diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index edd053d..ab19448 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -10,7 +10,7 @@ jobs: fail-fast: false matrix: version: - - '1.6' + - '1.9.2' os: - ubuntu-latest arch: diff --git a/Project.toml b/Project.toml index 2275f43..91c0c5d 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "RvSpectML" uuid = "1f61ac2c-3a1c-440a-925a-2707197041c8" authors = ["Eric B. Ford, Christian Gilbertson, Joe Ninan, Michael L. Palumbo III, Alex Wise, and contributors"] -version = "0.2.7" +version = "0.2.8" [deps] CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" @@ -45,15 +45,15 @@ EchelleCCFs = "0.2" EchelleInstruments = "0.2" FITSIO = "0.16, 0.17" FileIO = "1.4" -Interpolations = "0.12, 0.13, 0.14" +Interpolations = "0.12, 0.13, 0.14, 0.15" JLD2 = "0.2, 0.3, 0.4" KernelFunctions = "0.9.7, 0.10" -LsqFit = "0.11, 0.12, 0.13" +LsqFit = "0.11, 0.12, 0.13, 0.15" MultivariateStats = "0.7, 0.8, 0.9, 0.10" NaNMath = "0.3, 1" Optim = "1" PDMats = "0.10, 0.11" -Polynomials = "1, 1.1, 2, 3" +Polynomials = "1, 1.1, 2, 3, 4" ProgressMeter = "1.4" QuadGK = "2.4" Query = "1" @@ -61,11 +61,12 @@ RvSpectMLBase = "0.2" Scalpels = "0.1" SpecialFunctions = "1.0, 1.1, 2" StaticArrays = "1" +Statistics = "1" StatsBase = "0.33, 0.34" Stheno = "0.6, 0.7, 0.8" -TemporalGPs = "0.3, 0.4, 0.5, 0.6" +TemporalGPs = "0.6 - 0.6.7" ThreadedIterables = "0.2" -julia = "1.5, 1.6, 1.7, 1.8" +julia = "1.6" [extras] Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" diff --git a/docs/make.jl b/docs/make.jl index b2c7289..546328c 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -23,6 +23,8 @@ makedocs(; "Internals" => "internals.md", "Index" => "longlist.md", ], + checkdocs=:none, + #checkdocs=:exports, ) deploydocs(; diff --git a/docs/src/index.md b/docs/src/index.md index 6d232a4..d852e54 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -39,7 +39,7 @@ include("examples/calc_rvs_ccf_std.jl") - [EchelleInstruments](https://rvspectml.github.io/EchelleInstruments.jl/stable/) - [EchelleCCFs](https://rvspectml.github.io/EchelleCCFs.jl/stable) - [Scalpels](https://rvspectml.github.io/Scalpels.jl/stable/) -- [RvSpectMLPlots](https://rvspectml.github.io/RvSpectMLPlots.jl/stable/)^[unreg] +- [RvSpectMLPlots](https://rvspectml.github.io/RvSpectMLPlots.jl/stable/)* - [^unreg]: This package is not yet registerd in Julia's general registry yet. +* = This package is not yet registerd in Julia's general registry yet. diff --git a/docs/src/internals.md b/docs/src/internals.md index a7426dc..e44655e 100644 --- a/docs/src/internals.md +++ b/docs/src/internals.md @@ -11,60 +11,4 @@ Depth = 3 ``` ## Functions -### General purpose -```@autodocs -Modules = [RvSpectML ] -Public = false -Order = [ :function ] -``` - -### Radial Velocity Related -```@autodocs -Modules = [RvSpectML.DCPCA, RvSpectML.LineFinder ] #, RvSpectML.PPCA ] -Public = false -Order = [ :function ] -``` - -### Interpolation -```@autodocs -Modules = [RvSpectML.LinearInterpolation, RvSpectML.SincInterpolation, RvSpectML.TemporalGPInterpolation ] # RvSpectML.GPInterpolation, -Public = false -Order = [ :function] -``` - -## Other -```@autodocs -Modules = [Pipeline ] -Public = false -Order = [:function] -``` - -## Types -### General purpose -```@autodocs -Modules = [RvSpectML ] -Public = false -Order = [:type ] -``` - -### Radial Velocity Related -```@autodocs -Modules = [ RvSpectML.DCPCA, RvSpectML.LineFinder ] #, RvSpectML.PPCA ] -Public = false -Order = [:type ] -``` - -### Interpolation -```@autodocs -Modules = [RvSpectML.LinearInterpolation, RvSpectML.SincInterpolation, RvSpectML.TemporalGPInterpolation ] # RvSpectML.GPInterpolation, -Public = false -Order = [:type ] -``` - -## Other -```@autodocs -Modules = [Pipeline ] -Public = false -Order = [:type] -``` diff --git a/src/interp/gp_fast/low_level.jl b/src/interp/gp_fast/low_level.jl index df2c90d..3967d9d 100644 --- a/src/interp/gp_fast/low_level.jl +++ b/src/interp/gp_fast/low_level.jl @@ -10,7 +10,8 @@ Optional Inputs: function construct_gp_prior(; smooth_factor::Real = 1, σ²::Real = 0.5, l::Real = 5.8e-5) σ² *= smooth_factor l *= smooth_factor - k = σ² * transform(Matern52Kernel(), 1 / l) + #k = σ² * transform(Matern52Kernel(), 1 / l) + k = σ² * Matern52Kernel() ∘ ScaleTransform(1 / l) f_naive = GP(k) #f = to_sde(f_naive) # if develop issues with StaticArrays could revert to this f = to_sde(f_naive, SArrayStorage(Float64)) @@ -29,7 +30,8 @@ function construct_gp_prior(; smooth_factor_σ²::Real = 1, smooth_factor_l::Rea σ² *= smooth_factor_σ² * smooth_factor l *= smooth_factor_l * smooth_factor #k = σ² * transform(Matern52Kernel(), 1 / l) - k = σ² * with_lengthscale(Matern52Kernel(), 1 / l) + #k = σ² * with_lengthscale(Matern52Kernel(), 1 / l) + k = σ² * Matern52Kernel() ∘ ScaleTransform(1 / l) f_naive = GP(k) #f = to_sde(f_naive) # if develop issues with StaticArrays could revert to this f = to_sde(f_naive, SArrayStorage(Float64))