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Add a non-normative page "Upgrading from PEtab v1" to the v2 documentation. It lists the structural changes, explains the numerical consequences of the removal of `parameterScale`, describes how to reparametrize log-scaled parameters (`log10_k` with `k = 10^log10_k`), the `reparametrize` option of `petab1to2`, the other changes affecting objective values (log10 observables, truncated priors, default prior), and how to verify a conversion. References #680. The `petab1to2` section describes PEtab-dev/libpetab-python#539. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
The sphinx_rtd_theme sets `white-space: nowrap` on all table cells, which makes tables with longer text, such as the structural changes table in the migration guide, require horizontal scrolling. Override this in `custom.css` so that cell contents wrap. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
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Adds a non-normative page "Upgrading from PEtab v1" to the v2 documentation (
doc/v2/migration_guide.rst, linked from the v2 toctree after the tutorial).Contents: a quick path for the typical case; the structural changes (handled by
petab1to2) and what has to be done by hand; the numerical consequences of removingparameterScale, i.e., how PEtab v1 tools evaluated priors on log-scaled parameters (D2D, pyPESTO, libpetab-python at pinned commits), what PEtab v2 specifies, and why a faithful conversion reparametrizes log-scaled parameters aslog10_kwithk = 10^log10_kin the model; the step-by-step reparametrization recipe including measurement-table placeholders; thereparametrizeoption ofpetab1to2; the other changes affecting objective values (log10observables, truncated priors, default prior); and a verification procedure.Also allows line breaks in table cells (
doc/_static/custom.css), since the RTD theme'snowrapmade wider tables scroll horizontally.The spec page is not modified. Infinite bounds follow erratum E1 (#684). The
petab1to2section describespetab.v2.reparametrize_log(PEtab-dev/libpetab-python#560, merged) andpetab1to2(reparametrize=...)(PEtab-dev/libpetab-python#539, not merged yet; the option names may still change there). A second page on comparing objective values across tools will follow in a separate PR.References #680.
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👀 https://petab--683.org.readthedocs.build/en/683/v2/migration_guide.html