User-calibrated models #87
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Codecov ReportAttention: Patch coverage is
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## model_hashes_nicer #87 +/- ##
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- Coverage 57.85% 57.35% -0.50%
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Files 14 14
Lines 1554 1578 +24
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+ Hits 899 905 +6
- Misses 655 673 +18 ☔ View full report in Codecov by Sentry. |
…ctor `CandidateSpace` excluded hashes; add `end_iteration`; rename `candidates`->`start_iteration`; change workflow as described in changelog
…on; start updating famos cli notebook
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* make model hashes nicer; add model hash to model method * :class:`ModelHash` * support user-supplied models with no specified subspace * Skip virtual models in `models_to_yaml_list` (#66) * Action updates via dependabot (#92) * GHA: Add PyPI deployment workflow (#91) Related to #89 * Fix minimum Python requirement (#97) petab requires python>=3.10 * Doc: Fix heading levels in example (#96) Fixes the sphinx TOC and a typo. * Get rid of petab DeprecationWarnings (#93) Closes #90 * README.md: PyPI badge * Add some docs; ensure similar PEtab problems in distance calculation (#67) * File formats to RTD (#102) * Move test suite description to RTD (#101) Related to #95. * User-calibrated models (#87) * compute safe petab hash digest size; support custom digest size; refactor `CandidateSpace` excluded hashes; add `end_iteration`; rename `candidates`->`start_iteration`; change workflow as described in changelog * `ModelHash.__eq__`: support comparisons with `str` and partial hashes * repro: narrow bounds in test cases 1-8 * Add logo draft (#103) * add to RTD, closes #88 * Set up `setuptools_scm` (#100) Set up `setuptools_scm` and move most package configuration to `pyproject.toml`. Move git-based package URLs out of `pyproject.toml` (otherwise, PyPI upload will fail). Co-authored-by: Dilan Pathirana <[email protected]> * Doc: Update RTD landing page (#105) * Doc: Update RTD landing page Add a bit of content. #95. * Apply suggestions from code review Co-authored-by: Dilan Pathirana <[email protected]> * Formatting, spelling, links --------- Co-authored-by: Dilan Pathirana <[email protected]> * Switch from black/isort/... to ruff (#99) Replace black/isort/... by ruff. Run `pre-commit run --all-files`. Some additional rules should be enabled, but that will require additional effort. --------- Co-authored-by: Dilan Pathirana <[email protected]> * Update file format spec (#106) * add example to model space, to clarify compressed format Co-authored-by: Daniel Weindl <[email protected]> * Doc: fix list formatting (#107) * test case 0009: update predecessor model * Visualization methods (#36) * closes #104 --------- Co-authored-by: Daniel Weindl <[email protected]> Co-authored-by: Daniel Weindl <[email protected]> * Support SSR as criterion (#108) * closes #44 * changelog --------- Co-authored-by: Dilan Pathirana <[email protected]> Co-authored-by: Daniel Weindl <[email protected]> Co-authored-by: Daniel Weindl <[email protected]>
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Allow users to supply previously-calibrated models. Model selection should proceed as if the user did not provide any calibrated models. However, whenever a user-calibrated model is encountered during model selection, that model is not sent to the calibration tool. Instead, the user-calibrated model is included after the calibration tools returns its results.
This introduces a new workflow: instead of iterations of
petab_select.ui.candidates, tools must now use iterations ofpetab_select.ui.start_iterationandpetab_select.ui.end_iteration.