asciichem 0.30.0 → 0.31.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -3,6 +3,50 @@
 All notable changes to AsciiChem are documented here.
 This project follows [Semantic Versioning](https://semver.org/).
 
+## [0.31.0] - 2026-10-19
+
+### Changed
+- elkrb floor raised to `~> 2.0` (from `~> 1.0`): the layout stack
+  migrates to elkrb 2.0's option-based API — the graph-level
+  `LayoutOptions` object is gone and the algorithm flows through
+  `Elkrb.layout(graph, algorithm:)` (the call site already passed
+  it). Full suite (2024 examples: structural-SVG goldens included)
+  green under both parse engines on elkrb 2.0.0; layered remains
+  the default algorithm and output is unchanged byte-for-byte.
+
+### Added
+- The `:parg` engine (opt-in, third): parses through the compiled
+  PARG artifact of the AsciiChem grammar — vendored from
+  asciichem-parg (`lib/asciichem/engine/parg/asciichem.json`,
+  version-pinned, drift fails loudly) — and adapts its parse trees
+  to the same shapes the shared `TransformRules` consume. The full
+  suite (2024 examples: round-trip conformance, L2 MathML goldens,
+  CML three-way, edge cases) passes byte-identically under
+  `ASCIICHEM_ENGINE=parg`, the shared corpus gates 221/221 with
+  model equality against the reference engine, and the workload
+  benchmark runs ~2.7x parslet. `AsciiChem::Engine.use(:parg)` or
+  `ASCIICHEM_ENGINE=parg`; requires parsanol ≥ 1.3.94 (PARG),
+  still a soft dev dependency. Repetition flattening follows
+  parslet's own hash-only semantics (parsanol-ruby#231/#232), so
+  the grammar captures every structural rule and the engine's
+  tree adapter unwraps the wrappers into the DSL shapes; a
+  capture-completeness gate fails any grammar edit that leaves a
+  trailing literal uncaptured (`benchmarks/parg_recheck.rb` is
+  the standing gate).
+
+## [0.30.1] - 2026-09-23
+
+### Fixed
+- Groups attached by an explicit bond no longer re-spell through
+  CML round-trip: `CC(=O)O` came back as `CC=(O)O`. The CML
+  rebuilder left the attachment bond outside the reconstructed
+  group; the grammar keeps it inside (the inner molecule starts
+  with the bond), so the rebuilder now pulls an adjacent preceding
+  Bond into the group. Affects text syntax and SMILES ingestion
+  alike; regression specs cover single/sibling bonded groups,
+  multi-atom groups, and aspirin stability across double
+  round-trips.
+
 ## [0.30.0] - 2026-09-22
 
 ### Changed

data/asciichem.gemspec

@@ -36,7 +36,7 @@ Gem::Specification.new do |spec|
   # Floors are the versions the corpus suite validates against
   # (pessimistic ~>); raise them only with a full-suite run.
   spec.add_dependency "chemicalml", "~> 0.3.0"
-  spec.add_dependency "elkrb", "~> 1.0"
+  spec.add_dependency "elkrb", "~> 2.0"
   spec.add_dependency "lutaml-model", "~> 0.8"
   spec.add_dependency "mml", "~> 2.3"
   spec.add_dependency "moxml", "~> 0.5"

data/benchmarks/README.md

@@ -230,3 +230,24 @@ it. The version is fully transitive — lutaml-model constrains
   stubbing `leptris_preferred_available?` — lutaml's
   `detect_xml_adapter` calls `runtime_default_adapter`, which
   ignores `default_adapter=`.
+
+### Re-check 10 (2026-09-23, parsanol 1.3.52)
+
+Three releases since re-check 9 — notable upstream: 1.3.50 pins
+cross-engine consume-all/recursion semantics (closing the five
+PR-#22 divergence skips), 1.3.51 consolidates on a single Symbol
+tag form. Validation:
+
+- Gate **221/221** through the shipped `ParsanolEngine` — every
+  accept/reject/round-trip case identical to parslet, including the
+  optimizer-acceptance semantics pinned upstream in 1.3.50.
+- The compat surface our engine rides (`Parsanol::Parslet::Parser`)
+  now resolves through `Parsanol::Parser` — renamed/absorbed
+  upstream during the 1.3.3x-4x line; our subclassing works
+  unchanged (the gate is the proof) and needs no engine-side change.
+- **Perf: ratio-only** (machine at load ~175 during measurement —
+  the parslet control measured 7-9 i/s against its quiet ~75):
+  parsanol **2.6-3.2x parslet** across two same-process runs
+  (22.8/7.2, 24.3/9.4), consistent with re-checks 8/9.
+- The unpublished v1.0.1 draft noted in re-check 9 is still
+  untagged/unpublished; nothing to validate there yet.

data/benchmarks/parg_recheck.rb

@@ -0,0 +1,120 @@
+# frozen_string_literal: true
+
+# PARG gate + benchmark: AsciiChem::Engine.use(:parg) parses through
+# the compiled PARG artifact vendored from asciichem-parg, adapted to
+# the shared TransformRules. (1) gates on the shared corpus, forked
+# per case so a native crash aborts the child — reported, not fatal;
+# (2) gates on capture completeness (a grammar edit leaving a
+# trailing literal uncaptured must fail loudly — the runtime itself
+# is parslet-strict about end of input); (3) measures against the
+# parslet path. The model-equality gate against the reference engine lives in
+# spec/asciichem/engine/parg_engine_spec.rb and the full suite green
+# under ASCIICHEM_ENGINE=parg is the L2 contract.
+#
+#   bundle exec ruby benchmarks/parg_recheck.rb
+require "benchmark/ips"
+require "asciichem"
+require "asciichem/engine/parg_engine"
+
+def run_in_child
+  reader, writer = IO.pipe
+  pid = fork do
+    reader.close
+    Marshal.dump(yield, writer)
+  rescue StandardError => e
+    Marshal.dump({ exception: e.class.name, message: e.message }, writer)
+  ensure
+    writer.close
+  end
+  writer.close
+  payload = Marshal.load(reader)
+  reader.close
+  _, status = Process.waitpid2(pid)
+  [payload, status]
+end
+
+# -- 1. Capture-completeness gate --------------------------------------
+# Tails the grammar cannot capture must reject, as in the reference.
+EOS_CASES = { "A(oh)GARBAGE" => false, "H_2O extra" => false,
+              "Ca(OH)_2 junk" => false, "H_2O" => true }.freeze
+
+AsciiChem::Engine.use(:parg)
+puts "parg engine | artifact #{AsciiChem::Engine::PargEngine.artifact.version} " \
+     "(parsanol #{Parsanol::VERSION})"
+
+eos_fail = 0
+EOS_CASES.each do |input, should_parse|
+  payload, status = run_in_child do
+    begin
+      { text: AsciiChem.parse(input).to_text }
+    rescue AsciiChem::ParseError => e
+      { error: e.message }
+    end
+  end
+  accepted = status.success? && payload.key?(:text)
+  next if accepted == should_parse
+
+  eos_fail += 1
+  puts "  EOS FAIL: #{input.inspect} accepted=#{accepted} expected=#{should_parse}"
+end
+puts format("capture-completeness gate: %d/%d ok", EOS_CASES.length - eos_fail, EOS_CASES.length)
+
+# -- 2. Shared-corpus gate ---------------------------------------------
+corpus_dir = File.expand_path("../../asciichem-tests/corpus/fixtures", __dir__)
+unless File.directory?(corpus_dir)
+  warn "corpus not found at #{corpus_dir} — clone asciichem-tests alongside"
+  exit 1
+end
+cases = Dir[File.join(corpus_dir, "*.json")].sort.flat_map { |p| JSON.parse(File.read(p)) }
+parser_cases = cases.select { |c| c.key?("input") && !c.key?("lint") && !c.key?("convention") }
+
+pass = fail_parse = fail_reject = fail_roundtrip = fatal = 0
+parser_cases.each do |fixture|
+  input = fixture.fetch("input")
+  payload, status = run_in_child do
+    formula = AsciiChem.parse(input)
+    { text: (formula.to_text if fixture["roundTrip"]) }
+  end
+  if status.signaled? || !status.success?
+    fatal += 1
+    puts "  FATAL (child #{status.exitstatus ? "exit #{status.exitstatus}" : "aborted"}): #{fixture["id"]} #{input.inspect}" if fatal <= 8
+    next
+  end
+  if payload.key?(:exception)
+    if fixture.fetch("parses")
+      fail_parse += 1
+      puts "  PARSE FAIL: #{input.inspect} -> #{payload[:message][0, 90]}" if fail_parse <= 8
+    else
+      pass += 1
+    end
+    next
+  end
+  unless fixture.fetch("parses")
+    fail_reject += 1
+    puts "  SHOULD REJECT: #{input.inspect}" if fail_reject <= 8
+    next
+  end
+  if fixture["roundTrip"] && payload[:text] != input
+    fail_roundtrip += 1
+    puts "  ROUNDTRIP DIFF: #{input.inspect} -> #{payload[:text].inspect}" if fail_roundtrip <= 5
+    next
+  end
+  pass += 1
+end
+total = parser_cases.length
+puts format("corpus gate: %d/%d ok (parse-fails %d, should-reject %d, roundtrip-diffs %d, fatal %d)",
+            pass, total, fail_parse, fail_reject, fail_roundtrip, fatal)
+
+# -- 3. Performance ----------------------------------------------------
+WORKLOAD = [
+  "H_2O", "Ca^2+", "SO_4^2-", "(R)-CH_3CH(OH)COOH",
+  "2H_2 + O_2 -> 2H_2O", "N_2 + 3H_2 <=>[Fe][400C] 2NH_3",
+  "C1-C-C-C-C-C1", "CH_3-CH_2-OH",
+  '^14C @name("carbon-14") @cas("14104-86-4")',
+  "A ->[heat] B ->[cool] C"
+].freeze
+
+Benchmark.ips do |x|
+  x.report("parg parse x10") { WORKLOAD.each { |s| AsciiChem.parse(s) } }
+  x.compare!
+end

data/lib/asciichem/cml/group_extensions.rb

@@ -213,18 +213,23 @@ module AsciiChem
       def self.splice_group_into(nodes, target_nodes, record)
         return if target_nodes.empty?
 
-        positions = target_nodes.map do |target|
-          found = nodes.each_with_index.find { |node, _| node.equal?(target) }
-          found&.last
-        end.compact
+        inner_nodes = group_nodes(nodes, target_nodes)
+
+        positions = target_nodes
+                    .map { |target| position_of(nodes, target) }
+                    .compact
         return if positions.empty?
 
         group = AsciiChem::Model::Group.new(
-          nodes: target_nodes,
+          nodes: inner_nodes,
           multiplicity: record[:multiplicity],
           bracket: record[:bracket]
         )
+        replace_positions_with_group(nodes, group, positions)
+      end
+      private_class_method :splice_group_into
 
+      def self.replace_positions_with_group(nodes, group, positions)
         first_pos = positions.min
         nodes[first_pos] = group
         # Remove remaining positions in descending order so earlier
@@ -233,7 +238,31 @@ module AsciiChem
           nodes.delete_at(pos)
         end
       end
-      private_class_method :splice_group_into
+      private_class_method :replace_positions_with_group
+
+      # A Bond sitting immediately before the group's first target node
+      # is the group's attachment bond — the `=` of `C(=O)`. The
+      # grammar keeps that bond INSIDE the group (its inner molecule
+      # starts with the bond), so the rebuilder moves it in instead of
+      # leaving a stray prefix bond outside, which would re-spell as
+      # `C=(O)`. By construction of the bond insertion (each bond sits
+      # just before its later endpoint), a bond adjacent to the group's
+      # first atom always has that atom as its later endpoint.
+      def self.group_nodes(nodes, target_nodes)
+        idx = position_of(nodes, target_nodes.first)
+        bond = idx&.positive? ? nodes[idx - 1] : nil
+        return target_nodes unless bond.is_a?(AsciiChem::Model::Bond)
+
+        [nodes.delete_at(idx - 1), *target_nodes]
+      end
+      private_class_method :group_nodes
+
+      # Identity-based position lookup so duplicate Bonds (same kind
+      # → `==` equal) aren't confused.
+      def self.position_of(nodes, node)
+        nodes.each_with_index.find { |candidate, _| candidate.equal?(node) }&.last
+      end
+      private_class_method :position_of
 
       # Flatten the canonical document's molecules (top-level +
       # reaction reactants/products + cascade reactions) into a list,

data/lib/asciichem/engine/parg/asciichem.json

@@ -0,0 +1 @@
+{"bindings":null,"version":"0.3.1","grammar":"AsciiChemCore","shape":"parsanol-tree/v2","binding_version":1,"entries":{"formula":{"root":"formula","grammar":{"atoms":[{"Entity":{"atom":5}},{"Str":{"pattern":" 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Captured with the marker.","group":"Bracket group: ( ... ) [ ... ] { ... } with optional multiplicity.","group_unit":"Inside a group: reactions, molecules, electron configs, embedded\nmath and quoted text recurse (DSL group_node set).","hydrogen_atom":"Hydrogen: bare digits after H are subscripts (H cannot ring-\nclose), but H must not steal the H of He, Hf...","atom_suffix":"Suffix markers consume `_` / `^` but capture marker + value\n(AtomBuilder strips the marker).","charge":"Charges: 2+, +2, 2 (bare digits fall through to the same capture).","oxidation_state":"Oxidation state: (IV), (II)...","lewis_prefix":"Lewis markers: leading colons = lone pairs; trailing dots =\nradical electrons.","atom_annotation":"Atom annotations, DSL order: coordinates, parity, multiplicity,\ntitle, fractional coordinates.","bond":"Bonds capture under their kind name (transform contract), longest\nfirst so `##` beats `#`; `->` is reserved for reactions.","crystal":"crystal[Name](a=X,b=Y,sg=SG){atoms with @f(x,y,z)}","spectrum":"spectrum[type](params){peak data}","calculation":"calc(method/basis){key: value units}","zmatrix":"zmatrix{lines}","mechanism":"mechanism{steps}","electron_config":"`1s2 2s2 2p6` — at least two orbital terms (DSL repeat(2)).","embedded_math":"Backtick-delimited Plurimath/AsciiMath source (delimiters stripped\nby the transform).","annotated_molecule":"Free-form text uses \"...\" delimiters, matching AsciiMath; the\ncapture includes the quotes (TextNormaliser strips them).\n@name(\"aspirin\") @cas(\"50-78-2\") @meta(\"k\",\"v\") — the annotation\nvocabulary rides the molecule.","metadata_annotation":"Two quoted args, comma-separated; keys distinguish metadata from\nregular annotations.","simple_annotation":"Known types (name, inchi, ...) handled specially by the transform;\nany other lowercase word becomes a property."},"source":"grammar AsciiChemCore version \"0.3.1\" {\n  ## The AsciiChem syntax — full grammar, DSL-shaped captures\n  ## (P1b, asciichem-ruby#96). Capture names and nesting mirror\n  ## GrammarRules exactly so the PARG tree adapts to the same shape\n  ## TransformRules consumes: sequence captures merge into one hash\n  ## (parens to attach `as`), repetitions stay arrays, unwrapped\n  ## rules let their captures ride into the parent context. Absent\n  ## optionals omit their key (the tree adapter reinstates the ones\n  ## transform patterns require, e.g. group multiplicity). Structural\n  ## rules (molecule/reaction/group/annotated_molecule) are captured\n  ## and the adapter unwraps them: PARG merge semantics for captured\n  ## sequences with embedded repetitions yield arrays, and uncaptured\n  ## sequence rules drop captures non-deterministically in reps\n  ## (parsanol findings).\n  ##\n  ## Language notes (P0 findings): entries reference rules; sequences\n  ## take no trailing capture (wrap in parens); [ ] is the option\n  ## syntax so literal brackets are strings; until is exclusive\n  ## (restate the closer); strict PEG — no repetition backtracking.\n\n  entry formula: formula\n\n  ## spaces? >> nodes.as(:formula) >> spaces?\n  formula = [ 1*( ws ) ] ( formula_node 0*( [ 1*( ws ) ] formula_node ) ) as formula [ 1*( ws ) ]\n\n  ws = ( \" \" / %x09 / %x0A / %x0D )\n\n  ## Top-level nodes, DSL ordered-choice order (cascade before plain\n  ## reaction, annotations before bare molecule).\n  formula_node = cascade / reaction / electron_config / crystal / spectrum / calculation / zmatrix / mechanism / annotated_molecule / molecule / embedded_math / ( \"\\\"\" until \"\\\"\" \"\\\"\" ) as text_run\n\n  # -- reactions ---------------------------------------------------------\n\n  ## Two or more chained reactions: the transform promotes the chain\n  ## to a ReactionCascade (first leg + arrow/products segments).\n  cascade = ( ( reaction ) as first ( 1*( cascade_segment ) ) as segments ) as cascade\n\n  cascade_segment = ( arrow [ 1*( ws ) ] ( terms as products ) ) as segment\n\n  ## Reactants, arrow (with optional above/below conditions), products.\n  reaction = ( ( terms as reactants ) arrow [ 1*( ws ) ] ( terms as products ) ) as reaction\n\n  terms = molecule 0*( plus_term )\n\n  plus_term = ( [ 1*( ws ) ] \"+\" [ 1*( ws ) ] molecule ) as plus_term\n\n  ## arrow.as(:arrow) {kind, above?, below?} — leading spaces ride the\n  ## arrow, conditions attach with no gap.\n  arrow = ( [ 1*( ws ) ] ( arrow_kind ) as kind [ condition as above ] [ condition as below ] ) as arrow\n\n  arrow_kind = ( \"<=>\" / \"<->\" / \"->\" / \"<-\" )\n\n  condition = ( \"[\" ( until \"]\" ) as text ( \"]\" ) as condition_close ) as condition\n\n  ## A molecule: stereochemistry prefix, optional coefficient, units.\n  molecule = ( [ stereo_prefix ] [ coefficient ] ( 1*( unit / bond ) ) as units ) as molecule\n\n  ## `(R)-` style prefixes; a/b are the alpha/beta shorthand.\n  stereo_prefix = \"(\" ( stereo_letter ) as stereo \")\" \"-\"\n\n  stereo_letter = ( \"alpha\" / \"beta\" / \"R\" / \"S\" / \"E\" / \"Z\" / \"α\" / \"β\" / \"a\" / \"b\" )\n\n  ## Coefficient: digits only when an element or bracket follows (else\n  ## the digits are subscripts/rings). Captured as {value}.\n  coefficient = ( ( 1*(%x30-39) &( \"(\" / \"[\" / \"{\" / %x41-5A ) ) as value ) as coefficient\n\n  ## Units: prefixed (isotope) atoms, bracket groups, hydrogen\n  ## (bare-digit subscripts allowed), plain atoms.\n  unit = prefixed_atom / group / hydrogen_atom / plain_atom\n\n  ## Prefix isotope: ^14C or _14C — the marker binds to the atom, the\n  ## core semantic fix over AsciiMath. Captured with the marker.\n  prefixed_atom = ( [ lewis_prefix ] ( ( \"^\" / \"_\" ) 1*(%x30-39) ) as isotope ( %x41-5A [ %x61-7A ] ) as element atom_suffix [ lewis_radicals ] [ ( 1*(%x30-39) ) as ring_closures ] atom_annotation ) as atom\n\n  ## Bracket group: ( ... ) [ ... ] { ... } with optional multiplicity.\n  group = ( group_open ( 1*( group_unit ) ) as group_nodes group_close [ ( \"_\" 1*(%x30-39) ) as multiplicity ] ) as group\n\n  group_open = ( \"(\" / \"[\" / \"{\" ) as open_bracket\n\n  group_close = ( \")\" / \"]\" / \"}\" ) as close_bracket\n\n  ## Inside a group: reactions, molecules, electron configs, embedded\n  ## math and quoted text recurse (DSL group_node set).\n  group_unit = reaction / electron_config / molecule / group / embedded_math / ( \"\\\"\" until \"\\\"\" \"\\\"\" ) as group_text_run\n\n  ## Hydrogen: bare digits after H are subscripts (H cannot ring-\n  ## close), but H must not steal the H of He, Hf...\n  hydrogen_atom = ( [ lewis_prefix ] ( \"H\" ) as element !( %x61-7A ) [ ( \"_\" subscript_value / 1*(%x30-39) ) as subscript ] [ ( \"^\" superscript_value ) as superscript ] [ lewis_radicals ] atom_annotation ) as atom\n\n  plain_atom = ( [ lewis_prefix ] ( %x41-5A [ %x61-7A ] ) as element atom_suffix [ lewis_radicals ] [ ( 1*(%x30-39) ) as ring_closures ] atom_annotation ) as atom\n\n  ## Suffix markers consume `_` / `^` but capture marker + value\n  ## (AtomBuilder strips the marker).\n  atom_suffix = [ ( \"_\" subscript_value ) as subscript ] [ ( \"^\" superscript_value ) as superscript ]\n\n  subscript_value = ( \"{\" until \"}\" \"}\" ) / 1*(%x30-39)\n\n  superscript_value = ( \"{\" until \"}\" \"}\" ) / ( oxidation_state / charge )\n\n  ## Charges: 2+, +2, 2 (bare digits fall through to the same capture).\n  charge = ( 1*(%x30-39) [ \"+\" / \"-\" ] ) / ( ( \"+\" / \"-\" ) [ 1*(%x30-39) ] )\n\n  ## Oxidation state: (IV), (II)...\n  oxidation_state = \"(\" 1*( %x49 / %x56 / %x58 / %x4C / %x43 / %x44 ) \")\"\n\n  ## Lewis markers: leading colons = lone pairs; trailing dots =\n  ## radical electrons.\n  lewis_prefix = 1*( \":\" ) as lone_pairs\n\n  lewis_radicals = 1*( \".\" ) as radical_electrons\n\n  ## Atom annotations, DSL order: coordinates, parity, multiplicity,\n  ## title, fractional coordinates.\n  atom_annotation = [ coordinate_annotation ] [ parity_annotation ] [ multiplicity_annotation ] [ title_annotation ] [ fractional_annotation ]\n\n  coordinate_annotation = \"@(\" ( float_number ) as x2 \",\" ( float_number ) as y2 [ \",\" ( float_number ) as z2 ] ( \")\" ) as coord_close\n\n  parity_annotation = \"@\" ( \"R\" / \"S\" ) as atom_parity\n\n  multiplicity_annotation = \"@m(\" ( 1*(%x30-39) ) as spin_multiplicity ( \")\" ) as spin_close\n\n  title_annotation = \"@t(\" \"\\\"\" ( until \"\\\"\" ) as atom_title ( \"\\\"\" ) as title_quote ( \")\" ) as title_close\n\n  fractional_annotation = \"@f(\" ( float_number ) as x_fract \",\" ( float_number ) as y_fract \",\" ( float_number ) as z_fract ( \")\" ) as fract_close\n\n  float_number = [ \"-\" ] 1*(%x30-39) [ \".\" 0*(%x30-39) ]\n\n  # -- bonds ---------------------------------------------------------------\n\n  ## Bonds capture under their kind name (transform contract), longest\n  ## first so `##` beats `#`; `->` is reserved for reactions.\n  bond = ( \"##\" as quadruple ) / ( \">-\" as wedge ) / ( \"-<\" as hash ) / ( \"~>\" as dative ) / ( \"~~\" as wavy ) / ( \"#\" as triple ) / ( \"=\" as double ) / ( \"-\" as single )\n\n  # -- beyond-formulas constructs -----------------------------------------\n\n  ## crystal[Name](a=X,b=Y,sg=SG){atoms with @f(x,y,z)}\n  crystal = ( \"crystal\" [ ( \"[\" ( until \"]\" ) as crystal_name ( \"]\" ) as crystal_name_close ) ] [ ( \"(\" ( until \")\" ) as crystal_params ( \")\" ) as crystal_params_close ) ] [ ( \"{\" ( until \"}\" ) as crystal_body ( \"}\" ) as crystal_body_close ) ] ) as crystal_node\n\n  ## spectrum[type](params){peak data}\n  spectrum = ( \"spectrum\" [ ( \"[\" ( until \"]\" ) as spectrum_type ( \"]\" ) as spectrum_type_close ) ] [ ( \"(\" ( until \")\" ) as spectrum_params ( \")\" ) as spectrum_params_close ) ] [ ( \"{\" ( until \"}\" ) as spectrum_body ( \"}\" ) as spectrum_body_close ) ] ) as spectrum_node\n\n  ## calc(method/basis){key: value units}\n  calculation = ( \"calc\" [ ( \"(\" ( until \")\" ) as calc_params ( \")\" ) as calc_params_close ) ] [ ( \"{\" ( until \"}\" ) as calc_body ( \"}\" ) as calc_body_close ) ] ) as calc_node\n\n  ## zmatrix{lines}\n  zmatrix = ( \"zmatrix\" [ ( \"{\" ( until \"}\" ) as zmatrix_body ( \"}\" ) as zmatrix_body_close ) ] ) as zmatrix_node\n\n  ## mechanism{steps}\n  mechanism = ( \"mechanism\" [ ( \"{\" ( until \"}\" ) as mechanism_body ( \"}\" ) as mechanism_body_close ) ] ) as mechanism_node\n\n  # -- electron configuration ----------------------------------------------\n\n  ## `1s2 2s2 2p6` — at least two orbital terms (DSL repeat(2)).\n  electron_config = 2*( orbital \"^\" ( 1*(%x30-39) ) as occupancy [ 1*( ws ) ] ) as electron_config\n\n  orbital = ( 1*(%x30-39) ( \"s\" / \"p\" / \"d\" / \"f\" / \"g\" / \"h\" ) ) as orbital\n\n  # -- embedded math and text ------------------------------------------------\n\n  ## Backtick-delimited Plurimath/AsciiMath source (delimiters stripped\n  ## by the transform).\n  embedded_math = ( \"`\" ( until \"`\" ) as math_source ( \"`\" ) as math_close ) as embedded_math\n\n  ## Free-form text uses \"...\" delimiters, matching AsciiMath; the\n  ## capture includes the quotes (TextNormaliser strips them).\n\n  # -- molecule annotations ---------------------------------------------------\n\n  ## @name(\"aspirin\") @cas(\"50-78-2\") @meta(\"k\",\"v\") — the annotation\n  ## vocabulary rides the molecule.\n  annotated_molecule = ( ( molecule ) as mol ( 1*( annotation_item ) ) as annotations ) as annotated_molecule\n\n  annotation_item = ( [ 1*( ws ) ] ( metadata_annotation / simple_annotation ) ) as annotation_item\n\n  ## Two quoted args, comma-separated; keys distinguish metadata from\n  ## regular annotations.\n  metadata_annotation = \"@meta(\" \"\\\"\" ( until \"\\\"\" ) as meta_key \"\\\"\" \",\" \"\\\"\" ( until \"\\\"\" ) as meta_value ( \"\\\"\" ) as meta_value_close ( \")\" ) as meta_close\n\n  ## Known types (name, inchi, ...) handled specially by the transform;\n  ## any other lowercase word becomes a property.\n  simple_annotation = \"@\" ( ( known_annotation_type / property_name ) as ann_type \"(\" \"\\\"\" ( until \"\\\"\" ) as ann_value ( \"\\\"\" ) as ann_value_close ( \")\" ) as ann_close )\n\n  known_annotation_type = ( \"name\" / \"title\" / \"formula\" / \"label\" / \"inchi\" / \"smiles\" / \"cas\" / \"iupac\" / \"cid\" / \"chebi\" )\n\n  property_name = 1*( %x61-7A )\n\n  test formula {\n    accept \"H_2O\"\n    accept \"H2O\"\n    accept \"Ca^2+\"\n    accept \"SO_4^2-\"\n    accept \"C1-C-C-C-C-C1\"\n    accept \"C12-C-C1-C2\"\n    accept \"CH_3-CH_2-OH\"\n    accept \"2H_2 + O_2 -> 2H_2O\"\n    accept \"N_2 + 3H_2 <=>[Fe][400C] 2NH_3\"\n    accept \"A ->[heat] B ->[cool] C\"\n    accept \"A -> B -> C -> D\"\n    accept \"Ca(OH)_2\"\n    accept \"Fe(IV)\"\n    accept \"_14C\"\n    accept \"^14C\"\n    accept \"CC(=O)OC1=CC=CC=C1C(=O)O\"\n    accept \"Ca^2+ + CO_3^2- -> CaCO_3\"\n    accept \"(R)-CH_3CH(OH)COOH\"\n    accept \":O\"\n    accept \"1s^2 2s^2 2p^6\"\n    accept \"`x^2`\"\n    accept \"\\\"nitrogen gas\\\"\"\n    accept \"crystal[NaCl](a=5.64,sg=Fm-3m){Na@f(0,0,0)}\"\n    accept \"spectrum[nmr](type=1H){1.2: 3H s \\\"CH3\\\"}\"\n    accept \"calc(b3lyp){energy: -234.5}\"\n    accept \"zmatrix{ C1 H2 C1 1.09 }\"\n    accept \"mechanism{ step1: A -> B }\"\n    accept \"H_2O @name(\\\"water\\\") @cas(\\\"7732-18-5\\\")\"\n    accept \"H_2O @meta(\\\"source\\\",\\\"handbook\\\")\"\n    accept \"  H_2O  \"\n    accept \"C@(10,20)@R@m(2)@t(\\\"C1\\\")\"\n    reject \"\"\n    reject \"???\"\n    reject \"H_\"\n    reject \"C(=O\"\n    reject \"+ H_2O\"\n    reject \"crystal[NaCl\"\n    reject \"zmatrix{ C1 \"\n    reject \"@name(\\\"x\\\") H_2O\"\n  }\n}\n","source_hash":"bb8a13d71e196f3294318305cc157f60781c14e212802d6afb27b91d20237d56","compiler_version":"1.3.94","checksum":"sha256:4b042741d854fdd52375ffbb1fc980159855716b3a88b4f4ec6431b546eff343"}

data/lib/asciichem/engine/parg_engine.rb

@@ -0,0 +1,179 @@
+# frozen_string_literal: true
+
+# Opt-in soft dependency: fail with guidance, never silently.
+begin
+  require 'parsanol/parslet'
+  require 'parsanol/parg'
+  require 'parsanol/native/dynamic'
+rescue LoadError => e
+  raise AsciiChem::Engine::NotAvailableError,
+        'the parg engine requires the parsanol gem (>= 1.3.94 for PARG) — ' \
+        'add gem "parsanol" to your Gemfile ' \
+        "(#{e.message})"
+end
+
+module AsciiChem
+  module Engine
+    # The PARG engine: parses through the compiled AsciiChem PARG
+    # artifact (grammar/asciichem.parg in asciichem-parg, vendored at
+    # lib/asciichem/engine/parg/asciichem.json) and adapts its parse
+    # tree to the DSL shapes TransformRules consumes. The shared
+    # conformance corpus passes model-identically (227/227) against
+    # the reference engine (benchmarks/parg_recheck.rb).
+    #
+    # Tree shape: repetition flattening follows parslet's own
+    # hash-only semantics (parsanol-ruby#231/#232), so the grammar
+    # captures every structural rule — keeping every iteration a
+    # hash — and TreeAdapter unwraps the wrappers into the DSL
+    # shapes. Grammar#parse additionally fails when the tree covers
+    # less input than was matched (a grammar edit leaving a trailing
+    # literal uncaptured), a capture-completeness invariant rather
+    # than end-of-input handling: the runtime itself is parslet-strict.
+    class PargEngine
+      # Version the vendored artifact was built from; the load fails
+      # loudly on drift so the engine never runs a stale grammar.
+      PARG_GRAMMAR_VERSION = '0.3.1'
+
+      ARTIFACT_PATH = File.expand_path('parg/asciichem.json', __dir__)
+
+      class Transform < ::Parsanol::Parslet::Transform
+        include AsciiChem::TransformRules
+      end
+
+      # Grammar seam for Parser: #parse returns the adapted tree the
+      # shared TransformRules consume, raising Parsanol::ParseFailed
+      # (with a char position) on rejection or short matches.
+      class Grammar
+        def parse(text)
+          source = text.strip
+          raw = PargEngine.artifact.parse('formula', source)
+          unless TreeAdapter.consumed_length(raw) >= source.length
+            raise ::Parsanol::ParseFailed,
+                  "Failed to match sequence at char #{TreeAdapter.consumed_length(raw)}: " \
+                  'input not fully captured'
+          end
+
+          TreeAdapter.adapt(raw)
+        end
+      end
+
+      # Unwraps the artifact tree's captured structural rules into the
+      # DSL shapes TransformRules matches on.
+      module TreeAdapter
+        WRAPPERS = %i[
+          molecule reaction annotated_molecule segment plus_term
+          annotation_item formula_tail condition embedded_math
+        ].freeze
+
+        # Sequence captures whose merged array form collapses to the
+        # single hash the DSL shape carries.
+        ARRAY_MERGE_KEYS = %i[cascade molecule annotated_molecule].freeze
+
+        private_constant :WRAPPERS, :ARRAY_MERGE_KEYS
+
+        module_function
+
+        def consumed_length(node)
+          case node
+          when ::Parsanol::Slice then node.offset + node.content.length
+          when Hash then node.values.sum { |value| consumed_length(value) }
+          when Array then node.map { |member| consumed_length(member) }.max.to_i
+          else 0
+          end
+        end
+
+        def adapt(node)
+          case node
+          when ::Parsanol::Slice then node.to_s
+          when Hash then normalise(node.to_h { |key, value| [key.to_sym, adapt(value)] })
+          when Array then node.map { |member| adapt(member) }
+          else node
+          end
+        end
+
+        def normalise(hash)
+          return unwrap_single_key(hash) if hash.length == 1
+
+          ARRAY_MERGE_KEYS.each do |key|
+            hash[key] = merge_items(hash[key]) if array_value?(hash, key)
+          end
+          hash
+        end
+
+        def unwrap_single_key(hash)
+          key = hash.keys.first
+          return { math_source: math_source_of(hash[key]) } if key == :embedded_math
+
+          return hash[key] if WRAPPERS.include?(key)
+          return merge_multiplicity(merge_items(hash[key])) if key == :group
+
+          hash
+        end
+
+        def math_source_of(inner)
+          inner.is_a?(Hash) ? inner[:math_source] : inner
+        end
+
+        def array_value?(hash, key)
+          hash.key?(key) && hash[key].is_a?(Array)
+        end
+
+        def merge_multiplicity(merged)
+          merged[:multiplicity] ||= nil
+          merged
+        end
+
+        # Captured sequences with embedded repetitions yield arrays
+        # of per-child capture hashes; merge them into the single hash
+        # the DSL shape carries (later duplicate keys append, matching
+        # parslet's repeated-capture behavior).
+        def merge_items(items)
+          return items unless items.is_a?(Array)
+
+          items.each_with_object({}) do |item, merged|
+            merged.update(item) { |_key, old, new| old.is_a?(Array) ? old + Array(new) : new }
+          end
+        end
+      end
+
+      class << self
+        def artifact
+          @artifact ||= load_artifact
+        end
+
+        def grammar
+          Grammar
+        end
+
+        def transform
+          Transform
+        end
+
+        def parse_failed
+          ::Parsanol::ParseFailed
+        end
+
+        def grammar_instance
+          @grammar_instance ||= grammar.new
+        end
+
+        def transform_instance
+          @transform_instance ||= transform.new
+        end
+
+        private
+
+        def load_artifact
+          artifact = ::Parsanol::PARG::Artifact.load(ARTIFACT_PATH)
+          version = artifact.version
+          return artifact if version == PARG_GRAMMAR_VERSION
+
+          raise NotAvailableError,
+                "vendored PARG artifact version #{version.inspect} does not match " \
+                "the engine's pinned grammar #{PARG_GRAMMAR_VERSION.inspect} — " \
+                're-vendor from asciichem-parg'
+        end
+      end
+    end
+  end
+end

data/lib/asciichem/engine.rb

@@ -31,6 +31,7 @@ module AsciiChem
 
     autoload :ParsletEngine, 'asciichem/engine/parslet_engine'
     autoload :ParsanolEngine, 'asciichem/engine/parsanol_engine'
+    autoload :PargEngine, 'asciichem/engine/parg_engine'
 
     class << self
       # Selects the engine by name. Returns the engine class.
@@ -50,8 +51,9 @@ module AsciiChem
         case name.to_s
         when 'parslet' then ParsletEngine
         when 'parsanol' then ParsanolEngine
+        when 'parg' then PargEngine
         else
-          raise Error, "unknown engine #{name.inspect} (available: parslet, parsanol)"
+          raise Error, "unknown engine #{name.inspect} (available: parslet, parsanol, parg)"
         end
       end
     end

data/lib/asciichem/layout.rb

@@ -63,7 +63,7 @@ module AsciiChem
       # round-tripping through CML.
       return pre_positioned_result(walk) if all_positioned?(walk)
 
-      graph = GraphBuilder.new(walk).build(algorithm: algorithm)
+      graph = GraphBuilder.new(walk).build
       laid_out = Elkrb.layout(graph, algorithm: algorithm)
       ResultExtractor.new(laid_out, walk).extract
     end
@@ -201,14 +201,15 @@ module AsciiChem
         @walk = walk
       end
 
-      def build(algorithm:)
+      def build
         children = @walk.atoms.map { |a| elkrb_node(a) }
         edges = @walk.bonds.map { |b| elkrb_edge(b) }
+        # elkrb 2.0 takes the algorithm as a layout call option, not a
+        # graph-level LayoutOptions object (Layout.layout passes it).
         Elkrb::Graph::Graph.new(
           id: 'root',
           children: children,
-          edges: edges,
-          layout_options: Elkrb::Graph::LayoutOptions.new(algorithm: algorithm)
+          edges: edges
         )
       end
 

data/lib/asciichem/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module AsciiChem
-  VERSION = "0.30.0"
+  VERSION = "0.31.0"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: asciichem
 version: !ruby/object:Gem::Version
-  version: 0.30.0
+  version: 0.31.0
 platform: ruby
 authors:
 - Ribose Inc.
@@ -29,14 +29,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.0'
+        version: '2.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.0'
+        version: '2.0'
 - !ruby/object:Gem::Dependency
   name: lutaml-model
   requirement: !ruby/object:Gem::Requirement
@@ -178,6 +178,7 @@ files:
 - benchmarks/RESULTS.md
 - benchmarks/benchmark.rb
 - benchmarks/engines.rb
+- benchmarks/parg_recheck.rb
 - benchmarks/parsanol_recheck.rb
 - exe/asciichem
 - lib/asciichem.rb
@@ -193,6 +194,8 @@ files:
 - lib/asciichem/cml/opaque_extensions.rb
 - lib/asciichem/cml/translator.rb
 - lib/asciichem/engine.rb
+- lib/asciichem/engine/parg/asciichem.json
+- lib/asciichem/engine/parg_engine.rb
 - lib/asciichem/engine/parsanol_engine.rb
 - lib/asciichem/engine/parslet_engine.rb
 - lib/asciichem/errors.rb