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AllenSWDB / allenswdb.github.io

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Visual behavior section does not build correctly #9

Closed galenlynch closed 1 year ago

galenlynch commented 1 year ago

@corbennett 

/root/capsule/databook/visual-behavior/VB-BehaviorSessionData.md: WARNING: Executing notebook failed: CellExecutionError [mystnb.exec]
/root/capsule/databook/visual-behavior/VB-BehaviorSessionData.md:22: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header]
/root/capsule/databook/visual-behavior/VB-BehaviorSessionData.md: WARNING: Notebook exception traceback saved in: /root/capsule/scratch/_build/html/reports/visual-behavior/VB-BehaviorSessionData.err.log [mystnb.exec]
/root/capsule/databook/visual-behavior/VBN-SessionData.md:169: WARNING: image file not readable: resources/dlc_eye_label_example.png
/root/capsule/databook/visual-behavior/VBN-Tutorial-Aligning_Behavior_Data_to_Task_Events.md:28: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
/root/capsule/databook/visual-behavior/VBN-Tutorial-Aligning_Behavior_Data_to_Task_Events.md:54: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
/root/capsule/databook/visual-behavior/VBN-Tutorial-Aligning_Behavior_Data_to_Task_Events.md:172: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
/root/capsule/databook/visual-behavior/VBN-Tutorial-Aligning_Behavior_Data_to_Task_Events.md:192: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
/root/capsule/databook/visual-behavior/VBN-Tutorial-Aligning_Behavior_Data_to_Task_Events.md:204: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
/root/capsule/databook/visual-behavior/VBN-Tutorial-Aligning_Behavior_Data_to_Task_Events.md:216: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
/root/capsule/databook/visual-behavior/VBO-Dataset.md:47: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header]
/root/capsule/databook/visual-behavior/VBO-Dataset.md:51: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header]
/root/capsule/databook/visual-behavior/VBO-Dataset.md:55: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header]
/root/capsule/databook/visual-behavior/VBO-Dataset.md:61: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header]
/root/capsule/databook/visual-behavior/VBO-Dataset.md:158: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header]
/root/capsule/databook/visual-behavior/VBO-Dataset.md:206: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header]
/root/capsule/databook/visual-behavior/VBO-Dataset.md:250: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header]
/root/capsule/databook/visual-behavior/VBO-Dataset.md:357: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header]
/root/capsule/databook/visual-behavior/VBO-Dataset.md:377: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header]
/root/capsule/databook/visual-behavior/VBO-Dataset.md:391: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header]
/root/capsule/databook/visual-behavior/VBO-ExperimentData.md: WARNING: Executing notebook failed: CellExecutionError [mystnb.exec]
/root/capsule/databook/visual-behavior/VBO-ExperimentData.md:26: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header]
/root/capsule/databook/visual-behavior/VBO-ExperimentData.md:220: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
/root/capsule/databook/visual-behavior/VBO-ExperimentData.md:240: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
/root/capsule/databook/visual-behavior/VBO-ExperimentData.md:260: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
/root/capsule/databook/visual-behavior/VBO-ExperimentData.md:298: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
/root/capsule/databook/visual-behavior/VBO-ExperimentData.md:365: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
/root/capsule/databook/visual-behavior/VBO-ExperimentData.md:389: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
/root/capsule/databook/visual-behavior/VBO-ExperimentData.md:450: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
/root/capsule/databook/visual-behavior/VBO-ExperimentData.md:471: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
/root/capsule/databook/visual-behavior/VBO-ExperimentData.md: WARNING: Notebook exception traceback saved in: /root/capsule/scratch/_build/html/reports/visual-behavior/VBO-ExperimentData.err.log [mystnb.exec]
/root/capsule/databook/visual-behavior/VBO-Tutorial-Compare_trial_types.md: WARNING: Executing notebook failed: CellExecutionError [mystnb.exec]
/root/capsule/databook/visual-behavior/VBO-Tutorial-Compare_trial_types.md:283: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
/root/capsule/databook/visual-behavior/VBO-Tutorial-Compare_trial_types.md:303: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
/root/capsule/databook/visual-behavior/VBO-Tutorial-Compare_trial_types.md: WARNING: Notebook exception traceback saved in: /root/capsule/scratch/_build/html/reports/visual-behavior/VBO-Tutorial-Compare_trial_types.err.log [mystnb.exec]
/root/capsule/databook/visual-behavior/VBO-Tutorial-Downloading_data_and_navigating_the_manifest.md: WARNING: Executing notebook failed: CellExecutionError [mystnb.exec]
/root/capsule/databook/visual-behavior/VBO-Tutorial-Downloading_data_and_navigating_the_manifest.md: WARNING: Notebook exception traceback saved in: /root/capsule/scratch/_build/html/reports/visual-behavior/VBO-Tutorial-Downloading_data_and_navigating_the_manifest.err.log [mystnb.exec]
galenlynch commented 1 year ago

This code in databook/visual-behavior/VBO-Tutorial-Compare_trial_types.md doesn't seem to work:

trial = ophys_experiment.trials.query('hit').sample()
fig, axes = make_trial_plot(trial)

Here is the output:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[27], line 2
      1 trial = ophys_experiment.trials.query('miss').sample(random_state = 2)
----> 2 fig, axes = make_trial_plot(trial)

Cell In[23], line 77, in make_trial_plot(trial)
     74 fig, axes = plt.subplots(4, 1, figsize = (15, 8), sharex=True)
     76 for ax in axes:
---> 77     plot_stimuli(trial, ax)
     79 plot_running(trial, axes[0])
     81 plot_licks(trial, axes[1])

Cell In[23], line 6, in plot_stimuli(trial, ax)
      2 '''
      3 plot stimuli as colored bars on specified axis
      4 '''
      5 stimuli = stimulus_presentations.copy()
----> 6 stimuli = stimuli[(stimuli.end_time >= trial['start_time']) & 
      7                   (stimuli.start_time <= trial['stop_time'])]
      8 for idx, stimulus in stimuli.iterrows():
      9     ax.axvspan(stimulus['start_time'], stimulus['end_time'], color=stimulus['color'], alpha=0.5)

File /opt/envs/allensdk/lib/python3.8/site-packages/pandas/core/ops/common.py:72, in _unpack_zerodim_and_defer.<locals>.new_method(self, other)
     68             return NotImplemented
     70 other = item_from_zerodim(other)
---> 72 return method(self, other)

File /opt/envs/allensdk/lib/python3.8/site-packages/pandas/core/arraylike.py:62, in OpsMixin.__ge__(self, other)
     60 @unpack_zerodim_and_defer("__ge__")
     61 def __ge__(self, other):
---> 62     return self._cmp_method(other, operator.ge)

File /opt/envs/allensdk/lib/python3.8/site-packages/pandas/core/series.py:6237, in Series._cmp_method(self, other, op)
   6234 res_name = ops.get_op_result_name(self, other)
   6236 if isinstance(other, Series) and not self._indexed_same(other):
-> 6237     raise ValueError("Can only compare identically-labeled Series objects")
   6239 lvalues = self._values
   6240 rvalues = extract_array(other, extract_numpy=True, extract_range=True)

ValueError: Can only compare identically-labeled Series objects
galenlynch commented 1 year ago

I just disabled it...