matchms similarity: fix bug in RI filtering #300
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maximskorik
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* update test data * remove matches from output * update `write_outputs` to return serialized `Scores` json * update matchMS formatter tests * remove matches file from formatter.py * add matchms dependency * replace deprecated decorator * correct typos; update docs * update similarity and formatter help * remove duplicated help section * add maximskorik to authors * bump `matchms` version * finish `matchms_formatter` * update test data produced with erroneous ri_filtering (#300) * update test data * update zenodo link * update `matchms_formatter` test data * update link to zenodo in `matchms_filtering` * lint * Update tools/matchms/matchms_similarity.xml * reduced testdata * Started updating test data * annotate tests * reduce test_3 * update test_2 * truncate recetox_gc-ei_ms; update test_4 * update test_5 * update test_2 to test same format files * add descriptive test annotations * remove unused data * update matchms_formatter test data * put `MPLCONFIGDIR` to macros and add to `matchms_formatter` * remove `environment_variables` macros; config Fontconfig via envvar * remove indent Co-authored-by: Helge Hecht <helge.hecht@recetox.muni.cz>
maximskorik
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* initialize wrapper * add inputs and output * add tests * change param's help * add help * add tool to .shed.yml * update labels and help * add slider to score cutoff * add maximskorik to tool authors * add networking wrapper * add output format selection to inputs * update test params * update test data * remove matches from output * update `write_outputs` to return serialized `Scores` json * update matchMS formatter tests * remove matches file from formatter.py * add matchms dependency * replace deprecated decorator * correct typos; update docs * update similarity and formatter help * remove duplicated help section * add maximskorik to authors * bump `matchms` version * finish `matchms_formatter` * update test data produced with erroneous ri_filtering (#300) * update test data * update zenodo link * update `matchms_formatter` test data * update link to zenodo in `matchms_filtering` * use creators from macros * reformat wrapper * save `parser` to `args` variable * update method name * fix python wrapper * update varnames in xml wrapper * reformat call to wrapper * add dynamic output format * remove test data; check file contents instead * add test case; change parameters order * add more test cases * move citations to macros.xml * format help section * lint * fix output tag name * reformat python to pass linter * remove debugging `print` * Update tools/matchms/matchms_similarity.xml * reduced testdata * Started updating test data * annotate tests * reduce test_3 * update test_2 * truncate recetox_gc-ei_ms; update test_4 * update test_5 * update test_2 to test same format files * add descriptive test annotations * remove unused data * update matchms_formatter test data * put `MPLCONFIGDIR` to macros and add to `matchms_formatter` * remove `environment_variables` macros; config Fontconfig via envvar * remove indent * add envvars to the `networking` tool schema Co-authored-by: Helge Hecht <helge.hecht@recetox.muni.cz>
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Fix bug in RI masking.
Because
matchms.Scores.scoresproperty doesn't have a setterdoesn't update this attribute.
Closes #298