with sudo apt-get install -y -q openmpi-bin libopenmpi-dev

rainwoodman · 2018-01-24T01:07:40Z

It is trickier. This is running on the docker based images, so we need to use the apt add-on. I usually work with packages from anaconda; but I guess you want to avoid that dependency in travis tests? If miniconda's OK I'll just copy over the boilerplate we use everywhere else.

…

On Tue, Jan 23, 2018 at 7:02 AM, Andrea Zonca ***@***.***> wrote: with sudo apt-get install -y -q openmpi-bin libopenmpi-dev — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#18 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAIbTH3effCexw44k8QVA3uauEmZVfj0ks5tNfR9gaJpZM4RjYiy> .

zonca · 2018-01-26T14:02:33Z

also everything from anaconda would be fine

zonca · 2018-01-26T14:03:06Z

anyway it looks like it is working fine now

zonca · 2018-01-31T13:57:26Z

@rainwoodman do you think this Pull Request is ready for @bthorne93 to review and merge?

zonca · 2018-01-31T13:58:44Z

I can then refactor #15 to use runtests as well

rainwoodman · 2018-01-31T18:36:31Z

Yes, please. Travis is finally green!

drive tests with run-tests.

dabd30f

Unfortunately I couldn't test this because pip install healpy failed on my box with anaconda-5.0 cross compilation tools chain. It couldn't find cfitsio. We need a good binary package of healpy on conda.

rainwoodman added 13 commits January 19, 2018 11:59

Fetch template dir from PYSM root package.

ac9997a

templates looked like an asset of PYSM, so the path shall be calculated in the root package.

Clean up the use of path names in the tests.

3c30cfc

Mark a known failure.

58b2561

The test case appears to be broken -- no one produce the file (but it is removed after test) It's likely better to use a temporary file (but must be aware that if MPI is used the filename needs to be broadcasted).

fix syntax of xfail.

6b2043a

move test_data to the root dir of package.

e4194dd

Since the intention is not to distribute them with the package.

update paths for the new test_dir location.

3dfa8f9

allow multiple filename components.

3734d66

This avoids '/', which was also avoided in the old code.

fix the fallback path.

8e00d5d

use pytest for testing on travis.

86edc6b

use runtests.py in .travis.

3476979

typo

9381984

No MPI is installed on travis, so do single.

c7acf72

install openmpi and mpi4py in travis.

3f4a2f5

b-thorne approved these changes Feb 5, 2018

View reviewed changes

b-thorne merged commit 1918c0d into b-thorne:master Feb 5, 2018

zonca mentioned this pull request Feb 6, 2018

Run tests with runtests #17

Closed

rainwoodman deleted the runtests branch February 11, 2018 00:22

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drive tests with run-tests. #18

drive tests with run-tests. #18

rainwoodman commented Jan 18, 2018

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zonca commented Jan 19, 2018

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rainwoodman commented Jan 31, 2018

drive tests with run-tests. #18

drive tests with run-tests. #18

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rainwoodman commented Jan 18, 2018

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