Rename non-periodic into 0-dimensional

docs/src/faq.md

@@ -56,7 +56,7 @@ Note that `Auto` is equivalent to both `AllNodes` and `SingleNodes` when the [`S
 
 See [below](@ref ToposProStandard) for the reason why the `Standard` topology is **xbi** and not ToposPro's "3,4,8T15".
 
-## CrystalNets.jl incorrectly detects bonds or reports a periodic structure as "non-periodic"
+## CrystalNets.jl incorrectly detects bonds or reports a periodic structure as "0-dimensional"
 
 You can use the [Visualization](@ref) tutorial to identify which bonds are incorrectly
 detected or missing.

src/archive.jl

@@ -348,7 +348,7 @@ function make_archive(path, destination, verbose=false)
         for (i, (topology, nfold)) in enumerate(results)
             nfold == 0 && continue
             genome = string(topology)
-            if startswith(genome, "unstable") || genome == "non-periodic"
+            if startswith(genome, "unstable") || genome == "0-dimensional"
                 flag = true
                 push!(flagerror[]::Vector{Tuple{Vector{Int},String}}, (vmap, genome))
                 continue

src/precompile.jl

@@ -46,7 +46,7 @@ using PrecompileTools
         # sfv = topological_genome(CrystalNet(PeriodicGraph(REVERSE_CRYSTALNETS_ARCHIVE["*SFV"])))
         # 2D
         hcb = topological_genome(CrystalNet(PeriodicGraph(REVERSE_CRYSTALNETS_ARCHIVE["hcb"])))
-        # non-periodic
+        # 0-dimensional
         calfig = determine_topology(path_to_calfig; structure=StructureType.MOF, clusterings=[Clustering.Auto])
         # other calls to determine_topology
         determine_topology(path_to_abw; structure=StructureType.Zeolite)

src/query.jl

@@ -465,7 +465,7 @@ Return a dictionary linking each file name to the result.
 The result is the corresponding topology name, if known, or the topological
 genome preceded by an "UNKNOWN" mention otherwise. In case of error, the result
 is the exception preceded by a "FAILED with" mention. Finally, if the input does
-not represent a periodic structure, the result is "non-periodic".
+not represent a periodic structure, the result is "0-dimensional".
 
 It is strongly recommended to toggle warnings off (through [`toggle_warning`](@ref)) and
 not to export any file since those actions may critically reduce performance,
@@ -654,7 +654,7 @@ function export_report(path, results::Dict; keepext=true, fullunknown=false, clu
                     elseif !isempty(topo.error)
                         print(io, "ERROR")
                     elseif ndims(topo.genome) == 0
-                        print(io, "non-periodic")
+                        print(io, "0-dimensional")
                     elseif topo.unstable
                         print(io, "UNSTABLE")
                     elseif topo.name isa Nothing

src/types.jl

@@ -1013,7 +1013,7 @@ function Base.show(io::IO, x::TopologicalGenome)
     if !isempty(x.error)
         print(io, "FAILED with: ", x.error)
     elseif ndims(x.genome) == 0
-        print(io, "non-periodic")
+        print(io, "0-dimensional")
     elseif x.unstable
         print(io, "unstable ", x.genome)
     elseif x.name isa String
@@ -1034,7 +1034,7 @@ function Base.parse(::Type{TopologicalGenome}, s::AbstractString)
     if startswith(s, "UNKNOWN")
         return TopologicalGenome(PeriodicGraph(s[9:end]), nothing, false)
     end
-    s == "non-periodic" && return TopologicalGenome()
+    s == "0-dimensional" && return TopologicalGenome()
     if startswith(s, "unstable")
         return TopologicalGenome(PeriodicGraph(s[10:end]), nothing, true)
     end
@@ -1371,7 +1371,7 @@ struct InterpenetratedTopologyResult <: AbstractVector{Tuple{TopologyResult,Int}
     data::Vector{Tuple{TopologyResult,Int,Vector{Int}}}
 end
 function InterpenetratedTopologyResult(b::Bool)
-    if b # non-periodic
+    if b # 0-dimensional
         InterpenetratedTopologyResult([(TopologyResult(),0,Int[])])
     else # no topology computation
         InterpenetratedTopologyResult(Tuple{TopologyResult,Int,Vector{Int}}[])
@@ -1390,7 +1390,7 @@ function Base.show(io::IO, ::MIME"text/plain", x::InterpenetratedTopologyResult)
     end
     for (i, (topology, nfold)) in enumerate(x)
         if nfold == 0
-            print(io, "non-periodic")
+            print(io, "0-dimensional")
             continue
         end
         if compact
@@ -1422,7 +1422,7 @@ end
 
 function Base.parse(::Type{InterpenetratedTopologyResult}, x::AbstractString)
     s = split(x; limit=4)
-    length(s) == 1 && x == "non-periodic" && return InterpenetratedTopologyResult(true)
+    length(s) == 1 && x == "0-dimensional" && return InterpenetratedTopologyResult(true)
     isempty(s) && return InterpenetratedTopologyResult(false)
     if length(s) > 3 && s[2] == "interpenetrated" && s[3] == "substructures:"
         lines = split(s[4], '\n')

test/runtests.jl

@@ -145,9 +145,9 @@ import CrystalNets.Clustering: SingleNodes, AllNodes, Standard, PE, PEM
     fowwar = extract1(determine_topology(joinpath(cifs, "FOWWAR.cif"); kwargs..., bonding=Bonding.Input, clusterings=[Clustering.Standard]))
     @test string(fowwar) == "Standard: UNKNOWN 3 1 1 0 0 1 1 2 0 0 0 1 3 0 0 0 1 4 0 0 0 2 5 0 0 0 2 6 0 0 0 3 6 0 0 0 3 7 0 0 0 4 5 1 0 0 4 7 0 -1 0 5 5 0 1 1 5 8 0 0 0 6 6 0 0 1 6 8 0 1 0 7 7 0 1 1 7 8 1 1 0"
 
-    # Test non-periodic input
+    # Test 0-dimensional input
     calfig = extract1(determine_topology(joinpath(cifs, "CALFIG.cif"); kwargs..., clusterings=[Clustering.Auto]))
-    @test string(calfig) == "non-periodic"
+    @test string(calfig) == "0-dimensional"
 
     println(stderr, "The following @error about carbon cycle disorder is expected.")
     # Test carbon cycle disorder detection