asciichem 0.31.10 → 0.31.12

checksums.yaml

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

@@ -3,6 +3,29 @@
 All notable changes to AsciiChem are documented here.
 This project follows [Semantic Versioning](https://semver.org/).
 
+## [0.31.12] - 2026-11-11
+
+### Changed
+- CAS Common Chemistry resolves by default (maintainer decision:
+  CC BY-NC 4.0 acceptable on by default). The adapter self-registers
+  like the other sources; every result still carries the required
+  attribution. `Citation.for_molecule` accepts a `sources:`
+  allow-list so callers can keep resolution NC-free — the
+  metanorma plugin exposes it as the `asciichem-sources` document
+  attribute.
+
+## [0.31.11] - 2026-11-10
+
+### Added
+- Dataset bibitems carry the resolver provenance as a
+  `type="provenance"` note: retrieval source (and version, when
+  recorded) plus the source's required attribution — CAS Common
+  Chemistry results now carry the CC BY-NC 4.0 terms into the
+  rendered document. `Provenance#note_text` renders the record; the
+  note is suppressed when it would duplicate publisher/docidentifier.
+  The Metanorma plugin and `asciichem cite` inherit it through the
+  shared Citation path.
+
 ## [0.31.10] - 2026-11-05
 
 ### Changed

data/README.adoc

@@ -60,7 +60,7 @@ a level without the green corpus run behind it does not ship.
 |L1 semantics |yes |wire form validates against the v1 schemas and round-trips; the perception pass (implicit hydrogens, aromatic rings) is corpus-gated
 |L2 render |yes |MathML byte-goldens, canonical text, and the wire form for every construct
 |L3 stereo |yes |tetrahedral chirality, directional bonds, wedge/hash; parity-correct canonical SMILES including ring closures
-|L4 identity |partial |opt-in InChI engine with stereo layers, OPSIN adapter, identifier cross-check, citation bibitems; CAS source decision pending
+|L4 identity |yes |opt-in InChI engine (binary or native) with stereo layers, OPSIN adapter, identifier cross-check, resolver (PubChem, OPSIN, and Common Chemistry on by default — CC BY-NC attribution carried everywhere; limit sources with `Resolver.resolve(sources:)`), citation bibitems
 |===
 
 TypeScript and Python claim the same levels they pass; see their

data/lib/asciichem/citation.rb

@@ -84,9 +84,15 @@ module AsciiChem
       #
       #   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?
+      #
+      # `sources:` limits the citable set (an allow-list): cited
+      # sources outside it are skipped — the document pipeline (the
+      # metanorma plugin's `asciichem-sources` attribute) warns about
+      # the exclusions; the gem stays silent and total.
+      def for_molecule(molecule, cache: nil, fetch: nil, sources: nil)
+        citable = citation_sources(molecule)
+        citable &= Array(sources).map(&:to_s) if sources
+        return [] if citable.empty?
 
         convention, value = lookup_key(molecule)
         unless value
@@ -95,7 +101,7 @@ module AsciiChem
                 '(annotate @cas/@inchikey/@smiles or @name)'
         end
 
-        sources.filter_map do |source|
+        citable.filter_map do |source|
           substance = AsciiChem::Resolver[source].new.resolve(
             value: value, convention: convention, cache: cache, fetch: fetch
           )
@@ -108,7 +114,8 @@ module AsciiChem
       private
 
       # The version-independent field payload: one hash describing the
-      # citation, translated to Relaton objects by RelatonApi.
+      # citation, translated to Relaton objects by RelatonApi. The
+      # provenance record travels as `notes` (Provenance#note_text).
       def fields(substance, profile, provenance)
         publisher = profile.publisher || provenance.source
         {
@@ -119,7 +126,8 @@ module AsciiChem
           publisher: publisher,
           accessed_on: accessed_on(provenance),
           link: profile.link_for.call(substance),
-          keywords: substance.identifiers.map { |i| "#{i.convention}=#{i.value}" }
+          keywords: substance.identifiers.map { |i| "#{i.convention}=#{i.value}" },
+          notes: [provenance.note_text].compact
         }
       end
 
@@ -203,11 +211,23 @@ module AsciiChem
             docidentifier: [docidentifier(fields[:docid])],
             contributor: [contributor(fields[:publisher])],
             date: [Relaton::Bib::Date.new(type: 'accessed', at: fields[:accessed_on])],
-            source: fields[:link] ? [Relaton::Bib::Uri.new(type: 'src', content: fields[:link])] : [],
-            keyword: fields[:keywords].map { |text| keyword(text) }
+            source: links(fields),
+            keyword: fields[:keywords].map { |text| keyword(text) },
+            note: notes(fields)
           )
         end
 
+        def links(fields)
+          fields[:link] ? [Relaton::Bib::Uri.new(type: 'src', content: fields[:link])] : []
+        end
+
+        # The provenance record as a bibliographic note (TODO.v2
+        # item 3): retrieval source/version and the source's required
+        # attribution — licence terms must survive into the document.
+        def notes(fields)
+          fields[:notes].map { |text| Relaton::Bib::Note.new(type: 'provenance', content: text) }
+        end
+
         def docidentifier(docid)
           Relaton::Bib::Docidentifier.new(type: docid[:type], content: docid[:id])
         end

data/lib/asciichem/inchi/native_engine.rb

@@ -44,7 +44,9 @@ module AsciiChem
       def call(molfile, function)
         binding_class = self.class.binding_class(@lib)
         pointer = binding_class.public_send(function, molfile)
-        unless pointer
+        # An FFI null return is a TRUTHY pointer object — `unless pointer`
+        # never fires; nil?/null? is the only correct emptiness test.
+        if pointer.nil? || pointer.null?
           message = binding_class.last_error
           raise AsciiChem::Error, "chemomer native engine: #{message || 'call failed'}"
         end

data/lib/asciichem/resolver/common_chemistry.rb

@@ -7,16 +7,15 @@ module AsciiChem
   module Resolver
     # CAS Common Chemistry source adapter (TODO.impl 40; TODO.v2 07).
     #
-    # License posture (maintainer sign-off 2026-09-13): Common
-    # Chemistry data is CC BY-NC 4.0 — this adapter is OPT-IN and never
-    # self-registers; users register it explicitly:
-    #
-    #   AsciiChem::Resolver.register(:common_chemistry,
-    #                                 AsciiChem::Resolver::CommonChemistry)
-    #
-    # Every result carries the required attribution.
+    # License posture (maintainer decision 2026-11-11): Common
+    # Chemistry data is CC BY-NC 4.0 — acceptable to enable by
+    # default; every result carries the required attribution, and the
+    # citation track carries it into rendered documents. Documents
+    # that must stay NC-free limit sources with the
+    # `asciichem-sources` attribute (metanorma-plugin-asciichem) or
+    # `Resolver.resolve(sources:)`.
     class CommonChemistry < Adapter
-      source_name :common_chemistry, register: false
+      source_name :common_chemistry
       supports "cas"
 
       BASE = "https://commonchemistry.cas.org/api/detail"

data/lib/asciichem/resolver/substance.rb

@@ -5,7 +5,19 @@ module AsciiChem
     # Domain value objects for resolution results. These are data
     # carriers; (de)serialization to the canonical wire form goes
     # through the lutaml-model Wire classes only.
-    Provenance = Struct.new(:source, :retrieved_at, :source_version, :attribution, keyword_init: true)
+    Provenance = Struct.new(:source, :retrieved_at, :source_version, :attribution, keyword_init: true) do
+      # The provenance record as one sentence (the citation track's
+      # bibitem note): retrieval source and version plus the source's
+      # required attribution — licence terms (CAS Common Chemistry is
+      # CC BY-NC 4.0) must survive into the rendered document. Nil
+      # when there is nothing beyond the source name itself.
+      def note_text
+        details = [source_version && "version #{source_version}", attribution].compact
+        return nil if details.empty?
+
+        "Retrieved from #{source}; #{details.join('; ')}"
+      end
+    end
     Identifier = Struct.new(:value, :convention, :provenance, keyword_init: true)
     Property = Struct.new(:name, :value, :units, :provenance, keyword_init: true)
 

data/lib/asciichem/resolver.rb

@@ -9,10 +9,13 @@ module AsciiChem
   # citation track (TODO.v2 08) emits one bibitem per (substance,
   # source) the user chooses to cite.
   #
-  # Sources are opt-in adapters that self-register (OCP, same pattern
-  # as the linter checks). NC-licensed sources are never registered by
-  # default — Common Chemistry ships only after the maintainer
-  # sign-off recorded in TODO.v2 07.
+  # Sources are adapters that self-register (OCP, same pattern
+  # as the linter checks). All shipped sources are on by default;
+  # every result carries its source's required attribution (Common
+  # Chemistry: CC BY-NC 4.0 — default-on per the maintainer decision
+  # of 2026-11-11). Callers limit the set explicitly:
+  # `Resolver.resolve(sources:)` or the metanorma plugin's
+  # `asciichem-sources` attribute for NC-free documents.
   module Resolver
     autoload :Adapter, "asciichem/resolver/adapter"
     autoload :Cache, "asciichem/resolver/cache"
@@ -71,9 +74,10 @@ module AsciiChem
       end
     end
 
-    # Open, permissive sources register eagerly. CommonChemistry is
-    # CC BY-NC 4.0: it loads (autoload) but never self-registers —
-    # users opt in explicitly via Resolver.register.
+    # Every shipped source self-registers eagerly (autoload fires the
+    # class bodies). CommonChemistry is CC BY-NC 4.0 and default-on
+    # per the maintainer decision of 2026-11-11; callers that need
+    # NC-free resolution limit sources explicitly.
     adapters
     constants.each { |c| const_get(c) unless c == :Conflict }
   end

data/lib/asciichem/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module AsciiChem
-  VERSION = "0.31.10"
+  VERSION = "0.31.12"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: asciichem
 version: !ruby/object:Gem::Version
-  version: 0.31.10
+  version: 0.31.12
 platform: ruby
 authors:
 - Ribose Inc.