Introduce preference for automatic ascii visualization of system (#122)

.github/workflows/CI.yml

@@ -18,7 +18,6 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.6'
           - '1.9'
           - '1.10'
           - 'nightly'

Project.toml

@@ -6,19 +6,28 @@ version = "0.5.0"
 [deps]
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 PeriodicTable = "7b2266bf-644c-5ea3-82d8-af4bbd25a884"
+Preferences = "21216c6a-2e73-6563-6e65-726566657250"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"
 
+[weakdeps]
+AtomsView = "ee286e10-dd2d-4ff2-afcb-0a3cd50c8041"
+
+[extensions]
+AtomsBaseAtomsViewExt = "AtomsView"
+
 [compat]
+AtomsView = "0.1"
 PeriodicTable = "1"
+Preferences = "1.4"
 Requires = "1"
 StaticArrays = "1"
 Unitful = "1"
 UnitfulAtomic = "1"
-julia = "1.6"
+julia = "1.9"
 
 [extras]
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"

ext/AtomsBaseAtomsViewExt.jl

@@ -0,0 +1,8 @@
+module AtomsBaseAtomsViewExt
+    using AtomsBase
+    using AtomsView
+
+    function Base.show(io::IO, mime::MIME"text/html", system::AbstractSystem)
+        write(io, AtomsView.visualize_structure(system, mime))
+    end
+end

src/AtomsBase.jl

@@ -18,24 +18,10 @@ include("utils/visualize_ascii.jl")
 include("utils/show.jl")
 include("utils/atomview.jl")
 
-
 # prototype implementations
 include("implementation/atom.jl")
 include("implementation/flexible_system.jl")
 include("implementation/fast_system.jl")
 include("implementation/utils.jl")
 
-
-# TODO:
-#  - this should be converted to an extension
-#  - should work for AbstractSystem
-function __init__()
-    @require AtomsView="ee286e10-dd2d-4ff2-afcb-0a3cd50c8041" begin
-        function Base.show(io::IO, mime::MIME"text/html", system::FlexibleSystem)
-            write(io, AtomsView.visualize_structure(system, mime))
-        end
-    end
-end
-
-
 end

src/implementation/atom.jl

@@ -50,8 +50,8 @@ Supported `kwargs` include `species`, `mass`, as well as user-specific custom pr
 """
 function Atom(identifier::AtomId,
               position::AbstractVector{L},
-              velocity::AbstractVector{V} = _default_velocity(position); 
-              species = ChemicalSpecies(identifier),
+              velocity::AbstractVector{V}=_default_velocity(position);
+              species=ChemicalSpecies(identifier),
               mass::M=mass(species),
               kwargs...) where {L <: Unitful.Length, V <: Unitful.Velocity, M <: Unitful.Mass}
     Atom{length(position), L, V, M}(position, velocity, species,

src/utils/show.jl

@@ -1,4 +1,35 @@
 using Printf
+using Preferences
+
+"""
+Configures the printing behaviour of `show_system`, which is invoked when a rich `text/plain`
+display of an `AbstractSystem` is requested. This is for example the case in a Julia REPL.
+The following options can be configured:
+
+- `max_particles_list`: Maximal number of particles in a system until `show_system`
+  includes a listing of every particle. Default: 10
+- `max_particles_visualize_ascii`: Maximal number of particles in a system
+  until `show_system` includes a representation of the system in the form of
+  an ascii cartoon using `visualize_ascii`. Default 0, i.e. disabled.
+"""
+function set_show_preferences!(; max_particles_list=nothing, max_particles_visualize_ascii=nothing)
+    if !isnothing(max_particles_list)
+        @set_preferences!("max_particles_list" => max_particles_list)
+    end
+    if !isnothing(max_particles_visualize_ascii)
+        @set_preferences!("max_particles_visualize_ascii" => max_particles_visualize_ascii)
+    end
+    show_preferences()
+end
+
+"""
+Display the current printing behaviour of `show_system`.
+See [`set_show_preferences!](@ref) for more details on the keys.
+"""
+function show_preferences()
+    (; max_particles_list=@load_preference("max_particles_list", 10),
+       max_particles_visualize_ascii=@load_preference("max_particles_visualize_ascii", 0))
+end
 
 """
 Suggested function to print AbstractSystem objects to screen
@@ -7,9 +38,9 @@ function show_system(io::IO, system::AbstractSystem{D}) where {D}
     pbc = periodicity(system)
     print(io, typeof(system).name.name, "($(chemical_formula(system))")
     perstr = [p ? "T" : "F" for p in pbc]
-    print(io, ", pbc = ", join(perstr, ""))
+    print(io, ", periodicity = ", join(perstr, ""))
 
-    if !any(pbc)
+    if any(pbc)
         box_str = ["[" * join(ustrip.(bvector), ", ") * "]"
                    for bvector in cell_vectors(system)]
         bunit = unit(eltype(first(cell_vectors(system))))
@@ -22,11 +53,11 @@ function show_system(io::IO, ::MIME"text/plain", system::AbstractSystem{D}) wher
     pbc  = periodicity(system)
     print(io, typeof(system).name.name, "($(chemical_formula(system))")
     perstr = [p ? "T" : "F" for p in periodicity(system)]
-    print(io, ", pbc = ", join(perstr, ""))
+    print(io, ", periodicity = ", join(perstr, ""))
     println(io, "):")
 
     extra_line = false
-    if any(pbc) 
+    if any(pbc)
         extra_line = true
         box = cell_vectors(system)
         bunit = unit(eltype(first(cell_vectors(system))))
@@ -47,17 +78,15 @@ function show_system(io::IO, ::MIME"text/plain", system::AbstractSystem{D}) wher
         extra_line = true
         @printf io "    %-17s : %s\n" string(k) string(v)
     end
-    if length(system) < 10
+    if length(system) ≤ show_preferences().max_particles_list
         extra_line && println(io)
         for atom in system
             println(io, "    ", atom)
         end
         extra_line = true
     end
 
-    # TODO We will make this configurable in a follow-up PR
-    show_ascii = false
-    if show_ascii
+    if length(system) ≤ show_preferences().max_particles_visualize_ascii
         ascii = visualize_ascii(system)
         if !isempty(ascii)
             extra_line && println(io)

test/printing.jl

@@ -12,19 +12,23 @@ using Test
     box = tuple([[10, 0.0, 0.0], [0.0, 5, 0.0], [0.0, 0.0, 7]]u"bohr" ...)
 
     flexible_system = periodic_system(atoms, box; fractional=true, data=-12)
-    @test repr(flexible_system) == "FlexibleSystem(CSi, pbc = TTT)"
-    # TODO:  I'm not sure why the expended expression should be printed in 
-    #        this setting. Still needs to be looked at please; same below 
-    # FlexibleSystem(CSi, pbc = TTT, cell_vectors = [[10.0, 0.0, 0.0], [0.0, 5.0, 0.0], [0.0, 0.0, 7.0]]u"a₀")"""
+    @test repr(flexible_system) == """FlexibleSystem(CSi, periodicity = TTT, cell_vectors = [[10.0, 0.0, 0.0], [0.0, 5.0, 0.0], [0.0, 0.0, 7.0]]u"a₀")"""
     show(stdout, MIME("text/plain"), flexible_system)
 
     fast_system = FastSystem(flexible_system)
-    @test repr(fast_system) == "FastSystem(CSi, pbc = TTT)"
-    # FastSystem(CSi, periodic = TTT, cell_vectors = [[10.0, 0.0, 0.0], [0.0, 5.0, 0.0], [0.0, 0.0, 7.0]]u"a₀")
+    @test repr(fast_system) == """FastSystem(CSi, periodicity = TTT, cell_vectors = [[10.0, 0.0, 0.0], [0.0, 5.0, 0.0], [0.0, 0.0, 7.0]]u"a₀")"""
     show(stdout, MIME("text/plain"), fast_system)
     show(stdout, MIME("text/plain"), fast_system[1])
 end
 
+@testset "Printing atomic systems" begin
+    at = Atom(:Si, zeros(3) * u"m", ones(3)u"m/s"; extradata=42)
+    show(stdout, MIME("text/plain"), at)
+    box = tuple([[10, 0.0, 0.0], [0.0, 5, 0.0], [0.0, 0.0, 7]]u"bohr" ...)
+    flexible_system = periodic_system([at], box)
+    show(stdout, MIME("text/plain"), flexible_system)
+end
+
 @testset "Test ASCII representation of structures" begin
     @testset "3D standard system" begin
         atoms = [:Si => [0.0, -0.125, 0.0],
@@ -45,7 +49,7 @@ end
     @testset "3D with negative unit cell" begin
         atoms = [:Si => [0.75, 0.75, 0.75],
                  :Si => [0.0,  0.0,  0.0]]
-        box = tuple([[-2.73, -2.73, 0.0], [-2.73, 0.0, -2.73], [0.0, -2.73, -2.73]]u"Å" ...) 
+        box = tuple([[-2.73, -2.73, 0.0], [-2.73, 0.0, -2.73], [0.0, -2.73, -2.73]]u"Å" ...)
         system = periodic_system(atoms, box; fractional=true)
         println(visualize_ascii(system))
     end