Ecosyste.ms: Issues

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GitHub / matchms/matchms issues and pull requests

#415 - Error reading JSON with peak_comments

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

#414 - Fixed use of FingerprintSimilarity in Pipeline

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

#413 - Error when using MSP from NIST MS Search

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

#412 - Improve msp reading performance

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

#411 - cleaner regex

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

#410 - Updated load_from_mgf reader

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

#409 - Updated CI to trigger on all pushes onto a PR branch

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

#408 - Rearranged test in folders

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

#407 - save_as_msp fails if "write_peak_comments" is true and peak comments are empty

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

#406 - Fix pipelines with dedicated score names

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

#405 - Handled sparse array_type fingerprint similarity

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

#404 - Issue300

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

#403 - Try mamba for installing rdkit

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

#402 - Consider move to Python 3.8 and higher

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

#401 - switch to to_dict() method

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

#400 - Improve MSP output keys

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

#399 - Handled sparse array_type fingerprint similarity

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

#398 - Improve MSP output keys

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

#397 - Inner join does not remove non-matching pairs

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

#396 - Load all file types

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

#395 - Raise minimum python to 3.8?

Issue - State: closed - Opened by hechth over 1 year ago - 8 comments

#394 - try adding pillow to dependencies

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

#393 - Implemented MSP reading for GOLM style MSP and MSL style files

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

#392 - Support reading old NIST and GOLM MSP formats

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

#391 - Rearrange tests in folders

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

#390 - Fix use of FingerprintSimilarity in Pipelines

Issue - State: closed - Opened by hechth almost 2 years ago
Labels: bug

#388 - Pipelines with dedicated score names don't work

Issue - State: closed - Opened by hechth almost 2 years ago - 3 comments
Labels: bug, stale

#387 - Fix reading of fingerprints

Issue - State: closed - Opened by hechth almost 2 years ago - 6 comments
Labels: bug

#386 - Fix adduct masses (include electron mass where missing)

Pull Request - State: closed - Opened by florian-huber almost 2 years ago - 2 comments

#385 - Add new filter collections

Issue - State: closed - Opened by florian-huber almost 2 years ago - 1 comment
Labels: future developments, package quality

#384 - Add updated tutorial

Pull Request - State: open - Opened by florian-huber almost 2 years ago - 3 comments

#383 - Small Scores additions

Issue - State: closed - Opened by florian-huber almost 2 years ago - 2 comments
Labels: stale

#382 - Matchms future plans

Issue - State: open - Opened by florian-huber almost 2 years ago - 17 comments
Labels: future developments

#381 - Update docstrings in Scores class

Pull Request - State: closed - Opened by maximskorik almost 2 years ago - 1 comment

#380 - Switch to sparse scores and Pipeline

Issue - State: closed - Opened by florian-huber almost 2 years ago - 2 comments
Labels: stale

#379 - Make Scores JSON-serializer work with with ML-based similarity metrics

Issue - State: closed - Opened by maximskorik almost 2 years ago - 6 comments
Labels: bug

#378 - Configure SonarCloud CI to scan PRs from forks

Pull Request - State: closed - Opened by maximskorik almost 2 years ago

#377 - `reduce_to_number_of_peaks` will always raise a ValueError

Issue - State: closed - Opened by anupriyatripathi almost 2 years ago - 7 comments
Labels: stale

#376 - Towards Pipeline and sparse implementation release

Issue - State: closed - Opened by florian-huber almost 2 years ago - 10 comments
Labels: stale

#375 - Add pickle import/export function

Issue - State: closed - Opened by florian-huber almost 2 years ago - 2 comments

#374 - Adduct correction masses

Issue - State: closed - Opened by tharwood3 about 2 years ago - 8 comments

#373 - [feature request] add metadata to nodes in similarity network

Issue - State: closed - Opened by maximskorik about 2 years ago - 2 comments
Labels: enhancement, stale

#372 - [feature request] add functionality to export metadata in tabular format

Issue - State: closed - Opened by maximskorik about 2 years ago
Labels: enhancement

#371 - Refactor metadata harmonization to improve msp/mgf reading performance

Pull Request - State: closed - Opened by maximskorik about 2 years ago - 2 comments
Labels: performance

#370 - Pipeline merge

Pull Request - State: closed - Opened by florian-huber about 2 years ago

#369 - Performance test of sparse vs. dense implementation

Issue - State: closed - Opened by florian-huber about 2 years ago - 1 comment

#368 - Pipeline (using sparsestack)

Pull Request - State: closed - Opened by florian-huber about 2 years ago - 1 comment

#366 - Add option for progress bars.

Issue - State: closed - Opened by niekdejonge about 2 years ago - 4 comments
Labels: stale

#365 - check load_from_msp

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

#364 - error: ms_network.create_network(scores)

Issue - State: closed - Opened by guikool about 2 years ago - 7 comments

#363 - make structure similarity scoring easier to run

Issue - State: closed - Opened by niekdejonge about 2 years ago - 2 comments
Labels: stale

#362 - spectrum typing does not work with IDE's

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

#361 - save_spectra_in_fast_import_file_type

Issue - State: closed - Opened by niekdejonge about 2 years ago - 13 comments
Labels: stale

#360 - switch from numpy to np

Pull Request - State: closed - Opened by florian-huber over 2 years ago - 1 comment

#359 - Update save_as_msp.py

Pull Request - State: closed - Opened by Adafede over 2 years ago - 3 comments

#358 - con't read file ,it's empty generator.

Issue - State: closed - Opened by LXXiaogege over 2 years ago - 14 comments

#357 - Skip test using rdkit for first CI round

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

#356 - Tests failing because rdkit import

Issue - State: closed - Opened by florian-huber over 2 years ago - 1 comment

#355 - add save neutral loss, add to df

Issue - State: closed - Opened by volvox292 over 2 years ago - 5 comments
Labels: stale

#354 - numpy.core._exceptions.MemoryError

Issue - State: closed - Opened by r00bit over 2 years ago - 5 comments

#353 - Add export/import for Scores objects

Pull Request - State: closed - Opened by maximskorik over 2 years ago - 4 comments
Labels: enhancement

#349 - Add new exporting formats to Networking module

Pull Request - State: closed - Opened by maximskorik over 2 years ago - 1 comment

#347 - [feature request] SIMILE support

Issue - State: closed - Opened by Adafede over 2 years ago - 3 comments
Labels: stale

#346 - Added option to write appended to `msp` export

Pull Request - State: closed - Opened by hechth over 2 years ago - 3 comments
Labels: help wanted

#345 - Harmonize logging

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

#343 - Allow appending to file in export functions

Issue - State: closed - Opened by hechth over 2 years ago - 3 comments

#342 - Introduce order in writing metadata

Issue - State: closed - Opened by hechth over 2 years ago - 4 comments
Labels: stale

#340 - Extend `MetadataMatch` to store difference (possibly `MetadataDifference` subclass?)

Issue - State: closed - Opened by hechth over 2 years ago - 3 comments
Labels: enhancement, stale

#338 - Add option to disable key mapping when loading Spectra

Issue - State: closed - Opened by hechth over 2 years ago - 7 comments
Labels: stale

#336 - Sparse scores array

Issue - State: closed - Opened by florian-huber over 2 years ago - 5 comments

#333 - [feature request] Easily filter an MGF (or other spectral file) according to a list

Issue - State: closed - Opened by Adafede over 2 years ago - 6 comments
Labels: stale

#327 - Pipeline

Pull Request - State: closed - Opened by florian-huber almost 3 years ago - 2 comments

#326 - matchms to handle cfm-predict output?

Issue - State: closed - Opened by Adafede almost 3 years ago - 17 comments
Labels: stale

#325 - Parallelization

Issue - State: closed - Opened by florian-huber almost 3 years ago - 6 comments

#324 - New matchms pipeline

Issue - State: closed - Opened by florian-huber almost 3 years ago - 5 comments

#321 - Remove losses

Pull Request - State: closed - Opened by florian-huber almost 3 years ago - 4 comments

#320 - Consider splitting filters into different types

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

#319 - No longer store losses but compute on the fly

Issue - State: closed - Opened by florian-huber almost 3 years ago - 2 comments
Labels: stale

#318 - Switch to sparse stacked scores (using structured numpy array)

Pull Request - State: closed - Opened by florian-huber almost 3 years ago - 4 comments

#317 - Consider adding rapid upper-bound score methods

Issue - State: closed - Opened by florian-huber almost 3 years ago - 2 comments
Labels: stale

#316 - Implement sparse scores matrix

Pull Request - State: closed - Opened by florian-huber almost 3 years ago - 4 comments

#311 - Move spectrum plotting to separate library

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

#308 - make importing functions report issues

Issue - State: closed - Opened by florian-huber almost 3 years ago - 2 comments
Labels: stale

#304 - Expand import export testing

Pull Request - State: closed - Opened by florian-huber almost 3 years ago - 2 comments

#301 - improve (and expand) spectra exports

Issue - State: closed - Opened by florian-huber almost 3 years ago - 2 comments
Labels: stale

#300 - Improve MSP output keys

Issue - State: closed - Opened by florian-huber almost 3 years ago - 5 comments

#297 - Update .zenodo.json

Pull Request - State: closed - Opened by maximskorik almost 3 years ago - 1 comment

#286 - Consider pandas-like API extension

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

#281 - Using matchms to perform library search.

Issue - State: closed - Opened by adelabriere almost 3 years ago - 5 comments

#277 - Add handling MSP files with peak comments (issue #249)

Pull Request - State: closed - Opened by maximskorik almost 3 years ago - 5 comments

#276 - Remove assertion

Pull Request - State: closed - Opened by florian-huber almost 3 years ago - 2 comments

#269 - Move to matchms 1.0.0

Issue - State: closed - Opened by florian-huber about 3 years ago - 2 comments

#268 - Design calculate_scores_pipeline

Issue - State: closed - Opened by florian-huber about 3 years ago - 18 comments

#263 - Make filter "strictness" more consistent (and revisit design)

Issue - State: closed - Opened by florian-huber about 3 years ago - 3 comments

#255 - Create metadata_export.py

Pull Request - State: closed - Opened by florian-huber about 3 years ago - 1 comment

#247 - Return spectrum similarity score as pair or single value instead of matrix

Issue - State: closed - Opened by chetankm1992 over 3 years ago - 6 comments

#231 - Update CI_build.yml

Pull Request - State: closed - Opened by florian-huber over 3 years ago - 5 comments