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v2: Allow infinite `nominalValue`

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Bewertung

Schwierigkeit
4/5
Geschätzter Aufwand
1-2 Tage
Anfängerfreundlichkeit
55/100
Issue-Typ
Feature
Klarheit
Klar beschrieben
Aktivitätsstatus
Aktiv
Tech-Stack
python, yaml
Bereich
data

Rechercherichtung

Start by reading the PEtab v2 data format documentation and development requirements linked in the issue, then inspect how the specification defines and validates nominalValue. Compare the proposed allowance for inf and -inf with the existing handling of condition table values and the related issues #682 and #684. Done means the specification clearly permits infinite nominal values, keeps NaN invalid, and explains the behavior for estimated and fixed parameters.

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Beschreibung

In PEtab 2.0.0, nominalValue is NUMERIC, i.e., finite. The resolution of #682 kept it that way. We propose to allow inf and -inf as well, as erratum E2 to PEtab 2.0.0.

Motivation

PEtab v2 removed parameterScale. The list of changes from v1 says: "To obtain the same effect, the model parameters can be transformed in the model file" (documentation_data_format.rst#L176-L182). The development docs require that problems from earlier versions remain specifiable (development.rst#L249-L251).

With finite nominal values, a transformed parameter doesn't give the same effect. In v1, a parameter k1 with parameterScale=log can be fixed at nominalValue=0 (v1 nominal values are on linear scale). This is a common way to switch off a mechanism without changing the model. After the recommended transformation to log_k1, the same fixed value is -inf, which NUMERIC doesn't allow.

Proposal

  • nominalValue becomes NUMERIC or 'inf' or '-inf'. NaN stays invalid.
  • For estimate=false, the value is applied as specified. Undefined results such as 0 * inf are the responsibility of the model author. This already applies to infinite values set via the condition table, whose math expressions support inf and -inf.
  • For estimate=true, the nominal value has no role in the problem definition, so allowing infinite values there has no consequences. Among other things, it allows storing estimation results at the boundary of an infinite parameter domain.

Why an erratum

Like #682, this resolves a conflict between the stated intent of the spec (parameterScale can be replaced by transforming the model) and a type restriction. Admittedly, the conflicting statement is in the informative list of changes, and converters can avoid the issue by not transforming fixed parameters. Still, the restriction doesn't serve a purpose, and allowing infinite values makes the statement about replacing parameterScale accurate.

libpetab-python currently doesn't reject infinite nominal values, so existing tooling already accepts them.

Relates to #682, #684.

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Erste Schritte

  1. Lesen Sie das ganze Issue und danach den Beitragsleitfaden des Projekts.
  2. Schreiben Sie ins Issue, dass Sie es übernehmen — das erspart doppelte Arbeit.
  3. Forken Sie das Repository und arbeiten Sie in einem Branch.
  4. Öffnen Sie einen Pull Request, der die Issue-Nummer nennt.

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