Support for petab v2 experiments#332
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Codecov ReportAttention: Patch coverage is
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## develop #332 +/- ##
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+ Coverage 74.56% 74.66% +0.09%
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Files 56 56
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| if exp_id in experiments: # noqa: B023 | ||
| i = 1 | ||
| while f"{exp_id}_{i}" in experiments: # noqa: B023 | ||
| i += 1 | ||
| exp_id = f"{exp_id}_{i}" |
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Why would this occur? Ah, because no symbol is inserted between preeq_cond_id and sim_cond_id? Then maybe my suggestion with __ means you can remove this?
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There might be measurements for ('foo', 'bar') and (None, 'foo__bar') which would result in colliding experiment IDs. You never know...
petab/v2/petab1to2.py
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| { | ||
| v2.C.EXPERIMENT_ID: exp_id, | ||
| v2.C.CONDITION_ID: preeq_cond_id, | ||
| v2.C.TIME: float("-inf"), |
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Could use -TIME_STEADY_STATE, or add some TIME_PREEQUILIBRATION
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Added TIME_PREEQUILIBRATION
Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>
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Add basic support for PEtab version 2 experiments (see also PEtab-dev/PEtab#586, and PEtab-dev/PEtab#581). Follow-up to #334.
Partially supersedes #263, which was started before petab.v1/petab.v2 were introduced and before PEtab-dev/PEtab#586.
simulationConditionIds (but does not do full validation yet)