ENH Generic design support using `formulaic`#328

Merged

BorisMuzellec merged 34 commits intomainfrom

wilkinson_formulae

Nov 18, 2024

Commits on Oct 28, 2024

feat: set design matrices using formulaic (WIP)
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feat: set design matrices using formulaic (WIP)
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feat: check that there are no NaNs in the design matrix
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Commits on Oct 29, 2024

feat: implement support for pairwise categorical contrasts
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feat: allow directly inputing a contrast vector
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feat: allow setting design factors as in versions < 0.5.* for backward compatibiliy, but throw deprecation warning
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feat: improve summary message when a contrast vector was directly provided
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docs: update docstrings to reflect deprecation of design_factors
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chore: deprecate ref_level
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chore: deprecate continuous_factors
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chore: remove build_design_matrix and remove_underscores utils, as they are no longer used
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refactor: update lfc_shrink to reflect new design format
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tests: update edge case tests
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tests: update main tests
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docs: remove build_design_matrix from docs
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docs: add missing docstrings in new DeseqStats methods
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feat: add formulaic utils copied from pertpy
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build!: discontinue python 3.9
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docs: update minimal example
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docs: update data loading example
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docs: update step by step example
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fix: typo
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Commits on Oct 30, 2024

feat: implement a `to_picklable_anndata()` method to allow saving a dds without its unpicklable attributes
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docs: add API documentation for to_picklable_anndata
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docs: fix rst formatting
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Commits on Oct 31, 2024

refactor: throw a ValueError instead of an AssertionError when numerical constrasts have incorrect shapes
Boris MUZELLEC
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Commits on Nov 4, 2024

test: ignore anndata ImplicitModificationWarnings in test suite
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test: add _formulaic test suite from pertpy
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Commits on Nov 13, 2024

refactor: move .cond() to DeseqDataSet so that it can be used at DeseqStats initialization
Boris MUZELLEC
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Commits on Nov 14, 2024

docs: add more details on providing a design matrix directly
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tests: add a few tests when a design matrix is directly provided
Boris MUZELLEC
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Commits on Nov 18, 2024

refactor: throw ValueError instead of AssertionError in case of design with invalid type
Boris MUZELLEC
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docs: improve lfc_shrink example
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docs: document the new materializer attributes
Boris MUZELLEC
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