v2: writing a problem reformats all math expressions, including unchanged ones
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调研方向
Start with how sympify_petab parses expressions on load and how to_df writes them back via petab_math_str in the petab.v2 modules. The proposed fix needs a decision on storing the original string on the expression model, which is a design question for maintainers before any code. Done means an unchanged formula round-trips to its original text, while a changed expression is still printed from sympy.
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描述
In petab.v2, math expressions (observable and noise formulas, condition target values, observable/noise parameter overrides) are stored as sympy expressions, parsed with sympify_petab on load. On writing, to_df prints them with petab_math_str; the original string is not kept. Therefore, loading and writing a problem rewrites every expression, changed or not:
| Input | Written back |
|---|---|
a - (b - c) |
a - b + c |
(100*pApB + 200*pApA)/2 |
100*pApA + 50*pApB |
2 * x / 3 |
0.6666666666666666*x |
log10(x) |
log(x)/log(10) |
The results are mathematically equivalent, but this makes diffs between original and written problems hard to read. E.g., when converting PEtab v1 problems to v2 and writing them, actual changes (like reparametrized noise formulas) are mixed with reformatting of unchanged formulas.
Possible approach: when parsing a string, also store the original string (e.g., as a pydantic private attribute), and write it in to_df if the expression is still equal to the parsed one; otherwise, print the expression. This keeps the current API.
Alternatives considered:
- Storing strings and deriving sympy expressions on demand: breaks the current API.
- Parsing with
evaluate=False: reduces, but does not prevent, reformatting, and changes the expressions returned to users.
🤖 Drafted with AI assistance.
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