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plotly / dash-bio

Open-source bioinformatics components for Dash
https://dash-gallery.plotly.host/Portal/?search=Bioinformatics
MIT License
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Ideogram test for number of chromosomes fails intermittently. #260

Closed mkcor closed 5 years ago

mkcor commented 5 years ago

We've had this CI fail with Python 3.7 over and over again, so there must be a bug: intermittent_fail

We want this number of chromosomes to be deterministic.

mkcor commented 5 years ago

Sorry, this intermittent fail also happens with Python 3.6: fail_py36

mkcor commented 5 years ago

My understanding of test_chromosomes_wrong_input (https://github.com/plotly/dash-bio/blob/master/tests/test_ideogram.py#L297) is that a wrong chromosome name fails silently... Since 'D' isn't valid, it is simply ignored and only '1' and '3' are retained.

mkcor commented 5 years ago

What I've noticed is that, in the screenshots above and CI failures we keep seeing, num_chromosoms actually retained its former value instead of updating as expected. Therefore, I'll try increasing the value of parameter timeout in the wait_for function.

mkcor commented 5 years ago

This other example illustrates the above comment https://github.com/plotly/dash-bio/issues/260#issuecomment-476273274, where the second region wasn't found within 10 seconds (default timeout value): region_count

mkcor commented 5 years ago

Closing for now, because we haven't seen these failures lately (and PR #280, although no silver bullet, may improve things). Will reopen if necessary.