Climatology Test: Handing masked depths without zspan

[iwensu0313]

Summary

Copied changes from https://github.com/ioos/ioos_qc/pull/104. Added a test to replicate missing values and no zspan set scenario https://github.com/ioos/ioos_qc/issues/65#issuecomment-1033141944. Proposed fix is to set MISSING flag at the end of check() so it doesn't get overridden by the GOOD flag.

Details

• Added new test QartodClimatologyMissingTest to test_qartod.py to capture scenario described in #65. The scenario is when a user passes an array with a missing data point (which gets masked by ioos_qc) and does not set zspan (depth range). The result is that the missing value gets flagged w/ 1 (GOOD) instead of 9 (MISSING).
• qartod.py - the change is moving where we set the MISSING flag to the bottom of the check() function so that it doesn't get overridden when we set the GOOD flags.

At the start of check() we currently set UNKNOWN and MISSING flags

# Start with everything as UNKNOWN (2)
flag_arr = np.ma.empty(inp.size, dtype='uint8')
flag_arr.fill(QartodFlags.UNKNOWN)

# If the value is masked set the flag to MISSING
flag_arr[inp.mask] = QartodFlags.MISSING

However, in this line near the end of the check() function, the slice keeps good data points AND all masked values. And assigns them the QartodFlags.GOOD flag which is a value of 1.

flag_arr[(values_idx & ~fail_idx & ~suspect_idx)] = QartodFlags.GOOD

We do not want MISSING flags (9) to be overridden with a GOOD flag (1), so assigning the MISSING flags at the end can prevent this.

[iwensu0313]

Tests appear to have all passed, but pre-commit check failing. Need to investigate - converted to draft

[ocefpaf]

Tests appear to have all passed, but pre-commit check failing. Need to investigate - converted to draft

Don't worry too much about pre-commits. Those are only code standards and sometimes we can fix those with:

pre-commit.ci autofix

[iwensu0313]

Tests appear to have all passed, but pre-commit check failing. Need to investigate - converted to draft

Don't worry too much about pre-commits. Those are only code standards and sometimes we can fix those with:

pre-commit.ci autofix

Sounds good! I figured out how to fix this one. One of the pre-commit checks auto fixed the issue but the other one I had to fix manually in this commit https://github.com/ioos/ioos_qc/pull/107/commits/485d63535eb1f281f4b0473a364dea723c068ab8. I definitely support sticking w/ code standards :)