Support for (A)XSF XCrySDen file format (#22)

* Shamelessly copy from extxyz interface for xsf interface

* Fix typo in filename

* Rename XSF to XCrySDenStructureFormat

Project.toml

@@ -12,6 +12,7 @@ PeriodicTable = "7b2266bf-644c-5ea3-82d8-af4bbd25a884"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"
+XCrySDenStructureFormat = "02310045-4665-40c9-a658-98c497d2eca9"
 
 [compat]
 AtomsBase = "0.3"
@@ -22,6 +23,7 @@ PeriodicTable = "1"
 Reexport = "1"
 Unitful = "1"
 UnitfulAtomic = "1"
+XCrySDenStructureFormat = "0.1"
 julia = "1.6"
 
 [extras]

src/xsf.jl

@@ -0,0 +1,43 @@
+import XCrySDenStructureFormat as XSF
+
+"""
+Parse or write file using [XSF](https://github.com/azadoks/XCrySDenStructureFormat.jl)
+
+Supported formats:
+  - [XSF](http://www.xcrysden.org/doc/XSF.html)
+"""
+struct XsfParser <: AbstractParser end
+
+function supports_parsing(::XsfParser, file; save, trajectory)
+    _, ext = splitext(file)
+    ext in (".xsf", ".axsf")
+end
+
+function load_system(::XsfParser, file::AbstractString, index=nothing)
+    if isnothing(index)
+        frames = XSF.load_xsf(file)
+        isempty(frames) && error(
+            "XSF returned no frames. Check the passed file is a valid (a)xsf file."
+        )
+        return last(frames)
+    else
+        return XSF.load_xsf(file)[index]
+    end
+end
+
+function save_system(::XsfParser, file::AbstractString, system::AbstractSystem)
+    XSF.save_xsf(file, system)
+end
+
+function load_trajectory(::XsfParser, file::AbstractString)
+    XSF.load_xsf(file)
+end
+
+function save_system(::XsfParser, file::AbstractString, system::AbstractSystem)
+    XSF.save_xsf(file, system)
+end
+
+function save_trajectory(::XsfParser, file::AbstractString,
+                         systems::AbstractVector{<:AbstractSystem})
+    XSF.save_xsf(file, systems)
+end

test/xsf.jl

@@ -0,0 +1,37 @@
+using AtomsIO
+using Test
+using AtomsBaseTesting
+
+@testset "XSF system write / read" begin
+    system = make_test_system().system
+    mktempdir() do d
+        outfile = joinpath(d, "output.xsf")
+        save_system(XsfParser(), outfile, system)
+        system2 = load_system(XsfParser(), outfile)
+        test_approx_eq(system, system2; rtol=1e-6)
+    end
+end
+
+@testset "XSF trajectory write/read" begin
+    systems = [make_test_system().system for _ in 1:3]
+    mktempdir() do d
+        outfile = joinpath(d, "output.axsf")
+        save_trajectory(XsfParser(), outfile, systems)
+        newsystems = load_trajectory(XsfParser(), outfile)
+        for (system, newsystem) in zip(systems, newsystems)
+            test_approx_eq(system, newsystem; rtol=1e-6)
+        end
+        test_approx_eq(systems[end], load_system(XsfParser(), outfile);    rtol=1e-6)
+        test_approx_eq(systems[2],   load_system(XsfParser(), outfile, 2); rtol=1e-6)
+    end
+end
+
+@testset "ExtXYZ supports_parsing" begin
+    import AtomsIO: supports_parsing
+    prefix = "test"
+    save = trajectory = true
+    @test  supports_parsing(XsfParser(), prefix * ".xsf";    save, trajectory)
+    @test  supports_parsing(XsfParser(), prefix * ".axsf";   save, trajectory)
+    @test !supports_parsing(XsfParser(), prefix * ".bxsf";   save, trajectory)
+    @test !supports_parsing(XsfParser(), prefix * ".cif";    save, trajectory)
+end