PEtab v1 to v2 converter #281
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## develop #281 +/- ##
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+ Coverage 72.92% 74.01% +1.08%
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Files 72 73 +1
Lines 4717 4798 +81
Branches 1012 1029 +17
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+ Hits 3440 3551 +111
+ Misses 983 953 -30
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petab/v2/petab1to2.py
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| if str(yaml_config[petab.C.FORMAT_VERSION]) != "1": | ||
| # TODO: Other valid version numbers? |
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Currently 1.0.0 is possible
https://github.com/search?q=repo%3APEtab-dev%2Flibpetab-python+1.0.0&type=code
| if output_dir is None: | ||
| # TODO requires petab.v2.Problem | ||
| raise NotImplementedError("Not implemented yet.") | ||
| elif isinstance(yaml_config, dict): | ||
| raise ValueError("If output_dir is given, yaml_config must be a file.") | ||
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| if isinstance(yaml_config, Path | str): | ||
| yaml_file = str(yaml_config) | ||
| path_prefix = get_path_prefix(yaml_file) | ||
| yaml_config = load_yaml(yaml_config) | ||
| get_src_path = lambda filename: f"{path_prefix}/{filename}" # noqa: E731 | ||
| else: | ||
| yaml_file = None | ||
| path_prefix = None | ||
| get_src_path = lambda filename: filename # noqa: E731 | ||
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| get_dest_path = lambda filename: f"{output_dir}/{filename}" # noqa: E731 |
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Keeping file names the same when upgrading is nice, but this is more intuitive to me. Fine as is, if you think this is nicer for most users.
problem1 = petab.v1.Problem.get_problem(yaml_config, validate=True)
experiment_df, measurement_df = convert_measurement_df_1to2(problem1)
problem2 = petab.v2.Problem(
problem1.condition_df,
experiment_df,
measurement_df,
...,
)
problem2.validate(raise=True)
if output_dir:
# alternatively `to_files` if you want to keep file names consistent...
problem2.to_files_generic(output_dir)
return problem2There was a problem hiding this comment.
The thing is, if you had multiple measurement files, condition files, ... then you most likely still want to have them as separate files in your v2 problem. That's not possible anymore once you read them into a v1 Problem, they will all get merged. And I don't want to rename all files afterwards.
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Makes sense! I have thought elsewhere that tracking a file ID for e.g. measurements, as an index subset, could improve things a bit. If you're not against this, I can open an issue for it.
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Also happy to add that to this PR, today or tomorrow.
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I'm generally open to tracking that information somewhere. To be discussed how that could look in details.
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Also happy to add that to this PR, today or tomorrow.
I'd rather have it done separately. (That doesn't preclude changing anything that was introduced here.)
Draft. Closes PEtab-dev#272.
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Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>
Converter for PEtab v1 problems to PEtab v2 problems.
Allows converting a set of PEtab v1 files to v2 files or creating a petab.v2.Problem from v1 yaml file.
To be extended/adapted as v2 matures.
Closes #272.