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Update README overview table automatically (#205)
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Lines changed: 33 additions & 6 deletions

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‎README.md‎

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@@ -5,6 +5,7 @@ Contributions to the collection are very welcome. For this, please create a new
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## Overview
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<!-- START OVERVIEW TABLE -->
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| PEtab Problem ID | Conditions | Estimated Parameters | Events | Preequilibration | Postequilibration | Measurements | Observables | Noise distribution(s) | Species | References | SBML4Humans |
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|:---------------------------------------------------------------------------------------------|-------------:|-----------------------:|---------:|-------------------:|--------------------:|---------------:|--------------:|:------------------------|----------:|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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| [Alkan_SciSignal2018](Benchmark-Models/Alkan_SciSignal2018/) | 73 | 56 | 0 | 0 | 0 | 1733 | 12 | normal | 36 | [\[1\]](http://identifiers.org/doi/10.1126/scisignal.aat0229) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Alkan_SciSignal2018/model_Alkan_SciSignal2018.xml) |
@@ -39,7 +40,7 @@ Contributions to the collection are very welcome. For this, please create a new
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| [Weber_BMC2015](Benchmark-Models/Weber_BMC2015/) | 2 | 36 | 0 | 1 | 0 | 135 | 8 | normal | 7 | [\[1\]](http://identifiers.org/doi/10.1186/s12918-015-0147-1) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Weber_BMC2015/model_Weber_BMC2015.xml) |
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| [Zhao_QuantBiol2020](Benchmark-Models/Zhao_QuantBiol2020/) | 7 | 28 | 0 | 0 | 0 | 82 | 1 | normal | 5 | [\[1\]](http://identifiers.org/pubmed/32219006) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Zhao_QuantBiol2020/SBML_Zhao_QuantBiol2020.xml) |
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| [Zheng_PNAS2012](Benchmark-Models/Zheng_PNAS2012/) | 1 | 46 | 0 | 1 | 0 | 60 | 15 | normal | 15 | [\[1\]](http://identifiers.org/doi/10.1073/pnas.1201240109) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Zheng_PNAS2012/model_Zheng_PNAS2012.xml) |
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<!-- END OVERVIEW TABLE -->
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## License
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‎scripts/_helpers.py‎

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@@ -1,10 +1,12 @@
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from pathlib import Path
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benchmark_path = Path(__file__).parent.parent / 'Benchmark-Models'
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benchmark_path = Path(__file__).resolve().parent.parent / 'Benchmark-Models'
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petab_yamls = {
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petab_path.name: benchmark_path / petab_path.name / (petab_path.name + '.yaml')
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for petab_path in benchmark_path.glob('*')
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if petab_path.name != '.DS_Store'
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}
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petab_yamls = {k: petab_yamls[k] for k in sorted(petab_yamls)}
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readme_md = Path(__file__).resolve().parent.parent / "README.md"

‎scripts/overview.py‎

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@@ -9,7 +9,7 @@
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import pandas as pd
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import petab
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from _helpers import petab_yamls
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from _helpers import petab_yamls, readme_md
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markdown_columns = {
@@ -145,8 +145,12 @@ def get_overview_table() -> pd.DataFrame:
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return df
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start_overview_table = '\n<!-- START OVERVIEW TABLE -->\n'
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end_overview_table = '\n<!-- END OVERVIEW TABLE -->\n'
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def main(
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markdown: bool = False,
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markdown: bool = False,
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update_readme: bool = False,
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):
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df = get_overview_table()
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pd.options.display.width = 0
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)
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df.index.rename(markdown_columns[index_column], inplace=True)
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df.rename(columns=markdown_columns, inplace=True)
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print(df.to_markdown())
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markdown_overview = df.to_markdown()
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if update_readme:
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with open(readme_md, "r") as f:
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readme_content = f.read()
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before_table = readme_content.split(start_overview_table)[0]
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after_table = readme_content.split(end_overview_table)[1]
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new_readme_content = (
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before_table
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+ start_overview_table
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+ markdown_overview
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+ end_overview_table
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+ after_table
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)
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with open(readme_md, "w") as f:
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f.write(new_readme_content)
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else:
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print(markdown_overview)
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else:
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print(df)
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import sys
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markdown = False
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update_readme = False
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if '--markdown' in sys.argv:
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markdown = True
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main(markdown)
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if '--update' in sys.argv:
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markdown = True
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update_readme = True
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main(markdown=markdown, update_readme=update_readme)

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