Update python part to AtomsBase 0.4

.github/workflows/TagBot.yml

@@ -4,6 +4,22 @@ on:
     types:
       - created
   workflow_dispatch:
+    inputs:
+      lookback:
+        default: 3
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
 jobs:
   TagBot:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'

Project.toml

@@ -1,7 +1,7 @@
 name = "AtomsIO"
 uuid = "1692102d-eeb4-4df9-807b-c9517f998d44"
 authors = ["Michael F. Herbst <[email protected]> and contributors"]
-version = "0.2.3"
+version = "0.2.5"
 
 [deps]
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
@@ -15,10 +15,10 @@ UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"
 XCrySDenStructureFormat = "02310045-4665-40c9-a658-98c497d2eca9"
 
 [compat]
-AtomsBase = "0.3"
-AtomsBaseTesting = "0.1"
+AtomsBase = "0.4"
+AtomsBaseTesting = "0.2"
 Chemfiles = "0.10.41"
-ExtXYZ = "0.1.14"
+ExtXYZ = "0.2"
 PeriodicTable = "1"
 Reexport = "1"
 Unitful = "1"

lib/AtomsIOPython/Project.toml

@@ -1,16 +1,16 @@
 name = "AtomsIOPython"
 uuid = "9e4c859b-2281-48ef-8059-f50fe53c37b0"
 authors = ["Michael F. Herbst <[email protected]> and contributors"]
-version = "0.1.2"
+version = "0.1.3"
 
 [deps]
 ASEconvert = "3da9722f-58c2-4165-81be-b4d7253e8fd2"
 AtomsIO = "1692102d-eeb4-4df9-807b-c9517f998d44"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 
 [compat]
-ASEconvert = "0.1.4"
-AtomsBaseTesting = "0.1"
+ASEconvert = "0.1.8"
+AtomsBaseTesting = "0.2"
 AtomsIO = "0.2"
 Reexport = "1"
 julia = "1.6"

lib/AtomsIOPython/src/AtomsIOPython.jl

@@ -2,17 +2,15 @@ module AtomsIOPython
 using Reexport
 @reexport using AtomsIO
 
-include("ase.jl")
-
 export AseParser
+include("ase.jl")
 
-function __init__()
-    # Append python-based parsers to the parser list in AtomsIO.
+function AtomsIO.atomsio_extra_parsers(::AtomsIO.PythonParsers)
+    # Register the python-based parsers with AtomsIO
+    #
     # Note: For reproducibility reasons changing the order of these parsers is a
     # *breaking change* (as it alters the behaviour of AtomsIO.load_system).
-    # Moreover since not all users will want to rely on Python dependencies, it is
-    # crucial that the python-based parsers are *appended* to this list.
-    parsers = AbstractParser[AseParser(), ]
-    append!(AtomsIO.DEFAULT_PARSER_ORDER, parsers)
+    AbstractParser[AseParser(), ]
 end
+
 end

lib/AtomsIOPython/test/ase.jl

@@ -9,7 +9,7 @@ function make_ase_system(args...; drop_atprop=Symbol[], kwargs...)
 end
 
 @testset "ASE parser has been added" begin
-    @test AseParser() in AtomsIO.DEFAULT_PARSER_ORDER
+    @test AseParser() in AtomsIO.default_parsers()
 end
 
 @testset "ASE system write/read" begin

lib/AtomsIOPython/test/comparison.jl

@@ -20,7 +20,7 @@ using AtomsBaseTesting
 end
 
 @testset "Test structures from simple XYZ files parse the same" begin
-    drop_atprop  = [:covalent_radius, :vdw_radius, :velocity, :charge, :atomic_mass]
+    drop_atprop  = [:covalent_radius, :vdw_radius, :velocity, :charge, :mass]
     drop_sysprop = [:extra_data]
     data = make_test_system(; drop_atprop, drop_sysprop, cellmatrix=:lower_triangular)
     system = periodic_system(data.atoms, data.box; data.sysprop...)

src/extxyz.jl

@@ -3,7 +3,7 @@ import ExtXYZ
 """
 Parse or write file using [ExtXYZ](https://github.com/libAtoms/ExtXYZ.jl)
 
-Supported formats:  
+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

src/saveload.jl

@@ -1,15 +1,29 @@
-# The list of parsers in the order to try them.
-# Python-based parsers are appended once AtomsIOPython is loaded.
-# Note: For reproducibility reasons changing the order of these parsers is a
-# *breaking change* (as it alters the behaviour of AtomsIO.load_system).
-# Moreover since not all users will want to rely on Python dependencies, it is
-# crucial that the python packages are only *appended* to this list.
-const DEFAULT_PARSER_ORDER = AbstractParser[
-    ExtxyzParser(), XcrysdenstructureformatParser(), ChemfilesParser(),
-]
+
+# Mechanics to add additional parsers automatically in a well-defined order
+# Add marker structs here for every new "category" of parsers that become
+# dynamically available (e.g. the PythonParsers() defined in AtomsIOPython)
+struct PythonParsers end
+atomsio_extra_parsers(marker) = AbstractParser[]
+
+function default_parsers()
+    # The list of parsers in the order to try them.
+    # Python-based parsers are appended once AtomsIOPython is loaded,
+    # since this defines an appropriate method for the PythonParsers() marker struct.
+    #
+    # Note: For reproducibility reasons changing the order of these parsers is a
+    # *breaking change* (as it alters the behaviour of AtomsIO.load_system).
+    # Moreover since not all users will want to rely on Python dependencies, it is
+    # crucial that the python packages are only *appended* to this list.
+
+    AbstractParser[
+        ExtxyzParser(), XcrysdenstructureformatParser(), ChemfilesParser(),
+        atomsio_extra_parsers(PythonParsers())... # Add python parsers if they are available
+    ]
+end
 
 function determine_parser(file; save=false, trajectory=false)
-    idx_parser = findfirst(DEFAULT_PARSER_ORDER) do parser
+    parsers = default_parsers()
+    idx_parser = findfirst(parsers) do parser
         supports_parsing(parser, file; save, trajectory)
     end
     if isnothing(idx_parser)
@@ -22,7 +36,7 @@ function determine_parser(file; save=false, trajectory=false)
         end
         error(errormsg)
     end
-    DEFAULT_PARSER_ORDER[idx_parser]
+    parsers[idx_parser]
 end
 
 

test/chemfiles.jl

@@ -10,15 +10,16 @@ function make_chemfiles_system(D=3; drop_atprop=Symbol[], infinite=false, kwargs
                             extra_sysprop=(; extra_data=42.0), cellmatrix=:upper_triangular,
                             kwargs...)
     if infinite
-        system = isolated_system(data.atoms; data.sysprop...)
+        cell = IsolatedCell(3)
     else
-        system = periodic_system(data.atoms, data.box; data.sysprop...)
+        cell = PeriodicCell(; cell_vectors=data.box, periodicity=(true, true, true))
     end
+    system = AtomsBase.FlexibleSystem(data.atoms, cell; data.sysprop...)
     merge(data, (; system))
 end
 
 @testset "Chemfiles system write / read" begin
-    system = make_chemfiles_system(; drop_atprop=[:atomic_mass]).system
+    system = make_chemfiles_system(; drop_atprop=[:mass]).system
     mktempdir() do d
         outfile = joinpath(d, "output.cml")
         save_system(ChemfilesParser(), outfile, system)
@@ -30,7 +31,7 @@ end
 
 @testset "Chemfiles trajectory write/read" begin
     ignore_atprop = [:covalent_radius, :vdw_radius]
-    systems = [make_chemfiles_system(; drop_atprop=[:atomic_mass]).system for _ in 1:3]
+    systems = [make_chemfiles_system(; drop_atprop=[:mass]).system for _ in 1:3]
     mktempdir() do d
         outfile = joinpath(d, "output.cml")
         save_trajectory(ChemfilesParser(), outfile, systems)
@@ -41,7 +42,7 @@ end
 
         test_approx_eq(systems[end], load_system(ChemfilesParser(), outfile);
                        rtol=1e-6, ignore_atprop)
-        test_approx_eq(systems[2],   load_system(ChemfilesParser(), outfile, 2);
+        test_approx_eq(systems[2], load_system(ChemfilesParser(), outfile, 2);
                        rtol=1e-6, ignore_atprop)
     end
 end

test/xsf.jl

@@ -8,8 +8,7 @@ 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
-    xsf_drop_atprop = [:velocity, :charge, :atomic_mass, :vdw_radius, :covalent_radius,
-                       :magnetic_moment]
+    xsf_drop_atprop = [:velocity, :charge, :mass, :vdw_radius, :covalent_radius, :magnetic_moment]
     xsf_drop_sysprop = [:extra_data, :charge, :multiplicity]
     force = [randn(3)u"Eh_au/Å" for _ in 1:n_atoms]
     make_test_system(D; drop_atprop=append!(drop_atprop, xsf_drop_atprop),