Ecosyste.ms: Issues

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GitHub / iomega/ms2query issues and pull requests

#254 - Error running ms2query

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

#253 - updated_dois

Pull Request - State: closed - Opened by niekdejonge 6 months ago - 1 comment

#252 - Fix empty class annotation bug

Pull Request - State: closed - Opened by niekdejonge 6 months ago - 1 comment

#251 - Handle compound_name is not given in metadata.

Pull Request - State: closed - Opened by niekdejonge 6 months ago - 1 comment

#250 - Set matchms version to max 0.26.4

Pull Request - State: closed - Opened by niekdejonge 6 months ago - 1 comment

#249 - Failure to grab compound name from metadata dictionary

Issue - State: closed - Opened by wjcranda 6 months ago - 10 comments

#248 - Version 1.5.0 assertation error if wrong ion mode

Issue - State: closed - Opened by wjcranda 6 months ago - 1 comment

#247 - MS2Query version 0.3.2 library

Issue - State: closed - Opened by jamesjiadazhan 6 months ago - 1 comment

#246 - Update setup.py

Pull Request - State: closed - Opened by florian-huber 7 months ago

#245 - ImportError: cannot import name 'triu' from 'scipy.linalg'

Issue - State: closed - Opened by nici7 7 months ago - 6 comments

#244 - module 'matchms.filtering' has no attribute 'add_losses'

Issue - State: closed - Opened by jweinb 7 months ago - 9 comments

#243 - Update to testing version 3.9 - 3.11

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

#242 - Automatic zenodo upload failing

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

#241 - No additional metadata information

Issue - State: closed - Opened by Dmente92 8 months ago - 1 comment

#240 - Add nearest neighbor search

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

#238 - Remove pickle from docstring for loading files

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

#237 - Update ms2deepscore to 0.5.0

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

#236 - Allow searching for library compounds without mass spectrum

Issue - State: open - Opened by niekdejonge 11 months ago - 4 comments

#234 - “feature_id” column empty

Issue - State: closed - Opened by montmasis about 1 year ago - 4 comments

#233 - Update matchms version

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

#232 - Implement parquet

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

#231 - Replace pandas append with concat

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

#230 - Add do pubchem lookup parameter

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

#229 - The default value of add_compound_classes is wrongly documented

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

#228 - Add embeddings to sqlite

Pull Request - State: open - Opened by niekdejonge about 1 year ago - 14 comments

#227 - "Harmonizing annotations" degrades in peformance over time.

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

#226 - Add preselection cut off to settings

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

#225 - Added the add_compound_classes train_all_models

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

#224 - Added add_compound_classes parameter to SettingsTrainingModels

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

#223 - Add add compound classes to settings

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

#221 - Replace pickled dataframes

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

#220 - Isort

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

#219 - Added changes to changelog

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

#218 - Update matchms and pandas version.

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

#217 - Raise a value error if there are too little training spectra.

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

#216 - Fix readme

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

#215 - Update dummy data to match recent changes

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

#214 - Crash in `matchms` probably due to format change

Issue - State: closed - Opened by mapio about 1 year ago - 8 comments

#213 - Crash in `matchms` probably due to format change

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

#212 - Metric name changed, warnings and errors looking for `val_loss`.

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

#211 - Create your own library (without training new models) example does not work.

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

#210 - Update the example data in `dummy_data`

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

#209 - Set onnxruntime to <1.16

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

#208 - ONNX issue

Issue - State: closed - Opened by eeko-kon over 1 year ago - 4 comments

#207 - Change command line message --library

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

#206 - Set maximum ms2deepscore version

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

#205 - Added environment.yml file

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

#204 - Add yml file

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

#203 - Feature_id flag in python

Issue - State: closed - Opened by eeko-kon over 1 year ago - 6 comments

#202 - Make library creation more robust

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

#201 - Update hyperparameters for larger MS2DeepScore model

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

#200 - Check with newer MS2DeepScore models

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

#199 - Upgrade to new matchms release

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

#198 - Change the default additional metadata to retention_time

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

#197 - Update ms2query cleaning to use matchms pipeline

Issue - State: open - Opened by niekdejonge over 1 year ago
Labels: code structure

#196 - Training library (updated version)

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

#195 - Fix zenodo version

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

#194 - Error in applying MS2Query

Issue - State: closed - Opened by anani-a-missinou over 1 year ago - 9 comments

#193 - Change zenodo identifier to specific version

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

#192 - Split MS2Query in run and train

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

#191 - Store embeddings in different file format

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

#190 - Matchms new version

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

#189 - change version and changelog

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

#188 - Allow partial reuse of compound class annotations

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

#187 - Classes in sqlite

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

#186 - Return dataframe instead of results table

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

#185 - Replace analog search return results table with return dataframe

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

#184 - Classes in sqlite

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

#183 - MS2DeepScore

Issue - State: open - Opened by eeko-kon almost 2 years ago - 3 comments

#182 - weighted spectrum is unknown to the model

Issue - State: closed - Opened by thierrynieus almost 2 years ago - 4 comments

#181 - set pandasto <2.0.0

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

#180 - Remove matchmsextras dependency

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

#179 - Update setup.py

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

#178 - Clean up readme and downloading

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

#177 - Define zenodo doi

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

#176 - Implement onnx

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

#175 - urllib.error.URLError: <urlopen error [Errno 54] Connection reset by peer>

Issue - State: closed - Opened by eeko-kon almost 2 years ago - 1 comment

#174 - Add option to add metadata columns in command line

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

#173 - move to matchms>0.13<0.18

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

#172 - Add dot product (cosine score) to the results

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

#171 - moved command line function to init

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

#170 - Fix command line running

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

#169 - Update changelog

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

#168 - Finalize workflow k fold validation

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

#167 - make_adding_spectra_to_library_possible

Issue - State: closed - Opened by niekdejonge about 2 years ago - 1 comment
Labels: enhancement

#166 - make_more_user_friendly

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

#165 - Update utils.py

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

#164 - Allow different spellings of file types

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

#163 - Automatically split positive and negative mode query spectra

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

#162 - Add required preprocessing to readme

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

#161 - remove tensorflow warnings

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

#160 - Make training random forest with feature names

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

#159 - Remove library files creator from init to prevent dependency on rdkit

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

#158 - make command line runnable

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

#157 - split unit and integration tests

Issue - State: open - Opened by niekdejonge about 2 years ago
Labels: code structure

#156 - Paralalize MS2Query

Issue - State: open - Opened by niekdejonge over 2 years ago - 4 comments
Labels: computational performance