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Implement dict streaming #1

Merged
merged 11 commits into from
Sep 25, 2024
Merged

Implement dict streaming #1

merged 11 commits into from
Sep 25, 2024

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shirte
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@shirte shirte commented Sep 25, 2024

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* implement key-based access: config['description']
* add __repr__ method
* avoid that AutoConfiguration calls the _get_config method of the Model class (instead let _get_config returns an AutoConfiguration)
* make package and file-based configuration two exclusive options in AutoConfiguration
* add types
* derive DefaultConfiguration from DictConfiguration
* move yaml search code from AutoConfiguration to SearchYamlConfiguration
* implement proper merge mechanism in MergedConfiguration
* move code from AutoConfiguration to model classes
* introduce convenient Explorer._read method
* add another criterion to find the best reader in DepthFirstExplorer
* change type Generator[..., None, None] to Iterator[...]
* make ReaderRegistry aware of potential constructor arguments in individual reader classes
* move file-based code from Writer to a new class FileWriter
* implement new writer classes:  IteratorWriter, PandasWriter, and RecordListWriter.
* update the WriterRegistry to support registering and retrieving writers based on output format
* implement special case of filtering "H" in FilterByElement
* remove pipeline classes (they are replaced by list of preprocessing steps)
* remove pipeline registry since it is not needed anymore
* move code to Step / MapStep classes
* move class_decorator in utils submodule
* implement call_with_mappings that calls a method and assigns function arguments by name
* implement method to retrieve the file of a given class instance
* move code for assigning mol ids and names to separate classes (AssignMolId, AssignName)
* move code that takes care of adding missing columns to a separate class (EnforceSchema)
* let the base class Model handle prediction of molecules
* add all additional convenience code to SimpleModel (configuration, input, output)
* implement wrapper classes for input reading (ReadInput) and output writing (WriteOutput)
* merge different model classes into one class
* merge all scenario test cases into one file
@shirte shirte merged commit 7186d9d into molinfo-vienna:main Sep 25, 2024
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