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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

Added

Changed

Removed

[0.3.0] - 2023-05-12

Added

  • general class Data for input handling #141
  • DataFrame class to read and handle tabular metadata input #141
  • implementation of blocking time in PubChem #145

Changed

  • Spectra class is an instantiation of Data class #141
  • fix throttling freezing the app #144

Removed

  • retired NLM (ChemIDplus) service #140

[0.2.5] - 2022-10-15

Added

  • added Pytest config file pytest.ini and set it to automatically detect asynchronous tests #124

Changed

  • fixed Circuit Breaker implementation to be compatible with Python 3.9 #124

Removed

[0.2.4] - 2022-08-30

Changed

  • escaping of single quotes in IDSM arguments #102
  • unified environment and packaging management #115
  • apply circuit breaker pattern in WebConverter #113

Removed

  • removed test case from curator which fails in matchms > 0.14 #112

[0.2.3] - 2022-05-12

Added

  • KEGG ID conversions support to BridgeDb service #101

Changed

  • double quotes to single quotes in IDSM #102

[0.2.2] - 2022-04-27

Added

  • introduced error level into logging #95
  • logging of unknown errors in Annotator #90

Changed

  • the log file is now written continuously during annotation and the metrics added at the end of the file #92

Removed

[0.2.1] - 2022-04-05

Added

  • try-finally block to ensure the Monitor thread is always terminated #86

Changed

  • improved parsing of PubChem responses #84

[0.2.0] - 2022-03-19

Added

  • BridgeDb supporting conversion of several database IDs #76
  • ComputeConverter class for conversions based on computation instead of querying #75
  • ConverterBuilder which validates and initialises converters #75
  • reintroduced PubChem service using direct REST web interface #76

Changed

  • reorganised Converter class to support computation approach #75
  • renamed PubChem service to IDSM to avoid confusion #73

[0.1.3] - 2022-02-15

Added

  • multidict package requirement
  • tracking of attributes validation in log #68
  • CIR: Inchi -> SMILES conversion #66

Changed

  • passed multidict instead of frozendict to aiohttp.ClientSession.post (required by package)
  • take only first result when there are multiple hits in CIR conversions #69
  • support ISOMERIC_SMILES and CANONICAL_SMILES in PubChem instead of generic SMILES #67

[0.1.2] - 2022-01-06

Added

  • generate_options() function in Galaxy submodule to create all possible conversions supported by the tool in a format suitable for the galaxy tool form #58
  • monitoring of services status during annotation process #56
  • validation of obtained metadata #59

Changed

  • structure and contents of documentation #51

Removed

  • tests checking contents and consistency of individual services #54

[0.1.1] - 2021-12-07

Added

  • get_conversion_functions on the level of Converter

Changed

  • computation of all available jobs in Application

Removed

  • get_all_conversions on the level of Annotator

[0.1.0] - 2021-11-16

Added

  • Added conda environment files #35
  • Usage of IDSM SPARQL for PubChem service #25
  • Added logging and quantitative progress of annotation process #22
  • Generalised requests to obtain multiple values at once #20
  • Added asynchronous requests #15