Add :let keyword, more supported packages
nixo
parent
e86200172c
commit
e789251ce9
97
init.jl
97
init.jl
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@ -1,4 +1,4 @@
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const supported_packages = [:DataFrames, :NamedArrays, :Plots]
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const supported_packages = [:DataFrames, :NamedArrays, :Plots, :HypothesisTests, :CSVFiles]
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# Generic fallback
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orgshow(io::IO, Any, i; kwargs...) = show(io, i)
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@ -27,8 +27,17 @@ function orgshow(io::IO, ::MIME"text/csv", i::Array{T,2}; kwargs...) where T <:
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orgshow(io, MIME("text/org"), i; kwargs...)
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end
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function orgstring(e::Tuple{Exception,Any})
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string("ERROR,", e[1], "\n",
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"Stacktrace:\n",
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join(e[2], '\n'))
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end
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# The comma is needed to allow export as table
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orgshow(io::IO, ::MIME"text/org", e::Exception; kwargs...) = print(io, "ERROR,", e)
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function orgshow(io::IO, ::MIME"text/org", e::Tuple{Exception,Any};
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kwargs...)
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print(io, orgstring(e))
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end
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function orgshow(io::IO, ::MIME"text/org", t::NamedTuple)
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print(io, join(string.(keys(t)), ','))
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@ -48,6 +57,26 @@ function orgshow(io::IO, ::MIME"text/org",
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end
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end
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OrgAPApvalue(p) = p < 0.001 ? "< .001" : string("= ", round(p, sigdigits = 2))
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function define_HypothesisTests()
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Main.@eval function orgshow(io::IO,
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m::MIME"text/org",
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test::PowerDivergenceTest; kwargs...)
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println(io, join(["test", "df", "N", "stat", "p-value"], ','))
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print(io, join(["X^2", test.df, test.n, test.stat, pvalue(test)], ','))
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end
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Main.@eval function orgshow(io::IO,
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m::MIME"text/html",
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test::PowerDivergenceTest; kwargs...)
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print(io, string("X^2",
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" (", test.df, ", N = ", test.n,
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") = ",
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round(test.stat; digits = 2),
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", p ", OrgAPApvalue(pvalue(test))))
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end
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end
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function define_Plots()
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# Fallback: we will try to plot any image/png or image/svg
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Main.@eval function orgshow(io::IO,
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@ -65,9 +94,10 @@ function define_Plots()
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p::Plots.Plot; kwargs...)
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show(io, MIME("image/png"), plot(p; kwargs...))
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end
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Main.@eval function orgshow(io::IO, ::MIME"image/png", e::Exception; kwargs...)
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Main.@eval function orgshow(io::IO, ::MIME"image/png", e::Tuple{Exception,Any};
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kwargs...)
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let p = plot(showaxis = false, grid = false, bg = :yellow)
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annotate!([0.5], [0.5], (string("ERROR: ", e), :red))
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annotate!([0.5], [0.5], (orgstring(e), :red))
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orgshow(io, MIME("image/png"), p; kwargs...)
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end
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end
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@ -78,7 +108,10 @@ function define_Plots()
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end
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end
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Main.@eval function orgshow(io::IO, ::MIME"text/html", p::Plots.Plot; kwargs...)
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Plots._show(io, MIME("text/html"), plot(p; kwargs...))
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p = plot(p; kwargs...)
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p.attr[:html_output_format] = "png"
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# Plots._show(io::IO, MIME("text/html"), p::Plots.Plot; kwargs...)
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Plots._show(io, MIME("text/html"), p)
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end
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Main.@eval function orgshow(io::IO, ::MIME"image/svg+xml", p::Plots.Plot; kwargs...)
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show(io, MIME("image/svg+xml"), plot(p; kwargs...))
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@ -116,13 +149,30 @@ function define_DataFrames()
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end
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end
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function define_CSVFiles()
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Main.@eval function orgshow(io::IO, ::MIME"text/csv", d::CSVFiles.CSVFile)
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orgshow(io, MIME("text/org"), d)
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end
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Main.@eval function orgshow(io::IO, ::MIME"text/html", d::CSVFiles.CSVFile)
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show(io, MIME("text/html"), RES)
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end
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Main.@eval function orgshow(io::IO, ::MIME"application/json", d::CSVFiles.CSVFile)
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show(io, MIME("application/vnd.dataresource+json"), RES)
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end
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Main.@eval function orgshow(io::IO, ::MIME"text/org", d::CSVFiles.CSVFile)
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orgshow(io, MIME("text/org"), collect(d))
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end
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end
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function define_NamedArrays()
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Main.@eval function orgshow(io::IO, ::MIME"text/org",
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na::NamedArrays.NamedArray{T,2} where T <: Any)
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na::NamedArray{T,2} where T <: Any)
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n = names(na)
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a = collect(na)
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print(io, join(string.(na.dimnames), "/") * ',')
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print(io, join(n[2], ','') * '\n')
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# The char used by NamedArrays is '╲' but by default it's not
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# shown in pdf export
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print(io, join(string.(na.dimnames), " \\ ") * ',')
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print(io, join(n[2], ',') * '\n')
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print(io, join([join([string(n[1][i], ','),
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join([a[i,j]
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for j in 1:size(na,2)
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@ -130,7 +180,7 @@ function define_NamedArrays()
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for i in 1:size(na,1)
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], '\n'))
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end
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Main.@eval function orgshow(io::IO, ::MIME"text/org", na::NamedArrays.NamedArray{T,1} where T <: Any)
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Main.@eval function orgshow(io::IO, ::MIME"text/org", na::NamedArray{T,1} where T <: Any)
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n = names(na)
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a = collect(na)
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print(io, string(na.dimnames[1], ',', '\n'))
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@ -141,15 +191,16 @@ end
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define_package_functions(pkg::Symbol) = (@eval $pkg)()
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function OrgBabelImport(_imports; forced = false)
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function OrgBabelImport(imports; forced = false)
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"Load dependencies. Do this before calling OrgBabelReload()"
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# Reload this module, so that if new packages have been imported,
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# we can use them to save the output
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!forced && isempty(_imports) && return
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!forced && isempty(imports) && return
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println("$imports")
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try
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Main.eval(Meta.parse(
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"""begin
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$_imports
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$imports
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end"""))
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true
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catch e
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@ -183,29 +234,30 @@ function OrgBabelFormat(output_type::Symbol,
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dir, vars,
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src_file,
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silently::Bool,
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pure::Bool,
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kwargs)
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content = read(src_file, String)
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# Fake a prompt with the current input
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try
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println(string("\njulia> ", content))
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printstyled(IOContext(stdout, :color => true),
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"\njulia> ", color = :blue)
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println(content)
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catch
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end
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# Dispatch on output type
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code = pure ? "let $vars; $content; end" : "begin $vars; $content end"
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if output_type == :value
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# Run the code
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result = cd(dir) do
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try
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# Variable assignment
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Main.eval(Meta.parse(vars))
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# src block evaluation
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Main.eval(Meta.parse("begin $content end"))
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Main.eval(Meta.parse(code))
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catch e
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e
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(e, stacktrace())
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end
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end
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if !silently
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try
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print(result)
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display(MIME("text/plain"), result)
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catch e
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println("Error $e while showing results")
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end
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@ -236,12 +288,10 @@ function OrgBabelFormat(output_type::Symbol,
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redirect_stderr(f) do
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cd(dir) do
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try
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# Variable assignment
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Main.eval(Meta.parse(vars))
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# src block evaluation
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Main.eval(Meta.parse("begin $content end"))
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Main.eval(Meta.parse(code))
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catch e
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println(e)
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println(join(stacktrace(), '\n'))
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end
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end
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end
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@ -260,3 +310,4 @@ function OrgBabelFormat(output_type::Symbol,
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end
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OrgBabelReload()
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80
ob-julia.el
80
ob-julia.el
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@ -12,7 +12,7 @@
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:version "24.1"
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:type 'string)
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(defcustom org-babel-julia-startup-script
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(defcustom ob-julia-startup-script
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(concat (file-name-directory (or load-file-name (buffer-file-name)))
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"init.jl")
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"Julia file path to run at startup. Must be absolute."
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@ -52,6 +52,7 @@ There's no effect in non-session evaluations"
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(height . :any)
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(size . :any)
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(inline . :any)
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(let . :any)
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(import . :any)
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(using . :any)
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(async . :any)
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@ -81,7 +82,14 @@ There's no effect in non-session evaluations"
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(set (make-local-variable 'org-babel-julia-session-directory) dir)
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(save-window-excursion
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(require 'ess)
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(julia)
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;; load the julia startup script (defined in ob-julia-startup-script)
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;; pass it along with other arguments defined in inferior-julia-args
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(let* ((start-script-arg
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(concat (format "--load=%s" ob-julia-startup-script)))
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(inferior-julia-args (if inferior-julia-args
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(concat inferior-julia-args start-script-arg)
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start-script-arg)))
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(julia))
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(rename-buffer
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(if (bufferp session)
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(buffer-name session)
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@ -92,14 +100,7 @@ There's no effect in non-session evaluations"
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;; running the command
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(set-process-filter (get-buffer-process
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(org-babel-comint-buffer-livep session))
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'org-julia-async-process-filter)
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;; Initialization
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(let ((julia-init
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(with-temp-buffer
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(insert-file-contents org-babel-julia-startup-script)
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(buffer-string))))
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(ess-send-string (ess-get-process) julia-init nil))
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(current-buffer))))
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'org-julia-async-process-filter))))
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(defun org-babel-julia-get-session-name (params)
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"Extract the session name from the PARAMS.
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@ -153,8 +154,7 @@ This function is used for all async processing with and without session."
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;; This will evaluate the code again
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;; (cl-callf org-babel-process-params (nth 2 info))
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(setq params (nth 2 info))
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(setq cache (let ((c (cdr (assq :cache params))))
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(and c (string= "yes" c))))
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(setq cache (ob-julia-check-trueness params :cache))
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;; pass info to have a different hash
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(setq new-hash (if cache (org-babel-sha1-hash) nil))
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(org-babel-remove-result)
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@ -181,14 +181,14 @@ Does not rely on an ESS session."
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(make-process :name "*julia-async-process*"
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:filter #'org-julia-async-process-filter
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:command `(,org-babel-julia-command
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"--load" ,org-babel-julia-startup-script
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"--load" ,ob-julia-startup-script
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"--eval"
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,(format "include(%S);%s" tmpfile command)))
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(concat "julia-async:" uuid ":" outfile))
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(progn
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(shell-command
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(format "%s --load %s %s" org-babel-julia-command
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org-babel-julia-startup-script tmpfile))
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ob-julia-startup-script tmpfile))
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outfile))))
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(defun org-babel-julia-assign-to-var-or-array (var)
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@ -201,7 +201,7 @@ Does not rely on an ESS session."
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"Create a Matrix (Vector{Any,2} from `MATRIX' and assign it to `NAME'"
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(format "%s = [%s]" name
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(mapconcat (lambda (line) (mapconcat (lambda (e)
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(format "%s" e))
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(format "%S" e))
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line " ")) matrix ";")))
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(defun org-babel-julia-assign-to-var (name value)
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@ -290,19 +290,22 @@ else OUTFILE is used, and data is _write()_ to it."
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(format "OrgBabelImport(%S);OrgBabelReload();"
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(concat (if using (mapconcat (lambda (x) (concat "using " x))
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using "\n") "")
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"\n"
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(if import (mapconcat (lambda (x) (concat "import " x))
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import "\n") "")))
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"")
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(format
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"OrgBabelFormat(%s,%S,%S,%S,%S,%s,%S);"
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output-type outfile
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dir
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(mapconcat 'concat vars ";") srcfile
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(if org-babel-julia-silent-repl
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"true" "false")
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(org-babel-julia-make-kwargs `((width . ,width)
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(height . ,height)
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(size . ,size)))))))
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"OrgBabelFormat(%s,%S,%S,%S,%S,%s,%s,%S);"
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output-type outfile
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dir
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(mapconcat 'concat vars ";") srcfile
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(if org-babel-julia-silent-repl
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"true" "false")
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(if (ob-julia-check-trueness params :let)
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"true" "false")
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(org-babel-julia-make-kwargs `((width . ,width)
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(height . ,height)
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(size . ,size)))))))
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(defun org-babel-execute:julia-async (buffer session body block output params)
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(let* ((uuid (org-id-uuid))
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@ -361,14 +364,14 @@ If PARAMS is :async, insert a link, unless CALLBACK is true."
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(if inlined
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(with-temp-buffer
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(when (bound-and-true-p org-export-current-backend)
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(insert (format "@@%s:"
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(insert (format "#+begin_export %s\n"
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(if org-export-current-backend
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org-export-current-backend
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inlined))))
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(insert-file-contents results)
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(when (bound-and-true-p org-export-current-backend)
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(goto-char (point-max))
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(insert "@@"))
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(insert "\n#+end_export"))
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(buffer-string))
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(org-babel-result-cond (if res (split-string res) nil)
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(with-temp-buffer
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@ -391,27 +394,25 @@ table. To force a matrix, use matrix"
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((member "raw" results) 'raw)
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(t 'auto))))
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(defun ob-julia-check-trueness (params param)
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""
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(and (assoc param params)
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(let ((val (cdr (assoc param params))))
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(or
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(not val)
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(string= "t" val)
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(string= "yes" val)))))
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(defun org-babel-julia-async-p (params)
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"Check whether the session should be async or not."
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(let* ((res (cdr (assoc :results params)))
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(async (assoc :async params)))
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(and async
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(or
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(not (cdr async))
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(string= "t" (cdr async))
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(string= "yes" (cdr async)))
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(ob-julia-check-trueness params :async)
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(and (eq org-babel-current-src-block-location (org-babel-where-is-src-block-head)))
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(not (and res (stringp res) (member "silent" (split-string res)))))))
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(defun org-babel-julia-really-async-p ()
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;; (let*
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;; ((head (org-babel-where-is-src-block-head))
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;; (async (and (not (bound-and-true-p org-export-current-backend))
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;; head
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;; org-babel-current-src-block-location
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;; (equal org-babel-current-src-block-location
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;; head))))
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;; async)
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;; Disable async on export
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(not (bound-and-true-p org-export-current-backend)))
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;; Copied from ob-python
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@ -442,7 +443,6 @@ This function is called by `org-babel-execute-src-block'.
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BODY is the content of the src block
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PARAMS are the parameter passed to the block"
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;; org-babel-current-src-block-location ; this variable does not work >.<
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(message (format "body: %s, params: %s" body params))
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(save-excursion
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(let* ((buffer (buffer-name))
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(session (org-babel-julia-get-session-name params))
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18
readme.org
18
readme.org
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@ -19,7 +19,10 @@ See [[Implemented features]] for more details.
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(customized by =org-babel-julia-default-session=)
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3. If session has a values, use it's name
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3. Check if we want to use a session or not. Check if the session
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exists. Start the session accordingly.
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exists. Start the session accordingly. During startup, the file
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defined in =ob-julia-startup-script= is loaded. This file must define
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functions like OrgBabelFormat, to let emacs send code to
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execute. See =init.jl= for details.
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4. Is the evaluation async?
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1. YES:
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1. Register a filter function
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@ -100,7 +103,18 @@ sleep(1)
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Asynchronous evaluation is automatically disabled on export, or when a
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code block depends on one (=:var=)
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** Variables input (=:var=), Standard output
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** Variables input (=:var =:let=), Standard output
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As usual, you can set variables with the =:var= header. To make ob-julia
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behave like the julia REPL, variables are set in the global scope. If
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you want a block to be isolated, you can use the extra =:let= header
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argument: with this, the src block is inside a let block:
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#+begin_src julia :exports code :eval never
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let vars
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src_block
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end
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#+end_src
|
||||
|
||||
*** Inputs
|
||||
|
||||
|
|
|
|||
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Reference in New Issue