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Create standard/schema for a Model#130

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dilpath merged 61 commits intodevelopPEtab-dev/petab_select:developfrom mkstdPEtab-dev/petab_select:mkstdCopy head branch name to clipboardJan 6, 2025

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Commits on Nov 23, 2024

• closes #120

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Commits on Nov 29, 2024

• fix tests

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• update notebooks

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Commits on Dec 2, 2024

• Merge branch 'develop' into class_models

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• Update petab_select/ui.py

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• Update petab_select/ui.py

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• track iterations; fix ModelHash.get_model; add Model.__repr__

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• add analysis module

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• fixme: use pypesto PR branch

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• Merge branch 'develop' into analyze

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• unfix pypesto in tox.ini to use pyproject.toml

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Commits on Dec 3, 2024

• fix tests

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• test

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Commits on Dec 13, 2024

• sort iterations in group_by_iteration

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• add VIRTUAL_INITIAL_MODEL_HASH

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• method to convert Models to dataframe; update plotting code

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• update vis example to use iterations

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• update vis notebook

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• doc analysis methods briefly

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• typo

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• move models criterion getter to Models; add Models.values() for backwards compatibility; update plot code

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• update test

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Commits on Dec 14, 2024

• add Model.hashes

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• test case 0009: add caveat

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• fix notebooks

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• update expected test case results

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Commits on Dec 15, 2024

• start sorting of constants

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• refactor Model with mkstd

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• add some old petab parameter helpers to Model; add default_compare

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Commits on Dec 16, 2024

• remove constraint column (constraints aren't implemented yet)

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• update test cases 1-8 expected models

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• split ModelBase into VirtualModelBase to make virtual object; cast criteria to float in setter;

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• update cli.py

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• update plot.py

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• update models.py

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• update constants.py

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• update ui.py

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• refactor to remove PetabMixin

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• update model_subspace.py; fix selector sets

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Commits on Dec 17, 2024

• predecessor_model now always set to virtual or real model; update candidate_space.py

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• model subspace: require explicit parameter definitions; implement can_fix_all

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• update famos candidate space

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• fix standard type; support resolving relative paths in constructor

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• fix 0009 expected yaml

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• test case 0009: update expected.yaml

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• check subclass first

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• dedent

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• Merge branch 'analyze' into mkstd

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• add schema; add to RTD

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• subheadings

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Commits on Dec 18, 2024

• Update petab_select/model_subspace.py

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Commits on Jan 1, 2025

• update test_analyze.py

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• update test_famos.py

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• review: add link

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• fix link

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• update test_cli.py

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• fix link

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• fix test_model.py

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• temp fix pypesto

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• fix link

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Commits on Jan 6, 2025

• Merge branch 'develop' into mkstd

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