asciichem 0.25.0 → 0.26.0

checksums.yaml

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

@@ -3,6 +3,21 @@
 All notable changes to AsciiChem are documented here.
 This project follows [Semantic Versioning](https://semver.org/).
 
+## [0.26.0] - 2026-09-14
+
+### Added
+- The cite syntax (TODO.impl 45): `@cite("pubchem")` on a molecule
+  declares which source to cite it from; `Citation.for_molecule`
+  resolves the molecule's identifiers (registry keys preferred over
+  names) and emits one bibitem per cited source. Zero grammar
+  changes — `@cite` rides the property-annotation form by design.
+
+### Fixed
+- Molecule annotations now canonicalise with spaces between them
+  (`@name("Water") @cas("...")`), matching the TypeScript and Python
+  canonicalisers; Ruby was the outlier joining them without a
+  separator.
+
 ## [0.25.0] - 2026-09-14
 
 ### Added
@@ -435,7 +450,8 @@ This project follows [Semantic Versioning](https://semver.org/).
   `version`.
 - Comprehensive RSpec suite with round-trip conformance.
 
-[Unreleased]: https://github.com/asciichem/asciichem-ruby/compare/v0.25.0...HEAD
+[Unreleased]: https://github.com/asciichem/asciichem-ruby/compare/v0.26.0...HEAD
+[0.26.0]: https://github.com/asciichem/asciichem-ruby/compare/v0.25.0...v0.26.0
 [0.25.0]: https://github.com/asciichem/asciichem-ruby/compare/v0.24.0...v0.25.0
 [0.24.0]: https://github.com/asciichem/asciichem-ruby/compare/v0.23.0...v0.24.0
 [0.23.0]: https://github.com/asciichem/asciichem-ruby/compare/v0.22.0...v0.23.0

data/benchmarks/README.md

@@ -41,6 +41,16 @@ as a drop-in speedup for the reference grammar:
    revalidation against the whole corpus with no measured win to
    justify it yet.
 
-**Verdict: not adopted.** Revisit when Parsanol's native backend can
-be engaged for full grammars and shows measured wins on this
-workload; the shim path is a documented no.
+**Verdict: not adopted yet.** Two corrections to the spike (tracked
+upstream in parsanol-ruby#25):
+
+1. The native-DSL micro-benchmark ran in Parsanol's default `:ruby`
+   mode — the Rust core (`:native`) was never engaged, so the native
+   path is unmeasured, not disproven.
+2. The `SO_4^2-` failure is a candidate upstream bug (`repeat` of a
+   `maybe`-prefixed sequence fails at end-of-input; minimal repro in
+   the issue).
+
+Revisit trigger unchanged: engage the native backend for full
+grammars, fix the repetition-termination bug, and beat parslet on
+this workload — then re-run the corpus against the port.

data/lib/asciichem/citation.rb

@@ -81,6 +81,57 @@ module AsciiChem
         bibitem(substance).to_xml
       end
 
+      # The cite syntax (TODO.impl 45): a molecule annotated
+      # `@cite("pubchem")` (a property annotation — the grammar needs
+      # no extension) declares *which source to cite it from*. This
+      # resolves the molecule's identifiers and emits one bibitem per
+      # cited source. Returns [[source, bibitem]] pairs; empty when the
+      # molecule has no @cite annotations.
+      #
+      #   AsciiChem.parse('H_2O @name("water") @cite("pubchem")')
+      #   AsciiChem::Citation.for_molecule(formula.nodes.first).map(&:last)
+      def for_molecule(molecule, cache: nil, fetch: nil)
+        sources = citation_sources(molecule)
+        return [] if sources.empty?
+
+        convention, value = lookup_key(molecule)
+        unless value
+          raise Error,
+                "molecule carries no resolvable identifier for citation " \
+                "(annotate @cas/@inchikey/@smiles or @name)"
+        end
+
+        sources.filter_map do |source|
+          substance = AsciiChem::Resolver[source].new.resolve(
+            value: value, convention: convention, cache: cache, fetch: fetch)
+          next unless substance
+
+          [source, bibitem(substance)]
+        end
+      end
+
+      private
+
+      # The property annotation whose title is "cite": values are the
+      # source names to cite from.
+      def citation_sources(molecule)
+        molecule.properties
+                .select { |p| p.title == "cite" && p.value }
+                .map(&:value)
+      end
+
+      # First identifier the resolver can look up by, in preference
+      # order: unambiguous registry keys before names.
+      def lookup_key(molecule)
+        identifier = molecule.identifiers.find { |i| %w[cas inchikey pubchem-cid].include?(i.convention) }
+        return [identifier.convention, identifier.value] if identifier
+
+        name = molecule.names.first
+        return ["name", name.content] if name
+
+        nil
+      end
+
       private
 
       def title_base(substance)

data/lib/asciichem/formatter/text.rb

@@ -38,7 +38,7 @@ module AsciiChem
         molecule.labels.each { |l| parts << %(@label("#{l.value}")) if l.value }
         molecule.properties.each { |p| parts << %(@#{p.title}("#{p.value}")) if p.title && p.value }
         molecule.metadata.each { |m| parts << %(@meta("#{m.name}","#{m.content}")) }
-        parts.empty? ? "" : " #{parts.join}"
+        parts.empty? ? "" : " #{parts.join(" ")}"
       end
 
       def visit_atom(atom)

data/lib/asciichem/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module AsciiChem
-  VERSION = "0.25.0"
+  VERSION = "0.26.0"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: asciichem
 version: !ruby/object:Gem::Version
-  version: 0.25.0
+  version: 0.26.0
 platform: ruby
 authors:
 - Ribose Inc.