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888 undo the suppressing of xarray chunking warning #918

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merged 4 commits into from
Aug 5, 2024
Merged

888 undo the suppressing of xarray chunking warning #918

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757b536
undo suppressing of warning
veenstrajelmer Aug 5, 2024
47c4146
update minimal xugrid version
veenstrajelmer Aug 5, 2024
8e0a19c
chunks=auto in testcase
veenstrajelmer Aug 5, 2024
0b50401
try again
veenstrajelmer Aug 5, 2024
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4 changes: 0 additions & 4 deletions dfm_tools/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,3 @@
from dfm_tools import data
from dfm_tools.modelbuilder import *
from dfm_tools.observations import *

import warnings
# suppress chunks warning: https://github.com/Deltares/dfm_tools/issues/679
warnings.filterwarnings("ignore", category=UserWarning, message='The specified chunks separate the stored chunks along dimension "time" starting at index 1. This could degrade performance. Instead, consider rechunking after loading.')
4 changes: 2 additions & 2 deletions pyproject.toml
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Expand Up @@ -36,8 +36,8 @@ dependencies = [
"netcdf4>=1.5.4",
#bottleneck<1.3.3 pip install fails in py39
"bottleneck>=1.3.3",
#xugrid<0.9.0 does not support partitioned 1d2d grids
"xugrid>=0.9.0",
#xugrid<0.11.0 does not use all meshkernel attrs (https://github.com/Deltares/xugrid/pull/250) and is not rechunking partitions (https://github.com/Deltares/xugrid/pull/253)
"xugrid>=0.11.0",
#cdsapi<0.7.0 supports credentials from environment variables
"cdsapi>=0.7.0",
#pydap<3.4.0 is from May 2017 and does not support newer python versions
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20 changes: 9 additions & 11 deletions tests/test_external_packages.py
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Expand Up @@ -149,20 +149,18 @@ def test_xarray_decode_default_fillvals(tmp_path):
file_out = os.path.join(tmp_path, 'temp_fnc_default_fillvals_map.nc')
ds.to_netcdf(file_out)

# chunks=auto to avoid "UserWarning: The specified chunks separate the stored chunks along dimension "time" starting at index 1. This could degrade performance. Instead, consider rechunking after loading."
chunks = 'auto'

#open dataset with decode_fillvals
try:
uds = dfmt.open_partitioned_dataset(file_out,decode_fillvals=False)
except Exception as e:
# this raises "ValueError: connectivity contains negative values"
with pytest.raises(ValueError) as e:
# until xarray handles default fillvalues: https://github.com/Deltares/dfm_tools/issues/490
assert isinstance(e,ValueError)
if 'uds' in locals():
raise Exception("apparently xarray now decodes default fillvalues, so "
"`dfmt.decode_default_fillvals()` can be removed if minimum xarray "
"version is set as requirement")

# if xarray handles default fillvalues, `dfmt.decode_default_fillvals()` can be removed if minimum xarray version is set as requirement
uds = dfmt.open_partitioned_dataset(file_out, decode_fillvals=False, chunks=chunks)
assert "connectivity contains negative values" in str(e.value)

#this should be successful
uds2 = dfmt.open_partitioned_dataset(file_out,decode_fillvals=True)
uds2 = dfmt.open_partitioned_dataset(file_out, decode_fillvals=True, chunks=chunks)
fnc_new = uds2.grid.face_node_connectivity

assert fill_value_default in fnc_new
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