[FFroehlich]

Follows #573. Fixes in assignments_to_experiments, found while reviewing #573's refactor and by differential testing against simulation. Each one changes the converted problem, and each has a regression test that fails without the fix. None was introduced by the refactor.

Fixes

• A switch exactly at the start of a later period was lost when that period did not change any symbol of the assignment. With k1 := piecewise(0, time < 10, 1) and periods at 0 and 10, k1 stayed 0 after t = 10. Likewise time <= 0 after preequilibration. A later period now also sets the value when it differs from the value at the end of the previous period.
• Condition changes of symbols still used elsewhere were dropped. With k1 := dose * piecewise(0, time < 10, 1) and a reaction that also uses dose, the condition's dose = 2 was removed, so the reaction silently used the model value. Changes are now only dropped if nothing else (the model's math or conversion factors, an observable, a condition change) refers to the symbol.
• A condition change was re-evaluated wherever a switch used it, with the values at the switch. PEtab applies a condition once, at the start of its period, and all its changes simultaneously, with the values from before the period. With d1 = b1 + 0.5 at t = 2 and b1 = 2 at t = 3 (or b1 = 2 in the same condition), a switch to d1 at t = 5 used 2.5 instead of 1.7. Changes are now evaluated at the start of their period; one whose value refers to something not known there, e.g. a species, is rejected. As a side effect, switching times set to expressions such as t1 = t2 + 1 now convert instead of being rejected.
• Time-dependent initial assignments were converted into switches, but SBML evaluates an initial assignment once, at the start of the simulation, so k1 = piecewise(0, time < 10, 1) never switches. They now stay in the model, as the docstring's scope ("assignment rules") already said.
• At preequilibration, a value referring to model parameters outside the parameter table failed the lint (CheckInitialChangeSymbols), since preequilibration starts the experiment. Those parameters now take their model values, as at the first period.
• An assignment to a species or compartment crashed with an AttributeError; it now raises NotImplementedError.
• A problem without time-dependent assignments was still changed: an experiment that only preequilibrates got an empty period at t = 0, and periods were re-sorted. It is now returned as it was, after the lint.
• A ramp's slope parameter could clash with PEtab IDs, e.g. an observable parameter k1_slope, since it was only checked against SBML IDs. It is now named with Problem.get_unused_id.
• A switching time that a condition set from a parameter fixed by the parameter table was rejected, e.g. t1 = p + 1, although t1 := p + 1 in the assignment itself converts with p's nominal value. Fixed parameters now take their nominal values in condition changes too; switching times that depend on estimated parameters are still rejected.
• New condition values used the symbols parsed from SBML, without the assumptions of PEtab's symbols (petab_symbol, real), so they compared unequal to the same expressions parsed by PEtab, e.g. after reading the condition table back. They now use PEtab's symbols.

Test changes: test_assignments_to_experiments and _unused_condition_id used an initial assignment (k1 = ...) to mean a switching rule and now use an assignment rule (k1 := ...). _validate relied on an estimated parameter with a time-dependent initial assignment; it now uses an existing experiment default_experiment, to which the measurements without an experiment ID would also be assigned, which the final lint catches.

Module

As suggested in review, assignments_to_experiments and its helpers now live in their own module, petab.v2.assignments_to_experiments (moved unchanged; still exported from petab.v2.converters), and their tests in tests/v2/test_assignments_to_experiments.py. SbmlModel.get_referenced_ids() and ObservableTable.free_symbols are new, also from review.

Checked

• pytest tests/v2 tests/v1/test_petab.py tests/v1/test_sbml.py: 266 passed; pre-commit clean.
• The benchmark problems Brannmark_JBC2010, Fujita_SciSignal2010, Isensee_JCB2018 and Raimundez_PCB2020 (and Oliveira_NatCommun2021's error) convert identically before and after.
• Differential testing against simulation: random problems with dose sums, several and nested pieces, ramps, every inequality form, switching times set by conditions (often exactly at period starts), symbols shared with reactions, two converted assignments in one model, and condition values that are expressions in other parameters. Each experiment of the original and the converted problem is turned into SBML events with ExperimentsToSbmlConverter, simulated in BasiCO, and compared (rtol 1e-6). On this PR's head, 2093 problems match and none is rejected; in 7 more, COPASI fails on the original model, and the converted one matches it up to there. The same generator finds 59 mismatches in 300 problems on main. Not covered: preequilibration, experiments that start at t ≠ 0, and first periods with expression values (only parameter table symbols are allowed there).
• A second pass with an independent reference simulator (SciPy, integrating piecewise between all switching times and period starts; it agrees with BasiCO on 94 cross-checked simulations), covering what the first could not: experiments that start at t = -5, 2 or 5, preequilibration (with the documented semantics: converted assignments hold their value at time 0), parameter table entries whose estimated or fixed nominal values differ from the model's (in values, switching times and condition values), condition values that refer to parameter table symbols at the start and to a species in unrelated changes. Each problem also checks that the input stays unchanged, that conversion is deterministic and idempotent, and that the converted condition and experiment tables survive a round trip through their DataFrames. On this PR's head, 1415 of 1500 problems match and pass all checks; the other 85 are rejected because a switching time depends on an estimated parameter, as intended. On main, the same pass finds 21 mismatches and 16 lint failures of the converted problem in 200 problems.
• Where BasiCO disagrees with the reference simulator on an original problem (a switch of the assignment rule exactly at the time of a period's event, which COPASI mis-simulates; moving the switch by 0.001 removes the disagreement), the reference simulator agrees with the converted problem.

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[codecov-commenter]

Codecov Report

❌ Patch coverage is 93.61702% with 15 lines in your changes missing coverage. Please review.
✅ Project coverage is 79.06%. Comparing base (597c0a6) to head (3e6327d).

Files with missing lines	Patch %	Lines
petab/v2/assignments_to_experiments.py	93.05%	7 Missing and 8 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #574      +/-   ##
==========================================
+ Coverage   78.97%   79.06%   +0.09%     
==========================================
  Files          69       70       +1     
  Lines        8096     8155      +59     
  Branches     1450     1461      +11     
==========================================
+ Hits         6394     6448      +54     
- Misses       1215     1218       +3     
- Partials      487      489       +2     

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[FFroehlich]

did not review code in detail, but has now survived multiple rounds of fuzzing/adversarial review+testing.

[dweindl]

By now, I'd say that assignments_to_experiments deserves a separate module and separate test module. Fine to export it from petab.v2.converters.