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petab1to2: deterministic name for pre-existing experimentId column - #572
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| f"The measurement table has a column `{v2.C.EXPERIMENT_ID}`, " | ||
| "which is reserved in PEtab v2. " | ||
| f"It was renamed to `{renamed_experiment_id}`.", | ||
| # call to `petab1to2` |
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This refers to the stacklevel. The problem is that we have potentially different user entry points. Currently, the stacklevel assumes that a user called petab1to2. Clarified.
Rename a pre-existing `experimentId` column in v1 measurement tables to `experimentId_v1` (with a numeric suffix if taken) instead of `experiment_id_<uuid4>`, consistently across all measurement files, and warn about the rename. Closes PEtab-dev#568. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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…3494) Since PEtab-dev/libpetab-python#572, `petab1to2` warns when it renames a v1 measurement table column `experimentId`, which is reserved in PEtab v2. With warnings as errors, the v1→v2 auto-upgrade fails, and so do the JAX benchmark tests for Brannmark_JBC2010 and Isensee_JCB2018 (e.g., https://github.com/AMICI-dev/AMICI/actions/runs/40377463587/job/121764332167). The renamed column is not used for simulation, so the warning is ignored. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
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petab1to2renamed a pre-existingexperimentIdcolumn in v1 measurement tables toexperiment_id_<uuid4>, so repeated conversions of the same problem (e.g.,Brannmark_JBC2010,Isensee_JCB2018) produced different output.Now the column is renamed to
experimentId_v1(with a numeric suffix if that name is taken), chosen consistently across all measurement files, and a warning is emitted.Closes #568.
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