junit-results.xml

<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="1" skipped="0" tests="10" time="168.316" timestamp="2022-11-03T11:21:43.461711" hostname="james"><testcase classname="pd_parser.tests.test_parse_pd" name="test_inputs" time="0.359" /><testcase classname="pd_parser.tests.test_parse_pd" name="test_core" time="0.477" /><testcase classname="pd_parser.tests.test_parse_pd" name="test_resync" time="0.386" /><testcase classname="pd_parser.tests.test_parse_pd" name="test_two_pd_alignment" time="0.396" /><testcase classname="pd_parser.tests.test_parse_pd" name="test_beh_with_nas" time="0.418" /><testcase classname="pd_parser.tests.test_parse_pd" name="test_plotting" time="0.305" /><testcase classname="pd_parser.tests.test_parse_pd" name="test_parse_pd" time="19.320"><failure message="FileNotFoundError: [Errno 2] No such file or directory: 'bids-validator'">_bids_validate = &lt;function _bids_validate.&lt;locals&gt;._validate at 0x7f70fc5d7b50&gt;

    @pytest.mark.filterwarnings('ignore::RuntimeWarning')
    @pytest.mark.filterwarnings('ignore::DeprecationWarning')
    def test_parse_pd(_bids_validate):
        # load in data
        behf = op.join(basepath, 'pd_beh.tsv')
        events = _read_tsv(op.join(basepath, 'pd_events.tsv'))
        events_relative = _read_tsv(op.join(basepath, 'pd_relative_events.tsv'))
        raw_tmp = mne.io.read_raw_fif(op.join(basepath, 'pd_data-raw.fif'),
                                      preload=True)
        with raw_tmp.info._unlock():
            raw_tmp.info['dig'] = None
            raw_tmp.info['line_freq'] = 60
        out_dir = _TempDir()
        fname = op.join(out_dir, 'pd_data-raw.fif')
        raw_tmp.save(fname)
        # this needs to be tested with user interaction, this
        # just tests that it launches
        pd_parser.find_pd_params(fname, pd_ch_names=['pd'])
        plt.close('all')
        # test core functionality
        annot, samples = pd_parser.parse_pd(fname, beh=behf, pd_ch_names=['pd'],
                                            zscore=20, resync=0.125)
        plt.close('all')
        raw = mne.io.read_raw_fif(fname)
        raw.set_annotations(annot)
        events2, event_id = mne.events_from_annotations(raw)
        np.testing.assert_array_equal(
            events2[:, 0], [e for e in events['pd_parser_sample'] if e != 'n/a'])
        assert samples == events['pd_parser_sample']
        # test add_pd_off_events
        annot = pd_parser.add_pd_off_events(fname, off_event_name=off_event_name,
                                            zscore=20)
        raw.set_annotations(annot)
        assert off_event_name in annot.description
        events2, event_id = mne.events_from_annotations(raw)
        off_events = events2[events2[:, 2] == event_id[off_event_name]]
        np.testing.assert_array_equal(
            off_events[:, 0], [e for e in events['off_sample'] if e != 'n/a'])
        '''
        df = dict(trial=range(300), pd_parser_sample=samples, off_sample=list())
        i = 0
        for s in samples:
            df['off_sample'].append('n/a' if s == 'n/a' else off_events[i, 0])
            i += s != 'n/a'
        '''
        # test add_pd_relative_events
        pd_parser.add_relative_events(
            raw, behf,
            relative_event_keys=['fix_duration', 'go_time', 'response_time'],
            relative_event_names=['ISI Onset', 'Go Cue', 'Response'])
        annot, pd_ch_names, beh = _load_data(raw)
        raw.set_annotations(annot)
        events2, event_id = mne.events_from_annotations(raw)
        np.testing.assert_array_equal(events2[:, 0], events_relative['sample'])
        assert pd_ch_names == ['pd']
        np.testing.assert_array_equal(
            events2[:, 2], [event_id[tt] for tt in events_relative['trial_type']])
        # test add_pd_events_to_raw
        raw2 = pd_parser.add_events_to_raw(raw, keep_pd_channels=True)
        events3, event_id2 = mne.events_from_annotations(raw2)
        np.testing.assert_array_equal(events3, events2)
        assert event_id2 == event_id
        # test pd_parser_save_to_bids
        bids_dir = op.join(out_dir, 'bids_dir')
        pd_parser.save_to_bids(bids_dir, fname, '1', 'test', verbose=False)
&gt;       _bids_validate(bids_dir)

_bids_validate = &lt;function _bids_validate.&lt;locals&gt;._validate at 0x7f70fc5d7b50&gt;
annot      = &lt;Annotations | 1433 segments: Fixation (288), Go Cue (288), ISI Onset ...&gt;
beh        = {'fix_duration': [0.6, 0.7, 0.4, 0.4, 0.5, 0.7, ...], 'fix_onset_time': [40923.295, 40931.0775, 40938.977, 40946.7271,...8, 1.3289, 1.0254, 1.4241, 1.5237, ...], 'pd_parser_sample': ['n/a', 210633, 218529, 226292, 233756, 241635, ...], ...}
behf       = '/home/alexrockhill/projects/pd-parser/pd_parser/tests/data/pd_beh.tsv'
bids_dir   = '/tmp/tmp_mne_tempdir_4r2jt8dz/bids_dir'
event_id   = {'Fixation': 1, 'Go Cue': 2, 'ISI Onset': 3, 'Response': 4, ...}
event_id2  = {'Fixation': 1, 'Go Cue': 2, 'ISI Onset': 3, 'Response': 4, ...}
events     = {'off_sample': ['n/a', 211334, 218930, 226677, 234240, 242336, ...], 'pd_parser_sample': ['n/a', 210633, 218529, 226292, 233756, 241635, ...], 'trial': [0, 1, 2, 3, 4, 5, ...]}
events2    = array([[ 210633,       0,       1],
       [ 211333,       0,       3],
       [ 211334,       0,       5],
       ...,
       [2636340,       0,       3],
       [2636971,       0,       2],
       [2637579,       0,       4]])
events3    = array([[ 210633,       0,       1],
       [ 211333,       0,       3],
       [ 211334,       0,       5],
       ...,
       [2636340,       0,       3],
       [2636971,       0,       2],
       [2637579,       0,       4]])
events_relative = {'duration': [0.100006103515625, 0.0999908447265625, 0.100006103515625, 0.0999908447265625, 0.100006103515625, 0.10000...': ['Fixation', 'ISI Onset', 'Stim Off', 'Go Cue', 'Response', 'Fixation', ...], 'value': [1, 3, 5, 2, 4, 1, ...], ...}
fname      = '/tmp/tmp_mne_tempdir_4r2jt8dz/pd_data-raw.fif'
off_events = array([[ 211334,       0,       2],
       [ 218930,       0,       2],
       [ 226677,       0,       2],
       [ 2...       2],
       [2620448,       0,       2],
       [2628328,       0,       2],
       [2636324,       0,       2]])
out_dir    = '/tmp/tmp_mne_tempdir_4r2jt8dz'
pd_ch_names = ['pd']
raw        = &lt;Raw | pd_data-raw.fif, 1 x 2818158 (2819.8 s), ~7 kB, data not loaded&gt;
raw2       = &lt;Raw | pd_data-raw.fif, 1 x 2818158 (2819.8 s), ~7 kB, data not loaded&gt;
raw_tmp    = &lt;Raw | pd_data-raw.fif, 1 x 2818158 (2819.8 s), ~21.5 MB, data loaded&gt;
samples    = ['n/a', 210633, 218529, 226292, 233756, 241635, ...]

pd_parser/tests/test_parse_pd.py:425: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
pd_parser/tests/test_parse_pd.py:91: in _validate
    run_subprocess(cmd, shell=shell)
        bids_root  = '/tmp/tmp_mne_tempdir_4r2jt8dz/bids_dir'
        bids_validator_exe = ['bids-validator', '--config.error=41']
        cmd        = ['bids-validator', '--config.error=41', '/tmp/tmp_mne_tempdir_4r2jt8dz/bids_dir']
        shell      = False
&lt;decorator-gen-1&gt;:12: in run_subprocess
    ???
        args       = ()
        command    = ['bids-validator', '--config.error=41', '/tmp/tmp_mne_tempdir_4r2jt8dz/bids_dir']
        do_level_change = False
        kwargs     = {'shell': False}
        return_code = False
        verbose    = None
../mne-python/mne/utils/misc.py:127: in run_subprocess
    with running_subprocess(command, *args, **kwargs) as p:
        all_err    = ''
        all_out    = ''
        args       = ()
        command    = ['bids-validator', '--config.error=41', '/tmp/tmp_mne_tempdir_4r2jt8dz/bids_dir']
        control_stderr = True
        control_stdout = True
        err_q      = &lt;queue.Queue object at 0x7f70fc116350&gt;
        kwargs     = {'shell': False}
        out_q      = &lt;queue.Queue object at 0x7f70fc116410&gt;
        return_code = False
        verbose    = None
../../software/anaconda3/envs/mne/lib/python3.10/contextlib.py:135: in __enter__
    return next(self.gen)
        self       = &lt;contextlib._GeneratorContextManager object at 0x7f70fc116b90&gt;
../mne-python/mne/utils/misc.py:256: in running_subprocess
    p = subprocess.Popen(command, *args, **kwargs)
        after      = 'wait'
        args       = ()
        command    = ['bids-validator', '--config.error=41', '/tmp/tmp_mne_tempdir_4r2jt8dz/bids_dir']
        command_name = 'bids-validator'
        command_str = 'bids-validator --config.error=41 /tmp/tmp_mne_tempdir_4r2jt8dz/bids_dir'
        contexts   = ['stderr', 'stdout']
        env        = environ({'SHELL': '/bin/bash', 'SESSION_MANAGER': 'local/james:@/tmp/.ICE-unix/3548,unix/james:/tmp/.ICE-unix/3548', '...est', 'OLDPWD': '/home/alexrockhill', 'PYTEST_CURRENT_TEST': 'pd_parser/tests/test_parse_pd.py::test_parse_pd (call)'})
        kwargs     = {'shell': False, 'stderr': -1, 'stdout': -1}
        stdxxx     = 'stdout'
        verbose    = None
../../software/anaconda3/envs/mne/lib/python3.10/subprocess.py:969: in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
        args       = ['bids-validator', '--config.error=41', '/tmp/tmp_mne_tempdir_4r2jt8dz/bids_dir']
        bufsize    = -1
        c2pread    = 24
        c2pwrite   = 25
        close_fds  = True
        creationflags = 0
        cwd        = None
        encoding   = None
        env        = None
        errors     = None
        errread    = 26
        errwrite   = 27
        executable = None
        extra_groups = None
        f          = &lt;_io.BufferedReader name=26&gt;
        gid        = None
        gids       = None
        group      = None
        p2cread    = -1
        p2cwrite   = -1
        pass_fds   = ()
        pipesize   = -1
        preexec_fn = None
        restore_signals = True
        self       = &lt;Popen: returncode: 255 args: ['bids-validator', '--config.error=41', '/tmp/...&gt;
        shell      = False
        start_new_session = False
        startupinfo = None
        stderr     = -1
        stdin      = None
        stdout     = -1
        text       = None
        uid        = None
        umask      = -1
        universal_newlines = None
        user       = None
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = &lt;Popen: returncode: 255 args: ['bids-validator', '--config.error=41', '/tmp/...&gt;
args = ['bids-validator', '--config.error=41', '/tmp/tmp_mne_tempdir_4r2jt8dz/bids_dir']
executable = b'bids-validator', preexec_fn = None, close_fds = True
pass_fds = (), cwd = None, env = None, startupinfo = None, creationflags = 0
shell = False, p2cread = -1, p2cwrite = -1, c2pread = 24, c2pwrite = 25
errread = 26, errwrite = 27, restore_signals = True, gid = None, gids = None
uid = None, umask = -1, start_new_session = False

    def _execute_child(self, args, executable, preexec_fn, close_fds,
                       pass_fds, cwd, env,
                       startupinfo, creationflags, shell,
                       p2cread, p2cwrite,
                       c2pread, c2pwrite,
                       errread, errwrite,
                       restore_signals,
                       gid, gids, uid, umask,
                       start_new_session):
        """Execute program (POSIX version)"""
    
        if isinstance(args, (str, bytes)):
            args = [args]
        elif isinstance(args, os.PathLike):
            if shell:
                raise TypeError('path-like args is not allowed when '
                                'shell is true')
            args = [args]
        else:
            args = list(args)
    
        if shell:
            # On Android the default shell is at '/system/bin/sh'.
            unix_shell = ('/system/bin/sh' if
                      hasattr(sys, 'getandroidapilevel') else '/bin/sh')
            args = [unix_shell, "-c"] + args
            if executable:
                args[0] = executable
    
        if executable is None:
            executable = args[0]
    
        sys.audit("subprocess.Popen", executable, args, cwd, env)
    
        if (_USE_POSIX_SPAWN
                and os.path.dirname(executable)
                and preexec_fn is None
                and not close_fds
                and not pass_fds
                and cwd is None
                and (p2cread == -1 or p2cread &gt; 2)
                and (c2pwrite == -1 or c2pwrite &gt; 2)
                and (errwrite == -1 or errwrite &gt; 2)
                and not start_new_session
                and gid is None
                and gids is None
                and uid is None
                and umask &lt; 0):
            self._posix_spawn(args, executable, env, restore_signals,
                              p2cread, p2cwrite,
                              c2pread, c2pwrite,
                              errread, errwrite)
            return
    
        orig_executable = executable
    
        # For transferring possible exec failure from child to parent.
        # Data format: "exception name:hex errno:description"
        # Pickle is not used; it is complex and involves memory allocation.
        errpipe_read, errpipe_write = os.pipe()
        # errpipe_write must not be in the standard io 0, 1, or 2 fd range.
        low_fds_to_close = []
        while errpipe_write &lt; 3:
            low_fds_to_close.append(errpipe_write)
            errpipe_write = os.dup(errpipe_write)
        for low_fd in low_fds_to_close:
            os.close(low_fd)
        try:
            try:
                # We must avoid complex work that could involve
                # malloc or free in the child process to avoid
                # potential deadlocks, thus we do all this here.
                # and pass it to fork_exec()
    
                if env is not None:
                    env_list = []
                    for k, v in env.items():
                        k = os.fsencode(k)
                        if b'=' in k:
                            raise ValueError("illegal environment variable name")
                        env_list.append(k + b'=' + os.fsencode(v))
                else:
                    env_list = None  # Use execv instead of execve.
                executable = os.fsencode(executable)
                if os.path.dirname(executable):
                    executable_list = (executable,)
                else:
                    # This matches the behavior of os._execvpe().
                    executable_list = tuple(
                        os.path.join(os.fsencode(dir), executable)
                        for dir in os.get_exec_path(env))
                fds_to_keep = set(pass_fds)
                fds_to_keep.add(errpipe_write)
                self.pid = _posixsubprocess.fork_exec(
                        args, executable_list,
                        close_fds, tuple(sorted(map(int, fds_to_keep))),
                        cwd, env_list,
                        p2cread, p2cwrite, c2pread, c2pwrite,
                        errread, errwrite,
                        errpipe_read, errpipe_write,
                        restore_signals, start_new_session,
                        gid, gids, uid, umask,
                        preexec_fn)
                self._child_created = True
            finally:
                # be sure the FD is closed no matter what
                os.close(errpipe_write)
    
            self._close_pipe_fds(p2cread, p2cwrite,
                                 c2pread, c2pwrite,
                                 errread, errwrite)
    
            # Wait for exec to fail or succeed; possibly raising an
            # exception (limited in size)
            errpipe_data = bytearray()
            while True:
                part = os.read(errpipe_read, 50000)
                errpipe_data += part
                if not part or len(errpipe_data) &gt; 50000:
                    break
        finally:
            # be sure the FD is closed no matter what
            os.close(errpipe_read)
    
        if errpipe_data:
            try:
                pid, sts = os.waitpid(self.pid, 0)
                if pid == self.pid:
                    self._handle_exitstatus(sts)
                else:
                    self.returncode = sys.maxsize
            except ChildProcessError:
                pass
    
            try:
                exception_name, hex_errno, err_msg = (
                        errpipe_data.split(b':', 2))
                # The encoding here should match the encoding
                # written in by the subprocess implementations
                # like _posixsubprocess
                err_msg = err_msg.decode()
            except ValueError:
                exception_name = b'SubprocessError'
                hex_errno = b'0'
                err_msg = 'Bad exception data from child: {!r}'.format(
                              bytes(errpipe_data))
            child_exception_type = getattr(
                    builtins, exception_name.decode('ascii'),
                    SubprocessError)
            if issubclass(child_exception_type, OSError) and hex_errno:
                errno_num = int(hex_errno, 16)
                child_exec_never_called = (err_msg == "noexec")
                if child_exec_never_called:
                    err_msg = ""
                    # The error must be from chdir(cwd).
                    err_filename = cwd
                else:
                    err_filename = orig_executable
                if errno_num != 0:
                    err_msg = os.strerror(errno_num)
&gt;               raise child_exception_type(errno_num, err_msg, err_filename)
E               FileNotFoundError: [Errno 2] No such file or directory: 'bids-validator'

args       = ['bids-validator', '--config.error=41', '/tmp/tmp_mne_tempdir_4r2jt8dz/bids_dir']
c2pread    = 24
c2pwrite   = 25
child_exception_type = &lt;class 'OSError'&gt;
child_exec_never_called = False
close_fds  = True
creationflags = 0
cwd        = None
env        = None
env_list   = None
err_filename = 'bids-validator'
err_msg    = 'No such file or directory'
errno_num  = 2
errpipe_data = bytearray(b'OSError:2:')
errpipe_read = 28
errpipe_write = 29
errread    = 26
errwrite   = 27
exception_name = bytearray(b'OSError')
executable = b'bids-validator'
executable_list = (b'/home/alexrockhill/.rbenv/shims/bids-validator', b'/usr/local/opt/sphinx-doc/bin/bids-validator', b'/home/alexrockh...ill/software/freesurfer/tktools/bids-validator', b'/home/alexrockhill/software/freesurfer/mni/bin/bids-validator', ...)
fds_to_keep = {29}
gid        = None
gids       = None
hex_errno  = bytearray(b'2')
low_fds_to_close = []
orig_executable = 'bids-validator'
p2cread    = -1
p2cwrite   = -1
part       = b''
pass_fds   = ()
pid        = 614610
preexec_fn = None
restore_signals = True
self       = &lt;Popen: returncode: 255 args: ['bids-validator', '--config.error=41', '/tmp/...&gt;
shell      = False
start_new_session = False
startupinfo = None
sts        = 65280
uid        = None
umask      = -1

../../software/anaconda3/envs/mne/lib/python3.10/subprocess.py:1845: FileNotFoundError</failure></testcase><testcase classname="pd_parser.tests.test_parse_pd" name="test_long_events" time="0.326" /><testcase classname="pd_parser.tests.test_parse_pd" name="test_parse_audio" time="5.928" /><testcase classname="pd_parser.tests.test_parse_pd" name="test_cli" time="7.863" /><testcase time="0.000" /></testsuite></testsuites>