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general relativistic HMC #372

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general relativistic HMC #372

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7fc04d2
feat: port relativistic hmc from research repo
Jul 25, 2024
3813ba0
feat(wip): port reemannian hmc from research repo
Jul 25, 2024
8805885
Update src/AdvancedHMC.jl
yebai Jul 26, 2024
6b023f7
Update AdvancedHMC.jl
yebai Jul 26, 2024
3bbb17f
feat(wip): port reemannian hmc from research repo
Sep 18, 2024
cdef753
Apply suggestions from code review
xukai92 Oct 26, 2024
4ff42cf
chore: remove experimental notebook
Oct 26, 2024
1acbf8f
feat: port rest of the code from research repo
Oct 26, 2024
f446f0e
feat: port rest of the code from research repo
Oct 26, 2024
62077db
Merge branch 'master' into kx/general-relativistic
xukai92 Oct 26, 2024
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4 changes: 4 additions & 0 deletions Project.toml
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Original file line number Diff line number Diff line change
@@ -4,6 +4,7 @@ version = "0.6.2"

[deps]
AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
AdaptiveRejectionSampling = "c75e803d-635f-53bd-ab7d-544e482d8c75"
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A minor issue: Do we want to depend on ARS? Is it possible to turn this into a weak deps?

ArgCheck = "dce04be8-c92d-5529-be00-80e4d2c0e197"
DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
InplaceOps = "505f98c9-085e-5b2c-8e89-488be7bf1f34"
@@ -31,15 +32,18 @@ AdvancedHMCOrdinaryDiffEqExt = "OrdinaryDiffEq"

[compat]
AbstractMCMC = "5"
AdaptiveRejectionSampling = "0.1.1"
ArgCheck = "1, 2"
CUDA = "3, 4, 5"
DocStringExtensions = "0.8, 0.9"
InplaceOps = "0.3"
LinearAlgebra = "1.6"
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Duplicate with L53.

Suggested change
LinearAlgebra = "1.6"

LogDensityProblems = "2"
LogDensityProblemsAD = "1"
MCMCChains = "5, 6"
OrdinaryDiffEq = "6"
ProgressMeter = "1"
Random = "1.6"
Requires = "0.5, 1"
Setfield = "0.7, 0.8, 1"
SimpleUnPack = "1.1"
1 change: 1 addition & 0 deletions research/.gitignore
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
results
25 changes: 22 additions & 3 deletions research/Project.toml
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Original file line number Diff line number Diff line change
@@ -1,8 +1,27 @@
[deps]
AdaptiveRejectionSampling = "c75e803d-635f-53bd-ab7d-544e482d8c75"
AdvancedHMC = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
Comonicon = "863f3e99-da2a-4334-8734-de3dacbe5542"
DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
DiffResults = "163ba53b-c6d8-5494-b064-1a9d43ac40c5"
Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
DrWatson = "634d3b9d-ee7a-5ddf-bec9-22491ea816e1"
DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8"
FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41"
ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a"
MCMCDebugging = "6d524b87-5f90-4494-b601-374a5b87a94b"
MCMCDiagnosticTools = "be115224-59cd-429b-ad48-344e309966f0"
Match = "7eb4fadd-790c-5f42-8a69-bfa0b872bfbf"
MultivariateStats = "6f286f6a-111f-5878-ab1e-185364afe411"
Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
ReTest = "e0db7c4e-2690-44b9-bad6-7687da720f89"
ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
SparseDiffTools = "47a9eef4-7e08-11e9-0b38-333d64bd3804"
StatProfilerHTML = "a8a75453-ed82-57c9-9e16-4cd1196ecbf5"
VecTargets = "8a639fad-7908-4fe4-8003-906e9297f002"
Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
12 changes: 9 additions & 3 deletions research/README.md
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Original file line number Diff line number Diff line change
@@ -1,8 +1,14 @@
In order to use algorithms in this folder, please navigate to the AdvancedHMC folder and run
In order to use algorithms in this folder, please navigate to the `AdvancedHMC` folder and run


```
] activate research/
```julia
] activate research
] develop .
] instantiate
```

To run the tests, please run below from the `research` directory

```bash
julia --proj=@. test/runtests.jl
```
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