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♻️ Refactor: Model and Parameters#1135

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jsnel merged 45 commits intoglotaran:mainglotaran/pyglotaran:mainfrom joernweissenborn:refactor/model_and_parametersjoernweissenborn/pyglotaran:refactor/model_and_parametersCopy head branch name to clipboardNov 4, 2022

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• Added basic model.

  

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• Added megacomplexes model.

  

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• New Model can load from dict.

  

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• Basic idea for item fill.

  

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• Added get issues.

  

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• Added item fill.

  

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• Added model as_dict.

  

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• Added model markdown.

  

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• Added get parameter labels.

  

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• Added validate dataset datasetmodel megacomplexes.

  

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• Added global items.

  

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• Replaced old model with new.

  

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• Adapted optimization.

  

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• Adapted builtin megacomplexes.

  

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• Reimplemented ParameterGroup as Parameters.

  

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• Adapted yml load parameters.

  

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• All test are working again.

  

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• Fixed mypy issues and added docstrings for model package.

  

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• Fixed small bugs.

  

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• 🩹 Fixed benchmarks

  

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• ♻️ Refactored by Sourcery

  

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• Fixed project parameter generation.

  

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• 💥 Raised min python version to 3.10

  

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• Refactored clp penalties to have types.

  

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• Deprecated parameter group.

  

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• Fixed model as_dict aand validate.

  

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• Fixed unique megacomplex check.

  

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• Fixed damped oscillation megacomplex type.

  

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• Small fixes.

  

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• 🩹🗑️ Raised deprecation version for new deprecations to 0.9.0

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• 🧹 Renamed fuctions not conforming to snake case

  

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• ✨ Added equality check for Parameters

  

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• ♻️ Made nan_or_equal work with general values not only numeric

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• 👌 Added helper decorator to omit default values from repr in attrs class

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• 👌 Added proper repr to Parameters

  

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• 🧪🩹 Fixed and reactivated pandas tests

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• 🩹📚 Changed read the docs config to work with python 3.10

  

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• Fixed bug in interval item.

  

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• Fixed Parameters.copy.

  

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• Added test to check that initial parameters don't get overwritten.

  

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Commits on Nov 4, 2022

• Included review comments.

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• Updated changelog.

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• 🩹 Fixed integration benchmark

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• 👌Avoid redefining built-in type

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• 📚 Added change to changelog

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