asciichem 0.31.11 → 0.31.13

checksums.yaml

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data/CHANGELOG.md

@@ -3,6 +3,32 @@
 All notable changes to AsciiChem are documented here.
 This project follows [Semantic Versioning](https://semver.org/).
 
+## [0.31.13] - 2026-11-11
+
+### Fixed
+- `Resolver.resolve_all` isolates source-level failures: a live probe
+  found the Common Chemistry API now answers 401 without an API key
+  (CAS key-gated the endpoint); with it registered by default, that
+  401 raised through the multi-source fan-out and took the other
+  sources down with it. A source-level error now skips that source —
+  callers see what answered.
+
+### Changed
+- The README documents the full capability surface: structures,
+  lint, local identity, resolution with provenance, citations, and
+  the command line.
+
+## [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

data/README.adoc

@@ -45,6 +45,91 @@ formula.to_mathml  # => "<math>...</math>"
 formula.to_text    # => "H_2O"  (round trip)
 ----
 
+The parsed model is the canonical form: MathML, HTML, LaTeX, text,
+linear and 2D structural SVG, and CML are views over the same tree.
+
+=== Structures: SMILES and molfile in, AsciiChem out
+
+[source,ruby]
+----
+formula = AsciiChem.parse_smiles("CC(=O)Oc1ccccc1C(=O)O")
+formula.to_structural_svg   # 2D depiction, deterministic layout
+formula.to_smiles           # canonical aromatic SMILES
+formula.to_text             # AsciiChem text
+
+formula = AsciiChem.parse_molfile(molfile_text)   # V2000 in and out
+----
+
+=== Lint
+
+[source,ruby]
+----
+AsciiChem::Linter.run(formula)   # chemistry diagnostics: balance,
+                                 # valence, charge, isotopes, rings,
+                                 # identifier consistency, ...
+AsciiChem::Linter.errors?(formula) # => true/false
+----
+
+=== Local identity: InChI, AuxInfo, InChIKey
+
+[source,ruby]
+----
+require "asciichem/inchi"
+
+# the native chemomer engine (byte-exact vs the IUPAC oracle;
+# CHEMOMER_LIB points at the built cdylib) or the IUPAC binary:
+AsciiChem::Inchi.engine = AsciiChem::Inchi::NativeEngine.new
+
+identity = AsciiChem::Inchi.identity_for(molecule)
+identity.inchi     # "InChI=1S/C9H8O4/..."
+identity.inchikey  # "BSYNRYMUTXBXSQ-UHFFFAOYSA-N"
+----
+
+=== Resolution: identifiers to substance records
+
+[source,ruby]
+----
+require "asciichem/resolver"
+
+substance = AsciiChem::Resolver.resolve(value: "50-78-2", convention: "cas")
+substance.preferred_name        # => "Aspirin"
+substance.structure.to_smiles   # from the source record
+substance.identifiers.first.provenance.source   # "common_chemistry"
+
+# all shipped sources (PubChem, OPSIN, CAS Common Chemistry) resolve
+# by default; attribution rides every record. Limit the set when a
+# use must stay NC-free:
+AsciiChem::Resolver.resolve(value: "50-78-2", convention: "cas",
+                            sources: [:pubchem, :opsin])
+----
+
+=== Citations: dataset bibitems with provenance
+
+[source,ruby]
+----
+require "asciichem/citation"
+
+molecule = AsciiChem.parse("CC(=O)OC1=CC=CC=C1C(=O)O @cas(\"50-78-2\") @cite(\"pubchem\")").nodes.first
+AsciiChem::Citation.for_molecule(molecule)
+# => [["pubchem", #<Relaton bibitem>]] - one dataset-type bibitem per
+# (substance, source), anchored by InChIKey, with a provenance note
+# (retrieved from, version, attribution).
+----
+
+== Command line
+
+[source,sh]
+----
+asciichem convert -i "H_2O" -t mathml        # also: --from smiles|molfile
+asciichem identity -i aspirin.smiles --from smiles
+asciichem resolve --cas 50-78-2 --source common_chemistry
+asciichem validate -i 'H_2O @cas("50-78-2")'
+asciichem cite --cas 50-78-2 -t model-json
+asciichem lint -i "2H_2 + O_2 -> 2H_2O"
+asciichem roundtrip -i "C_6H_12O_6"
+asciichem parse-cml -i formula.xml
+----
+
 == Conformance
 
 The reference implementation of https://www.asciichem.org[the AsciiChem
@@ -60,7 +145,7 @@ 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
           )

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.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"
@@ -40,16 +43,23 @@ module AsciiChem
         raise Error, "unknown resolver source #{name.inspect} (registered: #{adapters.keys.sort.join(', ')})"
       end
 
-      # Resolves against every opt-in source, returning one Substance
-      # per source that answers (nil entries dropped). Sources answer
-      # in registration order.
+      # Resolves against every registered source (or the selected
+      # subset), returning one Substance per source that answers (nil
+      # entries dropped). Sources answer in registration order. A
+      # source-level failure (HTTP error, rejected request) skips that
+      # source — one dead or key-gated endpoint must not poison the
+      # others; callers see what answered.
       def resolve_all(value:, convention:, sources: nil, fetch: nil, cache: nil, refresh: false)
         selected = sources ? Array(sources).map { |s| self[s] } : adapters.values
         selected.filter_map do |adapter_class|
           adapter = adapter_class.new
           next unless adapter.supports?(convention)
 
-          adapter.resolve(value: value, convention: convention, fetch: fetch, cache: cache, refresh: refresh)
+          begin
+            adapter.resolve(value: value, convention: convention, fetch: fetch, cache: cache, refresh: refresh)
+          rescue AsciiChem::Error
+            nil
+          end
         end
       end
 
@@ -71,9 +81,10 @@ 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 = "0.31.11"
+  VERSION = "0.31.13"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: asciichem
 version: !ruby/object:Gem::Version
-  version: 0.31.11
+  version: 0.31.13
 platform: ruby
 authors:
 - Ribose Inc.