Ga/Ja_safe flags and mittleff clean-up

Manifest.toml

@@ -8,9 +8,9 @@ version = "0.5.0"
 
 [[Adapt]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "ffcfa2d345aaee0ef3d8346a073d5dd03c983ebe"
+git-tree-sha1 = "f1b523983a58802c4695851926203b36e28f09db"
 uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
-version = "3.2.0"
+version = "3.3.0"
 
 [[ArgTools]]
 uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
@@ -64,10 +64,10 @@ uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4"
 version = "0.8.7"
 
 [[Colors]]
-deps = ["ColorTypes", "FixedPointNumbers", "InteractiveUtils", "Reexport"]
-git-tree-sha1 = "ac5f2213e56ed8a34a3dd2f681f4df1166b34929"
+deps = ["ColorTypes", "FixedPointNumbers", "Reexport"]
+git-tree-sha1 = "82f4e6ff9f847eca3e5ebc666ea2cd7b48e8b47e"
 uuid = "5ae59095-9a9b-59fe-a467-6f913c188581"
-version = "0.12.6"
+version = "0.12.7"
 
 [[CompilerSupportLibraries_jll]]
 deps = ["Artifacts", "Libdl"]
@@ -338,6 +338,12 @@ git-tree-sha1 = "f8c673ccc215eb50fcadb285f522420e29e69e1c"
 uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
 version = "0.4.5"
 
+[[MittagLeffler]]
+deps = ["QuadGK", "SpecialFunctions"]
+git-tree-sha1 = "56200ea7b88fda91c7eb9422c52bce78c2fac7b5"
+uuid = "9c257583-4f8f-53fd-abd9-c69d5080dd54"
+version = "0.2.0"
+
 [[Mmap]]
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 
@@ -358,9 +364,9 @@ uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
 
 [[MutableArithmetics]]
 deps = ["LinearAlgebra", "SparseArrays", "Test"]
-git-tree-sha1 = "6b6bb8f550dc38310afd4a0af0786dc3222459e2"
+git-tree-sha1 = "ff3aa3e4dbc837f80c2031de2f90125c8b3793f3"
 uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0"
-version = "0.2.14"
+version = "0.2.15"
 
 [[NLopt]]
 deps = ["MathOptInterface", "MathProgBase", "NLopt_jll"]
@@ -492,9 +498,9 @@ uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [[StatsBase]]
 deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics"]
-git-tree-sha1 = "a83fa3021ac4c5a918582ec4721bc0cf70b495a9"
+git-tree-sha1 = "4bc58880426274277a066de306ef19ecc22a6863"
 uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-version = "0.33.4"
+version = "0.33.5"
 
 [[TOML]]
 deps = ["Dates"]

Project.toml

@@ -13,9 +13,9 @@ FunctionWrappers = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e"
 ImageFiltering = "6a3955dd-da59-5b1f-98d4-e7296123deb5"
 InverseLaplace = "e24f45a5-4790-5a38-8b2c-33d770a4e70f"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
+MittagLeffler = "9c257583-4f8f-53fd-abd9-c69d5080dd54"
 NLopt = "76087f3c-5699-56af-9a33-bf431cd00edd"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
-QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
@@ -28,7 +28,7 @@ FunctionWrappers = "1.1"
 ImageFiltering = "0.6"
 InverseLaplace = "0.3"
 JLD2 = "0.1"
+MittagLeffler = "0.2"
 NLopt = "0.6"
-QuadGK = "2.3"
 SpecialFunctions = "0.10"
-julia = "1.4"
+julia = "1.6"

README.md

@@ -72,9 +72,6 @@ If you use RHEOS in your work, please consider citing the following papers as ap
 
 + A. Bonfanti, J. L. Kaplan, G. Charras, A. J. Kabla (2020). _Fractional viscoelastic models for power-law materials_. Soft Matter, 16, 6002-6020, [https://doi.org/10.1039/D0SM00354A](https://doi.org/10.1039/D0SM00354A)
 
-## Embedded Dependencies
-#### [MittagLeffler.jl](https://github.com/jlapeyre/MittagLeffler.jl)
-
 ## Contributing to RHEOS
 If you believe you have found any bugs or invalid behaviour in RHEOS, please feel free to file an issue on this repository. You can also raise an issue if you feel that any part of the documentation needs clarification, or for any feature requests. Even better than just raising an issue, you could both raise an issue and issue a pull request which fixes that issue.
 

src/RHEOS.jl

@@ -4,13 +4,17 @@ __precompile__(true)
 module RHEOS
 
 # installed from Julia package repository
-using InverseLaplace
 using NLopt
 using JLD2
 using DataStructures
 using FunctionWrappers: FunctionWrapper
 using Dierckx
 
+# useful for the various model functions
+using InverseLaplace
+import MittagLeffler: mittleff as mittlefforiginal
+import SpecialFunctions: gamma
+
 import DSP.conv
 
 # Base and stdlib imports
@@ -77,8 +81,8 @@ export AFM, Tweezers
 
 ######################################################
 # bundled dependencies from rheos-cambridge forked repos
-MittLeffLiteDir = joinpath(@__DIR__, "..", "deps", "MittLeffLite", "MittLeffLite.jl")
-include(MittLeffLiteDir)
+#MittLeffLiteDir = joinpath(@__DIR__, "..", "deps", "MittLeffLite", "MittLeffLite.jl")
+#include(MittLeffLiteDir)
 
 include("base.jl")
 include("definitions.jl")

src/base.jl

@@ -199,7 +199,7 @@ Preprocessing base functionality
 Generate sigma/std deviation for gaussian smoothing kernel.
 
 Acts as a low pass filter. Information of time scale τ will be half power,
-faster will be increasingly cut. Called by smoothgauss function.
+faster will be increasingly cut. Called by smooth function.
 """
 function getsigma(τ::Real, samplerate::Real)
 

src/datagen.jl

@@ -90,7 +90,7 @@ time as its only argument. The original data's time signal is used.
 Normally used with a RheoTimeData generated using the `timeline` function.
 """
 function strainfunction(data::RheoTimeData, f::T) where T<:Function
-    log = data.log == nothing ? nothing : [data.log; RheoLogItem( (type=:process, funct=:strainfunction, params=(f=f,), keywords=()),
+    log = data.log === nothing ? nothing : [data.log; RheoLogItem( (type=:process, funct=:strainfunction, params=(f=f,), keywords=()),
                                     (comment="strain function applied to timeline",) ) ]
 
     return RheoTimeData(data.σ, convert(Vector{RheoFloat}, map(f, data.t)), data.t, log)
@@ -106,7 +106,7 @@ time as its only argument. The original data's time signal is used.
 Normally used with a `RheoTimeData` generated using the `timeline` function.
 """
 function stressfunction(data::RheoTimeData, f::T) where T<:Function
-    log = data.log == nothing ? nothing : [data.log; RheoLogItem( (type=:process, funct=:stressfunction, params=(f=f,), keywords=()),
+    log = data.log === nothing ? nothing : [data.log; RheoLogItem( (type=:process, funct=:stressfunction, params=(f=f,), keywords=()),
                                     (comment="stress function applied to timeline",) ) ]
     return RheoTimeData(convert(Vector{RheoFloat}, map(f, data.t)), data.ϵ, data.t, log)
 end