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More informative error message for error reading InferenceData from NetCDF #1637

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merged 4 commits into from
Mar 30, 2021
Merged

More informative error message for error reading InferenceData from NetCDF #1637

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e0da2fd
More informative error message.
rpgoldman Mar 26, 2021
d83dec9
Blacken and pylint.
rpgoldman Mar 26, 2021
626168c
Update Changelog for PR 1637.
rpgoldman Mar 29, 2021
c7eba46
Merge branch 'main' into err-reading-inf-data
OriolAbril Mar 30, 2021
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
* Improved retrieving or pointwise log likelihood in `from_cmdstanpy`, `from_cmdstan` and `from_pystan` ([1579](https://github.com/arviz-devs/arviz/pull/1579) and [1599](https://github.com/arviz-devs/arviz/pull/1599))
* Added interactive legend to bokeh `forestplot` ([1591](https://github.com/arviz-devs/arviz/pull/1591))
* Added interactive legend to bokeh `ppcplot` ([1602](https://github.com/arviz-devs/arviz/pull/1602))
* Add more helpful error message for HDF5 problems reading `InferenceData` from NetCDF ([1637](https://github.com/arviz-devs/arviz/pull/1637))

### Maintenance and fixes
* Enforced using coordinate values as default labels ([1201](https://github.com/arviz-devs/arviz/pull/1201))
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32 changes: 23 additions & 9 deletions arviz/data/inference_data.py
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Expand Up @@ -328,16 +328,30 @@ def from_netcdf(filename: str) -> "InferenceData":
InferenceData object
"""
groups = {}
with nc.Dataset(filename, mode="r") as data:
data_groups = list(data.groups)
try:
with nc.Dataset(filename, mode="r") as data:
data_groups = list(data.groups)

for group in data_groups:
with xr.open_dataset(filename, group=group) as data:
if rcParams["data.load"] == "eager":
groups[group] = data.load()
else:
groups[group] = data
return InferenceData(**groups)
for group in data_groups:
with xr.open_dataset(filename, group=group) as data:
if rcParams["data.load"] == "eager":
groups[group] = data.load()
else:
groups[group] = data
return InferenceData(**groups)
except OSError as e: # pylint: disable=invalid-name
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To use e (instead of err or something a bit longer that pylint considers optimal) as variable to raise errors from other errors, it may be worth it to add it to .pylintrc instead of having to disable the error every time

if e.errno == -101:
raise type(e)(
str(e)
+ (
" while reading a NetCDF file. This is probably an error in HDF5, "
"which happens because your OS does not support HDF5 file locking. See "
"https://stackoverflow.com/questions/49317927/"
"errno-101-netcdf-hdf-error-when-opening-netcdf-file#49317928"
" for a possible solution."
)
)
raise e

def to_netcdf(
self, filename: str, compress: bool = True, groups: Optional[List[str]] = None
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