Proposal for the introduction of extensions #537
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dweindl
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Mar 12, 2022
dweindl
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Mar 12, 2022
Co-authored-by: Daniel Weindl <[email protected]>
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May 24, 2022
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.
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Jul 20, 2022
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
dweindl
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Mar 10, 2023
* 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]>
dweindl
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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
dweindl
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Jul 3, 2024
* 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]>
dweindl
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Jul 3, 2024
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
dweindl
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Jul 3, 2024
* 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]>
dweindl
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Jul 3, 2024
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
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This pull request describes a proposal for the extension of PEtab (see #528) that allows changes to the format through extensions. The proposed development and acceptance procedure is described in the changes to development.rst . The other change the documentation to indicate that the PEtab YAML file becomes mandatory.
Required steps for changes to the PEtab specification
Note: this replaces #527, which was permanently closed when I accidentally deleted the corresponding repository