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remove --nan-to-num CLI parameter (#548)

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* remove --nan-to-num CLI parameter

* factor tests better

* lint - remove unused variables
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Bruce Martin
2019-01-10 15:03:03 -08:00
committed by GitHub
parent f876a0091a
commit 5d60505407
8 changed files with 34 additions and 183 deletions
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docs/faq.md
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@@ -86,12 +86,6 @@ cellxgene prepare data/ --output=data-processed.h5ad --recipe=zheng17
It should be easy to run `prepare` then call `cellxgene launch` a few times with different settings to explore different behaviors. We may explore adding other preprocessing options in the future.
#### When I start _cellxgene_, I get an error `Unexpected HTTP response 500, INTERNAL SERVER ERROR -- Out of range float values are not JSON compliant` in the web UI, or `Warning: JSON encoding failure - suggest trying --nan-to-num command line option` in the CLI. What can I do?
At the moment, _cellxgene_ is unable to transmit floating point NaN or Infinity values to the web UI (due to a limitation on data serialization method in use). We expect to resolve this in a future release, but in the meantime, you can work around this issue by starting cellxgene with the `--nan-to-num` command line option, ie, `cellxgene launch data.h5ad --nan-to-num`.
This option will convert all NaNs to zero, and all positive/negative infinities to the min/max of the data element within which the value was found (eg, +Infinity within an `obs` annotation will be converted to the maximum finite value in that annotation). This option will increase startup time, so we recommend only using it when the dataset contains NaN/Infinities.
#### I tried to `pip install cellxgene` and got a weird error I don't understand
This may happen, especially as we work out bugs in our installation process! Please create a new [Github issue](https://github.com/chanzuckerberg/cellxgene/issues), explain what you did, and include all the error messages you saw. It'd also be super helpful if you call `pip freeze` and include the full output alongside your issue.