Separate @iferror from @ifwarn

docs/src/faq.md

@@ -14,8 +14,8 @@ This is the focus of the [Visualization](@ref) tutorial.
 
 ## How can I silence warnings or remove exports?
 
-- From the module: see [`CrystalNets.toggle_warning`](@ref) and [`CrystalNets.toggle_export`](@ref)
-- From the executable: use the `--no-warn` and `--no-export` flags.
+- From the module: see [`CrystalNets.toggle_warning`](@ref), [`CrystalNets.toggle_error`](@ref) and [`CrystalNets.toggle_export`](@ref)
+- From the executable: use the `--no-warn`, `--no-error` and `--no-export` flags.
 
 For exports, each `export_...` keyword argument to [`Options`](@ref CrystalNets.Options) can be individually set to `false` or `""` to silence this particular export. See also the paragraph on [export options](@ref exports).
 

src/CrystalNets.jl

@@ -49,6 +49,7 @@ import Logging
 using ProgressMeter
 
 const DOWARN = Base.RefValue{Bool}(false)
+const DOERROR = Base.RefValue{Bool}(true)
 const DOEXPORT = Base.RefValue{Bool}(false)
 
 """
@@ -62,6 +63,17 @@ function toggle_warning(to=nothing)
     DOWARN[] = to isa Nothing ? !DOWARN[] : to
 end
 
+"""
+    toggle_error(to=nothing)
+
+Toggle @error visibility on (if `to == true`) or off (if `to == false`).
+Without an argument, toggle on and off repeatedly at each call.
+"""
+function toggle_error(to=nothing)
+    global DOERROR
+    DOERROR[] = to isa Nothing ? !DOERROR[] : to
+end
+
 """
     toggle_export(to=nothing)
 
@@ -75,6 +87,7 @@ end
 
 function __init__()
     toggle_warning("--no-warn" ∉ ARGS)
+    toggle_error("--no-error" ∉ ARGS)
     toggle_export("--no-export" ∉ ARGS)
     nothing
 end

src/executable.jl

@@ -85,6 +85,10 @@ function parse_commandline(args)
             help = "Discard all warnings and information messages."
             action = :store_true
 
+        "--no-error"
+            help = "Discard all @error messages."
+            action = :store_true
+
         "--no-export"
             help = "Do not automatically export the parsed input."
             action = :store_true
@@ -264,6 +268,9 @@ function main(args)
         if parsed_args[:no_warn]::Bool
             toggle_warning(false)
         end
+        if parsed_args[:no_error]::Bool
+            toggle_error(false)
+        end
         if parsed_args[:no_export]::Bool
             if !isnothing(parsed_args[:export_to])
                 return parse_error("""Cannot use both arguments "--export-to" and "--no-export".""")

src/input.jl

@@ -44,7 +44,7 @@ function parse_cif(file)
             @toggleassert loopisspecified
             if startswith(l[i:j], "data")
                 inloop = false
-                @ifwarn if haskey(all_data, "atom_site_fract_x")
+                @iferror if haskey(all_data, "atom_site_fract_x")
                     @error lazy"The CIF file $name may contain multiple inputs: only keeping the last one."
                 end
                 i, j, x = nextword(l, x)
@@ -82,7 +82,7 @@ function parse_cif(file)
                 loopspec = String[]
                 lastword = ""
             elseif j-i ≥ 4 && l[i:i+4] == "data_"
-                @ifwarn if haskey(all_data, "data") && haskey(all_data, "atom_site_fract_x")
+                @iferror if haskey(all_data, "data") && haskey(all_data, "atom_site_fract_x")
                     @error lazy"The CIF file $name may contain multiple inputs: only keeping the last one."
                 end
                 all_data["data"] = l[i+5:j]
@@ -259,12 +259,12 @@ function CIF(parsed::Dict{String, Union{Vector{String},String}})
             if x == 0 || y == 0
                 empty!(bonds)
                 missingatom = x == 0 ? bond_a[i] : bond_b[i]
-                @ifwarn @error lazy"""Atom $missingatom, used in a bond, has either zero or multiple placements in CIF file $(parsed["__name"]). This invalidates all bonds from the file, which will thus be discarded."""
+                @iferror @error lazy"""Atom $missingatom, used in a bond, has either zero or multiple placements in CIF file $(parsed["__name"]). This invalidates all bonds from the file, which will thus be discarded."""
                 break
             end
             d = 1.004f0*dists[i] # to avoid rounding errors
             if isnan(d) || (d != -Inf32 && (d ≤ 0f0 || isinf(d)))
-                @ifwarn @error lazy"""Invalid bond distance of $d between atoms $(bond_a[i]) and $(bond_b[i]) in CIF file $(parsed["__name"])."""
+                @iferror @error lazy"""Invalid bond distance of $d between atoms $(bond_a[i]) and $(bond_b[i]) in CIF file $(parsed["__name"])."""
                 continue
             end
             push!(bonds[x], (y, d))
@@ -680,7 +680,7 @@ function fix_valence!(graph::PeriodicGraph3D, pos, types, passH, passO, passCN,
         checked || @reduce_valence dofix 2 4 1
         anychecked |= checked
     end
-    @ifwarn anychecked && @error lazy"Found what looks like a disordered carbon ring for $(options.name): use of disordered input is not advised, please double-check the detected topology or provide a clean input."
+    @iferror anychecked && @error lazy"Found what looks like a disordered carbon ring for $(options.name): use of disordered input is not advised, please double-check the detected topology or provide a clean input."
     if !isempty(invalidatoms)
         s = String.(collect(invalidatoms))
         @ifwarn begin
@@ -718,13 +718,13 @@ function sanitize_removeatoms!(graph::PeriodicGraph3D, pos, types, mat, options)
             if flag && any(>(2.6), lengths)
                 # This warning could be out of a  @ifwarn because it reliably indicates
                 # cases where the input was not properly cleaned
-                @ifwarn @error lazy"Very suspicious connectivity found for $(options.name)."
+                @iferror @error lazy"Very suspicious connectivity found for $(options.name)."
                 flag = false
             end
         else
             at = get(atomic_numbers, t, nothing)
             if at === nothing
-                @ifwarn @error lazy"Unrecognized atom type \"$t\" in $(options.name) will be considered a dummy atom."
+                @iferror @error lazy"Unrecognized atom type \"$t\" in $(options.name) will be considered a dummy atom."
                 push!(toremove, i)
             elseif ismetal[at::Int]
                 for u in neighbors(graph, i)

src/types.jl

@@ -940,7 +940,7 @@ function UnderlyingNets(g::SmallPseudoGraph, options::Options)
     groups = UnderlyingNets()
     graph = g isa PeriodicGraph ? g : PeriodicGraph(g)
     dimensions = PeriodicGraphs.dimensionality(graph)
-    @ifwarn if haskey(dimensions, 0)
+    @iferror if haskey(dimensions, 0)
         @error "Detected substructure of dimension 0 in the input graph. It will be ignored for topology computation."
     end
     cell = Cell()

src/utils.jl

@@ -58,6 +58,20 @@ macro ifwarn(ex)
     end
 end
 
+macro iferror(ex)
+    return quote
+        if (DOERROR[]::Bool)
+            @static if VERSION < v"1.7-"
+                $(esc(ex))
+            else
+                Base.with_logger(minimal_logger) do
+                    $(esc(ex))
+                end
+            end
+        end
+    end
+end
+
 
 function recursive_readdir!(stored, prefix, path)
     for f in readdir(path; sort=false, join=false)