Issues with ExtXYZ fixed (#30)

Project.toml

@@ -1,7 +1,7 @@
 name = "AtomsIO"
 uuid = "1692102d-eeb4-4df9-807b-c9517f998d44"
 authors = ["Michael F. Herbst <info@michael-herbst.com> and contributors"]
-version = "0.2.2"
+version = "0.2.3"
 
 [deps]
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
@@ -18,7 +18,7 @@ XCrySDenStructureFormat = "02310045-4665-40c9-a658-98c497d2eca9"
 AtomsBase = "0.3"
 AtomsBaseTesting = "0.1"
 Chemfiles = "0.10.41"
-ExtXYZ = "0.1.11"
+ExtXYZ = "0.1.14"
 PeriodicTable = "1"
 Reexport = "1"
 Unitful = "1"

docs/make.jl

@@ -16,7 +16,6 @@ DocMeta.setdocmeta!(AtomsIO, :DocTestSetup, :(using AtomsIO, AtomsIOPython); rec
 makedocs(;
     modules=[AtomsIO, AtomsIOPython],
     authors="Michael F. Herbst <info@michael-herbst.com> and contributors",
-    repo="https://github.com/mfherbst/AtomsIO.jl/blob/{commit}{path}#{line}",
     sitename="AtomsIO",
     format=Documenter.HTML(;
         prettyurls=get(ENV, "CI", "false") == "true",
@@ -30,7 +29,6 @@ makedocs(;
         "file_formats.md",
     ],
     checkdocs=:exports,
-    strict=true
 )
 
 deploydocs(;

src/extxyz.jl

@@ -13,15 +13,33 @@ function supports_parsing(::ExtxyzParser, file; save, trajectory)
     ext in (".xyz", ".extxyz")
 end
 
+
+function _extxyz_read_frames(args...; kwargs...)
+    frames = nothing
+    try
+        frames = ExtXYZ.read_frames(args...; kwargs...)
+    catch e
+        # Version branch is needed because current_exceptions only
+        # appeared in 1.7
+        if VERSION ≥ v"1.7" && e isa TaskFailedException
+            cur_e = last(current_exceptions(e.task))
+            rethrow(cur_e.exception)
+        else
+            rethrow()
+        end
+    end
+    if isnothing(frames) || isempty(frames)
+        error("ExtXYZ returned no frames. Check the passed file is a valid (ext)xyz file.")
+    end
+    frames
+end
+
 function load_system(::ExtxyzParser, file::AbstractString, index=nothing)
     if isnothing(index)
-        frames = ExtXYZ.read_frames(file)
-        isempty(frames) && error(
-            "ExtXYZ returned no frames. Check the passed file is a valid (ext)xyz file."
-        )
+        frames = _extxyz_read_frames(file)
         return ExtXYZ.Atoms(last(frames))
     else
-        frame = only(ExtXYZ.read_frames(file, index))
+        frame = only(_extxyz_read_frames(file, index))
         return ExtXYZ.Atoms(frame)
     end
 end
@@ -31,7 +49,7 @@ function save_system(::ExtxyzParser, file::AbstractString, system::AbstractSyste
 end
 
 function load_trajectory(::ExtxyzParser, file::AbstractString)
-    ExtXYZ.Atoms.(ExtXYZ.read_frames(file))
+    ExtXYZ.Atoms.(_extxyz_read_frames(file))
 end
 
 function save_trajectory(::ExtxyzParser, file::AbstractString,

src/xsf.jl

@@ -4,7 +4,7 @@ import XCrySDenStructureFormat as XSF
 Parse or write file using [XCrySDenStructureFormat](https://github.com/azadoks/XCrySDenStructureFormat.jl).
 
 Supported formats:
-  - [XSF](http://www.xcrysden.org/doc/XSF.html) and [AXSF](XCrySDenStructureFormat)
+  - [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.
 """

test/failed_files.jl

@@ -13,6 +13,16 @@ using LinearAlgebra
     end
 end
 
+@testset "Zero atoms in XYZ" begin
+    @static if VERSION < v"1.7"
+        @test_throws TaskFailedException load_system("files/zero_atoms.xyz")
+    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")
+    end
+end
+
 @testset "XYZ from Lammps" begin
     @static if VERSION < v"1.8"
         @test_throws ErrorException load_system("files/lammps.xyz")

test/files/zero_atoms.xyz

@@ -0,0 +1,3 @@
+0
+
+