Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / matchms/matchms issues and pull requests

#727 - Question: why having `mz_power` in cosine score?

Issue - State: open - Opened by ctapobep 19 days ago

#726 - save_as_mgf is always in append mode

Issue - State: open - Opened by florian-huber 22 days ago
Labels: good first issue, workshop 2025

#725 - Retention time not converted correctly

Issue - State: open - Opened by florian-huber 22 days ago

#724 - Documentation outdated --> better introduce modules (e.g. filtering)

Issue - State: open - Opened by florian-huber 22 days ago
Labels: documentation, package quality, workshop 2025

#723 - Vendor mass spec formats

Issue - State: open - Opened by ctapobep about 1 month ago

#722 - Save empty spectrum list as empty file

Pull Request - State: open - Opened by wasimsandhu 2 months ago

#721 - Use Ruff for formatting

Issue - State: open - Opened by wasimsandhu 2 months ago

#720 - Add ecosystem dependency tests

Pull Request - State: closed - Opened by julianpollmann 3 months ago - 5 comments

#718 - Numpy compatibility

Issue - State: closed - Opened by julianpollmann 3 months ago
Labels: package quality

#717 - Feature/add fingerprint inchikey mapping

Pull Request - State: closed - Opened by julianpollmann 3 months ago

#716 - Add missing key conversions for RIKEN and NIST

Issue - State: open - Opened by hechth 3 months ago

#715 - Allow numpy 1.x and 2.x

Pull Request - State: closed - Opened by florian-huber 3 months ago

#714 - Incompatibilities with Numpy >= 2.0

Issue - State: closed - Opened by florian-huber 3 months ago - 1 comment

#713 - Preparing for release 0.28.0

Pull Request - State: closed - Opened by hechth 3 months ago - 2 comments

#712 - Enable metadata exporting with tab separators

Pull Request - State: closed - Opened by hechth 3 months ago - 2 comments

#711 - Enable metadata exporting with tab separators

Issue - State: closed - Opened by hechth 3 months ago

#710 - Release 0.28.0

Issue - State: closed - Opened by hechth 3 months ago

#709 - Updated matchms dependencies

Pull Request - State: closed - Opened by hechth 3 months ago - 2 comments

#708 - Add save as mzml

Issue - State: open - Opened by niekdejonge 4 months ago - 3 comments

#707 - Add save as mzml

Pull Request - State: open - Opened by niekdejonge 4 months ago

#706 - Remove printing dict during saving

Issue - State: closed - Opened by niekdejonge 5 months ago

#705 - Update utils.py

Pull Request - State: closed - Opened by niekdejonge 5 months ago - 2 comments

#704 - Store losses as part of spectra object

Issue - State: closed - Opened by rtlortega 7 months ago - 3 comments

#703 - Rename CudaMS -> SimMS, tweak description a bit

Pull Request - State: closed - Opened by tornikeo 7 months ago

#702 - IndexError in `.matrix` when all scores are 0

Pull Request - State: closed - Opened by tornikeo 7 months ago

#701 - Increased Test Coverage

Pull Request - State: closed - Opened by julianpollmann 7 months ago - 3 comments

#700 - fixed bug in mirrorplots when plotting only specific mz range

Pull Request - State: closed - Opened by hechth 7 months ago

#699 - Bump Version to 0.27.0

Pull Request - State: closed - Opened by julianpollmann 7 months ago

#698 - Parallel loading

Issue - State: closed - Opened by 1641004802 7 months ago - 2 comments

#697 - Only merge after CI action successes

Issue - State: closed - Opened by julianpollmann 7 months ago - 2 comments
Labels: stale

#696 - Update README.rst

Pull Request - State: closed - Opened by florian-huber 8 months ago - 1 comment

#695 - New Spectra class?

Issue - State: closed - Opened by florian-huber 8 months ago - 1 comment

#694 - Added encoding to loading and saving mgf

Pull Request - State: closed - Opened by niekdejonge 8 months ago - 2 comments

#693 - Updated numpy version will fail comparisons

Issue - State: closed - Opened by julianpollmann 8 months ago - 3 comments

#692 - Numpy replace njitted

Pull Request - State: closed - Opened by florian-huber 8 months ago - 2 comments

#691 - Update numba and numpy

Pull Request - State: closed - Opened by florian-huber 8 months ago - 1 comment

#690 - Fix/refactor spectrums to spectra

Pull Request - State: closed - Opened by julianpollmann 8 months ago - 3 comments

#689 - Fix/update actions

Pull Request - State: closed - Opened by julianpollmann 8 months ago - 1 comment

#688 - Design and implement a Spectra / Dataset class

Issue - State: open - Opened by florian-huber 8 months ago - 4 comments
Labels: future developments

#687 - Align talking and coding: `spectrums` --> `spectra`

Issue - State: closed - Opened by florian-huber 8 months ago - 3 comments

#686 - Remove None Spectra from Spectrum lists before exporting

Pull Request - State: closed - Opened by julianpollmann 8 months ago - 1 comment

#685 - Update docs

Pull Request - State: closed - Opened by julianpollmann 8 months ago

#684 - Added excempt label to stale.yml

Pull Request - State: closed - Opened by julianpollmann 8 months ago

#683 - Remove losses from test

Pull Request - State: closed - Opened by niekdejonge 8 months ago - 1 comment

#682 - Added mark stale issues workflow

Pull Request - State: closed - Opened by julianpollmann 8 months ago

#681 - replace losses attribute by property method

Pull Request - State: closed - Opened by florian-huber 8 months ago

#680 - Remove losses attribute from `Spectrum`

Issue - State: open - Opened by florian-huber 8 months ago - 2 comments

#679 - load_from_mgf leads to corrupt of vscode

Issue - State: closed - Opened by 1641004802 8 months ago - 2 comments

#678 - fix name position

Pull Request - State: closed - Opened by lionel42 8 months ago - 1 comment

#677 - fix merge mistake

Pull Request - State: closed - Opened by niekdejonge 8 months ago

#676 - Add repair parent mass from smiles

Pull Request - State: closed - Opened by niekdejonge 9 months ago - 1 comment

#675 - Fix repair adduct and parent mass not repairing correct parent mass

Pull Request - State: closed - Opened by niekdejonge 9 months ago - 1 comment

#674 - Add require correct ms level 2

Pull Request - State: closed - Opened by niekdejonge 9 months ago

#673 - Add check if monoisotopic mass could be determined

Pull Request - State: closed - Opened by niekdejonge 9 months ago - 1 comment

#672 - Handle None spectra when saving

Issue - State: closed - Opened by niekdejonge 9 months ago
Labels: good first issue

#671 - Fix saving bug

Pull Request - State: closed - Opened by niekdejonge 9 months ago

#670 - Future filters

Issue - State: open - Opened by niekdejonge 9 months ago

#669 - Notify that `cudams` repository has been moved

Pull Request - State: closed - Opened by tornikeo 9 months ago

#668 - Check for size equality when using is_symmetric

Pull Request - State: closed - Opened by tornikeo 9 months ago - 1 comment

#667 - `is_symmetric` needs more checks

Issue - State: closed - Opened by tornikeo 9 months ago - 1 comment

#666 - Add require correct ms level

Pull Request - State: closed - Opened by niekdejonge 9 months ago - 2 comments

#665 - Add check filters handle none

Pull Request - State: closed - Opened by niekdejonge 9 months ago - 1 comment

#664 - Add require number of peaks below maximum

Pull Request - State: closed - Opened by niekdejonge 9 months ago

#663 - Remove noise below frequent intensities

Pull Request - State: closed - Opened by niekdejonge 9 months ago

#662 - fix bug with mz window

Pull Request - State: closed - Opened by niekdejonge 9 months ago

#661 - Derive formula from smiles

Pull Request - State: closed - Opened by niekdejonge 9 months ago

#660 - Allow peaks with many floating types

Pull Request - State: closed - Opened by tornikeo 9 months ago - 3 comments

#659 - Require matching adduct precursor mz parent mass

Pull Request - State: closed - Opened by niekdejonge 9 months ago

#658 - Fix metadata match

Pull Request - State: closed - Opened by niekdejonge 9 months ago

#657 - Require matching ionmode and adduct

Pull Request - State: closed - Opened by niekdejonge 9 months ago

#656 - updated version and changelog

Pull Request - State: closed - Opened by hechth 9 months ago

#655 - Fail fast on loading missing mgf

Pull Request - State: closed - Opened by tornikeo 9 months ago - 1 comment

#654 - Fix rdkit version

Pull Request - State: closed - Opened by niekdejonge 9 months ago - 1 comment

#653 - Teeny readme clarification about poetry extras

Pull Request - State: closed - Opened by tornikeo 9 months ago - 1 comment

#652 - Importing should raise error if file does not exist

Issue - State: closed - Opened by niekdejonge 9 months ago

#651 - Save mgf msp once per iteration in pipeline

Pull Request - State: closed - Opened by tornikeo 9 months ago - 1 comment

#650 - Remove profile spectra

Pull Request - State: closed - Opened by niekdejonge 9 months ago

#649 - Derive formula from inchi

Pull Request - State: closed - Opened by niekdejonge 9 months ago

#648 - Skip errors when loading file for msp

Pull Request - State: closed - Opened by niekdejonge 9 months ago

#647 - File export crashed for non utf-8 characters

Issue - State: open - Opened by florian-huber 9 months ago - 2 comments
Labels: bug

#646 - SpectrumProcessor saving of spectra should maybe be one by one

Issue - State: open - Opened by florian-huber 9 months ago - 1 comment

#645 - add logging for writing spectra to file

Pull Request - State: closed - Opened by florian-huber 9 months ago

#643 - Avoid keyword args to `njit` functions

Issue - State: open - Opened by tornikeo 9 months ago

#642 - Use StackedSparseArray for MetadataMatch `sparse equal_match`

Pull Request - State: closed - Opened by zargham-ahmad 9 months ago - 4 comments

#641 - Installation of rdkit fails in CI pipeline

Issue - State: closed - Opened by florian-huber 10 months ago - 2 comments
Labels: bug

#640 - Propose dependency changes

Pull Request - State: closed - Opened by florian-huber 10 months ago - 3 comments

#639 - Outdated (and possibly too restrictive) dependency settings

Issue - State: closed - Opened by florian-huber 10 months ago - 3 comments

#638 - Vectorise matrix similarity functions

Pull Request - State: closed - Opened by tornikeo 10 months ago - 8 comments

#637 - Vectorize similarity calculations

Issue - State: closed - Opened by tornikeo 10 months ago - 1 comment

#636 - Don't use unstable sorting in similarity measures

Pull Request - State: closed - Opened by tornikeo 10 months ago

#635 - Consider additional score: Delta MZ

Issue - State: open - Opened by florian-huber 10 months ago

#634 - Consider additional score: MCES

Issue - State: open - Opened by florian-huber 10 months ago

#633 - BaseSimilarity.matrix method errors if all scores/matches are 0

Issue - State: open - Opened by tharwood3 10 months ago - 1 comment
Labels: bug

#632 - Save and load hdf5 representation

Issue - State: open - Opened by niekdejonge 10 months ago
Labels: enhancement

#631 - adding colors for mirrror spectra and tests

Pull Request - State: closed - Opened by lionel42 10 months ago

#630 - fix merge mistakes

Pull Request - State: closed - Opened by niekdejonge 10 months ago - 1 comment

#629 - Should we remove keys that are invalid and if so, which values should we accept?

Issue - State: open - Opened by hechth 10 months ago
Labels: discussion