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| Main Authors: | , , |
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| Format: | Recurso digital |
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Zenodo
2026
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| Online Access: | https://doi.org/10.5281/zenodo.19392782 |
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Table of Contents:
- <p>This pull request introduces several improvements and refactorings across the codebase and project configuration, with a focus on dependency management, code quality, and consistency in function definitions. The most significant changes include the integration of XML-based rules, a reorganization of dependency handling, and the standardization of QoI (Quantity of Interest) function definitions across example notebooks and scripts.</p> <p>Many thanks to @elmbeech for his PRs, contributions, and valuable suggestions.</p> <p><strong>GUI Enhancements</strong></p> <ul> <li>Support for rules defined in XML format</li> <li>Tab 1: Rule parameters displayed as nested combo boxes</li> <li>Improved readability of .ini file output</li> <li>Fix for a bug handling XML paths with attribute IDs for differentiation (thanks to @elmbeech for pointing this out)</li> </ul> <p><strong>Model Analysis context</strong></p> <ul> <li>Added an option to include functions within lambda expressions (@elmbeech)</li> <li>In <code>calculate_qoi_statistics</code>, added a verbose option and explicit memory freeing when reading database chunks (@elmbeech )</li> <li>Added <code>uq-physicell</code> and <code>pcdl</code> version information to the database metadata</li> </ul> <p><strong>Bayesian Optimization (BO) context</strong></p> <ul> <li>Added <code>uq-physicell</code>, <code>pcdl</code>, and <code>botorch</code> version information to the database metadata</li> </ul> <p><strong>Approximate Bayesian Computation (ABC) context</strong></p> <ul> <li>Added metadata to the database with <code>uq-physicell</code>, <code>pcdl</code>, and <code>pyabc </code> version information .</li> </ul> <p><strong>Code Consistency and Refactoring</strong></p> <ul> <li>All example notebooks and scripts have been updated to define QoI functions as Python lambda functions rather than string representations, ensuring consistency and enabling better serialization and reuse.</li> <li>The <code>CalibrationContext</code> class in <code>uq_physicell/abc/abc_context.py</code> and <code>uq_physicell/abc/bo_context.py</code> now ensures that <code>qoi_functions</code> are stored as strings for serialization.</li> <li>Use of flake8 in workflow test. (@elmbeech )</li> <li>Update installation options and dependencies (@elmbeech )</li> </ul>