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* Bump minor version to v0.37
* Remove selector/space stuff (#2458)
* Remove selector stuff from ESS
* Remove selector stuff from MH
* Remove selector stuff from HMC
* Remove selector stuff from Emcee
* Remove selector stuff from IS
* Add missing getspace methods
* Remove selector stuff for particle methods
* Fix an HMC selector bug
* Code style
* Fix Emcee selector bug
* Fix typo in ESS tests
* Fix some constructor overwrites
* Remove unnecessary tests
* Remove selector stuff from SGHMC
* Remove drop_space and other non-longer-necessary deprecation measures
* Bump minor version 0.37. Add a HISTORY.md entry
* Apply suggestions from code review
Co-authored-by: Penelope Yong <[email protected]>
* Remove unnecessary type parameters
Co-authored-by: Penelope Yong <[email protected]>
* Simplify constructors in particle_mcmc.jl
* Remove calls to setgid and updategid
---------
Co-authored-by: Penelope Yong <[email protected]>
* Bump Mooncake compat to 0.4.95
* Support for DynamicPPL v0.35 (#2488)
* Progress towards compat with DPPL v0.35
* More fixing of DPPL v0.35 stuff
* Fix LogDensityFunction argument order
* More minor bugfixes
* [TEMP] Commit Manifest pointing to DynamicPPL#release-0.35
* remove LogDensityProblemsAD (#2490)
* Remove LogDensityProblemsAD, part 1
* update Optimisation code to not use LogDensityProblemsAD
* Fix field name change
* Don't put chunksize=0
* Remove LogDensityProblemsAD dep
* Improve OptimLogDensity docstring
* Remove unneeded model argument to _optimize
* Fix more tests
* Remove essential/ad from the list of CI groups
* Fix HMC function
* more test fixes (#2491)
* Remove LogDensityProblemsAD, part 1
* update Optimisation code to not use LogDensityProblemsAD
* Fix field name change
* Don't put chunksize=0
* Remove LogDensityProblemsAD dep
* Improve OptimLogDensity docstring
* Remove unneeded model argument to _optimize
* Fix more tests
* Remove essential/ad from the list of CI groups
* Fix HMC function
* More test fixes
* Remove Manifest
* More fixes for DynamicPPL 0.35 (#2494)
* Remove test/dynamicppl/compiler.jl
* Remove old regression tests
* Remove vdemo2
* Fix last test
* Add HISTORY.md entry about DPPL 0.35
* Allow ESS to sample variables with different symbols
* Update a TODO note
---------
Co-authored-by: Penelope Yong <[email protected]>
* Fix call to DynamicPPL.initialize_parameters!!
* Remove `Zygote` (#2505)
* Remove `Zygote`; fix#2504
* Update test/test_utils/ad_utils.jl
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
* Add HISTORY.md entry about removing support for Zygote
---------
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Markus Hauru <[email protected]>
Co-authored-by: Penelope Yong <[email protected]>
Co-authored-by: Markus Hauru <[email protected]>
* Fix a Gibbs test
* Clean up exports (#2474)
* Regroup exports by package
* Export DynamicPPL.returned and DynamicPPL.prefix
* Stop exporting @logprob_str and @prob_str
* Remove DynamicPPL module export
* Remove DynamicPPL.LogDensityFunction re-export
* Remove BernoulliLogit, drop support for Distributions < 0.25.77
* Stop blanket re-exporting Libtask and Bijectors
* Manually specify AbstractMCMC exports
* Format
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
* Remove Bijectors.ordered export
* Re-export LinearAlgebra.I
* Replace Turing.Model -> DynamicPPL.Model
* Format
* Keep exporting LogDensityFunction
* Add note in docs
* Align Turing exports with docs API page
* Fix things like `predict` on docs API page
* Fix a Gibbs test
* Format
* Fix missing Bijectors import
* Update docs/src/api.md
Co-authored-by: Markus Hauru <[email protected]>
* Update docs/src/api.md
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
* Clean up broken docs links, remove unneeded deps
* Format
* Add changelog entry for exports
* Clean up exports in essential/Essential
* Apply suggestions from code review
Co-authored-by: Markus Hauru <[email protected]>
---------
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Markus Hauru <[email protected]>
Co-authored-by: Markus Hauru <[email protected]>
---------
Co-authored-by: Penelope Yong <[email protected]>
Co-authored-by: Hong Ge <[email protected]>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Copy file name to clipboardExpand all lines: HISTORY.md
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# Release 0.37.0
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## Breaking changes
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### Gibbs constructors
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0.37 removes the old Gibbs constructors deprecated in 0.36.
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### Remove Zygote support
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Zygote is no longer officially supported as an automatic differentiation backend, and `AutoZygote` is no longer exported. You can continue to use Zygote by importing `AutoZygote` from ADTypes and it may well continue to work, but it is no longer tested and no effort will be expended to fix it if something breaks.
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[Mooncake](https://github.com/compintell/Mooncake.jl/) is the recommended replacement for Zygote.
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### DynamicPPL 0.35
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Turing.jl v0.37 uses DynamicPPL v0.35, which brings with it several breaking changes:
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- The right hand side of `.~` must from now on be a univariate distribution.
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- Indexing `VarInfo` objects by samplers has been removed completely.
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- The order in which nested submodel prefixes are applied has been reversed.
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- The arguments for the constructor of `LogDensityFunction` have changed. `LogDensityFunction` also now satisfies the `LogDensityProblems` interface, without needing a wrapper object.
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For more details about all of the above, see the changelog of DynamicPPL [here](https://github.com/TuringLang/DynamicPPL.jl/releases/tag/v0.35.0).
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### Export list
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Turing.jl's export list has been cleaned up a fair bit. This affects what is imported into your namespace when you do an unqualified `using Turing`. You may need to import things more explicitly than before.
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- The `DynamicPPL` and `AbstractMCMC` modules are no longer exported. You will need to `import DynamicPPL` or `using DynamicPPL: DynamicPPL` (likewise `AbstractMCMC`) yourself, which in turn means that they have to be made available in your project environment.
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-`@logprob_str` and `@prob_str` have been removed following a long deprecation period.
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- We no longer re-export everything from `Bijectors` and `Libtask`. To get around this, add `using Bijectors` or `using Libtask` at the top of your script (but we recommend using more selective imports).
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+ We no longer export `Bijectors.ordered`. If you were using `ordered`, even Bijectors does not (currently) export this. You will have to manually import it with `using Bijectors: ordered`.
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On the other hand, we have added a few more exports:
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-`DynamicPPL.returned` and `DynamicPPL.prefix` are exported (for use with submodels).
|`@model`|[`DynamicPPL.@model`](@extref)| Define a probabilistic model |
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|`@varname`|[`AbstractPPL.@varname`](@extref)| Generate a `VarName` from a Julia expression |
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|`to_submodel`|[`DynamicPPL.to_submodel`](@extref)| Define a submodel |
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|`prefix`|[`DynamicPPL.prefix`](@extref)| Prefix all variable names in a model with a given symbol |
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|`LogDensityFunction`|[`DynamicPPL.LogDensityFunction`](@extref)| A struct containing all information about how to evaluate a model. Mostly for advanced users |
|`predict`|[`StatsAPI.predict`](https://turinglang.org/DynamicPPL.jl/stable/api/#Predicting)| Generate samples from posterior predictive distribution |
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### Querying model probabilities and quantities
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Please see the [generated quantities](https://turinglang.org/docs/tutorials/usage-generated-quantities/) and [probability interface](https://turinglang.org/docs/tutorials/usage-probability-interface/) guides for more information.
|`generated_quantities`|[`DynamicPPL.generated_quantities`](@extref)| Calculate additional quantities defined in a model |
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|`pointwise_loglikelihoods`|[`DynamicPPL.pointwise_loglikelihoods`](@extref)| Compute log likelihoods for each sample in a chain |
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|`logprior`|[`DynamicPPL.logprior`](@extref)| Compute log prior probability |
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|`logjoint`|[`DynamicPPL.logjoint`](@extref)| Compute log joint probability |
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|`LogDensityFunction`|[`DynamicPPL.LogDensityFunction`](@extref)| Wrap a Turing model to satisfy LogDensityFunctions.jl interface |
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|`condition`|[`AbstractPPL.condition`](@extref)| Condition a model on data |
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|`decondition`|[`AbstractPPL.decondition`](@extref)| Remove conditioning on data |
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|`conditioned`|[`DynamicPPL.conditioned`](@extref)| Return the conditioned values of a model |
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|`fix`|[`DynamicPPL.fix`](@extref)| Fix the value of a variable |
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|`unfix`|[`DynamicPPL.unfix`](@extref)| Unfix the value of a variable |
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|`OrderedDict`|[`OrderedCollections.OrderedDict`](https://juliacollections.github.io/OrderedCollections.jl/dev/ordered_containers/#OrderedDicts)| An ordered dictionary |
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### Extra re-exports from Bijectors
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Note that Bijectors itself does not export `ordered`.
|`returned`|[`DynamicPPL.returned`](https://turinglang.org/DynamicPPL.jl/stable/api/#DynamicPPL.returned-Tuple%7BModel,%20NamedTuple%7D)| Calculate additional quantities defined in a model |
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|`pointwise_loglikelihoods`|[`DynamicPPL.pointwise_loglikelihoods`](@extref)| Compute log likelihoods for each sample in a chain |
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|`logprior`|[`DynamicPPL.logprior`](@extref)| Compute log prior probability |
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|`logjoint`|[`DynamicPPL.logjoint`](@extref)| Compute log joint probability |
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|`condition`|[`AbstractPPL.condition`](@extref)| Condition a model on data |
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|`decondition`|[`AbstractPPL.decondition`](@extref)| Remove conditioning on data |
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|`conditioned`|[`DynamicPPL.conditioned`](@extref)| Return the conditioned values of a model |
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|`fix`|[`DynamicPPL.fix`](@extref)| Fix the value of a variable |
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|`unfix`|[`DynamicPPL.unfix`](@extref)| Unfix the value of a variable |
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|`OrderedDict`|[`OrderedCollections.OrderedDict`](@extref)| An ordered dictionary |
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