New options for visualization #59
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# A new visualization based on a force directed graph NEW: A new module 'force_graph.py' contains the logic to create a three-dimensional representation of cobra objects in a webpage. NEW: Two test cases for the creation of three-dimensional representations have been added.
NEW: An alternative python integration for Escher. This is independent of the original and therefore does not have the same version conflicts. NEW: The visualization via 3d-force-directed-graph has been extended by a Jupyter widget integration. The visualization can now be viewed directly in Jupyter notebook or JupyterLab.
… required for BioCyc and the other covers the new visualization options. UPDATED: Added some DocString and used ruff. UPDATED: The ReadtheDocs environment has changed to use mambaforge instead of the classic conda solver for the creation of the environment. UPDATED: 'environment.yml' The Python version was set to 3.11 as autoapi is not yet compatible with 3.12 and this causes problems while creating the documentation.
NEW: A new test for the Python side of the Force Directed Graph visualization. NEW: Added package.json for dependencies. NEW: Configuration file for Vite. UPDATED: gitignore now includes node_module folder UPDATED: anywidget added to environment.yml UPDATED: pyproject.toml now includes any widget as a dependency. UPDATED: Added JS part to readme with installation and bundling instructions. UPDATED: Both integrations now use a bundled js file. UPDATED: ForceGraphIntegration now contains a save and load function. Which saves the graph layout as CSV. REMOVED: Old Force Directed Graph test.
UPDATED: conf.py sphinxcontrib.bibtex commented out due to incompatibilities. jupyter_sphinx added for the visualization section. Theme changed from rtd to furo. Removed extra js definitions as they caused duplications of widgets. UPDATED: Visualization example in the documentation is now created using jupyter_sphinx. UPDATED: escher-custom enthält jetzt die Option für 'never_ask_before_quit' von escher. UPDATED [cobramod.pathway]: The visualization function now includes the possibility to choose between different visualization options.
UPDATED: sphinx-autoapi in environment.yml moved to pip because conda does not provide the beta version. UPDATED [project.toml]: Now incorporates the JavaScript files.
Extended type annotations and Docstrings for the two new widgets. The documentation has been adapted accordingly.
UPDATED (tox.ini): Tox now uses mypy again and no longer tests only one Python version but 3.10, 3.11 and 3.12. UPDATED (pyproject.toml): Anywidget was added to pyproject.toml and the build system was defined. UPDATED (escher.py): The Escher integration received a new method called save_html with which an HTML image of the widget can be saved. UPDATED (conf.py): Further settings for the creation of documentations explicitly written down. UPDATED (index.rst): The references within index.rst are now working again.
UPDATED: The visualization tests for Escher have been migrated to the built-in integration and now use Galata to be automatically compared to a reference. Opening created Escher maps is now no longer necessary. UPDATED: The canvas used by Escher is now square, with the height and width corresponding to the width of the Jupyter cell. NEW: Deprecation warning when using the original Escher integration.
UPDATED: GitHub action extended to include the required additional build step. UPDATED: Further visual tests moved to the Galata Test suite.
NEW: Auto generation of a coverage.svg using pytest-cov within the tox suite.
UPDATED: Tests no longer fail due to version errors. UPDATED: Escher has been removed from the tests and the tests that used to use Escher now use the integrated visualization . UPDATED: The tests for versioning are now in a separate file. NEW: CITATION.cff added
New GitHub action to update the reference screenshots of Galata.
Splitting the GitHub action into smaller steps instead of a monolithic run.
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