Skip to content

Latest commit

 

History

History
117 lines (94 loc) · 7.13 KB

CHANGELOG.md

File metadata and controls

117 lines (94 loc) · 7.13 KB
Raw

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[0.13.4] - 2024-10-30

Changed

  • re-enabled parallelism in alignment step #230

[0.13.3] - 2024-09-16

Changed

  • fixed not working eic splitting code #226

[0.13.2] - 2024-07-30

Changed

  • Moved import order in the hope it will fix the import bugs by @hechth in #224

[0.13.0] - 2024-07-29

Added

  • added tests for mzdata and mzxml formats #216

Changed

  • feature.alignment function refactored by @KristinaGomoryova in #221
  • remove_noise function updated by @KristinaGomoryova in #219
  • Updated correct time to use precomputed clusters by @zargham-ahmad in #220
  • Fix tests by @hechth in #222

Removed

  • removed outdated files by @hechth in #223

[0.12.0] - 2023-07-10

Changed

  • sample names in aligned tables no longer use _intensity and _rt suffixes #212

Removed

  • corner case in peak picking when an EIC was between 2 and 10 features #212

[0.11.0] - 2023-05-09

Added

  • implemented new clustering algorithm and included parallelism in unsupervised and hybrid #201

Changed

  • refactored adaptive.bin and combine.seq.3 #196
  • refactored find.match #193
  • Simplified Evaluation Conditions For Test Cases #197
  • Renamed proc.cdf to remove_noise #190
  • Fixed dimension bug adaptive.bin #200

Removed

[0.10.3] - 2023-03-27

Changed

  • introduced parallelism in feature.align #182

[0.10.2] - 2023-03-10

Added

Changed

  • fixed bug in recover.weaker related to sample name matching #180

Removed

[0.10.1] - 2023-02-02

Added

  • refactored rm.ridge.R #171
  • refactored and documented prof.to.features.R #170
  • added full testdata case for unsupervised.R and hybrid.R #177
  • added function to sort data in compute_clusters.R to return sorted data #177

Changed

  • updated remote files with the full data get links #177
  • fixed parameter value of recover.weaker in unsupervised.R and hybrid.R #177
  • reinstated returning tolerances from clusters and passed them in unsupervised.R and hybrid.R #178

Removed

  • removed NA check in concatenate_feature_tables #177

[0.10.0] - 2022-12-07

Added

  • added documentation from Rd files to code #78
  • added tests with realistic testdata for extract_features.R #42, #54
  • added tests for feature.align.R (#40), and adjust.time.R (#39)
  • added CI to repository's GitHub Actions #45,#49
  • added additional test cases for hybrid #133
  • added tests and testdata for run_filter.R #156
  • merge_features_and_known_table wrapper for augmentation of aligned features and known table #154

Changed

  • refactored feature.align.R #63#88#102
  • refactored adjust.time.R #64#102
  • refactored find.tol.time.R #91
  • refactored find.turn.point.R #91
  • refactored proc.cdf.R and adaptive.bin.R #137
  • refactored cont.index.R and renamed as run_filter.R #156
  • use proper sample IDs inside feature tables #153
  • exported functions in NAMESPACE #154
  • docstrings and documentation files for refactored functions #160
  • refactored parameter names to keep them more harmonized #167
  • moved some utility functions to a more suitable locations #164

Removed

  • extract_features and feature.align #154
  • improper usage of @examples #160
  • several obsolete utility functions #164
  • several outdated .Rd files #168
  • default argument values from low-level functions #168

[0.9.4] - 2022-05-10

Added

  • added complete tests for unsupervised and hybrid versions #19
  • added conda environments #20
  • added Docker development environment #31
  • added VSCode devcontainer configuration #31

Changed

  • fixed repository to comply with devtools::check() #27
  • refactored two.step.hybrid.R #34