Add flags to skip processing steps

[Hneuschmidt]

Add 3 flags to skip the downloading, s2 pre-processing and s3 pre-processing steps if so desired by the user. The user is responsible for making sure that the other command line arguments match the existing files downloaded or pre-processed in a previous run.

@radosuav this is a straightforward implementation of the "skipping steps CLI" discussed in #4 and #5 .

Please let me know if you have any comments / requests, especially on the following:

• Should it be possible to skip the fusion step? We could add another flag, but I am not sure what would be the use case for this
• Are the names of the flags fine, or do you have other (e.g. shorter) ideas?
• Should there be some output (e.g. logging) to remind the user, that steps are being skipped, and which files are being used for the processing?

Regarding the last point, I have refrained from adding any output because currently, the program only outputs what tqdm produces, as far as I know. I would be happy to add some logging when steps are skipped (or even print statements). Do you have any preference on this?

[radosuav]

Hi @Hneuschmidt and sorry for the delay, I overlooked this in the end of year rush! The code looks good, I would just set the default values to False, to keep the original behavior.

But I am thinking that maybe it would be better to have more granular control, especially for Sentinel-3 preprocessing. E.g. user might not want to redo the binning (which is most time consuming) but then would like to test different settings for the median composite. But not sure how to approach this, maybe just two flags:
skip_s3_pre_processing - skips the full preprocessing
skip_s3_binning - skips the binning but does other pre-processing steps

Regarding your questions:

Should it be possible to skip the fusion step? We could add another flag, but I am not sure what would be the use case for this

I also don't see the use case for this flag

Are the names of the flags fine, or do you have other (e.g. shorter) ideas?

I think they are nice and clear

Should there be some output (e.g. logging) to remind the user, that steps are being skipped, and which files are being used for the processing?

Maybe a simple print statement if something is skipped would be nice, just to avoid confusion