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WIP: Specification of Timecourses #581

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WIP: Specification of Timecourses #581

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fbergmann
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@fbergmann fbergmann commented May 22, 2024

This draft PR adds the descriptions from the Time course specification to the release/2.0.0 branch.

preview site is: https://petab--581.org.readthedocs.build/en/581/documentation_data_format.html#timecourses-table

FFroehlich and others added 17 commits March 10, 2023 07:32
* extract all changes from previous

* fixup

* allow hyphens in extension names

* fixup hyphens

* only require one toolbox that implements extension

* specify how to work with multiple PEtab problems

* specify we do not require a quorum number of votes

* allow test cases to be provided by the extension library

* Apply suggestions from code review

Co-authored-by: Daniel Weindl <[email protected]>

Co-authored-by: Daniel Weindl <[email protected]>
PEtab extensions were introduced in #537. We should be able to distinguish there between optional extensions and required extensions, i.e. those that modify the parameter estimation problem as such, and those that just add additional/optional information (e.g. annotations, info for visualization, ...). If some tool does not know about a certain optional extension, it can safely be ignored during import, if it does not know about a required extension, it should fail.

This PR adds a `required` attribute to extensions in the yaml file to indicate whether they are required for the mathematical interpretation of the PEtab problem.

Resolves #544
- remove preequilibrationConditionId
- remove simulationConditionId
- add timecourseID
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dweindl commented May 23, 2024

Thx Frank.

Maybe #541 and #542 can also be addressed here.

@@ -166,6 +170,56 @@ Detailed field description
If a compartment ID is provided, it is interpreted as the initial
compartment size.

- `expressions`

Expressions containing more than a single parameter ID or numberical
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Expressions containing more than a single parameter ID or numberical
Expressions containing more than a single parameter ID or numerical

Timecourses table
-----------------

The optional time courses tabke describes a sequence of different experimental
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The optional time courses tabke describes a sequence of different experimental
The optional time courses table describes a sequence of different experimental

@dweindl dweindl linked an issue May 30, 2024 that may be closed by this pull request
dweindl and others added 2 commits June 26, 2024 16:00
Previously, the math expression syntax wasn't specified. This was very problematic, because different libraries and programming languages have different names for the same functions, and more importantly, differ in operator precedence.


Co-authored-by: Dilan Pathirana <[email protected]>
Co-authored-by: dilpath <[email protected]>
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