Merge branch 'main' into compathelper/new_version/2023-05-02-00-55-24…

…-534-02600619793

.github/workflows/ci.yml

@@ -10,7 +10,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.6'
+          - '1.9.2'
         os:
           - ubuntu-latest
         arch:

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"
@@ -45,27 +45,28 @@ 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"
 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"

docs/make.jl

@@ -23,6 +23,8 @@ makedocs(;
         "Internals" => "internals.md",
         "Index" => "longlist.md",
     ],
+    checkdocs=:none,
+    #checkdocs=:exports,
 )
 
 deploydocs(;

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.

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]
-```

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))