Test Errors on a readonly file system

[satra]

Summary

When running nipype tests in a singularity container it fails because the tests try to create files in a read only file system.

Actual behavior

============================================= FAILURES ==============================================
____________________________ [doctest] nipype.interfaces.dcm2nii.Dcm2nii ____________________________
069 
070     Examples
071     ========
072 
073     >>> from nipype.interfaces.dcm2nii import Dcm2nii
074     >>> converter = Dcm2nii()
075     >>> converter.inputs.source_names = ['functional_1.dcm', 'functional_2.dcm']
076     >>> converter.inputs.gzip_output = True
077     >>> converter.inputs.output_dir = '.'
078     >>> converter.cmdline # doctest: +ALLOW_UNICODE
UNEXPECTED EXCEPTION: OSError(30, 'Read-only file system')
Traceback (most recent call last):

  File "/opt/conda/lib/python3.5/doctest.py", line 1321, in __run
    compileflags, 1), test.globs)

  File "<doctest nipype.interfaces.dcm2nii.Dcm2nii[5]>", line 1, in <module>

  File "/opt/conda/lib/python3.5/site-packages/nipype/interfaces/base.py", line 1678, in cmdline
    allargs = self._parse_inputs()

  File "/opt/conda/lib/python3.5/site-packages/nipype/interfaces/base.py", line 1911, in _parse_inputs
    value = self._gen_filename(name)

  File "/opt/conda/lib/python3.5/site-packages/nipype/interfaces/dcm2nii.py", line 198, in _gen_filename
    with open(config_file, "w") as f:

OSError: [Errno 30] Read-only file system: 'config.ini'

/opt/conda/lib/python3.5/site-packages/nipype/interfaces/dcm2nii.py:78: UnexpectedException
_________________________________________ test_level1design _________________________________________

    def test_level1design():
        l = Level1Design()
        runinfo = dict(cond=[{'name': 'test_condition', 'onset': [0, 10],
                              'duration':[10, 10]}],regress=[])
        runidx = 0
        contrasts = Undefined
        do_tempfilter = False
        orthogonalization = {}
        basic_ev_parameters = {'temporalderiv':False}
        convolution_variants = [
            ('custom', 7, {'temporalderiv':False, 'bfcustompath':'/some/path'}),
            ('hrf', 3, basic_ev_parameters),
            ('dgamma', 3, basic_ev_parameters),
            ('gamma', 2, basic_ev_parameters),
            ('none', 0, basic_ev_parameters)
            ]
        for key, val, ev_parameters in convolution_variants:
            output_num, output_txt = Level1Design._create_ev_files(l, os.getcwd(),
                                                                   runinfo, runidx,
                                                                   ev_parameters,
                                                                   orthogonalization,
                                                                   contrasts,
                                                                   do_tempfilter,
>                                                                  key)

../../interfaces/fsl/tests/test_Level1Design_functions.py:30: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../interfaces/fsl/model.py:227: in _create_ev_files
    self._create_ev_file(evfname, evinfo)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

self = <nipype.interfaces.fsl.model.Level1Design object at 0x2aab14958470>
evfname = '/opt/conda/lib/python3.5/site-packages/nipype/testing/data/ev_test_condition_0_1.txt'
evinfo = [[0, 10, 1], [10, 10, 1]]

    def _create_ev_file(self, evfname, evinfo):
>       f = open(evfname, 'wt')
E       OSError: [Errno 30] Read-only file system: '/opt/conda/lib/python3.5/site-packages/nipype/testing/data/ev_test_condition_0_1.txt'

../../interfaces/fsl/model.py:124: OSError
================== 2 failed, 2483 passed, 25 skipped, 7 xfailed in 317.66 seconds ===================

Expected behavior

Tests pass

How to replicate the behavior

pytest --doctest-modules -p no:cacheprovider /opt/conda/lib/python3.5/site-packages/nipype

Platform details:

please paste the output of: python -c "import nipype; print(nipype.get_info()); print(nipype.__version__)"

$ python -c "import nipype; print(nipype.get_info()); print(nipype.__version__)"
{'traits_version': '4.6.0', 'sys_version': '3.5.2 |Continuum Analytics, Inc.| (default, Jul  2 2016, 17:53:06) \n[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]', 'commit_source': 'archive substitution', 'sys_platform': 'linux', 'nibabel_version': '2.1.0', 'scipy_version': '0.19.0', 'pkg_path': '/opt/conda/lib/python3.5/site-packages/nipype', 'numpy_version': '1.11.3', 'nipype_version': '0.13.0-dev', 'networkx_version': '1.11', 'commit_hash': '%h', 'sys_executable': '/opt/conda/bin/python'}
0.13.0-dev

[mgxd]

@satra here's a more extensive list of tests that write to the filesystem

DOCTESTS:
nipype.interfaces.dcm2nii.Dcm2nii
nipype.interfaces.io.JSONFileGrabber
nipype.interfaces.niftyreg.regutils.RegAverage
nipype.interfaces.utility.base.IdentityInterface
nipype.interfaces.utility.base.Merge
nipype.interfaces.utility.base.Select
nipype.interfaces.utility.base.Split
nipype.interfaces.utility.wrappers.Function

STANDALONE:
../../interfaces/fsl/tests/test_Level1Design_functions.py
nipype/nipype/interfaces/niftyreg/regutils.py
nipype/nipype/pipeline/engine/tests/test_utils.py

is it crucial to have testing pass in readonly?

[oesteban]

Now that we use py.test, we should leverage the tmpdir fixture:

nipype/nipype/interfaces/tests/test_base.py

Lines 671 to 674 in 66411f4

	def test_CommandLine_output(tmpdir):
	# Create one file
	tmpdir.chdir()
	file = tmpdir.join('foo.txt')

[satra]

@mgxd - i think tmpdir's should always be writeable in these read only containers. we should test that out. so i agree with @oesteban that if it hasn't been used properly, we should fix those cases.

[oesteban]

One important note is using the path object correctly. Instead of:

nipype/nipype/interfaces/tests/test_base.py

Line 415 in 66411f4

tmp_json = os.path.join(str(tmpdir), 'settings.json')

We should have:

tmp_json = os.path.join(tmpdir.strpath, 'settings.json') 

Or if we were to write on that file right away:

fhandler = tmpdir.join('settings.json')
fhandler.write(txt)

[djarecka]

I can try to fix the tests if no one already done it, but I'm not sure if I understand your points, os.path.join(str(tmpdir), 'settings.json') is not doing exactly the same as os.path.join(tmpdir.strpath, 'settings.json')?

os.path.join(tmpdir.strpath, 'settings.json') returns LocalPath, not Str, but does it really change the problem?

[mgxd]

@djarecka I was going to add this into #2248 - but that may just handle a reworking of the bids interface so if you wanna tackle this that'd be good

[oesteban]

@djarecka:
It is very likely that os.path.join(str(tmpdir), 'settings.json') is completelly equivalent to os.path.join(tmpdir.strpath, 'settings.json'), but it is better to avoid any explicit call to __str__ and use the API of the fixture instead. That would prevent python 2/3 headaches (iff the fixture is fully compatible with both).

As refers to LocalPath, at least in Python 3:

>>> import os
>>> type(os.path.join('path', 'file'))
str

[djarecka]

@oesteban ok, sure I can change str() to strpath. I'm just missing the part how this possibly might help with readonly problem.

[oesteban]

It doesn't. But since we will revise and use more often the tmpdir fixture, I thought it would be a good opportunity for some housekeeping

[djarecka]

ok. I can change it. I'm still lost regarding the plan on changing doctests and fixing the issue, will just observe your conversation.

[oesteban]

This issue should be fairly easy to solve by making those failing test use the tmpdir fixture (which they don't currently use)

[djarecka]

but we're talking about doctest mostly, so you're thinking about creating "normal" tests from doctests or add pytest fixtures to doctests? Never done the latter, but it looks like it should be possible: https://docs.pytest.org/en/latest/doctest.html#the-doctest-namespace-fixture
will try