Bug - Saving error when 1-gram or 2-gram do not tags

[sarahlukens]

Version: 0.3dev0.r28, Error: nestor will crash in certain cases after clicking "UPDATE TAG EXTRACTION"

Steps to reproduce:

• Create new nestor project
• Leave some tagging element empty (such as Single word analysis or Multi word analysis)
• Will get save messages up to "Empty Docs:" ... "Docs must have at most xy tokens (xyth percentile)", then crashes python

Error message:

Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/nestor/ui/taggingUI_app.py", line 1510, in onClick_saveTrack self.completenessPlot.plot_it(nbins) File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/nestor/ui/taggingUI_app.py", line 2267, in plot_it color='xkcd:slate') File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/seaborn/distributions.py", line 231, in distplot kdeplot(a, vertical=vertical, ax=ax, color=kde_color, kde_kws) File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/seaborn/distributions.py", line 691, in kdeplot cumulative=cumulative, kwargs) File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/seaborn/distributions.py", line 294, in _univariate_kdeplot x, y = _scipy_univariate_kde(data, bw, gridsize, cut, clip) File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/seaborn/distributions.py", line 366, in _scipy_univariate_kde kde = stats.gaussian_kde(data, bw_method=bw) File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/scipy/stats/kde.py", line 172, in init self.set_bandwidth(bw_method=bw_method) File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/scipy/stats/kde.py", line 499, in set_bandwidth self._compute_covariance() File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/scipy/stats/kde.py", line 510, in _compute_covariance self._data_inv_cov = linalg.inv(self._data_covariance) File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/scipy/linalg/basic.py", line 975, in inv raise LinAlgError("singular matrix") numpy.linalg.linalg.LinAlgError: singular matrix Abort trap: 6

[rtbs-dev]

Having difficulty reproducing this.

leaving either tab completely empty and both

1. File>Save Project or
2. Report>Update Tag Extraction

are working fine for me. However, this could be related to #56 , since the KDE code is flagging. I think I'll remove KDE plotting, since there is already some code for getting nicely binned histograms in there (I don't think the KDE is really adding much?)

[rtbs-dev]

Should be fixed with 35b11c9 on master. Can you update and report back?

[rtbs-dev]

For now, since the KDE has been removed, I'm going to go ahead and close this. Feel free to comment if something else related to this goes wrong, I'll be happy to re-open.