Support for petab v2 experiments #332
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #332 +/- ##
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+ Coverage 74.56% 74.66% +0.09%
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Files 56 56
Lines 5521 5573 +52
Branches 959 976 +17
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+ Hits 4117 4161 +44
- Misses 1039 1040 +1
- Partials 365 372 +7 ☔ View full report in Codecov by Sentry. |
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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 <[email protected]>
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)