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Add embeddings to sqlite#228

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niekdejonge wants to merge 19 commits intomainiomega/ms2query:mainfrom add_embeddings_to_sqliteiomega/ms2query:add_embeddings_to_sqliteCopy head branch name to clipboard

+336-425

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Commits on Nov 23, 2023

• Add embeddings to sqlite file

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  eda20aa

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• Adjust library_files_creator to add embeddings to sqlite as well

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• Update test_library_files_creator.py

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• Add get_ms2deepscore_embeddings (from sqlite)

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• Add get_ms2deepscore_embeddings (from sqlite) to the test create sqlite file with embeddings

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Commits on Nov 24, 2023

• Add get_spec2vec_embeddings (from sqlite) to the test create sqlite file with embeddings

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  bc87818

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• UPdate ms2library to use new sqlite file

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  dcdf8ff

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• Fix mistake in test

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• Added missing compound classes again

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• Disable test_add_classifier_annotations.py since the classifier api is out

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  afdea16

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• Fix issue with check_expected_headers in tests

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Commits on Nov 26, 2023

• Include convert_to_dataframe in select_compound_classes

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  9a7b270

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• Add ms2deepscore model file name and spec2vec model file name to conftest

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  546f267

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• Move make_sqlfile_wrapper to method of LibraryFilesCreator

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• Allow for compound classes = False

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• isort

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• prospector

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• Remove pickled embeddings from tests and update select_files_for_ms2query

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• isort

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