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I am trying to mask clouds using the python API in Google Earth Engine, but the masked values are exporting as 0s instead of NAs. I am basically following the code here Apply cloud mask to Landsat Imagery in Google Earth Engine Python API

I have run the code in the GEE browser, and that actually exports the mask values as NAs, but not sure how to get the python API to do so.

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Quite some time has passed from your question so you may have solved already.
In any case, I've used the ee.Image.unmask method to replace the value of masked pixels in Sentinel 2 imagery. I typically go for values like -9999 rather than NAs, but I guess the method would do also in that case.

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