Detect if --verbose passed through Q2, and if so show logging messages #95
Assignees
Labels
enhancement
New feature or request
Comments
|
also should probs mention that this is like the lowest-priority issue in the universe |
fedarko
added a commit
that referenced
this issue
May 1, 2019
Due to problems with this making test output basically incomprehensible (due to an avalanche of debug text). Will eventually try to fix this (making --verbose in Q2 show these messages) in #95, but that's not a high-priority issue r/n.
fedarko
added a commit
to fedarko/qurro
that referenced
this issue
Jul 24, 2019
TL;DR -- I haven't touched a lot of this code in a while, and things
looked a bit gnarly.
The following things now result in a print message being sent:
- Empty samples being removed (prev was a logging.debug msg)
- Empty features being removed (prev was a logging.debug msg)
- Features in the table (that weren't in the rankings) being dropped
- Feature filtering (-x) being done:
- Starting and ending number of features are now printed, along
with the total number of features filtered.
Also, I removed the print_warning argument of
filter_unextreme_features(). Changing the way we invoke pytest (in
particular, removing the -s option, I think) means that print messages
that happen during the course of the Qurro python tests won't clutter
up the display. (A possible TODO: see if we can't use this behavior to
finally address biocore#95?) One nice thing about this was it allowed us to
simplify some of the -x-related code a bit.
Also added some documentation re: match_table_and_data() and
filter_unextreme_features(), for whomstever ends up looking at this
code in the future (...probably just me but whatevs). Open question:
does anyone except for me even read these commit messages? If you're
reading this right now, send me an email :P
fedarko
added a commit
to fedarko/qurro
that referenced
this issue
Jul 24, 2019
We can reasonably use --verbose in the Q2 examples now that biocore#95 stuff is sorted out. (Using --verbose in q2-qurro should be equivalent to the default invocation of standalone Qurro.) [ci skip]
This issue was closed.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Just showing logging messages all the time results in a deluge of output when running the python rrv tests. And checking if
pytestis insys.modulesor something similar when inplugin_setup.py(see here) doesn't seem to work, due to how QIIME 2 is set up.This means that for the moment
--verboseshows more stuff in the standalone code than in the Q2 code. I'm not super happy with that, but it isn't the worst thing. At least the logging statements are still in the code.The text was updated successfully, but these errors were encountered: