Update omps edr reader and hdf5_utils to handle OMPS SO2 data from FMI

[TAlonglong]

Update OMPS edr reader and hdf5_utils to handle OMPS SO2 DATA from FMI SAMPO.

The OMPS SO2 data from FMI SAMPO in hdf5 format contains references that need special handling. This update does this.

Also added dataset names special to the data from FMI SAMPO

• Closes Converting hdf5 attributes to string containing h5py.Reference of size 1 causes a AttributeError #630, closes satpy resample call -> numby.ndarray deepcopy error #883
• Tests added
• Tests passed
• Passes flake8 satpy
• Fully documented

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[TAlonglong]

Added updates after major help from @mraspaud, @pnuu and Timo

[djhoese]

This is related to #883 and #630 I think. @TAlonglong thanks for working on this. Any idea if this fixes things for these issues?

[TAlonglong]

Yes @djhoese both of them. One of them is mine. Forgot I issued that :-)

[djhoese]

Thanks again for this. I had a small suggestion on the name of the lon/lat datasets. Could you also add a test to the tests for the HDF5 utils module?

[mraspaud]

LGTM, just some consistency casing remarks

[mraspaud]

Also about consistency, should the dataset have same case and wording as the ones from the other files ?

[coveralls]

Coverage increased (+0.08%) to 89.605% when pulling 4820890 on TAlonglong:feature-omps-reader-update-for-sampo into 103d380 on pytroll:master.

[codecov]

Codecov Report

Merging #1126 into master will increase coverage by 0.08%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master    #1126      +/-   ##
==========================================
+ Coverage   89.52%   89.60%   +0.08%     
==========================================
  Files         200      200              
  Lines       29379    29484     +105     
==========================================
+ Hits        26301    26420     +119     
+ Misses       3078     3064      -14     

Impacted Files	Coverage Δ
satpy/readers/hdf5_utils.py	92.42% <100.00%> (+0.62%)	⬆️
satpy/readers/omps_edr.py	100.00% <100.00%> (+3.84%)	⬆️
satpy/tests/reader_tests/test_omps_edr.py	98.98% <100.00%> (+0.66%)	⬆️
satpy/readers/fci_l1c_fdhsi.py	96.15% <0.00%> (-0.03%)	⬇️
satpy/tests/writer_tests/test_cf.py	98.53% <0.00%> (ø)
satpy/tests/reader_tests/test_utils.py	100.00% <0.00%> (ø)
satpy/tests/reader_tests/test_ahi_hsd.py	100.00% <0.00%> (ø)
satpy/tests/reader_tests/test_geos_area.py	100.00% <0.00%> (ø)
satpy/tests/reader_tests/test_fci_l1c_fdhsi.py	100.00% <0.00%> (ø)
satpy/tests/reader_tests/test_seviri_l1b_hrit.py	100.00% <0.00%> (ø)
... and 6 more

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[TAlonglong]

I have renamed the datsets to match with the other dataset and marked them with sampo to reflect the data source.

for the test on the hdf5_utils it looks to me this is already covered.

[mraspaud]

I'm good with the changes, looks good to me. One last thing: the reader seems to be missing from the index.rst documentation table, can you update it @TAlonglong ?

[TAlonglong]

OK. Updated.

But I see that the data DIMENSION_LIST stuff we added is not tested. I tried to add test to handle this, but what ever I try the DIMENSION_LIST attribute I add never get to where this is used in the reader.

[mraspaud]

If you want to test the dimension list, it should ideally be a list of references. Actually in the files it looks like this:

variable.attrs['DIMENSION_LIST'] = np.array([np.array([ref1]), np.array([ref2])])

[TAlonglong]

OK, I tried with this: https://github.com/pytroll/satpy/pull/1126/files#diff-c736dc353b90f5ae010c5b8b42896df5R114 but the attribute I set here is not handled. So it never get into the data.attrs. And I dont understand why this attr I set just disapear.

[mraspaud]

I can try to have a look later

[mraspaud]

LGTM