Version 0.1.18: fixes to writeXYZ()

.github/workflows/CI.yml

@@ -24,6 +24,7 @@ jobs:
           - '1.6'
           - '1.7'
           - '1.8'
+          - '1.9'
           - '1'
         os:
           - ubuntu-latest

CHANGELOG.md

@@ -7,6 +7,15 @@ adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
 
+## [0.1.18]: 2024-02-06
+
+### Changed
+  - Ambiguity tests exclude `Base.Sort.defalg` on all versions due to a potential false positive.
+  - `writeXYZ()` methods are simplified and better documented.
+
+### Fixed
+  - `writeXYZ()` no longer references removed functions from prerelease versions.
+
 ## [0.1.17]: 2023-11-29
 
 This is the final feature release in the 0.1 series. All future 0.1 series releases will only

Project.toml

@@ -5,7 +5,7 @@ authors = [
     "Amber Lim <[email protected]>",
     "Patrick Cross <[email protected]>"
 ]
-version = "0.1.17"
+version = "0.1.18"
 
 [deps]
 ComputedFieldTypes = "459fdd68-db75-56b8-8c15-d717a790f88e"

src/filetypes.jl

@@ -30,11 +30,11 @@ end
 readXYZ(filename) = open(readXYZ, filename)
 
 """
-    writeXYZ(io::IO, data::AbstractVector{<:AbstractAtomPosition})
-    writeXYZ(io::IO, data::AbstractAtomList)
-    writeXYZ(io::IO, data::AbstractCrystal)
+    writeXYZ(io::IO, data)
+    writeXYZ(filename, data)
 
-Write an XYZ file based on a set of atomic coordinates.
+Write an XYZ file based on a set of atomic coordinate data. This data may be provided in any type
+that subtypes `AbstractVector{<:AbstractAtomPosition}`, or types convertible to `AtomList`.
 """
 function writeXYZ(io::IO, data::AbstractVector{<:AbstractAtomPosition})
     # Write the number of atoms
@@ -43,13 +43,13 @@ function writeXYZ(io::IO, data::AbstractVector{<:AbstractAtomPosition})
     println(io, "File written by Electrum.jl")
     # Write lines for all atoms
     for atom in data
-        println(io, atomname(atom), join([lpad(@sprintf("%f", n), 11) for n in coord(atom)]))
+        println(io, name(atom), join([lpad(@sprintf("%f", n), 11) for n in displacement(atom)]))
     end
     return nothing
 end
 
-writeXYZ(io::IO, data::AbstractAtomList) = writeXYZ(io, coord(cartesian(data)))
-writeXYZ(io::IO, data::AbstractCrystal) = writeXYZ(io, atoms(data))
+writeXYZ(io::IO, data::AtomList) = writeXYZ(io, data.atoms)
+writeXYZ(io::IO, data) = writeXYZ(io, AtomList(data))
 
 function writeXYZ(filename, data) 
     open(filename; write=true) do io

test/filetypes.jl

@@ -19,6 +19,16 @@
     @test iszero(h - g)
 end
 
+@testset "XYZ" begin
+    xyz_path = joinpath(tmpdir, "test.xyz")
+    writeXYZ(xyz_path, poscar)
+    xyz = readXYZ(xyz_path)
+    list = AtomList(poscar)
+    @test all(NamedAtom(xyz[n]) == NamedAtom(list[n]) for n in 1:4)
+    # atol is set to match number of printed digits
+    @test all(isapprox(displacement(xyz[n]), displacement(list[n]), atol=0.000001) for n in 1:4)
+end
+
 @testset "abinit outputs" begin
     den = v80_den["density_total"]
     wfk = v80_wfk["wavefunction"]

test/runtests.jl

@@ -3,7 +3,7 @@ using Test, Aqua, Electrum
 
 tmpdir = mktempdir()
 
-excluded_methods = Function[Base.unsafe_convert, Base.lstrip, Base.rstrip]
+excluded_methods = Function[Base.unsafe_convert, Base.lstrip, Base.rstrip, Base.Sort.defalg]
 # Base.getindex ambiguity was resolved in 1.9:
 # https://github.com/JuliaLang/julia/pull/41807
 # TODO: can we still try to test other methods for Base.getindex? It's pretty important...
@@ -12,9 +12,11 @@ if VERSION < v"1.9"
 end
 # Base.Sort.defalg ambiguity should be removed in 1.10:
 # https://github.com/JuliaLang/julia/pull/47383
+#= Aqua.jl seems to think there still is an ambiguity, however:
 if VERSION < v"1.10"
     push!(excluded_methods, Base.Sort.defalg)
 end
+=#
 
 Aqua.test_all(Electrum;
     ambiguities = (exclude = excluded_methods,)