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New visualization options

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@JanNiklasWeder JanNiklasWeder released this 16 May 19:40
· 4 commits to master since this release
v1.3.0
735e802
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Added

  • A new Escher binding independent of the original one [Escher-custom]
    • This integration is independent of the original and, therefore, does not have the same version conflicts.
  • A new Visualization option that displays cobra Objects as a Force Directed Graph
  • Introduced Galata as a new test suite
    • Galata automates the testing of visualization as it can compare reference images with outputs created in Jupyter Notebooks

Changed

  • cobramod.pathway
    • The visualization function now includes the possibility to choose between different visualization options
  • 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
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