WIP: Specification of Timecourses #581
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* 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
Co-authored-by: Dilan Pathirana <[email protected]>
- remove preequilibrationConditionId - remove simulationConditionId - add timecourseID
This was referenced May 23, 2024
This was referenced May 23, 2024
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| @@ -166,6 +170,56 @@ Detailed field description | |||
| If a compartment ID is provided, it is interpreted as the initial | |||
| compartment size. | |||
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| - `expressions` | |||
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| 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 | ||
| ----------------- | ||
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| 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 |
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]>
This was referenced Jun 29, 2024
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This draft PR adds the descriptions from the Time course specification to the
release/2.0.0branch.preview site is: https://petab--581.org.readthedocs.build/en/581/documentation_data_format.html#timecourses-table