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Attempt at implementation of VarNamedVector (Metadata alternative) #555

Merged
merged 222 commits into from
Oct 8, 2024
Merged

Attempt at implementation of VarNamedVector (Metadata alternative) #555

merged 222 commits into from
Oct 8, 2024

Commits on Oct 31, 2023

  1. initial implementation of VarNameVector

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Commits on Nov 7, 2023

  1. added some hacky getval and getdist get things to work for VarInfo

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  2. Apply suggestions from code review 

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Commits on Nov 12, 2023

  1. added arbitrary metadata field as discussed

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  2. renamed idcs to varname_to_index

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  3. renamed vns to varnames for VarNameVector

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  4. added keys impl for Metadata

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Commits on Nov 13, 2023

  1. added push! and update! for VarNameVector

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  2. added getindex_raw! and setindex_raw! for VarNameVector

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  3. added iterate and convert (for AbstractDict) impls for VarNameV… 

    …ector`
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  4. make the key and eltype part of the VarNameVector type

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  5. added more tests for VarNameVector

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  6. formatting

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  7. more testing for VarNameVector

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  8. minor changes to some comments

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  9. added a bunch more tests for VarNameVector + several bugfixes in the … 

    …process
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  10. formatting

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  11. added similar implementation for VarNameVector

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  12. formatting

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  13. removed debug statement

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  14. made VarInfo slighly more generic wrt. underlying metadata

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Commits on Nov 14, 2023

  1. Merge branch 'master' into torfjelde/varnamevector

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  2. fixed incorrect behavior in keys for Metadata

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  3. minor style changes to VarNameVector tests

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  4. style

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  5. added testing of update! with smaller sizes and fixed bug related t… 

    …o this
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  6. formatting

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  7. move functionality related to push! for VarNameVector into push!

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Commits on Nov 16, 2023

  1. Update src/varnamevector.jl 

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Commits on Nov 20, 2023

  1. Merge branch 'master' into torfjelde/varnamevector

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Commits on Dec 30, 2023

  1. several fixes to make sampling with VarNameVector + initiall tests for 

    sampling with VarNameVector
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  2. VarInfo + VarNameVector tests for all demo models

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  3. Merge remote-tracking branch 'origin/torfjelde/varnamevector' into to… 

    …rfjelde/varnamevector
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  4. Apply suggestions from code review 

    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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Commits on Dec 31, 2023

  1. added docs on the design of VarNameVector

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  2. Merge branch 'master' into torfjelde/varnamevector

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  3. Apply suggestions from code review 

    Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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  4. added note on update!

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Commits on Jan 1, 2024

  1. further elaboration of the design of VarInfo and VarNameVector

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  2. more writing improvements

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  3. added docstring to has_inactive_ranges and inactive_ranges_sweep!

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  4. moved docs on VarInfo design to a separate internals section

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  5. writing improvements for internal docs

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  6. further motivation of the design choices made in VarNameVector

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  7. improved writing

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  8. VarNameVector is now grown as much as needed

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Commits on Jan 2, 2024

  1. updated delete!

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  2. Significant changes to implementation of VarNameVector: 

    - "delete-by-mark" is now replaced by proper deletion.
- `inactive_ranges` replaced by `num_inactive`, which only keeps track
of the number of inactive entries for a given `VarName.
- `VarNameVector` is now a "grow-as-needed" structure where the
underlying also mimics the order that the user experiences.`
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  3. added copy when constructing VectorVarInfo from VarInfo

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  4. added missing isempty impl

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  5. remove impl of iterate and instead implemented pairs and values… 

    … iterators
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  6. added missing empty! for num_inactive

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  7. removed redundant shift_left! methd

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  8. fixed delete! for VarNameVector

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  9. added is_contiguous as an alterantive to !has_inactive

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  10. updates to internal docs

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  11. renamed sweep_inactive_ranges! to contiguify!

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  12. improvements to internal docs

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  13. more improvements to internal docs

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  14. moved additional methods description in internals to earlier in the doc

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  15. moved internals docs to a separate directory and split into files

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  16. more improvements to internals doc

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  17. formatting

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  18. added tests for delete! and fixed reference to old method

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  19. addition to delete! test

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  20. added values_as impls for VarNameVector

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  21. added docs for replace_valus and values_as for VarNameVector

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  22. fixed doctest

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  23. formatting

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  24. temporarily disable doctests so we can build docs

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  25. added missing compat entry for ForwardDiff in docs

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Commits on Jan 3, 2024

  1. moved some shared code into methods to make things a bit cleaner

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  2. added impl of merge for VarNameVector

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  3. renamed a few variables in merge impl for VarNameVector

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  4. forgot to include some changes in previous commit

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  5. added impl of subset for VarNameVector

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  6. fixed pairs impl for VarNameVector

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  7. added missing impl of subset for VectorVarInfo

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  8. added missing impl of merge_metadata for VarNameVector

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  9. added a bunch of from_vec_transform and tovec impls to make 

    `VarNameVector` work with `Cholesky`, etc.
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  10. make default args use from_vec_transform rather than FromVec

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  11. fixed values_as fro VarInfo with VarNameVector as metadata

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Commits on Jan 4, 2024

  1. fixed impl of getindex_raw when using integer index for `VarNameVec… 

    …tor`
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  2. added tests for getindex with Int index for VarNameVector

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  3. fix for setindex! and setindex_raw! for VarNameVector

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Commits on Jan 19, 2024

  1. introduction of from_vec_transform and tovec and its usage in `Va… 

    …rInfo`
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  2. moved definition of is_splat_symbol to the file where it's used

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  3. added VarInfo constructor with vector input for VectorVarInfo

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  4. make extract_priors take the rng as an argument

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  5. added replace_values for Metadata

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  6. make link and invlink act on the metadata field for VarInfo + 

    implementations of these for `Metadata` and `VarNameVector`
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  7. added temporary defs of with_logabsdet_jacobian and inverse for 

    `transpose` and `Bijectors.vec_to_triu`
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  8. added invlink_with_logpdf overload for ThreadSafeVarInfo

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  9. added is_transformed field to VarNameVector

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  10. removed unnecessary defintions of with_logabsdet_jacobian and 

    `inverse` for `transpose`
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  11. fixed issue where we were storing the wrong transformations in `VarNa… 

    …meVector`
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  12. make sure extract_priors doesn't mutate the varinfo

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  13. updated similar for VarNameVector and fixed invlink for `VarNam… 

    …eVector`
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  14. added handling of is_transformed in merge for VarNameVector

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  15. removed unnecesasry deepcopy from outer link

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  16. updated push! to also push! on is_transformed

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  17. skip tests for mutating linking when using VarNameVector

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  18. use same projection for Cholesky in VarNameVector as in VarInfo

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  19. fixed settrans!! for VarInfo with VarNameVector

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  20. fixed bug in set_flag!

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  21. fixed another typo

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  22. fixed return values of settrans!!

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Commits on Jan 20, 2024

  1. updated static transformation tests

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  2. Update test/simple_varinfo.jl 

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  3. Merge branch 'master' into torfjelde/varnamevector

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Commits on Jan 25, 2024

  1. Merge remote-tracking branch 'origin/torfjelde/varnamevector' into to… 

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  2. Merge branch 'master' into torfjelde/varnamevector

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  3. removed unnecessary impl of extract_priors

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  4. make short_varinfo_name of TypedVarInfo a bit more informative

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  5. moved impl of has_varnamevector for ThreadSafeVarInfo

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  6. added back extract_priors impl as we do need it

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  7. forgot to include tests for VarNameVector in runtests.jl

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  8. fix for relax_container_types in test/varnamevector.jl

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Commits on Jan 26, 2024

  1. fixed need_transforms_relaxation

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Commits on Jan 28, 2024

  1. updated some tests to not refer directly to FromVec

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  2. introduce from_internal_transform and its siblings

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  3. remove with_logabsdet_jacobian_and_reconstruct in favour of 

    `with_logabsdet_jacobian` with `from_linked_internal_transform`, etc.
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  4. added internal_to_linked_internal_transform + fixed a few bugs in 

    the linking as a resultt
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  5. added linked_internal_to_internal_transform as a complement to `int… 

    …eranl_to_linked_interanl_transform`
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  6. fixed bugs in invlink for VarInfo using `linked_internal_to_inter… 

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  7. more work on removing calls to reconstruct

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  8. removed redundant comment

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  9. added from_linked_vec_transform specialization for LKJ

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  10. more work on removing references to reconstruct

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  11. added copy in values_from_metadata to preserve behavior and avoid 

    refs to internal representation
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  12. remove reconstruct_and_link and invlink_and_reconstruct

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  13. replaced references to link_and_reconstruct and `invlink_and_recons… 

    …truct`
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  14. introduced recombine and replaced calls to reconstruct with n s… 

    …amples
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  15. completely removed reconstruct

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  16. renamed maybe_reconstruct_and_link to to_maybe_linked_internal and 

    `maybe_invlink_and_reconstruct` to `from_maybe_linked_internal`
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Commits on Jan 30, 2024

  1. added impls of from_*_internal_transform for ThreadSafeVarInfo

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  2. removed reconstruct from docs and from exports

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Commits on Jan 31, 2024

  1. renamed getval to getindex_internal and made dist an optional 

    argument for all the transform-related methods
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  2. updated docs + added description of how internals of transforms work

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  3. added a bunch of illustrations for the transforms docs + dot files us… 

    …ed to generated
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  4. temporarily removed VarNameVector completely

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  5. formatting

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  6. Update docs/src/internals/transformations.md 

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  7. Update docs/src/internals/transformations.md 

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  8. removed refs to VectorVarInfo

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Commits on Feb 1, 2024

  1. added impls of from_internal_transform for ThreadSafeVarInfo

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  2. reverted accidental removal of old VarInfo constructor

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  3. fixed incorrect recombine call

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  4. removed undefined refs to VarNameVector stuff in setup_varinfos

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  5. bump minior version because Turing breaks

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  6. fix: was using from_linked_internal_transform in 

    `from_internal_transform` for `ThreadSafeVarInfo`
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  7. removed getindex_raw

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  8. removed redundant docstrings

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  9. fixed tests

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  10. fixed comparisons in tests

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  11. try relative references for images in transformation docs

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Commits on Feb 3, 2024

  1. another attempt at fixing asset-references

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  2. Merge branch 'master' into torfjelde/transformations

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  3. fixed getindex diagrams in docs

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  4. minor changes to comments

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  5. remove Combinatorics as a test dep, as it's not needed for this PR

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  6. reverted unnecessary change

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  7. disable type-stability tests for models on older Julia versions

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  8. removed seemingly completely unused impl of setval!

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  9. Revert "temporarily removed VarNameVector completely" 

    This reverts commit 95dc8e3.
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Commits on Feb 6, 2024

  1. Revert "remove Combinatorics as a test dep, as it's not needed for th… 

    …is PR"

This reverts commit 071bebf.
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Commits on Aug 22, 2024

  1. Merge remote-tracking branch 'origin/master' into torfjelde/varnameve… 

    …ctor
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Commits on Sep 3, 2024

  1. More work on VarNameVector (#637) 

    * Update test/model.jl

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

* Apply suggestions from code review

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* Type-stability tests are now correctly using `rand_prior_true` instead
of `rand`

* `getindex_internal` now calls `getindex` instead of `view`, as the
latter can result in type-instability since transformed variables
typically result in non-view even if input is a view

* Removed seemingly unnecessary definition of `getindex_internal`

* Fixed references to `newmetadata` which has been replaced by `replace_values`

* Made implementation of `recombine` more explicit

* Added docstrings for `untyped_varinfo` and `typed_varinfo`

* Added TODO comment about implementing `view` for `VarInfo`

* Fixed potential infinite recursion as suggested by @mhauru

* added docstring to `from_vec_trnasform_for_size

* Replaced references to `vectorize(dist, x)` with `tovec(x)`

* Fixed docstring

* Update src/extract_priors.jl

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* Bump minor version since this is a breaking change

* Apply suggestions from code review

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* Update src/varinfo.jl

Co-authored-by: Tor Erlend Fjelde <[email protected]>

* Apply suggestions from code review

* Apply suggestions from code review

* Update src/extract_priors.jl

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* Added fix for product distributions of targets with changing support + tests

* Addeed tests for product of distributions with dynamic support

* Apply suggestions from code review

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* Fix typos, improve docstrings

* Use Accessors rather than Setfield

* Simplify group_by_symbol

* Add short_varinfo_name(::VectorVarInfo)

* Add tests for subset

* Export VectorVarInfo

* Tighter type bound for has_varnamevector

* Add some VectorVarName methods

* Add todo notes, remove dead code, fix a typo.

* Bug fixes and small improvements

* VarNameVector improvements

* Improve generated_quantities and its tests

* Improvement to VarNameVector

* Fix a test to work with VectorVarName

* Fix generated_quantities

* Fix type stability issues

* Various VarNameVector fixes and improvements

* Bump version number

* Improvements to generated_quantities

* Code formatting

* Code style

* Add fallback implementation of findinds for VarNameVector

* Rename VarNameVector to VarNamedVector

* More renaming of VNV. Remove unused VarNamedVector.metadata field.

* Rename FromVec to ReshapeTransform

* Progress towards having VarNamedVector as storage for SimpleVarInfo

* Fix unflatten(vnv::VarNamedVector, vals)

* More work on SimpleVarInfo{VarNamedVector}

* More tests for SimpleVarInfo{VarNamedVector}

* More tests for SimpleVarInfo{VarNamedVector}

* Respond to review feedback

* Add float_type_with_fallback(::Type{Union{}})

* Move some VNV functions to the correct file

* Fix push! for VNV

* Rename VNV.is_transformed to VNV.is_unconstrained

* Improve VNV docstring

* Add VNV inner constructor checks

* Reorganise parts of VNV code

* Documentation and small fixes for VNV

* Rename loosen_types!! and tighten_types, add docstrings and doctests

* Rename VarNameVector to VarNamedVector in docs

* Documentation and small fixes to VNV

* Fix subset(::VarNamedVector, args...) for unconstrained variables.

---------

Co-authored-by: Tor Erlend Fjelde <[email protected]>
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  2. Merge remote-tracking branch 'origin/master' into torfjelde/varnameve… 

    …ctor
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  3. Bump Bijectors dependecy

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  4. Remove dead TODO note

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  5. Remove old TODOs, improve VNV invlinking

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Commits on Sep 4, 2024

  1. Fix from_vec_transform for 0-dim arrays

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  2. Fix unflatten for VarInfo

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  3. Fix some VarInfo index getters

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  4. Change how VNV handles transformations, and other VNV stuff

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  5. Small docs fixes

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  6. Merge remote-tracking branch 'origin/master' into torfjelde/varnameve… 

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Commits on Sep 5, 2024

  1. Small fixes all over for VNV

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  2. Add comments

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  3. Fix some tests

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  4. Change long string formatting to support Julia 1.6

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  5. Small changes to ReshapeTransformation

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  6. Revert unrelated changes to ReverseDiff extension

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  7. Improve VarNamedVector VarInfo testing

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  8. Fix some depwarns

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  9. Improvements to test/simple_varinfo.jl

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  10. Fix for unset_flag!, better docstring

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  11. Add a comment about hasvalue/getvalue

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Commits on Sep 9, 2024

  1. Add @non_differentiable calls to work around Zygote limitations

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  2. Fix docs, workaround Zygote issue

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Commits on Sep 17, 2024

  1. Remove outdated workaround

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  2. Move has_varnamedvector(varinfo::VarInfo) to abstract_varinfo.jl

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  3. Make copies of logp and num_produce in subset

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  4. Rename getindex_raw to getindex_internal

    @mhauru
    mhauru committed Sep 17, 2024
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  5. Add push!(::VarNamedVector, ::Pair)

    @mhauru
    mhauru committed Sep 17, 2024
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Commits on Sep 24, 2024

  1. Improve VarNamedVector docs

    @mhauru
    mhauru committed Sep 24, 2024
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  2. Simplify VarNamedVector constructors

    @mhauru
    mhauru committed Sep 24, 2024
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Commits on Oct 2, 2024

  1. Change how VNV setindex! et al work

    @mhauru
    mhauru committed Oct 2, 2024
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  2. More improvements to VNV setters and their tests

    @mhauru
    mhauru committed Oct 2, 2024
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  3. Fix style issues in VNV

    @mhauru
    mhauru committed Oct 2, 2024
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  4. Update VNV docs. Add haskey to VarInfo

    @mhauru
    mhauru committed Oct 2, 2024
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  5. Merge remote-tracking branch 'origin/master' into torfjelde/varnameve… 

    …ctor
    @mhauru
    mhauru committed Oct 2, 2024
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  6. Fix VarInfo docs

    @mhauru
    mhauru committed Oct 2, 2024
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  7. Disable a test that only works for VectorVarInfo

    @mhauru
    mhauru committed Oct 2, 2024
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  8. Fix bug in isempty(::TypedVarInfo)

    @mhauru
    mhauru committed Oct 2, 2024
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Commits on Oct 3, 2024

  1. Make some doctests platform independent

    @mhauru
    mhauru committed Oct 3, 2024
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  2. Merge remote-tracking branch 'origin/master' into torfjelde/varnameve… 

    …ctor
    @mhauru
    mhauru committed Oct 3, 2024
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  3. Better implementation of haskey(::VarInfo, ::VarName) 

    Co-authored-by: Tor Erlend Fjelde <[email protected]>
    @mhauru @torfjelde
    mhauru and torfjelde authored Oct 3, 2024
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  4. Improve haskey for VarInfo

    @mhauru
    mhauru committed Oct 3, 2024
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  5. Make a VNV doctest more robust

    @mhauru
    mhauru committed Oct 3, 2024
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  6. Remote IndexStyle for VNV

    @mhauru
    mhauru committed Oct 3, 2024
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  7. Clean up an old comment

    @mhauru
    mhauru committed Oct 3, 2024
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  8. Fix haskey(::VarInfo, ::VarName)

    @mhauru
    mhauru committed Oct 3, 2024
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Commits on Oct 4, 2024

  1. Clarify a TODO note in varinfo.jl

    @mhauru
    mhauru committed Oct 4, 2024
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  2. Reintroduce Int indexing to VNV

    @mhauru
    mhauru committed Oct 4, 2024
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  3. Stop exporting any VNV stuff

    @mhauru
    mhauru committed Oct 4, 2024
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  4. Fix docs

    @mhauru
    mhauru committed Oct 4, 2024
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Commits on Oct 7, 2024

  1. Revert default VarInfo metadata type to Metadata

    @mhauru
    mhauru committed Oct 7, 2024
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  2. Fix a few trivial issues with Metadata

    @mhauru
    mhauru committed Oct 7, 2024
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  3. Docs bug fix

    @mhauru
    mhauru committed Oct 7, 2024
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  4. Fix type constraint

    @mhauru
    mhauru committed Oct 7, 2024
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