Ignore singleton coordinates without dims when attempting to generate bounds #281
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## main #281 +/- ##
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Coverage 100.00% 100.00%
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Files 9 14 +5
Lines 742 1143 +401
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pochedls
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Jul 26, 2022
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| # determine if the axis is also a dimension by determining | ||
| # if there is overlap between the CF axis names and the dimension | ||
| # names. If not, skip over axis for validation. | ||
| if len(set(CF_NAME_MAP[axis]) & set(self._dataset.dims.keys())) == 0: | ||
| continue | ||
|
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Just to make it clear what is going on...
For an axis like lat, set(CF_NAME_MAP[axis]) yields {"Y", "latitude", "lat"}.
set(self._dataset.dims.keys())) yields {'axis_nbounds', 'lat', 'lon', 'time'} .
set(...) & set(...) determines the intersection between these two groups. If there are elements in the resulting set (i.e., len(...) > 0, it means that the axis is also a dimension. If there are no elements in the set, then the axis is not a dimension.
If the axis is not a dimension, there is no need to find bounds and we skip adding bounds.
tomvothecoder
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* initial solution for #278 add unit test add comments for test, cleanup extraneous code initial work on #282 Bugfix/278 cannot generate bounds (#281) * initial solution for #278 * add unit test * add comments for test, cleanup extraneous code * PR review refactor - Add `types-python-dateutil` to `mypy` dependencies - Update `ref_date` var to `ref_dt_obj` to avoid mypy error `error: Unsupported operand types for + ("str" and "relativedelta")` - Use dictionary unpacking for units variable - Use `datetime.strptime` instead of `pd.datetime()` which runs into the `pd.Timestamp` limitation - Add logger.warning when non-CF compliant time coords cannot be decoded * Consider calendar type when decoding non-Cf time - Fix tests * Update xcdat/dataset.py Co-authored-by: pochedls <[email protected]> * Update xcdat/dataset.py Co-authored-by: pochedls <[email protected]> * Fix datetime reference * return more specific cftime datetime types * removing extraneous calendar specification * Refactor using xarray methods - Move try and except statements into `decode_non_cf_time()` - Extract function `_get_cftime_coords()` to encapsulate related logic from `decode_non_cf_time()` * Update docstrings and silence logger warnings in tests * Fix Timestamp limitation from dtype - Update logger warning * Add space in logger warning Co-authored-by: tomvothecoder <[email protected]>
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Description
This fixes an issue for datasets that have a singleton coordinate value (e.g., height = 2m), but not a corresponding dimension. When xcdat tries to add bounds, it hits an error, because the dimension is singleton.
Checklist
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