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fix: allow for numeric coercion after python_evalish_coerce #489

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fix: allow for numeric coercion after python_evalish_coerce #489

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10 changes: 9 additions & 1 deletion spras/config/algorithms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,14 @@
# This contains the dynamically generated algorithm schema for use in `schema.py`
__all__ = ['AlgorithmUnion']

def is_numeric(value: Any) -> bool:
"""Checks if the input value can be parsed by `float`."""
try:
float(value)
return True
except ValueError:
return False

def is_numpy_friendly(type: type[Any] | None) -> bool:
"""
Whether the passed in type can have any numpy helpers.
Expand All @@ -44,7 +52,7 @@ def python_evalish_coerce(value: Any) -> Any:
resources if wanted. This only prevents secret leakage.
"""

if not isinstance(value, str):
if not isinstance(value, str) or is_numeric(value):
return value

# These strings are in the form of function calls `function.name(param1, param2, ...)`.
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8 changes: 8 additions & 0 deletions test/test_config.py
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@ntalluri ntalluri Jun 15, 2026 •
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Reminder to add the test cases that tony had in #488

@tristan-f-r tristan-f-r Jun 16, 2026

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A few of these tests (link) would only serve to test Pydantic itself, but the tests which check for specific scientific notation would be good to ensure that the weak float test does capture all of the behavior we want.

Original file line number Diff line number Diff line change
Expand Up @@ -67,6 +67,9 @@ def get_test_config():
"include": True,
"runs": {
"strings": {"dummy_mode": ["terminals", "others"], "b": 3},
# We include slightly absurd numbers here for b
# to test https://github.com/Reed-CompBio/spras/issues/484.
"scientific": {"dummy_mode": "terminals", "b": ["1e-2", "1e2"]},
# spacing in np.linspace is on purpose
"singleton_string_np_linspace": {"dummy_mode": "terminals", "b": "np.linspace(0, 5,2,)"},
"str_array_np_logspace": {"dummy_mode": ["others", "all"], "g": "np.logspace(1,1)"}
Expand Down Expand Up @@ -296,6 +299,11 @@ def test_config_values(self):
OmicsIntegrator2Params(dummy_mode=DummyMode.others, b=3)
])

value_test_util('omicsintegrator2', 'scientific', OmicsIntegrator2Params, [
OmicsIntegrator2Params(dummy_mode=DummyMode.terminals, b=100),
OmicsIntegrator2Params(dummy_mode=DummyMode.terminals, b=0.01)
])

value_test_util('omicsintegrator2', 'singleton_string_np_linspace', OmicsIntegrator2Params, [
OmicsIntegrator2Params(dummy_mode=DummyMode.terminals, b=5.0),
OmicsIntegrator2Params(dummy_mode=DummyMode.terminals, b=0.0)
Expand Down
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