matchms/matchms issues and pull requests

#515 - Fix readthedocs

Issue - State: closed - Opened by florian-huber about 1 year ago - 1 comment

#514 - add str and repr methods

Pull Request - State: closed - Opened by florian-huber about 1 year ago - 2 comments

#513 - refactoring

Pull Request - State: closed - Opened by florian-huber about 1 year ago - 1 comment

#512 - Add peak changes to SpectrumProcessor

Issue - State: closed - Opened by niekdejonge about 1 year ago - 2 comments

#511 - Skipping spectra breaking pipeline

Issue - State: closed - Opened by niekdejonge about 1 year ago - 5 comments
Labels: stale

#510 - Small bug fixing (during running of pipeline)

Pull Request - State: closed - Opened by niekdejonge about 1 year ago - 5 comments

#509 - Add pubchem lookup

Pull Request - State: closed - Opened by niekdejonge over 1 year ago - 5 comments

#508 - Add blink to similarity scores

Issue - State: closed - Opened by florian-huber over 1 year ago - 2 comments
Labels: stale

#507 - Restructure metadata utils

Pull Request - State: closed - Opened by niekdejonge over 1 year ago - 3 comments

#506 - Modified cosine score ignores mass-shifted fragments with fewer charges than precursor

Issue - State: closed - Opened by biobeni over 1 year ago - 4 comments
Labels: stale

#505 - Improve adding filters in SpectrumProcessor

Pull Request - State: closed - Opened by niekdejonge over 1 year ago - 3 comments

#504 - Add str and repr methods to classes

Issue - State: closed - Opened by florian-huber over 1 year ago

#503 - Restructure metadata utils

Pull Request - State: closed - Opened by niekdejonge over 1 year ago - 1 comment

#502 - Add repair annotation filter

Issue - State: closed - Opened by niekdejonge over 1 year ago - 1 comment

#501 - Change processing report

Pull Request - State: closed - Opened by niekdejonge over 1 year ago - 1 comment

#500 - ProgressReport can count one changed spectrum multiple times

Issue - State: closed - Opened by niekdejonge over 1 year ago

#499 - Improve default pipelines

Pull Request - State: closed - Opened by niekdejonge over 1 year ago - 3 comments

#498 - Spectrum processor sorting

Pull Request - State: closed - Opened by niekdejonge over 1 year ago - 2 comments

#497 - Add progress bar to SimilarityNetwork

Issue - State: closed - Opened by florian-huber over 1 year ago - 2 comments
Labels: stale

#496 - Add default settings to processing steps

Pull Request - State: closed - Opened by niekdejonge over 1 year ago

#495 - How to handle duplicated filters in SpectrumProcessor

Issue - State: closed - Opened by niekdejonge over 1 year ago - 2 comments

#494 - Add default filters to yaml file

Issue - State: closed - Opened by niekdejonge over 1 year ago - 1 comment

#493 - Fix filter parameter setting

Pull Request - State: closed - Opened by niekdejonge over 1 year ago - 1 comment

#492 - Filter parameters in default pipelines are not used

Issue - State: closed - Opened by niekdejonge over 1 year ago

#491 - Remove lock file

Pull Request - State: closed - Opened by florian-huber over 1 year ago - 1 comment

#490 - Poetry related CI fails due to poetry.lock

Issue - State: closed - Opened by florian-huber over 1 year ago - 2 comments

#489 - try pypi build with Python 3.9

Pull Request - State: closed - Opened by florian-huber over 1 year ago

#488 - Tests don't pass

Issue - State: closed - Opened by niekdejonge over 1 year ago - 3 comments

#487 - remove unnecessary warning

Pull Request - State: closed - Opened by florian-huber over 1 year ago - 2 comments

#486 - Pr455 review

Pull Request - State: closed - Opened by florian-huber over 1 year ago

#485 - SpectrumProcessor should also report filters that do not make changes.

Issue - State: closed - Opened by niekdejonge over 1 year ago - 1 comment

#484 - logging level adjustments

Pull Request - State: closed - Opened by florian-huber over 1 year ago - 1 comment

#483 - Add workflow setters

Pull Request - State: closed - Opened by niekdejonge over 1 year ago

#482 - Add check for correct workflow

Pull Request - State: closed - Opened by niekdejonge over 1 year ago - 1 comment

#481 - Remove file names from yaml

Pull Request - State: closed - Opened by niekdejonge over 1 year ago

#480 - Add individual filters in yaml

Pull Request - State: closed - Opened by niekdejonge over 1 year ago

#479 - Move yaml file creation and loading outside Pipeline.py

Pull Request - State: closed - Opened by niekdejonge over 1 year ago - 1 comment

#478 - Store all filters in yaml file instead of predefined_processing_queries

Issue - State: closed - Opened by niekdejonge over 1 year ago - 1 comment

#477 - Complete filter order

Pull Request - State: closed - Opened by niekdejonge over 1 year ago

#476 - Add test that checks that ALL_FILTERS contains all filter functions

Issue - State: closed - Opened by niekdejonge over 1 year ago - 1 comment

#475 - Pipeline refactoring

Issue - State: closed - Opened by niekdejonge over 1 year ago

#474 - Make CI more lightweight

Issue - State: closed - Opened by florian-huber over 1 year ago - 1 comment

#473 - update pypi upload workflow

Issue - State: closed - Opened by florian-huber over 1 year ago - 2 comments

#472 - Change processing report to store filter step instead of field

Pull Request - State: closed - Opened by niekdejonge over 1 year ago

#471 - clean up rdkit imports

Issue - State: closed - Opened by hechth over 1 year ago - 2 comments
Labels: stale

#470 - update pipeline to use Processor class

Pull Request - State: closed - Opened by florian-huber over 1 year ago

#469 - Improve documentation adducts

Pull Request - State: closed - Opened by niekdejonge over 1 year ago - 2 comments

#468 - Add alexander Piciga to citations

Pull Request - State: closed - Opened by niekdejonge over 1 year ago

#467 - SpectrumProcessor class

Issue - State: closed - Opened by florian-huber over 1 year ago - 9 comments

#466 - Change project build system to poetry and minor bugfixes

Pull Request - State: closed - Opened by hechth over 1 year ago - 4 comments

#465 - Consider switching to black as a formatter

Issue - State: closed - Opened by hechth over 1 year ago - 4 comments
Labels: documentation, package quality, stale

#464 - Change build system to use poetry

Issue - State: closed - Opened by hechth over 1 year ago - 1 comment
Labels: enhancement, package quality

#463 - `pyyaml` could be a core dependency

Issue - State: closed - Opened by chanana over 1 year ago
Labels: bug

#462 - Error loading MoNA msp file, multiple warnings regarding inability to convert retention time to float

Issue - State: closed - Opened by jmmitc06 over 1 year ago - 3 comments
Labels: bug

#461 - Cannot Install the `master` branch with Python 3.11.4

Issue - State: closed - Opened by srivarra over 1 year ago - 3 comments
Labels: bug, package quality

#460 - silence unnecessary warnings

Pull Request - State: closed - Opened by florian-huber over 1 year ago - 1 comment

#459 - Save each spectrum (.ms) format

Issue - State: closed - Opened by anupriyatripathi over 1 year ago - 4 comments
Labels: question

#458 - Rename `get_ions_from_adduct` function

Issue - State: closed - Opened by hechth over 1 year ago - 2 comments
Labels: documentation, stale

#457 - Improve function name and documentation

Issue - State: closed - Opened by hechth over 1 year ago - 2 comments
Labels: documentation

#456 - `ModuleNotFoundError`: No module named 'matchms.filtering.filter_utils'

Issue - State: closed - Opened by chanana over 1 year ago - 3 comments
Labels: bug

#455 - Add filter class

Pull Request - State: closed - Opened by florian-huber over 1 year ago - 4 comments

#454 - refactor filter functions and their path structure

Pull Request - State: closed - Opened by florian-huber over 1 year ago - 2 comments

#453 - Make one function for import rdkit

Issue - State: closed - Opened by niekdejonge over 1 year ago - 1 comment
Labels: enhancement, package quality

#452 - _interpret_pepmass error

Issue - State: closed - Opened by ADablanc over 1 year ago - 9 comments
Labels: bug, stale

#451 - Require annotation

Pull Request - State: closed - Opened by niekdejonge over 1 year ago - 1 comment

#450 - remove macos Python 3.7

Pull Request - State: closed - Opened by florian-huber over 1 year ago - 1 comment

#449 - Add filter ionmode

Pull Request - State: closed - Opened by niekdejonge over 1 year ago - 1 comment

#448 - Add smiles from compound name

Pull Request - State: closed - Opened by niekdejonge over 1 year ago - 3 comments

#447 - rdkit log level implementation to supress warnings

Pull Request - State: closed - Opened by al-pi314 over 1 year ago - 10 comments

#446 - Warning interpret_pepmass

Issue - State: closed - Opened by niekdejonge over 1 year ago - 1 comment

#445 - Retire macOS python 3.7 support

Issue - State: closed - Opened by hechth over 1 year ago - 2 comments

#444 - Update CI from Node12 actions

Issue - State: closed - Opened by hechth over 1 year ago

#443 - Add metadata harmonization options to `load_spectra` function

Pull Request - State: closed - Opened by hechth over 1 year ago - 2 comments

#442 - Add metadata harmonization options to `load_spectra` function

Issue - State: closed - Opened by hechth over 1 year ago

#441 - Implement `save_spectra` method

Issue - State: closed - Opened by hechth over 1 year ago - 2 comments
Labels: enhancement

#440 - Interpret adducts

Pull Request - State: closed - Opened by niekdejonge over 1 year ago - 2 comments

#439 - Updated regex in get_peak_values function

Pull Request - State: closed - Opened by zargham-ahmad over 1 year ago - 2 comments

#438 - Removed filter_by_range non-inplace version

Pull Request - State: closed - Opened by zargham-ahmad over 1 year ago - 1 comment

#437 - Fixed reading peak_comments in json reader

Pull Request - State: closed - Opened by zargham-ahmad over 1 year ago - 4 comments

#436 - New filter functions for parent mass

Pull Request - State: closed - Opened by niekdejonge over 1 year ago - 3 comments

#435 - Added compare precursor_mz and parent mass

Pull Request - State: closed - Opened by niekdejonge over 1 year ago

#434 - Convert filtering functions to classes

Issue - State: open - Opened by niekdejonge over 1 year ago - 6 comments
Labels: future developments

#433 - Different Logging for Pipeline filtering

Issue - State: closed - Opened by niekdejonge over 1 year ago - 3 comments
Labels: future developments

#432 - Group filtering functions

Issue - State: closed - Opened by niekdejonge over 1 year ago - 8 comments
Labels: future developments, package quality

#431 - add more complications to pesticides.mgf

Pull Request - State: closed - Opened by florian-huber over 1 year ago - 1 comment

#430 - MGF import error due to pyteomics pepmass parsing

Issue - State: closed - Opened by florian-huber over 1 year ago - 4 comments
Labels: bug, stale

#429 - Update clean_compound_name.py

Pull Request - State: closed - Opened by niekdejonge over 1 year ago - 1 comment

#428 - Derive_adduct_from_name should remove multiple adducts

Issue - State: closed - Opened by niekdejonge over 1 year ago - 1 comment

#427 - added get compound from puchem

Pull Request - State: closed - Opened by niekdejonge over 1 year ago - 12 comments

#426 - Loading spectra in pipeline

Pull Request - State: closed - Opened by niekdejonge over 1 year ago - 1 comment

#425 - Pipeline should use load_spectra function

Issue - State: closed - Opened by niekdejonge over 1 year ago

#424 - fix potential regex risks

Pull Request - State: closed - Opened by florian-huber over 1 year ago - 2 comments

#423 - Fixed metadata export style bug

Pull Request - State: closed - Opened by zargham-ahmad over 1 year ago - 3 comments

#422 - Metadata export style bug

Issue - State: closed - Opened by hechth over 1 year ago

#421 - Parsing issues with matchms 0.19

Issue - State: closed - Opened by ADablanc over 1 year ago - 10 comments

#420 - Updated comment parsing logic

Pull Request - State: closed - Opened by zargham-ahmad over 1 year ago - 3 comments

#419 - add min_mz and max_mz

Pull Request - State: closed - Opened by florian-huber over 1 year ago - 3 comments

#418 - Updated harmonize_values function to remove invalid metadata

Pull Request - State: closed - Opened by zargham-ahmad over 1 year ago - 1 comment

#417 - Fix return type of `filter_by_range` to be either a Scores object or remove non-inplace method.

Issue - State: closed - Opened by hechth over 1 year ago

#416 - Removed fingerprint writing to file

Pull Request - State: closed - Opened by zargham-ahmad over 1 year ago - 1 comment

GitHub / matchms/matchms issues and pull requests