Ecosyste.ms: Issues

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GitHub / matchms/matchms issues and pull requests

#615 - Remove adduct and mol wt wrong

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

#614 - Derive ionmode from charge

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

#613 - Fix issue with single number of rows or columns

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

#612 - KeyError: 'num peaks'

Issue - State: open - Opened by 1641004802 8 months ago

#611 - Fix documentation error

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

#610 - Fix mz boundaries mirror plot

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

#609 - RuntimeError: Wrong peak format detected!

Issue - State: closed - Opened by 1641004802 8 months ago - 3 comments

#607 - fixed non respected specified mz boudaries

Pull Request - State: closed - Opened by lionel42 8 months ago - 3 comments

#606 - Do not consider lowest_idx again in find_matches

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

#605 - Fix array truth value error in Metadata tests

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

#604 - Support GOLM style MSP files

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

#603 - Development setup bugs

Issue - State: closed - Opened by hechth 10 months ago

#602 - Added `require_retention_time` and `require_retention_index` filters

Pull Request - State: closed - Opened by hechth 10 months ago - 6 comments

#601 - Reported changes when nothing is changed

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

#600 - Weird `repair_adduct_based_on_smiles` `derive_ionmode` logic?

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

#599 - Follow up on #593

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

#598 - fix bug for empty peak array and add test

Pull Request - State: closed - Opened by florian-huber 11 months ago

#597 - KeyError: 'scans' during matchms running

Issue - State: open - Opened by anani-a-missinou 11 months ago - 1 comment

#596 - Stabilize CosineGreedy by using mergesort on matches

Pull Request - State: closed - Opened by tornikeo 11 months ago

#595 - CosineGreedy is unstable

Issue - State: closed - Opened by tornikeo 11 months ago

#594 - fix isort

Pull Request - State: closed - Opened by Adafede 11 months ago - 1 comment

#593 - Re-organize some importing modules

Pull Request - State: closed - Opened by florian-huber 11 months ago - 3 comments

#592 - Re-organize some importing modules

Pull Request - State: closed - Opened by Adafede 11 months ago - 1 comment

#591 - Improvements for matchms cleaning pipeline

Issue - State: open - Opened by niekdejonge 11 months ago
Labels: future developments

#590 - Compound name missing in some database entries (matchms database cleaning)

Issue - State: open - Opened by Philipbear 12 months ago - 2 comments
Labels: enhancement, stale

#589 - Mismatch between adduct and ionmode after filtering pipeline

Issue - State: open - Opened by niekdejonge 12 months ago - 2 comments

#588 - Fix generating empty spectrums

Issue - State: closed - Opened by lionel42 12 months ago - 2 comments
Labels: bug

#587 - Don't repeatedly open mgf file when exporting

Pull Request - State: closed - Opened by niekdejonge 12 months ago

#586 - Save empty spectrum list as empty file

Issue - State: open - Opened by niekdejonge 12 months ago - 3 comments

#585 - Add filters `require_retentiontime` and `require_retentionindex`

Issue - State: closed - Opened by hechth 12 months ago - 1 comment

#584 - Pepmass string format breaks code

Issue - State: closed - Opened by niekdejonge 12 months ago - 2 comments
Labels: bug

#583 - Fix pepmass issue

Pull Request - State: closed - Opened by niekdejonge 12 months ago - 2 comments

#582 - Replace 'List' with 'list'

Pull Request - State: closed - Opened by kozo2 almost 1 year ago - 1 comment

#581 - adjust logger message

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

#580 - Fix inconsistencies in filtering pipline

Issue - State: open - Opened by florian-huber about 1 year ago - 1 comment
Labels: stale

#579 - improve export -->import consistency

Issue - State: open - Opened by florian-huber about 1 year ago - 2 comments
Labels: stale

#578 - Add check that ion_mass is not None

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

#577 - repair_smiles_of_salts can fail

Issue - State: closed - Opened by florian-huber about 1 year ago - 6 comments
Labels: bug

#576 - non-matchms logging messages are not added to pipeline logging

Issue - State: open - Opened by florian-huber about 1 year ago - 2 comments
Labels: stale

#575 - Update README.rst

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

#574 - Use poetry version in CONTRIBUTING.md

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

#572 - Allow one filter input type

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

#571 - Allow for only one filter type in SpectrumProcessor

Issue - State: open - Opened by niekdejonge about 1 year ago - 2 comments
Labels: stale

#570 - Small run pipeline changes

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

#569 - How could I speed up the similarity matrix computation?

Issue - State: open - Opened by JannikSchneider12 about 1 year ago - 6 comments

#568 - Update typehinting

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

#567 - Solve merge conflicts

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

#566 - Switch to tmp_path

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

#565 - Remove predefined pipelines

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

#564 - require_matching_compound_name_and_annotation

Issue - State: open - Opened by niekdejonge about 1 year ago - 1 comment
Labels: enhancement, future developments, stale

#563 - Performance-optimization of similarity computations (graph-based)

Issue - State: open - Opened by florian-huber about 1 year ago - 2 comments
Labels: performance

#562 - Create new predefined pipelines, with subgroups and update tests.

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

#561 - Remove predefined pipelines from SpectrumProcessor

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

#560 - Add export styles to Scores.to_dict()

Issue - State: open - Opened by florian-huber about 1 year ago - 1 comment
Labels: stale

#559 - Fix wrong pubchem annotations

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

#558 - Fix repair not matching annotation

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

#557 - add export_style parameter

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

#556 - Add export style to all export formats

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

#554 - Fix issue with parse metadata recognizing empty metadata as well.

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

#553 - Fix retention time for msp

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

#552 - Update require_parent_mass_match_smiles.py

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

#551 - WARNINGs and KeyError when `load_from_msp` MoNA LC-MS/MS Positive Mode MSP

Issue - State: closed - Opened by kozo2 about 1 year ago - 6 comments

#550 - Consider including option for MSn data

Issue - State: closed - Opened by florian-huber about 1 year ago - 6 comments
Labels: stale

#549 - Rdkit is not abe to load some smiles

Issue - State: closed - Opened by niekdejonge about 1 year ago - 4 comments
Labels: bug, stale

#548 - Metadata processing of some msp files fails fatally

Issue - State: closed - Opened by jmmitc06 about 1 year ago - 10 comments
Labels: bug

#547 - Enable setting key conversion with static method

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

#546 - Enable setting key conversion with static method

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

#545 - Consider switching to `ruff` as linter

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

#544 - MetadataMatch with "sparse" flag still allocates whole matrix

Issue - State: closed - Opened by hechth about 1 year ago - 2 comments
Labels: bug

#543 - Prevent accidental file overwriting

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

#542 - Automatically test readme

Issue - State: open - Opened by niekdejonge about 1 year ago - 3 comments

#541 - Add matchms version to logging and yaml file

Issue - State: open - Opened by niekdejonge about 1 year ago - 4 comments

#540 - Fixed string representation and added testcase for issue 452

Pull Request - State: closed - Opened by hechth about 1 year ago

#539 - fixed pepmass string parsing

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

#538 - Interpret pepmass doesn't handle strings

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

#537 - Pepmass overwritten

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

#536 - Store cleaning settings

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

#535 - Make initialize_spectrum_processor part of SpectrumProcessor init

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

#533 - Remove pepmass after running interpret_pepmass.py

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

#532 - Do not by default overwrite in interpret_pepmass

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

#531 - Convert filtering functions to classes

Pull Request - State: open - Opened by zargham-ahmad about 1 year ago

#530 - Add uneffective filters to report

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

#529 - Fix small issues

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

#528 - Design useful processor default pipelines

Issue - State: closed - Opened by florian-huber about 1 year ago - 3 comments
Labels: stale

#527 - Fix processing report

Pull Request - State: closed - Opened by niekdejonge about 1 year ago - 4 comments

#526 - Fix adduct missing charge

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

#525 - Complete library cleaning pipeline

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

#524 - Remove duplicated filters

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

#523 - Improve derive adduct from name

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

#522 - Further cleaning repair_not_matching_annotation

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

#521 - Minor cleaning 510

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

#520 - Revisit readthedocs documentation

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

#519 - Reconsider filter warnings and flow

Issue - State: closed - Opened by florian-huber about 1 year ago - 3 comments
Labels: stale

#518 - Add peak changes to processing report

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

#517 - Test dev pipeline fails

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

#516 - Update tutorial material

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