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Path management #324
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Right. Adding an argument for that to
Somewhat related, I was planning to introduce some object representing the problem-yaml and adding that to petab.Problem. A base directory could easily be added there. This would also provide access to file names that are otherwise lost, and could be used (in simple cases) as default arguments to |
Introduces Problem.config which contains the info from the PEtab yaml file. Sometimes it is convenient to have the original filenames around. Closes PEtab-dev#324.
When passing the problem configuration as `dict` to `Problem.from_yaml`, one should be able to specify the base path for resolving relative paths. See PEtab-dev#324. Closes PEtab-dev#324
Introduces Problem.config which contains the info from the PEtab yaml file. Sometimes it is convenient to have the original filenames around. Closes PEtab-dev#324.
Introduces Problem.config which contains the info from the PEtab yaml file. Sometimes it is convenient to have the original filenames around. Closes PEtab-dev#324.
Introduces Problem.config which contains the info from the PEtab yaml file. Sometimes it is convenient to have the original filenames around. Closes PEtab-dev#324.
Introduces Problem.config which contains the info from the PEtab yaml file. Sometimes it is convenient to have the original filenames around. Pydantic gives more helpful error messages than `jsonschema` in case of incorrect inputs. Later on, this could replace `jsonschema` completely. Closes #324.
When generating a
petab.Problem
from a yaml file, all files are automatically prefixed by the location of the yaml file. However when directly passing the correspondingdict
(potentially after manipulation), it is no longer possible to specify a prefix and the only way for the import to work correctly is toos.chdir
to the appropriate directory.Straightforward to add a corresponding command line argument, but I guess it would be generally great to store a prefix path somewhere in the generated
petab.Problem
, as this would make it easier to reference files within the problem (not part of the current spec afaik, but it would be great to have in the future).Opinions?
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