skip some tests when external dependency is not present

[yarikoptic]

may be it was already implemented and intended, I am just presenting my observation:

$> python -m pytest -v -k "not test_build_image" neurodocker 
================================================================= test session starts ==================================================================
platform linux -- Python 3.5.4, pytest-3.2.1, py-1.4.34, pluggy-0.4.0 -- /home/yoh/deb/perspect/neurodocker/venvs/dev/bin/python
cachedir: .cache
rootdir: /home/yoh/deb/perspect/neurodocker, inifile:
plugins: localserver-0.3.7, hypothesis-3.44.1
collected 66 items                                                                                                                                      

neurodocker/docker/tests/test_docker.py::test_docker_is_running PASSED
neurodocker/docker/tests/test_docker.py::TestBuildOutputLogger::test_start PASSED
neurodocker/docker/tests/test_docker.py::TestBuildOutputLogger::test_get_logs PASSED
neurodocker/docker/tests/test_docker.py::TestDockerImage::test___init__ PASSED
neurodocker/docker/tests/test_docker.py::TestDockerImage::test_build PASSED
neurodocker/docker/tests/test_docker.py::TestDockerContainer::test_start_cleanup PASSED
neurodocker/docker/tests/test_docker.py::TestDockerContainer::test_exec_run PASSED
neurodocker/docker/tests/test_docker.py::TestDockerContainer::test_cleanup PASSED
neurodocker/docker/tests/test_docker.py::test_copy_file_from_container PASSED
neurodocker/docker/tests/test_docker.py::test_copy_file_to_container PASSED
neurodocker/interfaces/tests/test_afni.py::TestAFNI::test_invalid_binaries PASSED
neurodocker/interfaces/tests/test_ants.py::TestANTs::test_invalid_binaries PASSED
neurodocker/interfaces/tests/test_ants.py::TestANTs::test_build_from_source_github PASSED
neurodocker/interfaces/tests/test_freesurfer.py::TestFreeSurfer::test_copy_license PASSED
neurodocker/interfaces/tests/test_mrtrix.py::TestMRtrix3::test_build_from_source PASSED
neurodocker/reprozip/tests/test_merge.py::test_merge_pack_files FAILED
neurodocker/reprozip/tests/test_trace.py::test_ReproZipMinimizer_no_ptrace SKIPPED
neurodocker/reprozip/tests/test_trace.py::test_ReproZipMinimizer PASSED
neurodocker/tests/test_generate.py::test__add_add PASSED
neurodocker/tests/test_generate.py::test__add_to_entrypoint PASSED
neurodocker/tests/test_generate.py::test__add_arg PASSED
neurodocker/tests/test_generate.py::test__add_base PASSED
neurodocker/tests/test_generate.py::test__add_cmd PASSED
neurodocker/tests/test_generate.py::test__add_copy PASSED
neurodocker/tests/test_generate.py::test__add_entrypoint PASSED
neurodocker/tests/test_generate.py::test__add_env_vars FAILED
neurodocker/tests/test_generate.py::test__add_exposed_ports PASSED
neurodocker/tests/test_generate.py::test__add_install PASSED
neurodocker/tests/test_generate.py::test__add_arbitrary_instruction PASSED
neurodocker/tests/test_generate.py::test__add_label PASSED
neurodocker/tests/test_generate.py::test_add_run PASSED
neurodocker/tests/test_generate.py::test__add_run_bash PASSED
neurodocker/tests/test_generate.py::test__add_volume PASSED
neurodocker/tests/test_generate.py::test__add_workdir PASSED
neurodocker/tests/test_generate.py::test_DockerfileUsers PASSED
neurodocker/tests/test_generate.py::TestDockerfile::test___repr__ PASSED
neurodocker/tests/test_generate.py::TestDockerfile::test___str__ PASSED
neurodocker/tests/test_generate.py::TestDockerfile::test__create_cmd PASSED
neurodocker/tests/test_generate.py::TestDockerfile::test_save PASSED
neurodocker/tests/test_neurodocker.py::test_generate PASSED
neurodocker/tests/test_neurodocker.py::test_generate_opts FAILED
neurodocker/tests/test_neurodocker.py::test_generate_from_json PASSED
neurodocker/tests/test_neurodocker.py::test_generate_no_print PASSED
neurodocker/tests/test_neurodocker.py::test_generate_save PASSED
neurodocker/tests/test_parser.py::TestSpecsParser::test__validate_keys PASSED
neurodocker/tests/test_utils.py::test_manage_pkgs PASSED
neurodocker/tests/test_utils.py::test_check_url PASSED
neurodocker/tests/test_utils.py::test_indent PASSED
neurodocker/tests/test_utils.py::test_save_load_json PASSED
neurodocker/tests/test_utils.py::test_set_log_level PASSED
neurodocker/tests/test_version.py::test_get_gitversion PASSED

================================================== FAILURES ===================================================
____________________________________________ test_merge_pack_files ____________________________________________

    def _check_deps():
        """Raise RuntimeError if a dependency is not found. These dependencies are
        not included in `requirements.txt`.
        """
        import shutil
    
        msg = "Dependency '{}' not found."
    
        if shutil.which('rsync') is None:
            raise RuntimeError(msg.format('rsync'))
        try:
>           import reprozip
E           ImportError: No module named 'reprozip'

neurodocker/reprozip/merge.py:47: ImportError

During handling of the above exception, another exception occurred:

    def test_merge_pack_files():
        tmpdir = tempfile.mkdtemp()
    
        cmd = ["du -sh /usr", "rm --help"]
        packpath = _create_packfile(cmd, tmpdir)
        new_name = "first-pack.rpz"
        os.rename(packpath, os.path.join(tmpdir, new_name))
    
        cmd = ["ls -l /", "grep --help"]
        _create_packfile(cmd, tmpdir)
    
        pattern = os.path.join(tmpdir, '*.rpz')
        packfiles = glob(pattern)
        assert packfiles, "packfiles not found"
    
        outfile = os.path.join(tmpdir, 'merged.rpz')
>       merge_pack_files(outfile=outfile, packfiles=packfiles)

neurodocker/reprozip/tests/test_merge.py:48: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
neurodocker/reprozip/merge.py:165: in merge_pack_files
    _check_deps()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

    def _check_deps():
        """Raise RuntimeError if a dependency is not found. These dependencies are
        not included in `requirements.txt`.
        """
        import shutil
    
        msg = "Dependency '{}' not found."
    
        if shutil.which('rsync') is None:
            raise RuntimeError(msg.format('rsync'))
        try:
            import reprozip
        except Exception:
>           raise RuntimeError(msg.format('reprozip'))
E           RuntimeError: Dependency 'reprozip' not found.

neurodocker/reprozip/merge.py:49: RuntimeError
_____________________________________________ test__add_env_vars ______________________________________________

    def test__add_env_vars():
        env = {'THIS': 'THAT'}
        truth = 'ENV THIS="THAT"'
        assert truth == DF._add_env_vars(env)
    
        env['A'] = 'B'
        truth = ('ENV THIS="THAT" \\\n    A="B"')
>       assert truth == DF._add_env_vars(env)
E       assert 'ENV THIS="TH...\\\n    A="B"' == 'ENV A="B" \\\n    THIS="THAT"'
E         - ENV THIS="THAT" \
E         -     A="B"
E         + ENV A="B" \
E         +     THIS="THAT"

neurodocker/tests/test_generate.py:72: AssertionError
_____________________________________________ test_generate_opts ______________________________________________

capsys = <_pytest.capture.CaptureFixture object at 0x7fd553b11ba8>

    def test_generate_opts(capsys):
        args = "generate -b ubuntu:17.04 -p apt --no-check-urls {}"
        main(args.format('--user=neuro').split())
        out, _ = capsys.readouterr()
        assert "USER neuro" in out
    
        main(args.format('--add path/to/file.txt /tmp/file.txt').split())
        out, _ = capsys.readouterr()
        assert 'ADD ["path/to/file.txt", "/tmp/file.txt"]' in out
    
        main(args.format('--copy path/to/file.txt /tmp/file.txt').split())
        out, _ = capsys.readouterr()
        assert 'COPY ["path/to/file.txt", "/tmp/file.txt"]' in out
    
        main(args.format('--env KEY=VAL KEY2=VAL').split())
        out, _ = capsys.readouterr()
>       assert 'ENV KEY="VAL" \\' in out
E       assert 'ENV KEY="VAL" \\' in '# Generated by Neurodocker v0.3.2-5-gf1376bf.\n#\n# Thank you for using Neurodocker. If you discover any issues\n# or...bf", \\\n    \\n  "generation_timestamp": "2018-01-12 10:42:29" \\\n    \\n}\' > /neurodocker/neurodocker_specs.json\n'

neurodocker/tests/test_neurodocker.py:71: AssertionError
============================================= 15 tests deselected =============================================
======================= 3 failed, 47 passed, 1 skipped, 15 deselected in 236.14 seconds =======================
python -m pytest -v -k "not test_build_image" neurodocker  12.78s user 0.19s system 5% cpu 3:56.79 total

it is on a Debian system in a virtualenv with python 3.5

[kaczmarj]

This is a great idea! Thanks @yarikoptic. I am in the process of refactoring this package to also generate Singularity definition files. That involves rewriting many of the tests, so I will be sure to implement this idea.

The refactoring is happening in the branch ref/to-yaml.

[effigies]

Ran into this as well. A fix would be appreciated. Let me know if you need help.

[djarecka]

I will close this issue since it's pretty old and the test has been rewritten, please feel free to reopen if the problem still exists