CHANGELOG.md

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.

[0.5.0] - 2026-03-10

Added

• Added smiles_to_formula and inchi_to_formula conversions to the RDKit converter.
• Added unit tests for smiles_to_formula.
• Added support for tabular files, which are treated like tsv files.

Changed

• Updated matchms dependency to ^0.30.0 in pyproject.toml.
• NA values are now rerun through the pipeline instead of being skipped.

Fixed

• Minor documentation and test improvements.
• Linting, documentation updates, dependencies.

[0.4.1] - 2025-05-19

Changed

• updated dependencies #157

[0.4.0] - 2024-03-13

Changed

• Update IDSM SPARQL queries to achieve better performance by @galgonek in #152
• Switched to poetry and added additional converters by @hechth in #155

[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