ms2query - 1.4.1

Full Changelog: https://github.com/iomega/ms2query/compare/1.4.0...1.4.1

- Python
Published by niekdejonge over 1 year ago

ms2query - 1.5.3

What's Changed

• updated ms2query library dois by @niekdejonge in https://github.com/iomega/ms2query/pull/253

Full Changelog: https://github.com/iomega/ms2query/compare/1.5.2...1.5.3

- Python
Published by niekdejonge over 1 year ago

ms2query - 1.5.2

What's Changed

• Handle compound_name is not given in metadata. by @niekdejonge in https://github.com/iomega/ms2query/pull/251
• Fix empty class annotation bug by @niekdejonge in https://github.com/iomega/ms2query/pull/252

Full Changelog: https://github.com/iomega/ms2query/compare/1.5.1...1.5.2

- Python
Published by niekdejonge over 1 year ago

ms2query - 1.5.1

What's Changed

• Set matchms version to max 0.26.4 by @niekdejonge in https://github.com/iomega/ms2query/pull/250 Set maximum scipy version.

Full Changelog: https://github.com/iomega/ms2query/compare/1.5.0...1.5.1

- Python
Published by niekdejonge over 1 year ago

ms2query - 1.5.0

What's Changed

• Remove pickle from docstring for loading files by @niekdejonge in https://github.com/iomega/ms2query/pull/238
• Update to testing version 3.9 - 3.11 by @niekdejonge in https://github.com/iomega/ms2query/pull/243

Full Changelog: https://github.com/iomega/ms2query/compare/1.4.0...1.5.0

- Python
Published by niekdejonge over 1 year ago

ms2query - 1.4.0

What's Changed

• Update ms2deepscore to 0.5.0 by @niekdejonge in https://github.com/iomega/ms2query/pull/237

Full Changelog: https://github.com/iomega/ms2query/compare/1.3.0...1.4.0

- Python
Published by niekdejonge almost 2 years ago

ms2query - 1.3.0

What's Changed

• Update dummy data to match recent changes by @niekdejonge in https://github.com/iomega/ms2query/pull/215
• Fix readme by @niekdejonge in https://github.com/iomega/ms2query/pull/216
• Added changes to changelog by @niekdejonge in https://github.com/iomega/ms2query/pull/219
• Isort by @niekdejonge in https://github.com/iomega/ms2query/pull/220
• Replace pickled dataframes by @niekdejonge in https://github.com/iomega/ms2query/pull/221
• Add add compound classes to settings by @niekdejonge in https://github.com/iomega/ms2query/pull/223
• Added addcompoundclasses parameter to SettingsTrainingModels by @mapio in https://github.com/iomega/ms2query/pull/224
• The default value of addcompoundclasses is wrongly documented by @mapio in https://github.com/iomega/ms2query/pull/229
• Add do pubchem lookup parameter by @mapio in https://github.com/iomega/ms2query/pull/230
• Replace pandas append with concat by @mapio in https://github.com/iomega/ms2query/pull/231
• Update matchms version by @niekdejonge in https://github.com/iomega/ms2query/pull/233
• Implement parquet by @niekdejonge in https://github.com/iomega/ms2query/pull/232

New Contributors

• @mapio made their first contribution in https://github.com/iomega/ms2query/pull/224

Full Changelog: https://github.com/iomega/ms2query/compare/1.2.4...1.3.0

- Python
Published by niekdejonge about 2 years ago

ms2query - 1.2.4

Full Changelog: https://github.com/iomega/ms2query/compare/1.2.2...1.2.4

- Python
Published by niekdejonge over 2 years ago

ms2query - 1.2.3

Fixes issue with onnxruntime version 1.16 by requiring onnxruntime < 1.16

- Python
Published by niekdejonge over 2 years ago

ms2query - 1.2.2

What's Changed

• Change the default additional metadata to retention_time by @niekdejonge in https://github.com/iomega/ms2query/pull/198

Full Changelog: https://github.com/iomega/ms2query/compare/1.2.1...1.2.2

- Python
Published by niekdejonge over 2 years ago

ms2query - 1.2.1

Fix bug with downloading library files

- Python
Published by niekdejonge over 2 years ago

ms2query - 1.2.0

What's Changed

• Now compatible with Matchms>=0.14

- Python
Published by niekdejonge almost 3 years ago

ms2query - 1.1.1

What's Changed

• change version and changelog by @niekdejonge in https://github.com/iomega/ms2query/pull/189

Full Changelog: https://github.com/iomega/ms2query/compare/1.1.0...1.1.1

- Python
Published by niekdejonge almost 3 years ago

ms2query - 1.0.1

Small bug fixes

- Python
Published by niekdejonge almost 3 years ago

ms2query - 1.0.0

What's Changed

Added

• Added compound classes to sqlite file
• Compound classes are now automatically added in the library file creation pipeline.
• Smiles are added from the specific spectrum instead of from the inchikey.

Removed

• Compound classes cannot be added from csv file anymore. Download the newest version of the sqlite file to have compoudn classes again.

Changed

• Zenodo link is set to latest version instead of specific version.

Code structure

• Unit tests had mayor reformatting
  • Better use of global fixtures
  • Remove pickled results table files

Full Changelog: https://github.com/iomega/ms2query/compare/0.7.4...1.0.0

- Python
Published by niekdejonge almost 3 years ago

ms2query - 0.7.4

What's Changed

• set pandas to <2.0.0 by @niekdejonge in https://github.com/iomega/ms2query/pull/181

Full Changelog: https://github.com/iomega/ms2query/compare/0.7.3.2...0.7.4

- Python
Published by niekdejonge almost 3 years ago

ms2query - 0.7.3.2

Fix tensorflow-metal version

- Python
Published by niekdejonge almost 3 years ago

ms2query - 0.7.3.1

Fix tensorflow macos M1 chip issues

- Python
Published by niekdejonge almost 3 years ago

ms2query - 0.7.3

Fix issues tensorflow macos.

- Python
Published by niekdejonge almost 3 years ago

ms2query - 0.7.2

What's Changed

• Clean up readme and downloading by @niekdejonge in https://github.com/iomega/ms2query/pull/178

Full Changelog: https://github.com/iomega/ms2query/compare/0.7.1...0.7.2

- Python
Published by niekdejonge almost 3 years ago

ms2query - 0.7.1

What's Changed

• Define zenodo doi by @niekdejonge in https://github.com/iomega/ms2query/pull/177

Full Changelog: https://github.com/iomega/ms2query/compare/0.7.0...0.7.1

- Python
Published by niekdejonge almost 3 years ago

ms2query - 0.7.0

What's Changed

• Implement onnx by @niekdejonge in https://github.com/iomega/ms2query/pull/176

Full Changelog: https://github.com/iomega/ms2query/compare/0.6.7...0.7.0

- Python
Published by niekdejonge almost 3 years ago

ms2query - 0.6.7

Updated Readme and citation file. New release to test automatic storing of MS2Query on Zenodo.

- Python
Published by niekdejonge about 3 years ago

ms2query - 0.6.6

What's Changed

• Add option to add metadata columns in command line by @niekdejonge in https://github.com/iomega/ms2query/pull/174

Full Changelog: https://github.com/iomega/ms2query/compare/0.6.5...0.6.6

- Python
Published by niekdejonge about 3 years ago

ms2query - 0.6.5

Fixed issue with matchms extras release

- Python
Published by niekdejonge about 3 years ago

ms2query - 0.6.4

Fix issue with running command line

- Python
Published by niekdejonge about 3 years ago

ms2query - 0.6.3

fix issue command line running

- Python
Published by niekdejonge about 3 years ago

ms2query - 0.6.2

Fixed run from command line issue

- Python
Published by niekdejonge about 3 years ago

ms2query - 0.6.1

Fixed issue with command line running

- Python
Published by niekdejonge about 3 years ago

ms2query - 0.6.0

What's Changed

• makemoreuser_friendly by @niekdejonge in https://github.com/iomega/ms2query/pull/166
• Update changelog by @niekdejonge in https://github.com/iomega/ms2query/pull/169

Full Changelog: https://github.com/iomega/ms2query/compare/0.5.7...0.6.0

- Python
Published by niekdejonge about 3 years ago

ms2query - 0.5.7

What's Changed

• Finalize workflow k fold validation by @niekdejonge in https://github.com/iomega/ms2query/pull/168

Full Changelog: https://github.com/iomega/ms2query/compare/0.5.6...0.5.7

- Python
Published by niekdejonge about 3 years ago

ms2query - 0.5.6

Full Changelog: https://github.com/iomega/ms2query/compare/0.5.5...0.5.6

- Python
Published by niekdejonge over 3 years ago

ms2query - 0.5.5

Full Changelog: https://github.com/iomega/ms2query/compare/0.5.4...0.5.5

- Python
Published by niekdejonge over 3 years ago

ms2query - 0.5.4

- Python
Published by niekdejonge over 3 years ago

ms2query - 0.5.3

Full Changelog: https://github.com/iomega/ms2query/compare/0.5.2...0.5.3

Set tensorflow to <=2.4.1

- Python
Published by niekdejonge over 3 years ago

ms2query - 0.5.2

What's Changed

• remove tensorflow warnings by @niekdejonge in https://github.com/iomega/ms2query/pull/161

Full Changelog: https://github.com/iomega/ms2query/compare/0.5.1...0.5.2

- Python
Published by niekdejonge over 3 years ago

ms2query - 0.5.1

What's Changed

• Remove library files creator from init to prevent dependency on rdkit by @niekdejonge in https://github.com/iomega/ms2query/pull/159

Full Changelog: https://github.com/iomega/ms2query/compare/0.5.0...0.5.1

- Python
Published by niekdejonge over 3 years ago

ms2query - 0.5.0

What's Changed

• Added k fold cross validation script by @niekdejonge in https://github.com/iomega/ms2query/pull/152

Added

• Training models is now fully automatic (no need for notebooks)
• Functions for creating benchmarking results
• Functions for doing kfoldcross_validation
• Functions for visualizing benchmarking results ### Changed
• Method for creating new library files
• Cleaning spectra functions for running are now combined with cleaning spectra functions for training

Full Changelog: https://github.com/iomega/ms2query/compare/0.4.3...0.5.0

- Python
Published by niekdejonge over 3 years ago

ms2query - 0.4.3

What's Changed

• Prevent memory issues ms2deepscore by @niekdejonge in https://github.com/iomega/ms2query/pull/154

Full Changelog: https://github.com/iomega/ms2query/compare/0.4.1...0.4.3

- Python
Published by niekdejonge over 3 years ago

ms2query - 0.4.1

What's Changed

• reduce memory tanimoto by @niekdejonge in https://github.com/iomega/ms2query/pull/151

Full Changelog: https://github.com/iomega/ms2query/compare/0.4.0...0.4.1

- Python
Published by niekdejonge over 3 years ago

ms2query - 0.4.0

What's Changed

• Improve library files creation by @niekdejonge in https://github.com/iomega/ms2query/pull/146
• Improve ease of use downloading library and running ms2query by @niekdejonge in https://github.com/iomega/ms2query/pull/148
• Improve library files creation by @niekdejonge in https://github.com/iomega/ms2query/pull/149

Full Changelog: https://github.com/iomega/ms2query/compare/0.3.3...0.4.0

- Python
Published by niekdejonge over 3 years ago

ms2query - 0.3.3

What's Changed

• Create sqlite without spectrum by @niekdejonge in https://github.com/iomega/ms2query/pull/142
• Create smaller sqlite file by @niekdejonge in https://github.com/iomega/ms2query/pull/143

Full Changelog: https://github.com/iomega/ms2query/compare/0.3.2...0.3.3

- Python
Published by niekdejonge over 3 years ago

ms2query - 0.3.2

Added

• Updated notebooks for performance analysis
• Solved bug in downloading library

Changed

• Made handling different pandas versions more flexible

Full Changelog: https://github.com/iomega/ms2query/compare/0.3.1...0.3.2

- Python
Published by niekdejonge over 3 years ago

ms2query - 0.3.1

What's Changed

• change zenodo link with default library files by @niekdejonge in https://github.com/iomega/ms2query/pull/133
• Change numbering spectra by @niekdejonge in https://github.com/iomega/ms2query/pull/135

Full Changelog: https://github.com/iomega/ms2query/compare/0.3.0...0.3.1

- Python
Published by florian-huber about 4 years ago

ms2query - 0.3.0

What's Changed

• Analyze case studies by @niekdejonge in https://github.com/iomega/ms2query/pull/107
• Change run ms2query by @niekdejonge in https://github.com/iomega/ms2query/pull/114
• Add notebooks for cleaning GNPS dataset by @niekdejonge in https://github.com/iomega/ms2query/pull/116
• Use random forest by @niekdejonge in https://github.com/iomega/ms2query/pull/119
• test python version dependent pickle 5 install by @florian-huber in https://github.com/iomega/ms2query/pull/124
• parentmass -> precursormz and notebook re-run/update by @florian-huber in https://github.com/iomega/ms2query/pull/118
• Remove and restructure unused code by @niekdejonge in https://github.com/iomega/ms2query/pull/130
• Add isort by @florian-huber in https://github.com/iomega/ms2query/pull/128
• switch to newer matchms and spec2vec versions by @florian-huber in https://github.com/iomega/ms2query/pull/127

Full Changelog: https://github.com/iomega/ms2query/compare/0.2.4...0.3.0

- Python
Published by niekdejonge about 4 years ago

ms2query - 0.2.4

What's Changed

• solved issues downloading zenodo by @niekdejonge in https://github.com/iomega/ms2query/pull/113

Full Changelog: https://github.com/iomega/ms2query/compare/0.2.3...0.2.4

- Python
Published by niekdejonge over 4 years ago

ms2query - 0.2.3

What's Changed

• Make running user friendlier by @niekdejonge in https://github.com/iomega/ms2query/pull/108
• Refactor ms2library by @niekdejonge in https://github.com/iomega/ms2query/pull/109

Full Changelog: https://github.com/iomega/ms2query/compare/0.2.2...0.2.3

- Python
Published by niekdejonge over 4 years ago

ms2query - 0.2.2

Release were result table was added

- Python
Published by niekdejonge over 4 years ago

ms2query - 0.2.1

Changed release workflow, so pip package is also updated.

- Python
Published by niekdejonge over 4 years ago

ms2query - 0.2.0

Added

• Move library parts to Sqlite #56
• Define spectrum processing functions #61
• Extend CI workflow and add Sonarcloud #62
• Average inchikey score and neighbourhood score #78

Removed

• Streamlit web app (will now be future development) #83

Changed

• Refactored library matching #65
• Split workflow into true matches and analog search #72
• Refactored library files creation #74

- Python
Published by niekdejonge over 4 years ago

ms2query - 0.1.0

Initial release of MS2Query.

- Python
Published by florian-huber about 5 years ago