Merge pull request #7 from marcom/pkgexts

Use package extensions when available instead of Requires.jl

Project.toml

@@ -5,30 +5,32 @@ version = "0.2.1"
 
 [deps]
 BioStockholm = "eeb925a3-6f9d-43e6-829e-e0ea03b76ecf"
-CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 ColorSchemes = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
 Luxor = "ae8d54c2-7ccd-5906-9d76-62fc9837b5bc"
+PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 R2R_jll = "1e27f72a-4876-5c10-8678-3341fdb8ba55"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 Scratch = "6c6a2e73-6563-6170-7368-637461726353"
-PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
-UnicodePlots = "b8865327-cd53-5732-bb35-84acbb429228"
 ViennaRNA = "05a721ad-238d-4945-8c85-8b5c1fff3465"
 
 [compat]
 BioStockholm = "0.1"
 CairoMakie = "0.10"
 ColorSchemes = "3.18"
 Luxor = "3.3"
+PrecompileTools = "1"
 R2R_jll = "=1.0.6"
 Requires = "1.3"
 Scratch = "1.1"
-PrecompileTools = "1"
 UnicodePlots = "3"
 ViennaRNA = "0.9,0.10"
 julia = "1.6"
 
+[extensions]
+CairoMakieExt = "CairoMakie"
+UnicodePlotsExt = "UnicodePlots"
+
 [extras]
 BioStockholm = "eeb925a3-6f9d-43e6-829e-e0ea03b76ecf"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
@@ -37,4 +39,8 @@ UnicodePlots = "b8865327-cd53-5732-bb35-84acbb429228"
 ViennaRNA = "05a721ad-238d-4945-8c85-8b5c1fff3465"
 
 [targets]
-test = ["BioStockholm", "Test", "UnicodePlots", "ViennaRNA"]
+test = ["BioStockholm", "CairoMakie", "Test", "UnicodePlots", "ViennaRNA"]
+
+[weakdeps]
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+UnicodePlots = "b8865327-cd53-5732-bb35-84acbb429228"

README.md

@@ -59,13 +59,10 @@ plot_structure(dbn; sequence=seq,
 ```
 
 There is also an experimental `PlotRNA.plot_structure_makie` which
-looks a bit nicer but currently has a rather large time to first plot
-(on julia-1.9: about 10 seconds for `using CairoMakie, PlotRNA` and 10
-seconds for `PlotRNA.plot_structure_makie("(((...)))")`). Subsequent
-plots are very fast though. To use this function, you must load
-CairoMakie before PlotRNA. Code using CairoMakie is only loaded
-optionally with Requires.jl, as otherwise PlotRNA's package load time
-is a lot higher.
+looks a bit nicer but has a larger time to first plot (on julia-1.9:
+about 9 seconds for `using CairoMakie, PlotRNA` and 7 seconds for
+`PlotRNA.plot_structure_makie("(((...)))")`). Subsequent plots are
+very fast though.
 
 ```julia
 using CairoMakie, PlotRNA
@@ -77,7 +74,6 @@ PlotRNA.plot_structure_makie("(((...)))")
 Plotting in the terminal is supported via UnicodePlots with
 coordinates generated by ViennaRNA.
 
-
 ```julia
 using UnicodePlots, PlotRNA
 PlotRNA.uniplot("(((...)))")

src/plot_structure_makie.jl → ext/CairoMakieExt.jl

@@ -1,10 +1,20 @@
-# Note: we have to use the dot before CairoMakie as we are using
-# Requires.jl to only compile this code if CairoMakie is available
-using .CairoMakie: Makie, Axis, Colorbar, ColorTypes, DataAspect, Figure,
-    hidedecorations!, hidespines!, lines!, scatter!, text!,
-    xlims!, ylims!
+module CairoMakieExt
 
-function plot_structure_makie(
+using PrecompileTools: @compile_workload
+using PlotRNA
+using ViennaRNA: FoldCompound, Pairtable, basepairs, partfn, plot_coords, prob_of_basepairs
+if isdefined(Base, :get_extension)
+    using CairoMakie: Makie, Axis, Colorbar, ColorTypes, DataAspect,
+                      Figure, hidedecorations!, hidespines!, lines!,
+                      scatter!, text!, xlims!, ylims!
+else
+    using ..CairoMakie: Makie, Axis, Colorbar, ColorTypes, DataAspect,
+                        Figure, hidedecorations!, hidespines!, lines!,
+                        scatter!, text!, xlims!, ylims!
+end
+
+# Note: docstring is in src/PlotRNA.jl
+function PlotRNA.plot_structure_makie(
     structure::AbstractString;
     sequence::AbstractString=" "^length(structure),
     savepath::String = "",
@@ -77,3 +87,10 @@ function plot_structure_makie(
     end
     return f
 end
+
+@compile_workload begin
+    PlotRNA.plot_structure_makie("(((...)))")
+    PlotRNA.plot_structure_makie("(((...)))"; sequence="GGGAAACCC")
+end
+
+end # module

src/uniplot.jl → ext/UnicodePlotsExt.jl

@@ -1,23 +1,29 @@
+module UnicodePlotsExt
+
 # Secondary structure plotting to terminal with UnicodePlots
 
 # TODO
 # - smaller plots for smaller structures, e.g. (((...))), (((((....)))))
 # - bad aspect ratio for some structure, e.g. "Gladio" from Eterna100
 #   "((....))..(...(...(..(.(..(...(((.(((...((((....)))).((((((.((((((.((((((.((((((.((((((((((.((((((.(((((.((((.((((..((((...)))).))).)))))).))))).)))))).)))))))).)))))).)))))).)))))).))))))).)))...(((.(((((.(..((((.(..((((.(..((((.(..(((((((.((((((.(((((.((((((.(((.((((((....))))))..)))).)))).))))).)))))).)))))))).)..)))).)..)))).)..)))).)..))))).((((....))))...))).)))...)..).)..)...)...)..((....))"
 
-# Note: we have to use the dot before UnicodePlots as we are using
-# Requires.jl to only compile this code if UnicodePlots is available
+using PrecompileTools: @compile_workload
+using PlotRNA
 import ViennaRNA
-import .UnicodePlots
+if isdefined(Base, :get_extension)
+    import UnicodePlots
+else
+    import ..UnicodePlots
+end
 
-# the docstring is in PlotRNA.jl so it's always available, even if
-# this file wasn't loaded because of @require
-function uniplot(dbn; title="", width=:auto, height=:auto)
+# Note: docstring is in src/PlotRNA.jl
+function PlotRNA.uniplot(dbn::AbstractString; title::AbstractString="",
+                         width::Symbol=:auto, height::Symbol=:auto)
     n = length(dbn)
     n > 0 || throw(ArgumentError("secondary structure dbn has length 0"))
     x, y = ViennaRNA.plot_coords(ViennaRNA.Pairtable(dbn))
     plot = UnicodePlots.lineplot(x, y; border=:none, labels=false, title, width, height)
-    pt = Pairtable(dbn)
+    pt = ViennaRNA.Pairtable(dbn)
     for i = 1:n
         j = pt[i]
         if i < j
@@ -27,3 +33,9 @@ function uniplot(dbn; title="", width=:auto, height=:auto)
     end
     return plot
 end
+
+@compile_workload begin
+    PlotRNA.uniplot("(((...)))")
+end
+
+end # module

src/PlotRNA.jl

@@ -1,13 +1,21 @@
 module PlotRNA
 
 using PrecompileTools: @compile_workload
-using Requires: @require
-
 export VARNA, R2R, plot_structure
 
-function __init__()
-    @require CairoMakie="13f3f980-e62b-5c42-98c6-ff1f3baf88f0" include("plot_structure_makie.jl")
-    @require UnicodePlots="b8865327-cd53-5732-bb35-84acbb429228" include("uniplot.jl")
+# for julia < v1.9 we use Requires.jl instead of package extensions
+@static if !isdefined(Base, :get_extension)
+    using Requires: @require
+end
+@static if !isdefined(Base, :get_extension)
+    function __init__()
+        @require CairoMakie="13f3f980-e62b-5c42-98c6-ff1f3baf88f0" include(
+            normpath(@__DIR__, "..", "ext", "CairoMakieExt.jl")
+        )
+        @require UnicodePlots="b8865327-cd53-5732-bb35-84acbb429228" include(
+            normpath(@__DIR__, "..", "ext", "UnicodePlotsExt.jl")
+        )
+    end
 end
 
 include("plot_structure.jl")
@@ -17,23 +25,22 @@ include("r2r.jl")
 @compile_workload begin
     plot_structure("(((...)))")
     plot_structure("(((...)))"; sequence="GGGAAACCC")
-    # TODO: how to precompile but using @require from Requires.jl?
-    #       measure: are these precompile statements improving TTFP?
-    #uniplot("(((...)))")
-    #plot_structure_makie("(((...)))")
-    #plot_structure_makie("(((...)))"; sequence="GGGAAACCC")
 end
 
-# We define the docstrings of plot_structure_makie and uniplot here so they're always
-# available, even if they weren't loaded via @require in __init__().
+
+# Predefine docstrings of functions that are only available when other
+# packages are also loaded, either via package extensions (julia >=
+# v1.9) or Requires.jl (julia < v1.9).
+#
+#  - plot_structure_makie (needs CairoMakie)
+#  - uniplot (needs UnicodePlots)
 
 """
     plot_structure_makie(structure; [sequence, savepath, layout_type, colorscheme])
 
 Plot a secondary structure to a PNG image or PDF file depending on `savepath` ending.
 
-Using this function requires CairoMakie to have been loaded before
-PlotRNA with `using CairoMakie, PlotRNA`.
+Using this function requires CairoMakie to be loaded.
 """
 function plot_structure_makie end
 
@@ -43,8 +50,7 @@ function plot_structure_makie end
 Plot secondary structure using UnicodePlots, usually to show inside a
 terminal.
 
-Using this function requires UnicodePlots to have been loaded before
-PlotRNA with `using UnicodePlots, PlotRNA`.
+Using this function requires UnicodePlots to be loaded.
 """
 function uniplot end