v0.9 (#62)

* Prepare for Julia 1.7

* Update cell ID selection for velocity space in benchmark

Project.toml

@@ -1,7 +1,7 @@
 name = "Vlasiator"
 uuid = "7d2ba682-ad6e-4e20-80d9-3f2d4a610bb4"
 authors = ["Hongyang Zhou <hongyang.zhou@helsinki.fi>"]
-version = "0.8.30"
+version = "0.9.0"
 
 [deps]
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
@@ -16,7 +16,6 @@ RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
-UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
 WriteVTK = "64499a7a-5c06-52f2-abe2-ccb03c286192"
 
 [compat]
@@ -27,9 +26,8 @@ PyPlot = "2.9"
 RecipesBase = "1.1"
 Requires = "1.1"
 StaticArrays = "1.2"
-UnPack = "1.0"
 WriteVTK = "1.9"
-julia = "1.6"
+julia = "1.7"
 
 [extras]
 LazyArtifacts = "4af54fe1-eca0-43a8-85a7-787d91b784e3"

benchmark/benchmarks.jl

@@ -26,7 +26,7 @@ SUITE["read"]["DCCRG_select_large"] =
 SUITE["read"]["FG"] = @benchmarkable readvariable($meta, "fg_b")
 file = joinpath(directory, files[1])
 meta = load(file)
-SUITE["read"]["VDF"] = @benchmarkable readvcells($meta, 2; species="proton")
+SUITE["read"]["VDF"] = @benchmarkable readvcells($meta, 5; species="proton")
 
 SUITE["VTK"] = BenchmarkGroup(["conversion"])
 file = joinpath(directory, files[3])

src/Vlasiator.jl

@@ -3,7 +3,6 @@ module Vlasiator
 using Requires
 using StaticArrays
 using Printf: @sprintf
-using UnPack
 using LinearAlgebra: ×, dot, ⋅, norm, normalize!
 using Statistics: mean
 using EzXML

src/plot/plots.jl

@@ -1,10 +1,10 @@
 # Using user recipes from Plots.
 
-using RecipesBase, Printf, UnPack
+using RecipesBase, Printf
 
 # Build a recipe which acts on a custom type.
 @recipe function f(meta::MetaVLSV, var::AbstractString; op=:mag, axisunit=RE, normal=:y)
-   @unpack ncells, coordmin, coordmax = meta
+   (;ncells, coordmin, coordmax) = meta
    if ndims(meta) == 1
       data = readvariable(meta, var)
 

src/plot/pyplot.jl

@@ -77,7 +77,7 @@ function PyPlot.quiver(meta::MetaVLSV, var::AbstractString, ax=nothing;
 end
 
 function set_vector(meta::MetaVLSV, var, comp, axisunit::AxisUnit)
-   @unpack ncells, coordmin, coordmax = meta
+   (;ncells, coordmin, coordmax) = meta
    if occursin("x", comp)
       v1_ = 1
       if occursin("y", comp)
@@ -145,7 +145,7 @@ function PyPlot.pcolormesh(meta::MetaVLSV, var::AbstractString, ax=nothing; op=:
       # check if origin and normal exist in kwargs
       normal = haskey(kwargs, :normal) ? kwargs.data.normal : :y
       origin = haskey(kwargs, :origin) ? kwargs.data.origin : 0.0
-      kwargs = Base.structdiff(kwargs.data, (normal = normal, origin = origin))
+      kwargs = Base.structdiff(values(kwargs), (normal = normal, origin = origin))
       c = pcolormeshslice(meta, var, ax; op, axisunit, colorscale, addcolorbar, vmin, vmax,
          normal, origin, kwargs...)
       return c
@@ -261,7 +261,7 @@ end
 
 "Configure customized plot."
 function set_plot(c, ax, pArgs::PlotArgs, cticks, addcolorbar)
-   @unpack str_title, strx, stry, cb_title = pArgs
+   (;str_title, strx, stry, cb_title) = pArgs
 
    if addcolorbar
       cb = colorbar(c; ax, ticks=cticks, fraction=0.04, pad=0.02)
@@ -353,7 +353,7 @@ Plot mesh cell centers from axis view `projection`. `projection` should be eithe
 """
 function plotmesh(meta::MetaVLSV, ax=nothing; projection="3d", origin=0.0, marker="+",
    kwargs...)
-   @unpack coordmin, coordmax, cellid = meta
+   (;coordmin, coordmax, cellid) = meta
    if projection in ("x", "y", "z")
       dirp, dir1, dir2 =
          if projection == "x"

src/utility/plot.jl

@@ -29,7 +29,7 @@ end
 
 "Set plot-related arguments of `var` in `axisunit`."
 function set_args(meta::MetaVLSV, var, axisunit::AxisUnit; normal::Symbol=:none, origin=0.0)
-   @unpack ncells, coordmin, coordmax = meta
+   (;ncells, coordmin, coordmax) = meta
 
    if normal == :x
       seq = @SVector [2,3]
@@ -124,7 +124,7 @@ end
 
 "Return `data` of `var` on a uniform 2D mesh on the finest AMR level."
 function prep2dslice(meta::MetaVLSV, var, normal, op, pArgs::PlotArgs)
-   @unpack idlist, indexlist = pArgs
+   (;idlist, indexlist) = pArgs
 
    data3D = readvariable(meta, var)
 

src/vlsv/vlsvreader.jl

@@ -318,7 +318,7 @@ Return variable value of `var` from the vlsv file. By default `sorted=true`, whi
 that for DCCRG grid the variables are sorted by cell ID.
 """
 function readvariable(meta::MetaVLSV, var, sorted::Bool=true)
-   @unpack fid, footer, cellindex = meta
+   (;fid, footer, cellindex) = meta
    if (local symvar = Symbol(var)) in keys(variables_predefined)
       data = variables_predefined[symvar](meta)
       return data
@@ -359,7 +359,7 @@ Read a variable `var` in a collection of cells `ids`.
 """
 function readvariable(meta::MetaVLSV, var, ids)
    startswith(var, "fg_") && error("Currently does not support reading fsgrid!")
-   @unpack fid, footer, cellid, cellindex = meta
+   (;fid, footer, cellid, cellindex) = meta
 
    if (local symvar = Symbol(var)) in keys(variables_predefined)
       data = variables_predefined[symvar](meta, ids)
@@ -548,8 +548,8 @@ Read velocity cells from a spatial cell of ID `cid`, and return a map of velocit
 ids and corresponding value.
 """
 function readvcells(meta::MetaVLSV, cid; species="proton")
-   @unpack fid, footer = meta
-   @unpack vblock_size = meta.meshes[species]
+   (;fid, footer) = meta
+   (;vblock_size) = meta.meshes[species]
    bsize = prod(vblock_size)
 
    local offset::Int, nblocks::Int

src/vlsv/vlsvutility.jl

@@ -7,7 +7,7 @@ Return cell ID containing the given spatial `location`, excluding domain boundar
 Only accept 3D location.
 """
 function getcell(meta::MetaVLSV, loc)
-   @unpack coordmin, coordmax, dcoord, ncells, cellid, maxamr = meta
+   (;coordmin, coordmax, dcoord, ncells, cellid, maxamr) = meta
 
    coordmin[1] < loc[1] < coordmax[1] || error("x coordinate out of bound!")
    coordmin[2] < loc[2] < coordmax[2] || error("y coordinate out of bound!")
@@ -202,7 +202,7 @@ end
 Return a given cell's coordinates.
 """
 function getcellcoordinates(meta::MetaVLSV, cid::Integer)
-   @unpack ncells, coordmin, coordmax = meta
+   (;ncells, coordmin, coordmax) = meta
    cid -= 1 # for easy divisions
 
    xcell, ycell, zcell = ncells
@@ -237,7 +237,7 @@ end
 Return velocity cells' coordinates of `species` and `vcellids`.
 """
 function getvcellcoordinates(meta::MetaVLSV, vcellids; species="proton")
-   @unpack vblocks, vblock_size, dv, vmin = meta.meshes[species]
+   (;vblocks, vblock_size, dv, vmin) = meta.meshes[species]
 
    bsize = prod(vblock_size)
    blockid = @. vcellids ÷ bsize
@@ -278,7 +278,7 @@ end
 Get density from VDF, n = ∫ f(r,v) dV.
 """
 function getdensity(meta::MetaVLSV, VDF; species="proton")
-   @unpack dv = meta.meshes[species]
+   (;dv) = meta.meshes[species]
    n = zero(eltype(VDF))
 
    @inbounds @simd for f in VDF
@@ -288,7 +288,7 @@ function getdensity(meta::MetaVLSV, VDF; species="proton")
 end
 
 function getdensity(meta::MetaVLSV, vcellids, vcellf; species="proton")
-   @unpack dv = meta.meshes[species]
+   (;dv) = meta.meshes[species]
 
    n = zero(eltype(vcellf))
 
@@ -305,7 +305,7 @@ end
 Get bulk velocity from VDF, u = ∫ v * f(r,v) dV / n.
 """
 function getvelocity(meta::MetaVLSV, VDF; species="proton")
-   @unpack dv, vmin = meta.meshes[species]
+   (;dv, vmin) = meta.meshes[species]
    u = zeros(eltype(VDF), 3)
 
    @inbounds for k in axes(VDF,3), j in axes(VDF,2), i in axes(VDF,1)
@@ -326,7 +326,7 @@ function getvelocity(meta::MetaVLSV, VDF; species="proton")
 end
 
 function getvelocity(meta::MetaVLSV, vcellids, vcellf; species="proton")
-   @unpack dv, vmin = meta.meshes[species]
+   (;dv, vmin) = meta.meshes[species]
 
    VDF = flatten(meta.meshes[species], vcellids, vcellf)
 
@@ -339,7 +339,7 @@ end
 Get pressure tensor from VDF, pᵢⱼ = m/3 * ∫ (v - u)ᵢ(v - u)ⱼ * f(r,v) dV.
 """
 function getpressure(meta::MetaVLSV, VDF; species="proton")
-   @unpack dv, vmin = meta.meshes[species]
+   (;dv, vmin) = meta.meshes[species]
    p = zeros(eltype(VDF), 6)
 
    u = getvelocity(meta, VDF; species)
@@ -415,7 +415,7 @@ density as `f`. The value ranges from [0, +∞], with 0 meaning not Maxwellian-d
 all, and +∞ a perfect Maxwellian distribution.
 """
 function getmaxwellianity(meta, VDF; species="proton")
-   @unpack dv, vmin = meta.meshes[species]
+   (;dv, vmin) = meta.meshes[species]
 
    n = getdensity(meta, VDF)
    u = getvelocity(meta, VDF)
@@ -440,7 +440,7 @@ function getmaxwellianity(meta, VDF; species="proton")
 end
 
 function isInsideDomain(meta::MetaVLSV, point)
-   @unpack coordmin, coordmax = meta
+   (;coordmin, coordmax) = meta
 
    if coordmin[1] < point[1] ≤ coordmax[1] &&
       coordmin[2] < point[2] ≤ coordmax[2] &&
@@ -458,7 +458,7 @@ Returns cell IDs, distances and coordinates for every cell in a line between two
 points `point1` and `point2`. May be improved later with preallocation!
 """
 function getcellinline(meta::MetaVLSV, point1, point2)
-   @unpack coordmin, coordmax, ncells = meta
+   (;coordmin, coordmax, ncells) = meta
 
    if !isInsideDomain(meta, point1)
       throw(DomainError(point1, "point location outside simulation domain!"))
@@ -531,7 +531,7 @@ order to the cut plane and can be used to select data onto the plane.
 """
 function getslicecell(meta::MetaVLSV, sliceoffset, idim, minCoord, maxCoord)
    idim ∉ (1,2,3) && @error "Unknown slice direction $idim"
-   @unpack ncells, maxamr, cellid, cellindex = meta
+   (;ncells, maxamr, cellid, cellindex) = meta
 
    nsize = ncells[idim]
    sliceratio = sliceoffset / (maxCoord - minCoord)
@@ -582,7 +582,7 @@ Generate scalar data on the finest refinement level given cellids `idlist` and v
 `data` on the slice perpendicular to `normal`.
 """
 function refineslice(meta::MetaVLSV, idlist, data, normal)
-   @unpack ncells, maxamr = meta
+   (;ncells, maxamr) = meta
 
    dims = let ratio = 2^maxamr
       if normal == :x
@@ -718,7 +718,7 @@ Fill the DCCRG mesh with quantity of `vars` on all refinement levels.
 - `vtkGhostType::Array{UInt8}`: cell status (to be completed!).
 """
 function fillmesh(meta::MetaVLSV, vars; verbose=false)
-   @unpack maxamr, fid, footer, ncells, cellid, cellindex = meta
+   (;maxamr, fid, footer, ncells, cellid, cellindex) = meta
 
    nvarvg = findall(!startswith("fg_"), vars)
    nv = length(vars)
@@ -837,7 +837,7 @@ Convert VLSV file to VTK format.
 - `verbose=false`: display logs during conversion.
 """
 function write_vtk(meta::MetaVLSV; vars=[""], ascii=false, maxamronly=false, verbose=false)
-   @unpack ncells, maxamr, dcoord, coordmin = meta
+   (;ncells, maxamr, dcoord, coordmin) = meta
 
    append = ascii ? false : true
 
@@ -918,7 +918,7 @@ Save `data` of name `vars` at AMR `level` into VTK image file of name `file`.
 """
 function save_image(meta::MetaVLSV, file, vars, data, vtkGhostType, level, ascii=false,
    append=true)
-   @unpack coordmin, dcoord, ncells = meta
+   (;coordmin, dcoord, ncells) = meta
    origin = (coordmin[1], coordmin[2], coordmin[3])
    ratio = 2^level
    spacing = (dcoord[1] / ratio, dcoord[2] / ratio, dcoord[3] / ratio)