Update py-elephant to 1.1.0

added 1 commit

• fd4de9f5 - enable new version of py-elephant

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thanks @moritzkern :)

from what I can see in the logs one test fails:

elephant/test/test_spike_train_synchrony.py:454: 
elephant/spike_train_synchrony.py:359: TypeError
E                   TypeError: 'SpikeTrainList' object does not support item assignment

Full failed test log

 =================================== FAILURES ===================================
_ SynchrofactDetectionTestCase.test_correct_transfer_of_spiketrain_attributes __
self = <elephant.test.test_spike_train_synchrony.SynchrofactDetectionTestCase testMethod=test_correct_transfer_of_spiketrain_attributes>
def test_correct_transfer_of_spiketrain_attributes(self):

    # for delete=True the spiketrains in the block are changed,
    # test if their attributes remain correct

    sampling_rate = 1 / pq.s

    spiketrain = neo.SpikeTrain([1, 1, 5, 0] * pq.s,
                                t_stop=10 * pq.s)

    block = neo.Block()

    group = neo.Group(name='Test Group')
    block.groups.append(group)
    group.spiketrains.append(spiketrain)

    segment = neo.Segment()
    block.segments.append(segment)
    segment.block = block
    segment.spiketrains.append(spiketrain)
    spiketrain.segment = segment

    spiketrain.annotate(cool_spike_train=True)
    spiketrain.array_annotate(
        spike_number=np.arange(len(spiketrain.times.magnitude)))
    spiketrain.waveforms = np.sin(
        np.arange(len(spiketrain.times.magnitude))[:, np.newaxis]
        + np.arange(len(spiketrain.times.magnitude))[np.newaxis, :])

    correct_mask = np.array([False, False, True, True])

    # store the correct attributes
    correct_annotations = spiketrain.annotations.copy()
    correct_waveforms = spiketrain.waveforms[correct_mask].copy()
    correct_array_annotations = {key: value[correct_mask] for key, value in
                                 spiketrain.array_annotations.items()}

    # perform a synchrofact search with delete=True
    synchrofact_obj = Synchrotool(
        [spiketrain],
        spread=0,
        sampling_rate=sampling_rate,
        binary=False)


  synchrofact_obj.delete_synchrofacts(


        mode='delete',
        in_place=True,
        threshold=2)

elephant/test/test_spike_train_synchrony.py:454:

self = <elephant.spike_train_synchrony.Synchrotool object at 0x7f8b6373e9d0>
threshold = 2, in_place = True, mode = 'delete'
def delete_synchrofacts(self, threshold, in_place=False, mode='delete'):
    """
    Delete or extract synchronous spiking events.

    Parameters
    ----------
    threshold : int
        Threshold value for the deletion of spikes engaged in synchronous
        activity.

          * `deletion_threshold >= 2` leads to all spikes with a larger or
             equal complexity value to be deleted/extracted.
          * `deletion_threshold <= 1` leads to a ValueError, since this
             would delete/extract all spikes and there are definitely more
             efficient ways of doing so.

    in_place : bool, optional
        Determines whether the modification are made in place
        on ``self.input_spiketrains``.
        Default: False
    mode : {'delete', 'extract'}, optional
        Inversion of the mask for deletion of synchronous events.

          * ``'delete'`` leads to the deletion of all spikes with
            complexity >= `threshold`,
            i.e. deletes synchronous spikes.
          * ``'extract'`` leads to the deletion of all spikes with
            complexity < `threshold`, i.e. extracts synchronous spikes.

        Default: 'delete'

    Raises
    ------
    ValueError
        If `mode` is not one in {'delete', 'extract'}.

        If `threshold <= 1`.

    Returns
    -------
    list of neo.SpikeTrain
        List of spiketrains where the spikes with
        ``complexity >= threshold`` have been deleted/extracted.

          * If ``in_place`` is True, the returned list is the same as
            ``self.input_spiketrains``.
          * If ``in_place`` is False, the returned list is a deepcopy of
            ``self.input_spiketrains``.

    """

    if not self.annotated:
        self.annotate_synchrofacts()

    if mode not in ['delete', 'extract']:
        raise ValueError(f"Invalid mode '{mode}'. Valid modes are: "
                         f"'delete', 'extract'")

    if threshold <= 1:
        raise ValueError('A deletion threshold <= 1 would result '
                         'in the deletion of all spikes.')

    if in_place:
        spiketrain_list = self.input_spiketrains
    else:
        spiketrain_list = deepcopy(self.input_spiketrains)

    for idx, st in enumerate(spiketrain_list):
        mask = st.array_annotations['complexity'] < threshold
        if mode == 'extract':
            mask = np.invert(mask)
        new_st = st[mask]
        if in_place and st.segment is not None:
            segment = st.segment

            try:
                # replace link to spiketrain in segment
                new_index = self._get_spiketrain_index(
                    segment.spiketrains, st)
                segment.spiketrains[new_index] = new_st

E                   TypeError: 'SpikeTrainList' object does not support item assignment
elephant/spike_train_synchrony.py:359: TypeError 

Any ideas?

Hey @elmath ,

Sry, I forgot to update Elephants requirement for neo>0.13.0. .

Related to issues in !486 (merged) .

added 1 commit

• 4b999abc - add requirement for neo>0.13.0

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OK, in that case, I'll need to merge !486 (merged) first. Thanks!

added 4 commits

• b3a21d95 - Update Neo
• f06f725c - Update py-elephant to 1.1.0
• fb24ee4f - enable new version of py-elephant
• 4bca4179 - add requirement for neo>0.13.0

Compare with previous version

Thanks, for resolving !486 (merged) so promptly. Please let me know if there is anything else

added 4 commits

• 0e51d7a3 - 1 commit from branch technical-coordination/project-internal/devops/platform:master
• e7b46aa4 - Update py-elephant to 1.1.0
• eb6e3256 - enable new version of py-elephant
• 58026c95 - add requirement for neo>0.13.0

Compare with previous version

merged