[dweindl]

PEtab v2 has no parameterScale. To estimate a parameter <id> on log scale, or to specify a prior for log10(<id>), the v2 spec recommends replacing <id> by a new parameter log10_<id> with <id> = 10^log10_<id>.

This adds petab.v2.reparametrize_log(problem, parameter_ids, ...), which does this for the given parameters on a copy of the problem and returns the copy and the mapping of old to new parameter IDs:

• parameter table: log-transformed bounds (dropped for non-estimated parameters) and nominal value; priors from the priors argument, or derived from log-normal, log-laplace and log-uniform priors on <id> (other priors on <id> raise; priors of non-estimated parameters raise NotImplementedError unless dropped via priors={<id>: None})
• SBML model: new parameter log10_<id> and initial assignment <id> = 10^log10_<id> (replacing any existing one; <id> stays constant=true)
• observable/noise formulas and condition target values: <id> → 10^log10_<id>
• measurement overrides: replaced by the new IDs, numeric overrides are log-transformed, and the placeholder ph is replaced by 10^ph in the formulas

A lower bound of 0 becomes -inf, following PEtab-dev/PEtab#682. If other estimated parameters have priors, such a parameter needs an explicit prior, since the default uniform(lb, ub) would be improper; otherwise, a ValueError is raised. A nominal value of 0 becomes -inf, assuming PEtab-dev/PEtab#685 is accepted, e.g., for parameters fixed at 0.

Problems with required extensions are not supported.

Base e (log_<id>) is supported as well. The procedure follows the one described in the proposed v1→v2 migration guide (PEtab-dev/PEtab#680).

Split off from #539, which uses this in petab1to2(reparametrize=...) to preserve v1 parameter-scale priors.

🤖 Generated with Claude Code

[codecov-commenter]

Codecov Report

❌ Patch coverage is 94.18605% with 10 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.85%. Comparing base (e654711) to head (98e2737).

Files with missing lines	Patch %	Lines
petab/v2/reparametrize.py	94.93%	4 Missing and 4 partials ⚠️
petab/v2/models/_sbml_utils.py	81.81%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #560      +/-   ##
==========================================
+ Coverage   78.44%   78.85%   +0.41%     
==========================================
  Files          68       69       +1     
  Lines        7876     8043     +167     
  Branches     1406     1445      +39     
==========================================
+ Hits         6178     6342     +164     
  Misses       1214     1214              
- Partials      484      487       +3     

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[dilpath]

Thanks!