Merge pull request #27 from henry2004y/artifact

Use artifact for test data

.github/workflows/CI.yml

@@ -11,6 +11,7 @@ on:
     tags: '*'
     paths-ignore:
       - 'README.md'
+      - 'examples/**'
 env:
   JULIA_NUM_THREADS: 1
 jobs:

Artifacts.toml

@@ -0,0 +1,7 @@
+[testdata]
+git-tree-sha1 = "94103fd4bc493f5a2ddd9ec6ccd381cc07ebd7bf"
+lazy = true
+
+    [[testdata.download]]
+    url = "https://github.com/henry2004y/batsrus_data/raw/master/batsrus_data.tar.gz"
+    sha256 = "a69460d2c73509aedbb833caa7bfad0cd2a8ddb75404c6c5765cd801b0891965"

Project.toml

@@ -1,7 +1,7 @@
 name = "Batsrus"
 uuid = "e74ebddf-6ac1-4047-a0e5-c32c99e57753"
 authors = ["Hongyang Zhou <[email protected]>"]
-version = "0.3.9"
+version = "0.3.10"
 
 [deps]
 Dierckx = "39dd38d3-220a-591b-8e3c-4c3a8c710a94"
@@ -30,8 +30,9 @@ WriteVTK = "1.9"
 julia = "1.6"
 
 [extras]
+LazyArtifacts = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
 SHA = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "SHA"]
+test = ["Test", "LazyArtifacts", "SHA"]

docs/src/man/log.md

@@ -5,7 +5,18 @@ Because of the embarrassing parallelism nature of postprocessing, it is quite ea
 
 For the plotting, streamline tracing and particle tracing, a common problem is the grid and related interpolation process. Now I have [FieldTracer.jl](https://github.com/henry2004y/FieldTracer.jl) and [TestParticle.jl](https://github.com/henry2004y/TestParticle.jl) designed specifically for these tasks.
 
-### VTK AMR Grid Structure
+## Test Data
+
+If you don't have SWMF data at hand, Batsrus.jl provides some test data for you to begin with.
+```
+using LazyArtifacts
+
+datapath = artifact"testdata" # where you can find multiple test data files
+```
+
+These are also used in the standard test. These will be automatically downloaded from [batsrus_data](https://github.com/henry2004y/batsrus_data) if you run the package test locally.
+
+## VTK AMR Grid Structure
 
 `vtkOverlappingAMR` implements a somewhat strict Berger-Collela AMR scheme:
 1. All grids are Cartesian.

src/Batsrus.jl

@@ -13,6 +13,8 @@ struct FileList
    name::String
    "file type"
    type::String
+   "directory"
+   dir::String
    "file size"
    bytes::Int
    "number of snapshots"

src/io.jl

@@ -42,8 +42,7 @@ function readdata(filenameIn::AbstractString; dir=".", npict=1, verbose=false)
       throw(ArgumentError("Ambiguous filename $(filenameIn)!"))
    end
 
-   filename = joinpath(dir, filename[1])
-   filelist, fileID, pictsize = getfiletype(filename)
+   filelist, fileID, pictsize = getfiletype(filename[1], dir)
 
    verbose &&
       @info "filename=$(filelist.name)\n"*"npict=$(filelist.npictinfiles)"
@@ -251,10 +250,10 @@ end
 
 
 "Obtain file type."
-function getfiletype(filename)
-
-   fileID = open(filename, "r")
-   bytes = filesize(filename)
+function getfiletype(filename, dir)
+   file = joinpath(dir, filename)
+   fileID = open(file, "r")
+   bytes = filesize(file)
    type  = ""
 
    # Check the appendix of file names
@@ -283,7 +282,7 @@ function getfiletype(filename)
             type = "binary"
          else
             throw(ArgumentError(
-               "Error in getfiletype: incorrect formatted file: $(filename)"))
+               "Error in getfiletype: incorrect formatted file: $filename"))
          end
 
          if lenhead == 500
@@ -296,7 +295,7 @@ function getfiletype(filename)
       npictinfiles = bytes ÷ pictsize
    end
 
-   filelist = FileList(filename, type, bytes, npictinfiles)
+   filelist = FileList(filename, type, dir, bytes, npictinfiles)
 
    filelist, fileID, pictsize
 end
@@ -740,16 +739,16 @@ end
 Displaying file header information.
 """
 function showhead(file::FileList, head, io=stdout)
-   println(io, "filename  = $(file.name)")
-   println(io, "filetype  = $(file.type)")
-   println(io, "headline  = $(head.headline)")
-   println(io, "iteration = $(head.it)")
-   println(io, "time      = $(head.time)")
-   println(io, "gencoords = $(head.gencoord)")
-   println(io, "ndim      = $(head.ndim)")
-   println(io, "neqpar    = $(head.neqpar)")
-   println(io, "nw        = $(head.nw)")
-   println(io, "nx        = $(head.nx)")
+   println(io, "filename : $(file.name)")
+   println(io, "filetype : $(file.type)")
+   println(io, "headline : $(head.headline)")
+   println(io, "iteration: $(head.it)")
+   println(io, "time     : $(head.time)")
+   println(io, "gencoords: $(head.gencoord)")
+   println(io, "ndim     : $(head.ndim)")
+   println(io, "neqpar   : $(head.neqpar)")
+   println(io, "nw       : $(head.nw)")
+   println(io, "nx       : $(head.nx)")
 
    if head.neqpar > 0
       println(io, "parameters  = $(head.eqpar)")

test/runtests.jl

@@ -1,6 +1,6 @@
 # Tests of BATSRUS.jl
 
-using Batsrus, Test, SHA
+using Batsrus, Test, SHA, LazyArtifacts
 using Batsrus.UnitfulBatsrus, Unitful
 
 function filecmp(path1::AbstractString, path2::AbstractString)
@@ -25,10 +25,11 @@ function filecmp(path1::AbstractString, path2::AbstractString)
 end
 
 @testset "Batsrus.jl" begin
+   datapath = artifact"testdata"
    @testset "Reading 1D ascii" begin
       filename = "1d__raw_2_t25.60000_n00000258.out"
-      data = readdata(filename, dir="data", verbose=true)
-      @test startswith(repr(data), "filename  = data")
+      data = readdata(filename, dir=datapath, verbose=true)
+      @test startswith(repr(data), "filename : 1d")
       @test Batsrus.setunits(data.head, "NORMALIZED")
       @test isa(data.head, NamedTuple)
       @test extrema(data.x) == (-127.5, 127.5)
@@ -37,7 +38,7 @@ end
 
    @testset "Reading 2D structured binary" begin
       filename = "z=0_raw_1_t25.60000_n00000258.out"
-      data = readdata(filename, dir="data")
+      data = readdata(filename, dir=datapath)
       @test data.head.time == 25.6f0
       @test extrema(data.x) == (-127.5f0, 127.5f0)
       @test extrema(data.w) == (-0.79985905f0, 1.9399388f0)
@@ -50,7 +51,7 @@ end
 
    @testset "Reading 3D structured binary" begin
       filename = "3d_raw.out"
-      data = readdata(filename, dir="data")
+      data = readdata(filename, dir=datapath)
       plotrange = [-50.0, 50.0, -0.5, 0.5]
       X, Z, p = cutdata(data, "p"; dir="y", sequence=1, plotrange)
       @test p[1] ≈ 0.560976f0
@@ -60,39 +61,37 @@ end
    end
 
    @testset "Log" begin
-      logfilename = "data/log_n000001.log"
+      logfilename = joinpath(datapath, "log_n000001.log")
       head, data = readlogdata(logfilename)
       @test isa(head, NamedTuple)
       @test extrema(data) == (-0.105, 258.0)
    end
 
    @testset "VTK" begin
-      filename = "data/3d_bin.dat"
+      filename = joinpath(datapath, "3d_bin.dat")
       head, data, connectivity = readtecdata(filename)
       @test maximum(connectivity) ≤ head[:nNode] # check if it's read correctly
       convertTECtoVTU(head, data, connectivity)
       sha_str = bytes2hex(open(sha1, "out.vtu"))
       @test sha_str == "5b04747666542d802357dec183177f757754a254"
       rm("out.vtu")
 
-      filetag = "data/3d_mhd_amr/3d__mhd_1_t00000000_n00000000"
-      run(`tar -C data -zxf data/3d_mhd_amr.tar.gz`)
+      filetag = joinpath(datapath, "3d_mhd_amr/3d__mhd_1_t00000000_n00000000")
       batl = Batl(readhead(filetag*".info"), readtree(filetag)...)
       # local block index check
       @test Batsrus.find_grid_block(batl, [1.0, 0.0, 0.0]) == 4 
       @test Batsrus.find_grid_block(batl, [100.0, 0.0, 0.0]) == -100
       connectivity = getConnectivity(batl)
       sha_str = bytes2hex(sha256(string(connectivity)))
       @test sha_str == "c6c5a65a46d86a9ba4096228c1516f89275e45e295cd305eb70c281a770ede74"
-      rm("data/3d_mhd_amr", recursive=true)
    end
 
    @testset "Plotting" begin
       using PyPlot
       ENV["MPLBACKEND"]="agg" # no GUI
       @testset "1D ascii" begin
          filename = "1d__raw_2_t25.60000_n00000258.out"
-         data = readdata(filename, dir="data", verbose=false)
+         data = readdata(filename, dir=datapath, verbose=false)
          plotdata(data, "p", plotmode="line")
          line = gca().lines[1]
          @test line.get_xdata() ≈ data.x
@@ -101,7 +100,7 @@ end
 
       @testset "2D structured binary" begin
          filename = "z=0_raw_1_t25.60000_n00000258.out"
-         data = readdata(filename, dir="data")
+         data = readdata(filename, dir=datapath)
          plotdata(data, "p bx;by", plotmode="contbar streamover")
          @test isa(gca(), PyPlot.PyObject)
          contourf(data, "p")
@@ -123,7 +122,7 @@ end
 
       @testset "2D AMR Cartesian" begin
          filename = "bx0_mhd_6_t00000100_n00000352.out"
-         data = readdata(filename, dir="data")
+         data = readdata(filename, dir=datapath)
          plotdata(data, "P", plotmode="contbar")
          ax = gca()
          @test isa(ax, PyPlot.PyObject)
@@ -133,7 +132,7 @@ end
    @testset "Units" begin
       @test 1.0bu"R" > 2.0bu"Rg"
       filename = "y=0_var_1_t00000000_n00000000.out"
-      data = readdata(filename, dir="data")
+      data = readdata(filename, dir=datapath)
       varunit = getunit(data, "Rho")
       @test varunit == bu"amucc"
       varunit = getunit(data, "Ux")