Standardise :lp -> :logjoint
#1161
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## breaking #1161 +/- ##
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Coverage 79.99% 79.99%
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* v0.39 * Update DPPL compats for benchmarks and docs * remove merge conflict markers * Remove `NodeTrait` (#1133) * Remove NodeTrait * Changelog * Fix exports * docs * fix a bug * Fix doctests * Fix test * tweak changelog * FastLDF / InitContext unified (#1132) * Fast Log Density Function * Make it work with AD * Optimise performance for identity VarNames * Mark `get_range_and_linked` as having zero derivative * Update comment * make AD testing / benchmarking use FastLDF * Fix tests * Optimise away `make_evaluate_args_and_kwargs` * const func annotation * Disable benchmarks on non-typed-Metadata-VarInfo * Fix `_evaluate!!` correctly to handle submodels * Actually fix submodel evaluate * Document thoroughly and organise code * Support more VarInfos, make it thread-safe (?) * fix bug in parsing ranges from metadata/VNV * Fix get_param_eltype for TSVI * Disable Enzyme benchmark * Don't override _evaluate!!, that breaks ForwardDiff (sometimes) * Move FastLDF to experimental for now * Fix imports, add tests, etc * More test fixes * Fix imports / tests * Remove AbstractFastEvalContext * Changelog and patch bump * Add correctness tests, fix imports * Concretise parameter vector in tests * Add zero-allocation tests * Add Chairmarks as test dep * Disable allocations tests on multi-threaded * Fast InitContext (#1125) * Make InitContext work with OnlyAccsVarInfo * Do not convert NamedTuple to Dict * remove logging * Enable InitFromPrior and InitFromUniform too * Fix `infer_nested_eltype` invocation * Refactor FastLDF to use InitContext * note init breaking change * fix logjac sign * workaround Mooncake segfault * fix changelog too * Fix get_param_eltype for context stacks * Add a test for threaded observe * Export init * Remove dead code * fix transforms for pathological distributions * Tidy up loads of things * fix typed_identity spelling * fix definition order * Improve docstrings * Remove stray comment * export get_param_eltype (unfortunatley) * Add more comment * Update comment * Remove inlines, fix OAVI docstring * Improve docstrings * Simplify InitFromParams constructor * Replace map(identity, x[:]) with [i for i in x[:]] * Simplify implementation for InitContext/OAVI * Add another model to allocation tests Co-authored-by: Markus Hauru <[email protected]> * Revert removal of dist argument (oops) * Format * Update some outdated bits of FastLDF docstring * remove underscores --------- Co-authored-by: Markus Hauru <[email protected]> * implement `LogDensityProblems.dimension` * forgot about capabilities... * use interpolation in run_ad * Improvements to benchmark outputs (#1146) * print output * fix * reenable * add more lines to guide the eye * reorder table * print tgrad / trel as well * forgot this type * Allow generation of `ParamsWithStats` from `FastLDF` plus parameters, and also `bundle_samples` (#1129) * Implement `ParamsWithStats` for `FastLDF` * Add comments * Implement `bundle_samples` for ParamsWithStats -> MCMCChains * Remove redundant comment * don't need Statistics? * Make FastLDF the default (#1139) * Make FastLDF the default * Add miscellaneous LogDensityProblems tests * Use `init!!` instead of `fast_evaluate!!` * Rename files, rebalance tests * Implement `predict`, `returned`, `logjoint`, ... with `OnlyAccsVarInfo` (#1130) * Use OnlyAccsVarInfo for many re-evaluation functions * drop `fast_` prefix * Add a changelog * Improve FastLDF type stability when all parameters are linked or unlinked (#1141) * Improve type stability when all parameters are linked or unlinked * fix a merge conflict * fix enzyme gc crash (locally at least) * Fixes from review * Make threadsafe evaluation opt-in (#1151) * Make threadsafe evaluation opt-in * Reduce number of type parameters in methods * Make `warned_warn_about_threads_threads_threads_threads` shorter * Improve `setthreadsafe` docstring * warn on bare `@threads` as well * fix merge * Fix performance issues * Use maxthreadid() in TSVI * Move convert_eltype code to threadsafe eval function * Point to new Turing docs page * Add a test for setthreadsafe * Tidy up check_model * Apply suggestions from code review Fix outdated docstrings Co-authored-by: Markus Hauru <[email protected]> * Improve warning message * Export `requires_threadsafe` * Add an actual docstring for `requires_threadsafe` --------- Co-authored-by: Markus Hauru <[email protected]> * Standardise `:lp` -> `:logjoint` (#1161) * Standardise `:lp` -> `:logjoint` * changelog * fix a test --------- Co-authored-by: Markus Hauru <[email protected]> Co-authored-by: Markus Hauru <[email protected]>
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Closes #1140, as discussed in today's meeting.