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CHANGELOG.md

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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.

[dev] - unreleased

[0.4.1] - 2024-04-24

Changed

  • updated _assign_ri_value function to delete the RI key if the value is not greater than 0 #122

[0.4.0] - 2024-02-13

Added

  • reading RI values from the comments field #112
  • column name sanitizing and mapping using matchms #118
  • support for parquet and mgf formats #116
  • functions to check whether RI and RT are present #115

Changed

  • updated dependencies to newest versions #116
  • changed build system to use poetry #109

Removed

[0.3.4] - 2023-02-21

Changed

  • pinned pint >=0.17,<0.20 and matchms >=0.14.0,<0.18.0 for dependency issues

[0.3.3] - 2022-07-22

Added

Changed

  • replaced asserts with ValueError as asserts can be disabled. #91
  • updated matchms dependency to >= 0.14.0. #90

Removed

  • removed test cases which include data that has None retention times. #90

[0.3.2] - 2022-02-11

Added

  • data/Data.py: Added update_possible_rt_keys() and update_possible_ri_keys() methods for Data class. Now users can supply their own identifiers for RT/RI columns (csv files) and identifiers (msp) in their data. #74
  • General: Added missing documentation and updated README. #80
  • setup.py: Added versions for dependencies. #80
  • utils.py: Added method to check if array is sorted. #82
  • data/SimpleData.py: Added class for in-memory data which is read-only. #82

Changed

  • data/Data.py: Unified default RT/RI column identifiers between PandasData and MatchMSData classes. #74
  • data/MatchMSData.py: MatchMSData class now looks up for RT and RI identifiers from within default identifiers list instead of hardcoded 'retentiontime' & 'retentionindex' keys. #74
  • compute/Kovats.py: Computation is now real piece-wise linear interpolation and doesn't assume a step width of 100 but interpolates in the actual interval. #76

Removed

  • data/Data.py: Removed read method from class and contructor -> all child classes must now explicitly implement and call the superclass constructor. #82

[0.3.1] - 2021-12-9

Changed

  • data/PandasData.py: _read_into_dataframe() now deduces a proper delimiter via Python's csv.Sniffer class. #73

[0.3.0] - 2021-09-03

Added

  • main.py + cli/LoadDataAction.py: Added required passing of filetype and rt unit. #64 #67 #68

Changed

  • utils.py: get_extension function now returns extension without . #68
  • data/Data.py: Added filetype to constructor and made rt_unit non-optional. #67 #68
  • data/MatchMSData.py: Added filetype to constructor and made rt_unit non-optional. #67 #68
  • data/PandasData.py: Added filetype to constructor and made rt_unit non-optional. #67 #68

[0.2.0] - 2021-08-18

Added

  • Added __eq__ to PandasData and MatchMSData #51
  • Added __eq__ to ComputationMethod class and subclasses #52
  • data/PandasData.py: Added reading tsv files. #49
  • Command line interface functionality #29
    • utils.py: get_extension function
    • tests/fixtures/data.py: Added load_test_file function

Changed

  • data/MatchMSData.py: _assign_ri_value now converts all values to float and stores them as string in metadata field
  • data/MatchMSData.py _read_retention_indices now calls retention_indices property setter to store values
  • tests/fixtures/data.py: Changed loading of test data
  • compute/CubicSpline.py: compute now returns an array of floats #61
  • compute/Kovats.py: compute now returns a list of floats #61

[0.1.0] - 2021-07-12

Added

  • Reading data from CSV and MSP files #8#15#36
  • Computing Kovats retention index #25
  • Computing RI based on cubic splines #33
  • Added CI actions to GitHub #43
  • Added writing data back to memory for MSP, CSV and tsv files #7#14#19