v0.4.0

What's Changed

• Update to matchms 0.20.X and include Spec2Vec similarity score by @maximskorik in #321
• recetox-aplcms: update to 0.12.0 by @xtrojak in #390
• Include test-data in .shed.yml for riassigner and recetox_xmsannotator by @cat-bro in #391
• Update matchms to 0.22.0 by @hechth in #395
• updated CI and PR github actions from IUC by @hechth in #400
• updated PAT by @hechth in #401
• matchms: added filters and test and fixed linter warnings by @zargham-ahmad in #402
• Added matchms add key tool by @zargham-ahmad in #404
• Improved formatter.py performance by @zargham-ahmad in #403
• matchms convert: add MS-LIMA MSP style by @zargham-ahmad in #408
• Molecular optimization tool by @wverastegui in #394
• deployment CI fix by @zargham-ahmad in #410
• add dummy tests for aplcms by @hechth in #411
• bumped galaxy version in all wrapers to trigger toolshed update by @hechth in #413
• Update matchms to 0.23.1 by @hechth in #416
• Add EDAM identifiers: Retip and recetox-msfinder by @zargham-ahmad in #420
• Update matchms molecular networking tool by @hechth in #436
• Updated matchms version to 0.24.0 by @zargham-ahmad in #442
• Added tool: matchms_subsetting_tool by @zargham-ahmad in #437
• fix matchms outputs to existing types by @bernt-matthias in #438
• Added tool: matchms_metadata_merge by @zargham-ahmad in #428
• updated python in matchms merge and subsetting tool by @zargham-ahmad in #446
• Removes coordination complexes compounds by @wverastegui in #441
• Updated recetox-msfinder output and version by @zargham-ahmad in #451
• Update matchms_formatter.xml with OPENBLAS_NUM_THREADS=1 by @hechth in #452
• try more threads by @hechth in #453
• try adding RLIMIT_NPROC and removed explicit pandas dependency by @hechth in #455
• re-added pandas dependency by @hechth in #456
• Implemented matchms remove key tool by @hechth in #460
• matchms_filtering: Added derive_precursor_mz_from_parent_mass filter by @zargham-ahmad in #475
• Updated matchms filtering tool to use matchms function by @zargham-ahmad in #478
• Updated recetox_msfinder to v3.5.2-rcx2 by @zargham-ahmad in #483
• Disabled key conversion in matchms tools by @zargham-ahmad in #484
• Qcxms by @zargham-ahmad in #421
• Read RI from comments and add them to RI column field by @wverastegui in #486
• High-res peak overwriting with theoretical MS tool by @wverastegui in #487
• matchms metadata match: added formula to "equal_match" options by @zargham-ahmad in #489
• fix use_theoretical_mz_annotations tools by @hechth in #492
• next attempt by @hechth in #493
• Update qcxms_prod_run.xml by @hechth in #494
• QCxMS New Version by @zargham-ahmad in #497
• matchms add key, matchms remove key: Added multiple keys handling by @zargham-ahmad in #502
• MeOX & TMS GC-Derivatization Tool by @wverastegui in #503
• CI update by @hechth in #506
• Change output csv types to tsv by @zargham-ahmad in #504
• Updated MSMetaEnhancer to 0.4.0 by @zargham-ahmad in #512
• Fixed GFN1-xTB selection issue in qcxms_neutral_run tool by @zargham-ahmad in #513
• Updated RAMClustR tool by @zargham-ahmad in #514
• matchms scores formatter: added key parameter by @zargham-ahmad in #520
• Isolib tool first version by @hechth in #521
• Update isolib.xml by @hechth in #522
• isolib: fix rt column reading and writing by @hechth in #525
• Updated riassigner to 0.4.1 by @zargham-ahmad in #532
• Update WaveICA to outputs by @zargham-ahmad in #533
• Updated WaveICA to allow integer class column type by @zargham-ahmad in #537
• Tool for GC annotation by @wverastegui in #536
• Fixed typos by @wverastegui in #538
• Updated RAMClustR to allow tsv for rectetox-aplcms inputs by @zargham-ahmad in #539
• RAMClustR: fixed sample name reading for tabular inputs by @zargham-ahmad in #541
• Update ci.yaml by @hechth in #543
• updated matchms to 0.25.0 by @hechth in #544
• Update matchms help.xml by @hechth in #546
• styling all R files in folder by @hechth in #548
• Implemented dedicated require filters matchms tool by @zargham-ahmad in #517
• Update msmetaenhancer.xml by @hechth in #550
• Updated matchms remove spectra tool by @hechth in #553
• WaveICA: Added boolean parameter to output feature table and metadata table separately by @zargham-ahmad in #555
• Expanded creator tag by @wverastegui in #556
• Added boolean to retain molecule name by @wverastegui in #557
• Updated matchms to 0.27.0 by @zargham-ahmad in #558
• EDAM annotations for QCxMS and xTB tools by @wverastegui in #560

New Contributors

• @cat-bro made their first contribution in #391
• @bernt-matthias made their first contribution in #438

Full Changelog: v0.3.0...v0.4.0

Release v0.3.0

What's Changed

• matchms: add tabular datatype explicitly by @martenson in #206
• RAMClustR tool form improvement by @xtrojak in #220
• Bump RIAssigner to 0.3.2 by @hechth in #222
• MSMetaEnhancer log as an optional output by @xtrojak in #223
• Update CI to use planemo action by @martenson in #228
• Implemented basic RI filtering via matchms by @hechth in #227
• enable upload to MTS by @martenson in #231
• Update MSME to v0.2.0 by @xtrojak in #241
• upload all repos with green light to MTS by @martenson in #236
• waveica: remove obsolete file from shed.yml by @martenson in #245
• update biotransformer to 3.0 by @martenson in #235
• detect errors in all tools by @martenson in #247
• add new tool: msp_split by @wverastegui in #234
• Update MSME version to v0.2.1 by @xtrojak in #252
• Update RAMClustR to version 1.2.4 by @xtrojak in #254
• MSME matchms logging level by @xtrojak in #259
• MSME v0.2.2 by @xtrojak in #262
• Tool to merge MSP files by @wverastegui in #263
• Update MSME to v0.2.3 by @xtrojak in #267
• Add apLCMS Two-Step Hybrid wrapper by @maximskorik in #264
• apLCMS split to steps by @xtrojak in #265
• apLCMS: input collections by @xtrojak in #269
• RAMClustR: Add define experiment wrapper to shed by @xtrojak in #280
• galaxytools: update Zenodo badge in README.md by @maximskorik in #287
• matchms similarity: Added NeutralLossesCosine metric by @zargham-ahmad in #281
• matchms similarity: fix bug in RI filtering by @maximskorik in #300
• Update MSMetaEnhancer to v0.2.4 by @xtrojak in #297
• RAMClustR: removed quotes in SpecAbundance output by @zargham-ahmad in #303
• Fixed similarity bug for RI filtering & fixed formatter bug by @hechth in #302
• WaveICA: Separate input and formats support by @zargham-ahmad in #304
• matchms: switch to Scores objects by @maximskorik in #289
• matchms: add wrapper for matchMS networking subpackage by @maximskorik in #286
• Update MSMetaEnhancer to v0.2.5 by @xtrojak in #306
• Update version of actions in workflows by @xtrojak in #309
• Update MSME v0.2.5 version galaxy1 by @xtrojak in #311
• msfinder wrapper by @zargham-ahmad in #313
• add wrapper for training Spec2Vec in Galaxy by @maximskorik in #314
• add mzml-validation tool by @maximskorik in #319
• Msfinder version update by @zargham-ahmad in #324
• recetox-aplcms v0.10.1 by @xtrojak in #317
• Update help.xml by @xtrojak in #325
• RIAssigner 0.3.4 by @hechth in #331
• Update recetox-aplcms to v0.10.3 by @xtrojak in #329
• Reworked msp_split tool by @hechth in #343
• Tool to convert mass spectral libraries by @hechth in #339
• Updated recetox_aplcms_align_features with cluster by @zargham-ahmad in #345
• MSMetaEnhancer: get rid of Fontconfig error by @xtrojak in #347
• MSMetaEnhancer 0.3.0 by @xtrojak in #352
• Polish RMassBank by @xtrojak in #351
• Add matchms tool for metadata extraction by @xtrojak in #356
• Add matchms_metadata_export to shed by @xtrojak in #357
• update to recetox-aplcms 0.11.0 by @hechth in #353
• Fixed bug in recetox-aplcms remove_noise by @hechth in #362
• Updated matchms_convert tool by @zargham-ahmad in #358
• Updated Labels in recetox_aplcms tools by @zargham-ahmad in #346
• Update utils.R to fix bug introduced in PR merge by @hechth in #363
• Bump biotransformer to version 3.0_20230403 by @xtrojak in #360
• Remove aplcms_to_ramclustr_converter by @xtrojak in #366
• RAMClustR: update to 1.3.0 by @zargham-ahmad in #364
• Create add_issue_to_project.yml by @hechth in #344
• Create project_automation.yaml by @hechth in #372
• Update slash.yaml by @hechth in #377
• Add EDAM identifiers to recetox-aplcms suite by @hechth in #375
• Add EDAM identifiers to ramclustr by @zargham-ahmad in #376
• MSMetaEnhancer: Add EDAM identifiers by @xtrojak in #379
• BioTransformer: fix tests by @xtrojak in #385
• RIAssigner: Add EDAM identifiers by @xtrojak in #381
• Updated waveica for new outputs from recetox-aplcms by @zargham-ahmad in #378
• BioTransformer: Add EDAM identifiers by @xtrojak in #382
• Cleanup xmsannotator wrappers by @xtrojak in #367

New Contributors

• @wverastegui made their first contribution in #234
• @zargham-ahmad made their first contribution in #281

Full Changelog: v0.2.0...v0.3.0

Release v0.2.0

Merge pull request #217 from xtrojak/ramclustr-define-experiment

RAMClustR experimental design input

Initial release

Merge pull request #78 from martenson/update_ci

bring CI fixes from upstream

Zenodo Release

Merge pull request #78 from martenson/update_ci

bring CI fixes from upstream