Add files from Turing repo #12

devmotion · 2020-11-30T14:59:44Z

This PR adds relevant files from the Turing repo in a Turing/ subfolder, together with their history.

The files were extracted with git-filter-repo:

git clone [email protected]:TuringLang/Turing.jl.git
cd Turing
git filter-repo --path src/contrib/inference/AdvancedSMCExtensions.jl --path src/core/container.jl --path src/inference/AdvancedSMC.jl --path test/core/container.jl --path test/inference/AdvancedSMC.jl --path-rename '':Turing/
git remote add origin [email protected]:TuringLang/AdvancedPS.jl.git
git pull --allow-unrelated-histories origin master
git checkout -b Turing
git push -u origin Turing

Hopefully this simplifies reviews of PRs such as #11 (see, e.g., #11 (comment)) since it would be clearer what parts of the existing implementation in Turing were changed. Moreover, by keeping the history it might be easier to track down changes and understand the implementation better.

- Dict --> Array - push! : preallocate memory - forkc: remove forkc for the particles with only one chilcren.

Appveyor test

# Conflicts: # README.md

Benchmarks

Moved some untested functions to a separate branch.

Turing now works with Julia 0.5

# Conflicts: # README.md # docs/source/index.rst

# Conflicts: # src/core/compiler.jl # test/assume.jl # test/clonetask.jl # test/noparam.jl # test/predict.jl # test/runtests.jl

New interface and Gibbs sampling

Unify Mamba.Chain and Turing.Chain.

Unify rand interface

# Conflicts: # src/samplers/hmc.jl # src/samplers/sampler.jl # test/gibbs.jl

Remove sample macro

Refactor VarInfo

* Update Turing to AbstractMCMC 0.4 * Update sampling interface guide * Simplify resume_from handling in particle methods * Actually pass the RNG * Use cat instead of vcat to avoid mysterious type issues * Revert hack * Add error message Co-authored-by: Hong Ge <[email protected]>

* squash commit * minor fixes * bump DAD compat version * test fixes * use ForwardDiff for non-AD tests * Update Project.toml Co-Authored-By: David Widmann <[email protected]> * apply David's suggestions * Update src/Turing.jl Co-Authored-By: David Widmann <[email protected]> * David's comment * David's and Will's comments * Update Project.toml Co-Authored-By: David Widmann <[email protected]> * Update Project.toml Co-Authored-By: David Widmann <[email protected]> * Update src/core/ad.jl Co-Authored-By: David Widmann <[email protected]> * Update src/core/ad.jl Co-Authored-By: David Widmann <[email protected]> * Update src/core/ad.jl Co-Authored-By: David Widmann <[email protected]> * indentation Co-authored-by: David Widmann <[email protected]>

* Remove distribution wrappers (~> DynamicPPL) * Remove asssume/observer fallback code (~> DynamicPPL) * Update imports/exports/qualified names * Remove unnecessary code from utils (is in DPPL now) * fix rebase * bump DPPL compat version Co-authored-by: mohamed82008 <[email protected]>

Update Turing to AbstractMCMC 1.0, AdvancedMH 0.5, and DynamicPPL 0.6

* Use `propagate!` instead of `Libtask.consume` * Fix tests

* Make Turing compatible with DynamicPPL 0.7 * Uncomment test that should be fixed upstream * Updating variables in MH currently only works for `VarInfo` * Use DynamicPPL 0.7.1

* Allow sampling from the prior * Apply suggestions from code review Co-authored-by: Hong Ge <[email protected]> * Use `getlogp` instead of `getlp` * Add seed and increase number of samples Co-authored-by: Hong Ge <[email protected]>

* Fix particle filters with adaptive resampling and add documentation Fixes TuringLang/DynamicPPL.jl#104 * Fix and extend tests of `ParticleContainer` * Move logevidence tests from DynamicPPL * Add more convenient constructors for Particle Gibbs * Relax type annotations * Check for approximate equality only * Add docstring and reference

* Make GibbsComponent a simple trait (fix 1306) * Simplify isgibbscomponent; implement some other suggestions * Temporary fix for Distributions dependency

Co-authored-by: David Widmann <[email protected]>

* Remove `Turing.DEBUG` * Remove `_debug` * Update advi.jl Co-authored-by: Hong Ge <[email protected]>

Co-authored-by: Cameron Pfiffer <[email protected]>

yebai · 2020-11-30T15:20:07Z

Thanks, @devmotion - this is very helpful!

yebai · 2020-11-30T15:24:52Z

@devmotion maybe we can rename these files in a new PR, so that changes in #11 can be recognised by Github?

devmotion · 2020-11-30T15:27:07Z

Sure, I just wanted to keep this PR clean.

devmotion · 2020-11-30T15:29:54Z

Maybe it would be good as well to generate the default package layout with an empty module in a separate PR first, e.g., with PkgTemplates?

yebai · 2020-11-30T15:31:16Z

Maybe it would be good as well to generate the default package layout with an empty module in a separate PR first, e.g., with PkgTemplates?

Sounds good to me!

adscib and others added 30 commits April 29, 2016 13:34

Import of existing Turing code.

4e5f1ad

Re-organisation.

87a08d3

More efficient implementation of ParticleContainer.

51857e5

- Dict --> Array - push! : preallocate memory - forkc: remove forkc for the particles with only one chilcren.

Improved efficiency of io.jl.

97a1886

Added some comments.

9598d72

Revert all Int64 to Int.

5c04c67

Merge pull request #10 from yebai/appveyor_test

9f924e6

Appveyor test

Merged with master.

a551c22

Merge branch 'master' into benchmarks

8dc5640

# Conflicts: # README.md

Merge pull request #8 from yebai/benchmarks

672cd4d

Benchmarks

Add a switch to SMC to enable replay coroutines.

fea283d

Fix a bug in container

6fb9230

Moved some untested functions to a seprate branch.

fd53695

Merge pull request #36 from yebai/test-coverage

434661f

Moved some untested functions to a separate branch.

Fix bug in TArray.

082d503

Merge pull request #38 from yebai/master-julia-0.5

9e96a94

Turing now works with Julia 0.5

Merge branch 'master' into development

f3c5d88

# Conflicts: # README.md # docs/source/index.rst

Merge branch 'development'

1f2ebf2

# Conflicts: # src/core/compiler.jl # test/assume.jl # test/clonetask.jl # test/noparam.jl # test/predict.jl # test/runtests.jl

Fix Gibbs sampler bug

ec137fd

Merge pull request #73 from yebai/new-interface

62ac590

New interface and Gibbs sampling

Unify Mamba.Chain and Turing.Chain into one type.

0163d26

Merge pull request #116 from yebai/unify-chain

a2c15f0

Unify Mamba.Chain and Turing.Chain.

Fixed PG.

be46b72

Remove Task.storage and use flatten names internally

4725d9c

Merge pull request #130 from yebai/unify-rand-interface

3416493

Unify rand interface

Merge branch 'master' into remove-sample-macro

17751a0

# Conflicts: # src/samplers/hmc.jl # src/samplers/sampler.jl # test/gibbs.jl

Merge pull request #134 from yebai/remove-sample-macro

d8eafad

Remove sample macro

Add statistics

928c73f

Make accumulating of log weight more roboust (#218)

4a9e06d

Merge pull request #220 from yebai/refactor-vi

f2fdefd

Refactor VarInfo

devmotion and others added 23 commits February 18, 2020 14:10

Use reset_num_produce! (#1117)

0e677e0

Add concretize before generating Chains

e12b9af

Improved particle filter error message. (#900)

b477acb

Update to DynamicPPL 0.6

5c254fc

Merge pull request #1224 from devmotion/update

65d92c1

Update Turing to AbstractMCMC 1.0, AdvancedMH 0.5, and DynamicPPL 0.6

Add constructors and documentation for SMC (#1228)

785381b

Use propagate! instead of Libtask.consume (#1237)

ef6d0cc

* Use `propagate!` instead of `Libtask.consume` * Fix tests

Simplify ParticleContainer and add better tests for propagate! (#1242)

03b2c8f

Make Turing compatible with Libtask 0.4 (#1248)

3fdaadc

Make Turing compatible with DynamicPPL 0.7.1 (#1249)

40afdd4

* Make Turing compatible with DynamicPPL 0.7 * Uncomment test that should be fixed upstream * Updating variables in MH currently only works for `VarInfo` * Use DynamicPPL 0.7.1

Allow sampling from the prior (#1243)

95f2ab0

* Allow sampling from the prior * Apply suggestions from code review Co-authored-by: Hong Ge <[email protected]> * Use `getlogp` instead of `getlp` * Add seed and increase number of samples Co-authored-by: Hong Ge <[email protected]>

Use non-global RNGs

12e187a

Make GibbsComponent a simple trait (fix #1306) (#1307)

1848f32

* Make GibbsComponent a simple trait (fix 1306) * Simplify isgibbscomponent; implement some other suggestions * Temporary fix for Distributions dependency

Fixes for MCMCChains 4 (#1324)

b5176d1

residual sampling weird weighting (#1345)

ffab788

Co-authored-by: David Widmann <[email protected]>

Remove DEBUG (#1342)

1eb1645

* Remove `Turing.DEBUG` * Remove `_debug` * Update advi.jl Co-authored-by: Hong Ge <[email protected]>

Fix random test errors (#1469)

bfb4f3e

Update to AbstractMCMC 2 (#1428)

16fae46

Co-authored-by: Cameron Pfiffer <[email protected]>

Merge branch 'master' of github.com:TuringLang/AdvancedPS.jl

2c978d0

yebai merged commit 248846c into master Nov 30, 2020

delete-merged-branch bot deleted the Turing branch November 30, 2020 15:19

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