matchms - processing and similarity evaluation of mass spectrometry data. - 0.30.2

What's Changed

• Fixed metadata export by @hechth in https://github.com/matchms/matchms/pull/814
• prepare release 0.30.2 by @hechth in https://github.com/matchms/matchms/pull/815

Full Changelog: https://github.com/matchms/matchms/compare/0.30.1...0.30.2

Scientific Software - Peer-reviewed - Python
Published by hechth 6 months ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.30.1

What's Changed

• Fix msp import set key as numpy scalar instead of value by @julianpollmann in https://github.com/matchms/matchms/pull/807
• Bump requests from 2.32.3 to 2.32.4 by @dependabot in https://github.com/matchms/matchms/pull/808
• matchms fails when reading spectra where abundance is in scientific notation by @hechth in https://github.com/matchms/matchms/pull/809
• Bump urllib3 from 2.4.0 to 2.5.0 in https://github.com/matchms/matchms/pull/811

Full Changelog: https://github.com/matchms/matchms/compare/0.30.0...0.30.1

Scientific Software - Peer-reviewed - Python
Published by julianpollmann 6 months ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.30.0

What's Changed

• add support for python 3.13 by @julianpollmann in https://github.com/matchms/matchms/pull/804
• upgrade numPy from >1.24 to >=2.0.0

Full Changelog: https://github.com/matchms/matchms/compare/0.29.0...0.30.0

Scientific Software - Peer-reviewed - Python
Published by julianpollmann 7 months ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.29.0

What's Changed

Added

• Implemented preliminary mzSpecLib export #757
• added BinnedEmbeddingSimilarity and BaseEmbeddingSimilarity Classes #749
• added Fingerprints Class to compute and store inchikey-fingerprint mapping for a list of spectra #717
• some reference spectra were added #781

Changed

• compound_name is now always the first attribute to be written for each spectrum #762
• added option to use different peak separators for msp export #762
• filtering: cloning of Spectra is now optional in filtering and disabled in SpectrumProcessor. Enable cloning for the use of ProcessingReport with create_report = True #754
• importing now supports pathlib.Path #738
• exporting: empty spectra are saved as empty file instead of not saving at all #722
• exporting: save_as_mgf now supports write and append mode #741
• importing: load_mgf supports StringIO #745
• importing: fixed bug load_from_usi API call #759
• filtering: normalize_intensities will now set intensities to 0 instead of None when peak intensities are 0 #750
• Support GOLM style MSP files #763
• omit prospector, isort, black in favor of ruff #790

New Contributors

• @wasimsandhu made their first contribution in https://github.com/matchms/matchms/pull/722
• @mvisani made their first contribution in https://github.com/matchms/matchms/pull/745
• @roman-bushuiev made their first contribution in https://github.com/matchms/matchms/pull/738
• @acquayefrank made their first contribution in https://github.com/matchms/matchms/pull/741
• @oolonek made their first contribution in https://github.com/matchms/matchms/pull/748
• @Knerten0815 made their first contribution in https://github.com/matchms/matchms/pull/750
• @LucaCappelletti94 made their first contribution in https://github.com/matchms/matchms/pull/781

Full Changelog: https://github.com/matchms/matchms/compare/0.28.2...0.29

Scientific Software - Peer-reviewed - Python
Published by julianpollmann 8 months ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.28.2

What's Changed

• Allow numpy 1.x and 2.x by @florian-huber in https://github.com/matchms/matchms/pull/715

Full Changelog: https://github.com/matchms/matchms/compare/0.28.1...0.28.2

Scientific Software - Peer-reviewed - Python
Published by florian-huber about 1 year ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.28.1

Includes changes to the readme for PyPI compatability.

Full Changelog: https://github.com/matchms/matchms/compare/0.28.0...0.28.1

Scientific Software - Peer-reviewed - Python
Published by hechth about 1 year ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.28.0

What's Changed

• Increased Test Coverage by @julianpollmann in https://github.com/matchms/matchms/pull/701
• Rename CudaMS -> SimMS, tweak description a bit by @tornikeo in https://github.com/matchms/matchms/pull/703
• Update utils.py by @niekdejonge in https://github.com/matchms/matchms/pull/705
• Updated matchms dependencies by @hechth in https://github.com/matchms/matchms/pull/709
• IndexError in .matrix when all scores are 0 by @tornikeo in https://github.com/matchms/matchms/pull/702
• add logging for writing spectra to file by @florian-huber in https://github.com/matchms/matchms/pull/645
• Enable metadata exporting with tab separators by @hechth in https://github.com/matchms/matchms/pull/712

Full Changelog: https://github.com/matchms/matchms/compare/0.27.0...0.28.0

Scientific Software - Peer-reviewed - Python
Published by hechth about 1 year ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.27.0

[0.27.0] -2024-07-10

Changed

• Avoid using unstable sorting while sorting collected matching peaks #636.
• Losses will no longer be stored as part of a Spectrum object, but will be computed on the fly (using spectrum.losses or spectrum.compute_losses(loss_mz_from, loss_mz_to))#681
• Jaccard/Tanimoto @njit/numba-based similarity functions were replaced by 10-50x faster numpy matrix multiplications #638.
• Dependencies were updated to allow newer numpy and numba versions 691.
• Renamed method names and parameters to align spectrums -> spectra
• Python support changed from 3.8 - 3.11 to 3.9 to 3.12, and dependency versions were updated 640.

Removed

• add_losses() filter was removed. Losses will no longer be stored as part of a Spectrum object, but will be computed on the fly #681.

Fixed

• Remove empty spectra before exporting to file #686.
• Name position in mirror plots #678.

Scientific Software - Peer-reviewed - Python
Published by julianpollmann over 1 year ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.26.4

What's Changed

• Derive formula from smiles by @niekdejonge in https://github.com/matchms/matchms/pull/661
• Add check filters handle none by @niekdejonge in https://github.com/matchms/matchms/pull/665
• fix merge mistake by @niekdejonge in https://github.com/matchms/matchms/pull/677
• Add require number of peaks below maximum by @niekdejonge in https://github.com/matchms/matchms/pull/664

Full Changelog: https://github.com/matchms/matchms/compare/0.26.3...0.26.4

Scientific Software - Peer-reviewed - Python
Published by niekdejonge over 1 year ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.26.3

What's Changed

• Fix repair adduct and parent mass not repairing correct parent mass by @niekdejonge in https://github.com/matchms/matchms/pull/675
• Add repair parent mass from smiles by @niekdejonge in https://github.com/matchms/matchms/pull/676

Full Changelog: https://github.com/matchms/matchms/compare/0.26.2...0.26.3

Scientific Software - Peer-reviewed - Python
Published by niekdejonge over 1 year ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.26.2

What's Changed

• Add check if monoisotopic mass could be determined by @niekdejonge in https://github.com/matchms/matchms/pull/673
• Add require correct ms level 2 by @niekdejonge in https://github.com/matchms/matchms/pull/674

Full Changelog: https://github.com/matchms/matchms/compare/0.26.1...0.26.2

Scientific Software - Peer-reviewed - Python
Published by niekdejonge over 1 year ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.26.1

What's Changed

• Fix saving bug by @niekdejonge in https://github.com/matchms/matchms/pull/671

Full Changelog: https://github.com/matchms/matchms/compare/0.26.0...0.26.1

Scientific Software - Peer-reviewed - Python
Published by niekdejonge over 1 year ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.26.0

What's Changed

• Fix metadata match by @niekdejonge in https://github.com/matchms/matchms/pull/658
• Remove profile spectra by @niekdejonge in https://github.com/matchms/matchms/pull/650
• Merge require precursor mz by @niekdejonge in https://github.com/matchms/matchms/pull/623
• Fail fast on loading missing mgf by @tornikeo in https://github.com/matchms/matchms/pull/655
• fix bug with mz window by @niekdejonge in https://github.com/matchms/matchms/pull/662
• Require matching ionmode and adduct by @niekdejonge in https://github.com/matchms/matchms/pull/657
• Allow peaks with many floating types by @tornikeo in https://github.com/matchms/matchms/pull/660
• Require matching adduct precursor mz parent mass by @niekdejonge in https://github.com/matchms/matchms/pull/659
• Remove noise below frequent intensities by @niekdejonge in https://github.com/matchms/matchms/pull/663
• Notify that cudams repository has been moved by @tornikeo in https://github.com/matchms/matchms/pull/669
• Check for size equality when using is_symmetric by @tornikeo in https://github.com/matchms/matchms/pull/668
• Save mgf msp once per iteration in pipeline by @tornikeo in https://github.com/matchms/matchms/pull/651

Full Changelog: https://github.com/matchms/matchms/compare/0.25.0...0.26.0

Scientific Software - Peer-reviewed - Python
Published by niekdejonge over 1 year ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.25.0

What's Changed

• Added require_retention_time and require_retention_index filters by @hechth in https://github.com/matchms/matchms/pull/602
• Remove adduct and mol wt wrong by @niekdejonge in https://github.com/matchms/matchms/pull/615
• Fix repair parent mass is mol wt by @niekdejonge in https://github.com/matchms/matchms/pull/619
• Added require_formula and require_compound_name filters by @zargham-ahmad in https://github.com/matchms/matchms/pull/627
• Renamed repairadductbasedonsmiles.py to repairadductandparent… by @niekdejonge in https://github.com/matchms/matchms/pull/620
• fix merge mistakes by @niekdejonge in https://github.com/matchms/matchms/pull/630
• Add repair adduct based on parent mass by @niekdejonge in https://github.com/matchms/matchms/pull/622
• Return processing report by @niekdejonge in https://github.com/matchms/matchms/pull/628
• adding colors for mirrror spectra and tests by @lionel42 in https://github.com/matchms/matchms/pull/631
• Teeny readme clarification about poetry extras by @tornikeo in https://github.com/matchms/matchms/pull/653
• Fix rdkit version by @niekdejonge in https://github.com/matchms/matchms/pull/654
• Use StackedSparseArray for MetadataMatch sparse equal_match by @zargham-ahmad in https://github.com/matchms/matchms/pull/642
• updated version and changelog by @hechth in https://github.com/matchms/matchms/pull/656

New Contributors

• @lionel42 made their first contribution in https://github.com/matchms/matchms/pull/631

Full Changelog: https://github.com/matchms/matchms/compare/0.24.4...0.25.0

Scientific Software - Peer-reviewed - Python
Published by hechth over 1 year ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.24.4

What's Changed

• Return processing report by @niekdejonge in https://github.com/matchms/matchms/pull/625

Full Changelog: https://github.com/matchms/matchms/compare/0.24.3...0.24.4

Scientific Software - Peer-reviewed - Python
Published by niekdejonge over 1 year ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.24.3

What's Changed

• Fix mz boundaries mirror plot by @niekdejonge in https://github.com/matchms/matchms/pull/610
• Fix documentation error by @niekdejonge in https://github.com/matchms/matchms/pull/611
• Do not consider lowestidx again in findmatches by @tornikeo in https://github.com/matchms/matchms/pull/606
• Fix issue with single number of rows or columns by @niekdejonge in https://github.com/matchms/matchms/pull/613
• Derive ionmode from charge by @niekdejonge in https://github.com/matchms/matchms/pull/614
• Remove repair precursor by @niekdejonge in https://github.com/matchms/matchms/pull/618

Full Changelog: https://github.com/matchms/matchms/compare/0.24.2...0.24.3

Scientific Software - Peer-reviewed - Python
Published by niekdejonge over 1 year ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.24.2

What's Changed

• Fix pepmass issue by @niekdejonge in https://github.com/matchms/matchms/pull/583
• Follow up on #593 by @Adafede in https://github.com/matchms/matchms/pull/599

Full Changelog: https://github.com/matchms/matchms/compare/0.24.1...0.24.2

Scientific Software - Peer-reviewed - Python
Published by niekdejonge almost 2 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.24.1

Fixed

• Fix to handle spectra with empty peak arrays. #598
• Fix instability introduced in CosineGreedy by np.argsort. #595

Changed

• Speed up savetomgf by preventing repetitive file opening
• Code refactoring for import functions #593.

Scientific Software - Peer-reviewed - Python
Published by florian-huber almost 2 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.24.0

What's Changed

Added

• Option to set custom key replacements #547
• Option to set the export style in save_as_mgf and save_as_json to choose other than matchms styles such as nist, riken, gnps #557
• Added a save spectra function. To automatically save in the specified file format. #543
• Add saving function in SpectrumProcessor #543 ### Fixed
• Fixed bug when loading empty metadata in msp #548
• Handle missing precursor_mz in representation and #452 introduced by #514#540
• Fixed retention time harmonization for msp files #551
• Fix closing mgf file after loading and prevent reopening. #555

Changed

• Renamed derivesmilesfrompubchemcompoundnamesearch to deriveannotationfromcompoundname. #559
• Deriveannotationfromcompoundname does not add smile or inchi when this cannot be interpreted by rdkit. #559
• Refactored SpectrumProcessor. Reduced code repetition and improved modularity. Matchms filters can now be added as functions and in a different position than specified. #565
• The default pipelines now stores matchms functions instead of string representation. #565
• The option to add predefined pipelines to SpectrumProcessor has been removed. Predefined pipelines can now just be added by adding the default_pipelines (which is a list) to the filters parameter. #565

PR's since previous release

• Fixed string representation and added testcase for issue 452 by @hechth in https://github.com/matchms/matchms/pull/540
• Enable setting key conversion with static method by @hechth in https://github.com/matchms/matchms/pull/547
• Update requireparentmassmatchsmiles.py by @niekdejonge in https://github.com/matchms/matchms/pull/552
• add export_style parameter by @florian-huber in https://github.com/matchms/matchms/pull/557
• Fix wrong pubchem annotations by @niekdejonge in https://github.com/matchms/matchms/pull/559
• Switch to tmp_path by @florian-huber in https://github.com/matchms/matchms/pull/566
• Prevent accidental file overwriting by @niekdejonge in https://github.com/matchms/matchms/pull/543
• Fix retention time for msp by @niekdejonge in https://github.com/matchms/matchms/pull/553
• Fix issue with parse metadata recognizing empty metadata as well. by @niekdejonge in https://github.com/matchms/matchms/pull/554
• Create new predefined pipelines, with subgroups and update tests. by @niekdejonge in https://github.com/matchms/matchms/pull/562
• Fix repair not matching annotation by @niekdejonge in https://github.com/matchms/matchms/pull/558
• Remove predefined pipelines by @niekdejonge in https://github.com/matchms/matchms/pull/565
• Change requireminimumofhighpeaks to requireminimumnumberofhig… by @niekdejonge in https://github.com/matchms/matchms/pull/573

Full Changelog: https://github.com/matchms/matchms/compare/0.23.1...0.24.0

Scientific Software - Peer-reviewed - Python
Published by niekdejonge about 2 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.23.1

Full Changelog: https://github.com/matchms/matchms/compare/0.23.0...0.23.1

Scientific Software - Peer-reviewed - Python
Published by hechth about 2 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.23.0

What's Changed

• Fix filter parameter setting by @niekdejonge in https://github.com/matchms/matchms/pull/493
• Restructure metadata utils by @niekdejonge in https://github.com/matchms/matchms/pull/503
• Change processing report by @niekdejonge in https://github.com/matchms/matchms/pull/501
• add str and repr methods by @florian-huber in https://github.com/matchms/matchms/pull/514
• Add default settings to processing steps by @niekdejonge in https://github.com/matchms/matchms/pull/496
• refactoring by @florian-huber in https://github.com/matchms/matchms/pull/513
• Spectrum processor sorting by @niekdejonge in https://github.com/matchms/matchms/pull/498
• Improve default pipelines by @niekdejonge in https://github.com/matchms/matchms/pull/499
• Add repair annotation by @niekdejonge in https://github.com/matchms/matchms/pull/505
• Restructure metadata utils by @niekdejonge in https://github.com/matchms/matchms/pull/507
• Add pubchem lookup by @niekdejonge in https://github.com/matchms/matchms/pull/509
• Add peak changes to processing report by @niekdejonge in https://github.com/matchms/matchms/pull/518
• Minor cleaning 510 by @florian-huber in https://github.com/matchms/matchms/pull/521
• Small bug fixing (during running of pipeline) by @niekdejonge in https://github.com/matchms/matchms/pull/510
• Further cleaning repairnotmatching_annotation by @niekdejonge in https://github.com/matchms/matchms/pull/522
• Improve derive adduct from name by @niekdejonge in https://github.com/matchms/matchms/pull/523
• Remove duplicated filters by @niekdejonge in https://github.com/matchms/matchms/pull/524
• Complete library cleaning pipeline by @niekdejonge in https://github.com/matchms/matchms/pull/525
• Fix adduct missing charge by @niekdejonge in https://github.com/matchms/matchms/pull/526
• Fix small issues by @niekdejonge in https://github.com/matchms/matchms/pull/529
• Add uneffective filters to report by @niekdejonge in https://github.com/matchms/matchms/pull/530
• Remove pepmass after running interpret_pepmass.py by @niekdejonge in https://github.com/matchms/matchms/pull/533
• Make initializespectrumprocessor part of SpectrumProcessor init by @niekdejonge in https://github.com/matchms/matchms/pull/535
• Store cleaning settings by @niekdejonge in https://github.com/matchms/matchms/pull/536
• fixed pepmass string parsing by @hechth in https://github.com/matchms/matchms/pull/539

Full Changelog: https://github.com/matchms/matchms/compare/0.22.0...0.23.0

Scientific Software - Peer-reviewed - Python
Published by hechth about 2 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.22.0

matchms 0.22.0

Added

• New SpectrumProcessing class to be the central hub for all filter functions #455. Also takes care that filters are executed in a useful order. This is also integrated into the Pipeline class.

Changed

• Adjustment to logger levels to remove uninformative warnings #484 and #487.
• Extensive code refactoring and cleaning.
• Pipeline class refactoring, Loading of yaml file happens outside Pipeline class #479
• Yaml file now stores individual filters in the correct order #480
• File names are not stored in yaml file anymore, they are now supplied when calling run in Pipeline #481
• Yaml does not store logging information and spectrum files anymore #481 and #482

Scientific Software - Peer-reviewed - Python
Published by florian-huber over 2 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.21.2

matchms 0.21.2

Changed

• no more warning if precursor m/z field is updated but change is < 0.001 in interpret_pepmass filter step #460.
• using poetry as a build system #466

Fixed

• reading MoNA msp files which specify RT in minutes #462
• added missing pyyaml dependency #463

Scientific Software - Peer-reviewed - Python
Published by florian-huber over 2 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.21.1

What's Changed

• rdkit log level implementation to supress warnings by @al-pi314 in https://github.com/matchms/matchms/pull/447
• refactor filter functions and their path structure by @florian-huber in https://github.com/matchms/matchms/pull/454

New Contributors

• @al-pi314 made their first contribution in https://github.com/matchms/matchms/pull/447

Full Changelog: https://github.com/matchms/matchms/compare/0.21.0...0.21.1

Scientific Software - Peer-reviewed - Python
Published by hechth over 2 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.21.0

matchms 0.21.0

Added

• New filter functions to repair a smiles that do not match parent mass #440
  • Updated adduct conversion and known adducts
  • added repairadductbasedonsmiles
  • added repairparentmassismol_wt
  • added repairprecursorisparentmass
  • added repairsmilesof_salts
  • added requireparentmassmatchsmiles
  • added function to combine this in repairparentmassmatchsmiles_wrapper
• Added repairsmilesfromcompoundname #448
• Added requirecorrectionmode #449
• Added requirevalidannotation #451

Changed

• Use pandas for loading adducts dict
• Moved functions from addparentmass to deriveprecursormzandparent_mass from
• Updated reiteratepeakcomments function to convert the peak_comments keys to float #437
• Removed filterbyrange non-inplace version #438
• Updated regex in getpeakvalues function #439

Fixed

• Fixed mistake in calculating parent mass from adduct
• Added metadata_harmonization parameter to load_spectra function #443

Scientific Software - Peer-reviewed - Python
Published by florian-huber over 2 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.20.0

Matchms 0.20.0

Added

• minmz, maxmz and title parameters to spectrum plot (mostly array plot) #419

Changed

• Fixed pipeline filter #414
• Removed fingerprint writing to file #416
• Updated harmonize_values function to remove invalid metadata #418
• Fixed metadata export style bug #423
• Updated comment parsing logic in loadfrommsp #420
• Minor changes to regular expressions in cleancompoundname #424

Scientific Software - Peer-reviewed - Python
Published by niekdejonge over 2 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.19.0

matchms 0.19.0

Added

• Added function to infer filetype when loading spectra
• CI test runs now include Python 3.10

Changed

• Support reading old NIST and GOLM MSP formats #392
• expanded options to handle different metadata key styles for (msp) file export #300
• light refactoring of Metadata constructor to reduce spectra reading time #371
• two minor corrections of adduct masses (missing electron mass) #374
• Arranged test in folders #408
• Updated datatype of peakcomments returned by loadfrom_mgf reader #410

Fixed

• Support sparse score arrays also for FingerprintSimilarity scores #389

Scientific Software - Peer-reviewed - Python
Published by florian-huber over 2 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.18.0

matchms 0.18.0

This represents a major update of matchms with several potential breaking changes. Two main shifts are the addition of a Pipeline API (using a new Pipeline class) and the novel underlying representation of scores by sparse arrays (in Scores).

Added

• new Pipeline class to define entire matchms workflows. This includes importing one or several datasets, processing using matchms filtering/processing functions as well as similartiy computations. Also allows to import/export workflows as yaml files.

Changed

• major change of Scores class. Internally, scores are now stored as a stacked sparse array. This allows to store several different scores for spectrum-spectrums pairs in an efficient way. Also makes it possible to run large-scale comparisons in particular when pipelines start with rapid selective similarity scoring methods such as MetadataMatch or PrecursorMzMatch.
• Scoring/similarity methods now also get a .sparse_array() method (next to the previous .pair() and .matrix() methods).

Fixed

• minor fix in interpret_pepmass function.

Scientific Software - Peer-reviewed - Python
Published by florian-huber almost 3 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.17.0

matchms 0.17.0

Added

• Scores: added functionality for writing and reading Scores objects to/from disk as JSON and Pickle files #353
• save_as_msp() now has a mode option (write/append) #346

Changed

• Developer-remark: switched from import numpy to import numpy as np

Scientific Software - Peer-reviewed - Python
Published by florian-huber about 3 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.16.0

matchms 0.16.0

Main change is an expansion of the network exporting options!

Added

• Spectrum objects now also have .mz and .intensities properties #339
• SimilarityNetwork: similarity-network graphs can now be exported to cyjs, gexf, gml, and node-link JSON formats #349

Changed

• metadata filtering: made prefilter check for SMILES and InChI more lenient, eventually resulting in longer runtimes but more accurate checks #337

Scientific Software - Peer-reviewed - Python
Published by florian-huber over 3 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.15.0

matchms 0.15.0

Added neutral losses similarity score (cosine-type score) and a few small fixes.

Added

• new spectral similarity score: NeutralLossesCosine which is based on matches between neutral losses of two spectra #329

Changed

• added key conversion: "precursor_type" to "adduct" #332
• added key conversion: "rtinseconds" to "retention_time" #331

Fixed

• handling of duplicate entries in spectrum files (e.g. as field and again in the comments field in msp files) by ugrade of pickydict to 0.4.0 #332

Scientific Software - Peer-reviewed - Python
Published by florian-huber almost 4 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.14.0

matchms 0.14.0

This is the first of a few releases to work our way towards matchms 1.0.0, which also means that a few things in the API will likely change. Here the main change is that Spectrum.metadata is no longer a simple Python dictionary but became a Metadata object. In this context metadata field-names/keys will now be harmonized by default (e.g. "Precursor Mass" will become "precursor_mz). For list of conversions see matchms key conversion table.

Added

• new MetadataMatchsimilarity measure in matchms.similarity. This can be used to find matches between metadata entries and currently supports either full string matches or matches of numerical entries within a specified tolerance #315
• metadata is now stored using new Metadata class which automatically applied restrictions to used field names/keys to avoid confusion between different format styles #293
• all metadata keys must be lower-case, spaces will be changed to underscores.
• Known key conversions are applied to metadata entries using a matchms key conversion table
• new interpret_pepmass() filter to handle different pepmass entries found in data [#298][https://github.com/matchms/matchms/issues/298]

Changed

• Metadata harmonization will now happen by default! This includes changing field name style and applying known key conversions. To avoid the key conversions user have to make this explicit by setting metadata_harmonization=False #293
• Spikes class has become Fragments class #293
• Change import style (now: isort 5 and slightly different style) #323

Fixed

• can now handle charges that come as a string of type "2+" or "1-" #301
• new Metadataclass fixes issue of equality check for different entry orders #285

Scientific Software - Peer-reviewed - Python
Published by florian-huber almost 4 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.13.0

matchms 0.13.0

Mainly changed (and expanded) plotting functionalities and a few minor fixes.

Added

• Updated and extended plotting functionality, now located in matchms.plotting. Contains three plot types: plot_spectrum() or spectrum.plot(), plot_spectra_mirror() or spectrum.plot_against() and plot_spectra_array() #303

Changed

• Spectrum objects got an update of the basic spectrum plots spectrum.plot() #303
• require_precursor_mz() filter will now also discard nonsensical m/z values < 10.0 (value can be adapted by user) #309

Fixed

• Updated to new url for load_from_usi function (old link was broken) #310
• Small bug fix: add_retention filters can now properly handle TypeError for empty list. #314

Scientific Software - Peer-reviewed - Python
Published by florian-huber almost 4 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.12.0

Matchms 0.12.0

Contains a number of small fixes and improvments. Most notable the now possible handling of peak-comments which can also be imported and exported from and to msp files.

Added

• peak comments (as an mz: comment dictionary) are now part of metadata and can be addressed via a Spectrum() object peak_comments property #284
• peak comments are dynamically updated whenever the respective peaks are changed #277

Changed

• Major refactoring of unit test layout now using a spectrum builder pattern #261
• Spikes object now has different getitem method that allows to extract specific peaks as mz/intensity pair (or array) #291
• add_parent_mass() filter now better handles existing entries (including fields "parentmass", "exactmass" and "parentmass") #292
• minor improvement of compound name cleaning in derive_adduct_from_name() filter #280
• save_as_msp() now writes peak comments (if present) to the output file #277
• load_from_msp() now also reads peak comments #277

Fixed

• able to handle spectra containg empty/zero intensities #289

Scientific Software - Peer-reviewed - Python
Published by florian-huber almost 4 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.11.0

matchms 0.11.0

Matchms now includes proper logging with the option to write the logging messages to a file.

Added

• matchms logger, replacing all former print statments to better control logging output #271
• add_logging_to_file(), set_matchms_logger_level(), reset_matchms_logger() functions to adapt logging output to user needs #271

Changed

• save_to_msp() can now also write to files with other than ".msp" extensions such as ".dat" #276

Scientific Software - Peer-reviewed - Python
Published by florian-huber about 4 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.10.0

New filters (add_retention_time() and add_retention_index()) and new ability of Spectrum() objects to compute hashes. Plus some linting and code improvements.

Added

• Spectrum() objects now also allows generating hashes, e.g. hash(spectrum) #259
• Spectrum() objects can generate .spectrum_hash() and .metadata_hash() to track changes to peaks or metadata #259
• load_from_mgf() now accepts both a path to a mgf file or a file-like object from a preloaded MGF file #258

• Added add_retention filters with function add_retention_time() and add_retention_index() #265

  Changed

• Code linting triggered by pylint update #257

• Refactored add_parent_mass() filter can now also handle missing charge entries (if ionmode is known) #252

Scientific Software - Peer-reviewed - Python
Published by florian-huber about 4 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.9.2

Minor update.

Added

• Support for Python 3.9 #240

Changed

• Use bool instead of numpy.bool to avoid warnings #245

Scientific Software - Peer-reviewed - Python
Published by florian-huber over 4 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.9.1

This release is about a few smaller fixes.

Fixed

• Correctly handle charge=0 entries in add_parent_mass filter #236
• Reordered written metadata in MSP export for compatibility with MS-FINDER & MS-DIAL #230
• Update README.rst to fix fstring-quote python example #226

Scientific Software - Peer-reviewed - Python
Published by florian-huber over 4 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.9.0

Most important additions are a new matchms.networking module which allows to create a graph/network based on spectral similarities, and a now possible export of spectra to .msp files using save_as_msp(). This release further contains a number of small improvements and extensions as listed here:

Added

• new matchms.networking module which allows to build and export graphs from scores objects #198
• Expand list of known negative ionmode adducts and conversion rules #213
• .to_numpy method for Spikes class which allows to run spectrum.peaks.to_numpy #214
• save_as_msp() function to export spectrums to .msp file #215

Changed

• add_precursor_mz() filter now also checks for metadata in keys precursormz and precursor_mass #223
• load_from_msp() now handles .msp files containing multiple peaks per line separated by ; #221
• add_parent_mass() now includes overwrite_existing_entry option (default is False) #225

Fixed

• add_parent_mass() filter now makes consistent use of cleaned adducts #225

Scientific Software - Peer-reviewed - Python
Published by florian-huber over 4 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.8.2

This release deals with a number of minor bugs that were encountered when working with data from various sources and data formats.

Added

• Added filter function 'requireprecursormz' and added 1 assert function in 'ModifiedCosine' #191
• make_charge_int() to convert charge field to integer #184

Changed

• now deprecated: make_charge_scalar(), use make_charge_int() instead #183

Fixed

• Make load_from_msp work with different whitespaces #192
• Very minor bugs in add_parent_mass #188

Scientific Software - Peer-reviewed - Python
Published by florian-huber almost 5 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.8.1

This release is about fixing the Bioconda install by adding the package data which is necessary for the adduct handling.

Added

• helper functions to clean adduct strings, clean_adduct() #170

Scientific Software - Peer-reviewed - Python
Published by florian-huber almost 5 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.8.0

This release is mostly about a substantial extension of the adduct handling. A .csv table of known adducts is used to calculate the (estimated) compound mass from the precursor m/z and the adduct properties (add_parent_mass).

Added

• helper functions to clean adduct strings, clean_adduct() #170

Changed

• more thorough adduct cleaning effecting derive_adduct_from_name() and derive_ionmode() #171
• significant expansion of add_parent_mass() filter to take known adduct properties into account #170

Fixed

• too unspecific formula detection (and removal) from given compound names in derive_formula_from_name #172
• no longer ignore nmax setting in `reducetonumberof_peaks` filter #177

Scientific Software - Peer-reviewed - Python
Published by florian-huber almost 5 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.7.0

Handling of scores has been changed in a way that might break some pipelines: Scores for similarity measures that return more than one measure (e.g. cosine or modified cosine) are now structured arrays that can be called by e.g. scores["score"].

Added

• scores_by_query and scores_by reference now accept sort=True to return sorted scores #153

Changed

• Scores.scores is now returning a structured array #153

Fixed

• Minor bug in add_precursor_mz #161
• Minor bug in Spectrum class (missing metadata deepcopy) #153
• Minor bug in Spectrum class (eq method was not working with numpy arrays in metadata) #153

Scientific Software - Peer-reviewed - Python
Published by florian-huber almost 5 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.6.2

Changed

• Considerable performance improvement for CosineGreedy and CosineHungarian #159

Scientific Software - Peer-reviewed - Python
Published by florian-huber about 5 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.6.1

Added

PrecursorMzMatch for deriving precursor m/z matches within a given tolerance #156

Changed

Raise error for improper use of reduce_to_number_of_peaks filter #151
Renamed ParentmassMatch to ParentMassMatch #156

Fixed

Fix minor issue with msp importer to avoid failing with unknown characters #151

Scientific Software - Peer-reviewed - Python
Published by florian-huber about 5 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.6.0

Added

• Four new peak filtering functions #119
• scorebyreference and scorebyquery methods to Scores #142
• is_symmetric option to speed up all-vs-all type score calculation #59
• Support for Python 3.8 #145

Changed

• Refactor similarity scores to be instances of BaseSimilarity class #135
• Marked Scores.calculate() method as deprecated #135

Removed

• calculate_parallel function #135
• Scores.calculate_parallel method #135
• similarity.FingerprintSimilarityParallel class (now part of similarity.FingerprintSimilarity) #135
• similarity.ParentmassMatchParallel class (now part of similarity.ParentmassMatch) #135

Scientific Software - Peer-reviewed - Python
Published by florian-huber over 5 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.5.2

Changed

• Revision of JOSS manuscript. #137

Scientific Software - Peer-reviewed - Python
Published by florian-huber over 5 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.5.1

Documentation updates:

Added

• Basic submodule documentation and more code examples #128

Changed

• Extended, updated, and corrected documentation for filter functions #118

Scientific Software - Peer-reviewed - Python
Published by florian-huber over 5 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.5.0

Added

• Read mzML and mzXML files to create Spectrum objects from it #110
• Read msp files to create Spectrum objects from it #102
• Peak weighting option for CosineGreedy and ModifiedCosine score #96
• Peak weighting option for CosineHungarian score #112
• Similarity score based on comparing parent masses #79
• Method for instantiating a spectrum from the metabolomics USI #93

Changed

• CosineGreedy function is now numba based #86
• Extended readthedocs documentation #82

Fixed

• Incorrect denominator for cosine score normalization #98

Scientific Software - Peer-reviewed - Python
Published by florian-huber over 5 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.4.0

Added

• Filter add_fingerprint to derive molecular fingerprints #42
• Similarity scores based on molecular fingerprints #42
• Add extensive compound name cleaning and harmonization #23
• Faster cosine score implementation using numba #29
• Cosine score based on Hungarian algorithm #40
• Modified cosine score #26
• Import and export of spectrums from json files #15
• Doc strings for many methods #49
• Examples in doc strings which are tested on CI #49

Changed

• normalize_intensities filter now also normalizes losses #69

Scientific Software - Peer-reviewed - Python
Published by florian-huber over 5 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.3.4

Changed

• Fix verify step in conda publish workflow

Scientific Software - Peer-reviewed - Python
Published by fdiblen over 5 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.3.3

Added

• Build workflow runs the tests after installing the package

Changed

• tests were removed from the package (see setup.py)

Scientific Software - Peer-reviewed - Python
Published by fdiblen over 5 years ago

matchms - processing and similarity evaluation of mass spectrometry data. - 0.3.2

Added

• Workflow improvements
  • Use artifacts in build workflow
  • List artifact folder in build workflow

Changed

• Workflow improvements #244
  • merge anaconda and python build workflows
  • fix conda package install command in build workflow
  • publish only on ubuntu machine
  • update workflow names
  • test conda packages on windows and unix separately
  • install conda package generated by the workflow
  • split workflows into multiple parts
  • use default settings for conda action
• data folder is handled by setup.py but not meta.yml

Removed

• remove python build badge #244
• Moved spec2vec similarity related functionality from matchms to iomega/spec2vec
• removed build step in build workflow
• removed conda build scripts: conda/build.sh and conda/bld.bat
• removed conda/condarc.yml
• removed condabuildconfig.yaml
• removed testing from publish workflow

Scientific Software - Peer-reviewed - Python
Published by fdiblen over 5 years ago