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Add `reparametrize_log` and `petab1to2(reparametrize=...)` - #539

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dweindl wants to merge 6 commits into

PEtab-dev:mainfrom

dweindl:petab1to2-reparametrize-log

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Add `reparametrize_log` and `petab1to2(reparametrize=...)`#539
dweindl wants to merge 6 commits into
PEtab-dev:mainfrom
dweindl:petab1to2-reparametrize-log

Commits on Oct 15, 2026
- Add `reparametrize_log` and `petab1to2(reparametrize=...)`
  
  dweindl
  and
  claude
  committed
  bdad27e
- Improve error for placeholders that can't be log-transformed
  
  dweindl
  and
  claude
  committed
  0afcdff
- Use `math.log10` in `reparametrize_log` for base 10
  
  dweindl
  and
  claude
  committed
  724c3d0
- Define reparametrized model parameters by initial assignments
  
  dweindl
  and
  claude
  committed
  83d3402
- Skip log-scaled parameters with a lower bound of 0 in `petab1to2`
  
  dweindl
  and
  claude
  committed
  fd3334d
- Address review comments on log reparametrization
  
  dweindl
  and
  claude
  committed
  4be4d4a