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
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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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Resolved merge conflicts. This needs to be updated to match the new mostly-agreed-upon format in #586
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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. * updates the required fields in the measurement table * updates some validation functions to not expect the old `simulationConditionId`s (but does not do full validation yet) * extends PEtab v1 up-conversion to create a new experiment table. --------- Co-authored-by: Dilan Pathirana <[email protected]>
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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