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CHANGELOG.md

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Changelog

[Unreleased]

Planned

  • Parallelization of downloads and cross-references
  • Visualization with other tools than Escher
  • Deprecation of SolCyc
  • Deprecation of PairDictionary
  • Deprecation of Escher's official binding

[1.3.0]

Added

  • A new Escher binding independent of the original one [Escher-custom]
  • A new Visualization option that displays cobra Objects as a Force Directed Graph
  • Introduced Galata as a new test suite
    • Galata automates testing of visualisation as it can compare reference images with outpus created in Jupyter Notebooks

Changed

  • Type checks
    • Reintroduced MyPy as Ruff does not check types according to ruff's FAQ
  • GitHub Actions
    • GitHub Actions now run tests on Windows and macOS once again
    • New workflow for the creation of Galata reference images
    • GitHub Action has been divided into smaller sections to provide a better overview of failed steps
  • Documentation
    • Now uses Furo as a theme
    • Provides additional live examples of the new visualization options
  • Tests
    • Tests no longer check for specific database versions, this is only done in a controlled manner for the db_version module
    • Tests for visualization using Escher now use Escher-Custom
    • Several visualization tests were replaced by an equivalent test using Galata
  • environment.yml
    • Some dependencies now use their conda-forge package to reduce build time
    • 'sphinx-autoapi' was set to a dev version to be able to create the documentation using python 3.12
  • Maintenance
    • Several adjustments due to announced deprecations

[1.2.0]

Added

  • Memote example files added to docs
  • Curation and visualization logs are now separated by date in a 'logs' dir
  • Usage of credentials for BioCyc database
  • New structure cobramod.retrieval.Data. It is in charge of parsing into different objects
  • Extra functions in utils

Changed

  • Set object bug fixed [#50]
  • Escher is an optional dependency
  • Pre-hooks uses now ruff instead of flake8 and black.
  • Behaviour to open files if escher is not installed changed to not open browsers
  • Dropped support for python 3.8 and 3.9
  • Logging format is more human-friendly
  • Dropped support of mypy. Black is replaced with ruff
  • New pyproject.toml
  • Test data updated (19.02.24)
  • Function available_databases replaced by cobramod.retrieval.Databases
  • Structure for retrieval refactored and new parsing sub-packaged created
  • DataVersion moved to parsing package
  • Updated structure of test module
  • Removed multiple "private" methods and functions.
  • Docs files updated to these new changes
  • Test updated to uses new changes
  • Updating functions to not use deprecated pandas functions

Removed

  • Deprecated config files
  • Deprecation warning for SolCyc (Database appears to be shutdown)