Update package to use package extensions

Project.toml

@@ -3,16 +3,23 @@ uuid = "1692102d-eeb4-4df9-807b-c9517f998d44"
 authors = ["Michael F. Herbst <[email protected]> and contributors"]
 version = "0.2.3"
 
-[deps]
-AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
+[weakdeps]
 Chemfiles = "46823bd8-5fb3-5f92-9aa0-96921f3dd015"
 ExtXYZ = "352459e4-ddd7-4360-8937-99dcb397b478"
+XCrySDenStructureFormat = "02310045-4665-40c9-a658-98c497d2eca9"
+
+[extensions]
+AtomsIOChemfilesExt = "Chemfiles"
+AtomsIOExtXYZExt = "ExtXYZ"
+AtomsIOXCrySDenStructureFormatExt = "XCrySDenStructureFormat"
+
+[deps]
+AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 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"
@@ -33,4 +40,4 @@ Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["AtomsBaseTesting", "LinearAlgebra", "Pkg", "Test"]
+test = ["AtomsBaseTesting", "LinearAlgebra", "Pkg", "Test", "Chemfiles", "ExtXYZ", "XCrySDenStructureFormat"]

src/chemfiles.jl → ext/AtomsIOChemfilesExt.jl

@@ -1,18 +1,10 @@
+module AtomsIOChemfilesExt
+
 import Chemfiles
 using Logging
-using Unitful
-using UnitfulAtomic
-
-"""
-Parse or write file using [Chemfiles](https://github.com/chemfiles/Chemfiles.jl).
-
-Supported formats:  
-  - [CIF](https://www.iucr.org/resources/cif) files
-  - [Gromacs](http://manual.gromacs.org/archive/5.0.7/online/trj.html) / [LAMMPS](https://lammps.sandia.gov/doc/dump.html) / [Amber](http://ambermd.org/netcdf/nctraj.xhtml) trajectory files
-"""
-struct ChemfilesParser <: AbstractParser end
+using AtomsIO, Unitful, UnitfulAtomic
 
-function supports_parsing(::ChemfilesParser, file; save, trajectory)
+function AtomsIO.supports_parsing(::ChemfilesParser, file; save, trajectory)
     format = Logging.with_logger(NullLogger()) do
         Chemfiles.guess_format(file)
     end
@@ -29,32 +21,34 @@ function supports_parsing(::ChemfilesParser, file; save, trajectory)
 end
 
 
-function load_system(::ChemfilesParser, file::AbstractString, index=nothing)
+function AtomsIO.load_system(::ChemfilesParser, file::AbstractString, index=nothing)
     Chemfiles.Trajectory(file, 'r') do trajectory
         cfindex = something(index, length(trajectory)) - 1  # chemfiles is 0-based
         convert(AbstractSystem, Chemfiles.read_step(trajectory, cfindex))
     end
 end
 
-function save_system(::ChemfilesParser, file::AbstractString, system::AbstractSystem)
+function AtomsIO.save_system(::ChemfilesParser, file::AbstractString, system::AbstractSystem)
     Chemfiles.Trajectory(file, 'w') do trajectory
         write(trajectory, convert(Chemfiles.Frame, system))
     end
 end
 
-function load_trajectory(::ChemfilesParser, file::AbstractString)
+function AtomsIO.load_trajectory(::ChemfilesParser, file::AbstractString)
     Chemfiles.Trajectory(file, 'r') do trajectory
         map(0:length(trajectory)-1) do ci  # Chemfiles is 0-based
             convert(AbstractSystem, Chemfiles.read_step(trajectory, ci))
         end
     end
 end
 
-function save_trajectory(::ChemfilesParser, file::AbstractString,
+function AtomsIO.save_trajectory(::ChemfilesParser, file::AbstractString,
                          systems::AbstractVector{<:AbstractSystem})
     Chemfiles.Trajectory(file, 'w') do trajectory
         for system in systems
             write(trajectory, convert(Chemfiles.Frame, system))
         end
     end
 end
+
+end

src/extxyz.jl → ext/AtomsIOExtXYZExt.jl

@@ -1,14 +1,9 @@
-import ExtXYZ
-
-"""
-Parse or write file using [ExtXYZ](https://github.com/libAtoms/ExtXYZ.jl)
+module AtomsIOExtXYZExt
 
-Supported formats:  
-  - [XYZ](https://openbabel.org/wiki/XYZ) and [extxyz](https://github.com/libAtoms/extxyz#extended-xyz-specification-and-parsing-tools) files
-"""
-struct ExtxyzParser <: AbstractParser end
+import ExtXYZ
+using AtomsIO
 
-function supports_parsing(::ExtxyzParser, file; save, trajectory)
+function AtomsIO.supports_parsing(::ExtxyzParser, file; save, trajectory)
     _, ext = splitext(file)
     ext in (".xyz", ".extxyz")
 end
@@ -34,7 +29,7 @@ function _extxyz_read_frames(args...; kwargs...)
     frames
 end
 
-function load_system(::ExtxyzParser, file::AbstractString, index=nothing)
+function AtomsIO.load_system(::ExtxyzParser, file::AbstractString, index=nothing)
     if isnothing(index)
         frames = _extxyz_read_frames(file)
         return ExtXYZ.Atoms(last(frames))
@@ -44,15 +39,17 @@ function load_system(::ExtxyzParser, file::AbstractString, index=nothing)
     end
 end
 
-function save_system(::ExtxyzParser, file::AbstractString, system::AbstractSystem)
+function AtomsIO.save_system(::ExtxyzParser, file::AbstractString, system::AbstractSystem)
     ExtXYZ.write_frame(file, ExtXYZ.write_dict(system))
 end
 
-function load_trajectory(::ExtxyzParser, file::AbstractString)
+function AtomsIO.load_trajectory(::ExtxyzParser, file::AbstractString)
     ExtXYZ.Atoms.(_extxyz_read_frames(file))
 end
 
-function save_trajectory(::ExtxyzParser, file::AbstractString,
+function AtomsIO.save_trajectory(::ExtxyzParser, file::AbstractString,
                          systems::AbstractVector{<:AbstractSystem})
     ExtXYZ.write_frames(file, ExtXYZ.write_dict.(systems))
 end
+
+end

ext/AtomsIOXCrySDenStructureFormatExt.jl

@@ -0,0 +1,37 @@
+module AtomsIOXCrySDenStructureFormatExt
+
+import XCrySDenStructureFormat as XSF
+using AtomsIO
+
+function AtomsIO.supports_parsing(::XcrysdenstructureformatParser, file; save, trajectory)
+    _, ext = splitext(file)
+    ext in (".xsf", ".axsf")
+end
+
+function AtomsIO.load_system(::XcrysdenstructureformatParser, file::AbstractString, index=nothing)
+    frames = XSF.load_xsf(file)
+    isempty(frames) && error(
+        "XSF returned no frames. Check the passed file is a valid (a)xsf file."
+    )
+    if isnothing(index)
+        return last(frames)
+    else
+        return frames[index]
+    end
+end
+
+function AtomsIO.save_system(::XcrysdenstructureformatParser,
+                     file::AbstractString, system::AbstractSystem)
+    XSF.save_xsf(file, system)
+end
+
+function AtomsIO.load_trajectory(::XcrysdenstructureformatParser, file::AbstractString)
+    XSF.load_xsf(file)
+end
+
+function AtomsIO.save_trajectory(::XcrysdenstructureformatParser, file::AbstractString,
+                         systems::AbstractVector{<:AbstractSystem})
+    XSF.save_xsf(file, systems)
+end
+
+end

src/AtomsIO.jl

@@ -4,12 +4,9 @@ using Reexport
 import PeriodicTable
 
 include("parser.jl")
-include("chemfiles.jl")
-include("extxyz.jl")
-include("xsf.jl")
-include("saveload.jl")
+export AbstractParser, ChemfilesParser, ExtxyzParser, XcrysdenstructureformatParser
 
+include("saveload.jl")
 export load_system, save_system, load_trajectory, save_trajectory
-export AbstractParser
-export ChemfilesParser, ExtxyzParser, XcrysdenstructureformatParser
+
 end

src/parser.jl

@@ -1,2 +1,32 @@
 abstract type AbstractParser end
+
+
+"""
+Parse or write file using [Chemfiles](https://github.com/chemfiles/Chemfiles.jl).
+
+Supported formats:
+  - [CIF](https://www.iucr.org/resources/cif) files
+  - [Gromacs](http://manual.gromacs.org/archive/5.0.7/online/trj.html) / [LAMMPS](https://lammps.sandia.gov/doc/dump.html) / [Amber](http://ambermd.org/netcdf/nctraj.xhtml) trajectory files
+"""
+struct ChemfilesParser <: AbstractParser end
+
+"""
+Parse or write file using [ExtXYZ](https://github.com/libAtoms/ExtXYZ.jl)
+
+Supported formats:
+  - [XYZ](https://openbabel.org/wiki/XYZ) and [extxyz](https://github.com/libAtoms/extxyz#extended-xyz-specification-and-parsing-tools) files
+"""
+struct ExtxyzParser <: AbstractParser end
+
+
+"""
+Parse or write file using [XCrySDenStructureFormat](https://github.com/azadoks/XCrySDenStructureFormat.jl).
+
+Supported formats:
+  - [XSF](http://www.xcrysden.org/doc/XSF.html) and [AXSF](http://www.xcrysden.org/doc/XSF.html)
+    atomic structure files. These are the files typically used by the
+    [XCrySDen](http://www.xcrysden.org/) visualisation program.
+"""
+struct XcrysdenstructureformatParser <: AbstractParser end
+
 supports_parsing(::AbstractParser, file; save, trajectory) = false

test/chemfiles.jl

@@ -1,5 +1,5 @@
-using AtomsIO
 using Test
+using AtomsIO
 using AtomsBaseTesting
 using Unitful
 using UnitfulAtomic

test/extxyz.jl

@@ -1,7 +1,3 @@
-using AtomsIO
-using Test
-using AtomsBaseTesting
-
 @testset "ExtXYZ system write / read" begin
     system = make_test_system().system
     mktempdir() do d

test/failed_files.jl

@@ -1,6 +1,3 @@
-using Test
-using AtomsIO
-using Unitful
 using LinearAlgebra
 
 # Tests parsing files, where previously users reported problems
@@ -19,7 +16,7 @@ end
     elseif VERSION < v"1.8"
         @test_throws ErrorException load_system("files/zero_atoms.xyz")
     else
-        @test_throws "ExtXYZ frame contains zero atoms." load_system("files/zero_atoms.xyz")
+        @test_throws "ExtXYZ returned no frames. Check the passed file is a valid (ext)xyz file." load_system("files/zero_atoms.xyz")
     end
 end
 

test/runtests.jl

@@ -1,5 +1,9 @@
 using Test
 using Pkg
+using AtomsIO, AtomsBaseTesting
+using Unitful, UnitfulAtomic
+
+using Chemfiles, ExtXYZ, XCrySDenStructureFormat
 
 const GROUP = get(ENV, "GROUP", "Core")
 const GROUP_COVERAGE = !isempty(get(ENV, "GROUP_COVERAGE", ""))

test/safe_load.jl

@@ -1,7 +1,3 @@
-using Test
-using AtomsIO
-using AtomsBaseTesting
-
 @testset "save / load / determine_parser" begin
     system = make_test_system().system
 

test/xsf.jl

@@ -1,10 +1,3 @@
-using AtomsIO
-using Test
-using AtomsBaseTesting
-using Unitful
-using UnitfulAtomic
-
-
 function make_xsf_system(D=3; drop_atprop=Symbol[], drop_sysprop=Symbol[], kwargs...)
     @assert D == 3  # Only 3D systems are supported
     n_atoms = 5     # Copied from AtomsBaseTesting.make_test_system, used for making forces