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refactor Spectrum class#193

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CunliangGeng merged 30 commits intodevNPLinker/nplinker:devfrom 11-27-refactor_SpectrumNPLinker/nplinker:11-27-refactor_SpectrumCopy head branch name to clipboardDec 19, 2023

+193-241

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Commits on Dec 19, 2023

• remove property losses and method has_loss

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• remove propery is_library

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• remove attribute growth_media and methods add_strain and get_growth_medium

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• remove unused methods set_annotations and has_annotations

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• remove unused method get_metadata_value

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• remove unused method to_jcamp_str

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• remove attribute n_peaks

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• remove attributes max_ms2_intensity and total_ms2_intensity

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• remove unused attribute edges

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• remove parameter and attribute parent_mz

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• remove parameter and attribute id

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• adjust the order of parameter spectrum_id to 1st place

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• refactor method __init__

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• reorder methods and properties

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• remove method __cmp__

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• remove unused method __lt__

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• update methods __str__ and __repr__

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• change attribute normalised_peaks to property

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• split arguments peaks to two args mz and intensity

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• change the return type of property peaks to numpy 2D array

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• move method keep_top_k to the class SpecLib

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• remove property normalised_peaks

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• change default value of argument rt

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• remove arg annotations and add attribute gnps_annotations

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• remove unused global variable GNPS_KEY

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• add typing for attribute gnps_id

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• add typings and docstring for strains attribute and has_strain method

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• update class docstrings

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• update Spectrum loader

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• add unit tests for Spectrum class

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