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`sympify_petab` returns `Integer` for Python/numpy integers, but `Float` for numeric strings

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Avaliação

Dificuldade
2/5
Tempo estimado
1-3 horas
Facilidade para iniciantes
50/100
Tipo de issue
Bug
Clareza
Razoavelmente clara
Status de atividade
Ativa
Stack de tecnologia
python
Domínio
data

Direção de pesquisa

Start with sympify_petab in the petab.v1.math module and its docstring, which already says integers become floats. Reproduce the four calls in the issue to see the current Integer/Float split. Deciding whether to convert Python and numpy integers to sp.Float is a maintainer call, since existing callers would see a different return type. Done means the agreed behaviour is implemented and the v2 round-trip comparison holds.

Escrita pelo modelo de indexação a partir do texto da issue.

Descrição

sympify_petab converts numeric strings to sp.Float, but Python and numpy integers to sp.Integer:

import numpy as np
from petab.v1.math import sympify_petab

sympify_petab("2")          # Float: 2.00000000000000
sympify_petab(2.0)          # Float: 2.00000000000000
sympify_petab(2)            # Integer: 2
sympify_petab(np.int64(2))  # Integer: 2

Since sympy 1.13, sp.Integer(2) != sp.Float(2), so the type matters for comparisons. And integer arithmetic stays exact: sympify_petab(1) / sympify_petab(3) gives 1/3, while sympify_petab("1") / sympify_petab("3") gives 0.333333333333333.

In petab.v2, which parses all math fields with sympify_petab, this has the following effects:

  • For the same file content, the type depends on pandas' dtype inference for the whole column. A targetValue of 2 is parsed as Integer if all target values in the condition table are integers, and as Float if any other row contains a non-integer or an expression.
  • Objects created from Python integers, e.g. Change(target_id="k1", target_value=2), do not compare equal to the same objects after writing and reading them back, because the value is written as 2.0 and read back as Float.

PEtab numbers are floating point (the sympify_petab docstring also says "integer values are converted to floats", which currently only holds for strings). Converting integers to sp.Float in sympify_petab would make this consistent. However, this would change the return value for existing callers that pass Python integers.

🤖 Drafted with AI assistance.

Linguagem predominante
Python
Estrelas
18
Forks
9
Merge médio
1d 21h
PRs com merge (30d)
25

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