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labscript-suite-temp-2 / lyse

lyse is an analysis framework. It coordinates the running of python analysis scripts on experiment data as it becomes availiable, updating plots in real time.
BSD 2-Clause "Simplified" License
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Incompatibilities with pandas 0.20.1 #20

Closed philipstarkey closed 7 years ago

philipstarkey commented 7 years ago

Original report (archived issue) by Shaun Johnstone (Bitbucket: shjohnst, GitHub: shjohnst).

lyse is not currently compatible with pandas 0.20.1

The second shot to have a singleshot analysis routine run on it is replaced with nan's after the first singleshot analysis routine runs on it.

philipstarkey commented 7 years ago

Original comment by Chris Billington (Bitbucket: cbillington, GitHub: chrisjbillington).

Thanks. I'll take a look at this next Monday.

There are some fairly roundabout ways of manipulating dataframes in lyse, because the functionality to do what we wanted more directly was not available when we started using pandas. Pandas seems to be changing rapidly, maybe there are more kosher ways of doing these things now. I assume the problem you're describing probably comes down to something in dataframe_utilities.replace_with_padding() since that's where the replacing of a row happens after an analysis routine runs.

philipstarkey commented 7 years ago

Original comment by Chris Billington (Bitbucket: cbillington, GitHub: chrisjbillington).

Fix in pull request #15, feel free to merge it and see how it goes. I don't advise pulling from my fork to test because my default branch is a warzone. But I've tested the fix and it seems to fix the issue for me.

philipstarkey commented 7 years ago

Original comment by David Meyer (Bitbucket: dihm, GitHub: dihm).

I can also confirm that pull request #15 fixes this issue on my systems.

On a related tangent, I noticed in the Release notes for pandas 0.20 that the .ix indexer is starting the deprecation process. Would it be a good thing to update it now to .iloc? The only instance I found was line 1321 of lyse main.py

philipstarkey commented 7 years ago

Original comment by Chris Billington (Bitbucket: cbillington, GitHub: chrisjbillington).

Thanks for testing David, I'll merge the pull request, and have changed .ix to .iloc.

philipstarkey commented 7 years ago

Original comment by Chris Billington (Bitbucket: cbillington, GitHub: chrisjbillington).

Fixed issue #20, dataframe_utilities.replace_with_padding() not working on pandas 0.20.1.

→ \<\<cset 27e91cfc7cde4c8e39b3a0d138f7e11462a718b3>>

philipstarkey commented 7 years ago

Original comment by Chris Billington (Bitbucket: cbillington, GitHub: chrisjbillington).

Merged in cbillington/lyse/bugfix (pull request #15)

Fixed issue #20

→ \<\<cset 4cf4a3802b4e78d858db4a28842bc58d18d862d5>>