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Use get to avoid KeyError on missing cmiles attribute #300

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merged 14 commits into from
Oct 21, 2024
Merged

Use get to avoid KeyError on missing cmiles attribute #300

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f64d35b
use `get` to avoid KeyError on missing cmiles attribute
ntBre Oct 4, 2024
2ab5d7e
add failing test for #299
ntBre Oct 7, 2024
bbb9a06
warn with MissingCMILESWarning instead of printing
ntBre Oct 7, 2024
abd6d7c
check that a warning is emitted
ntBre Oct 7, 2024
0934011
run pre-commit hooks
ntBre Oct 7, 2024
1dbd9a0
switch to logging from warnings
ntBre Oct 9, 2024
e70ec87
move individual warnings to info level to hide by default
ntBre Oct 9, 2024
4b06d4c
call basicConfig first to fully initialize logger
ntBre Oct 9, 2024
4677298
track total number of missing CMILES and warn at the end
ntBre Oct 9, 2024
eedf0d6
extend the warning message to mention loading from an opt dataset
ntBre Oct 9, 2024
666c343
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 9, 2024
f93d7fe
update release notes
ntBre Oct 15, 2024
a4a7b03
fix extra colon
ntBre Oct 15, 2024
89b0564
fix minor typos
ntBre Oct 21, 2024
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8 changes: 4 additions & 4 deletions openff/qcsubmit/results/results.py
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Original file line number Diff line number Diff line change
Expand Up @@ -321,9 +321,9 @@ def from_datasets(
"canonical_isomeric_explicit_hydrogen_mapped_smiles"
)
if not cmiles:
cmiles = entry.attributes[
cmiles = entry.attributes.get(
"canonical_isomeric_explicit_hydrogen_mapped_smiles"
]
)
if not cmiles:
print(f"MISSING CMILES! entry = {entry_name}")
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@j-wags j-wags Oct 7, 2024 •
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(blocking) Could you change this to be warnings.warn with a new warning type like MissingCMILESWarning?

continue
Expand Down Expand Up @@ -470,9 +470,9 @@ def from_datasets(
"canonical_isomeric_explicit_hydrogen_mapped_smiles"
)
if not cmiles:
cmiles = entry.attributes[
cmiles = entry.attributes.get(
"canonical_isomeric_explicit_hydrogen_mapped_smiles"
]
)
if not cmiles:
print(f"MISSING CMILES! entry = {entry_name}")
continue
Expand Down
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