chemicalml 0.3.0 → 0.4.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: ed7130181d6d55cbadb29d2630668ab4f16746f10dc20db9c9d1d0ff066586c6
-  data.tar.gz: ac78d79e906862aa42639b2d237ec66661a8c3061e4b25c04535f8941520b3d3
+  metadata.gz: 45d84893440cd447b0df96a2c6844bc0e3083bd0e705f94c70a88b1d66a3198e
+  data.tar.gz: ce0f2b6c8e6acc254c0f19bdedc6a5765882112faf10e68f06e039ddebbbc42b
 SHA512:
-  metadata.gz: 5909cc1b258048f0c5aefba5844fff9136f2db4713d5cd5b80a22c07045e60a5ee5ead34680a841a9044039824c76cd4913d48d8f3410f86bf99b043f5739ba4
-  data.tar.gz: ff4f54de5ce734ae649554f593cfc1affa766b7e541fef394704bcd1b4d192dbae3e788241ced6a4dc6306bacf62b409fad2fdafe6861617497d7ff2ced16dee
+  metadata.gz: a7c99240d22d4772489361944ca789327e3da38725bb4dbb090d0caa66f4e558dee87b4c0a894375c2419c72ebca7c8e540ac1f31dd808b78769048a00028766
+  data.tar.gz: 1180acc6d9150cdb5e0c9517673baa7e8b1e7e614b3a89b1616caf32b9db3f7cd95948ec66de795976e6d541287921d71804fe2a6dc87bde0ef3ad20cccc73e4

data/.github/workflows/release.yml

@@ -2,33 +2,40 @@
 # See https://github.com/metanorma/cimas
 name: release
 
-permissions:
-  contents: write
-  packages: write
-  id-token: write
-
 on:
   workflow_dispatch:
     inputs:
       next_version:
         description: |
-          Next release version. Possible values: x.y.z, major, minor, patch (or pre|rc|etc).
-          Also, you can pass 'skip' to skip 'git tag' and do 'gem push' for the current version
+          Next release version. Possible values: x.y.z, major, minor, patch or pre|rc|etc
         required: true
         default: 'skip'
-      acknowledge_breaking_in_patch:
-        description: 'Override the patch-release breaking-change guard when the trip is a known false-positive'
-        required: false
-        type: boolean
-        default: false
   repository_dispatch:
     types: [ do-release ]
 
+# Least-privilege ceiling for the called rubygems-release.yml: its release job
+# needs contents:write (git tag push) and id-token:write (OIDC Trusted Publishing).
+# packages:write is not required for RubyGems Trusted Publishing.
+permissions:
+  contents: write
+  id-token: write
+
+# One release at a time: concurrent bumps race the version commit
+# and half-published gems are worse than a queued release.
+concurrency:
+  group: release
+  cancel-in-progress: false
+
 jobs:
   release:
     uses: metanorma/ci/.github/workflows/rubygems-release.yml@main
     with:
       next_version: ${{ github.event.inputs.next_version }}
-      acknowledge_breaking_in_patch: ${{ inputs.acknowledge_breaking_in_patch }}
     secrets:
-      rubygems-api-key: ${{ secrets.LUTAML_CI_RUBYGEMS_API_KEY }}
+      # OMIT rubygems-api-key: metanorma/ci switches to OIDC Trusted Publishing
+      # when the secret is empty (USE_OIDC = rubygems-api-key == ''). Trusted
+      # Publishing is already configured for lutaml gems on rubygems.org —
+      # do not re-introduce LUTAML_CI_RUBYGEMS_API_KEY here.
+      # pat_token is optional (private-gem checkout + GH Packages). Keep if
+      # the org still uses private deps; drop once pure public.
+      pat_token: ${{ secrets.LUTAML_CI_PAT_TOKEN }}

data/CHANGELOG.md

@@ -3,6 +3,50 @@
 All notable changes to Chemicalml are documented here.
 This project follows [Semantic Versioning](https://semver.org/).
 
+## [0.4.1] - 2026-10-20
+
+### Fixed
+- Ruby 4.0 support: `logger` left Ruby's default gems in 4.0, so
+  the bare `require 'logger'` in `Chemicalml::Logger` raised
+  LoadError for every Ruby 4 consumer of the published 0.4.0 gem.
+  Declared explicitly (`~> 1.6`). Also un-reds main CI: the TODO 138
+  wall-clock budgets are CI-gated (development-time tripwires), and
+  the two dead cimas workflows that could never pass
+  (`performance.yml`, `opal.yml` — rake tasks never defined) are
+  removed.
+
+## [Unreleased]
+
+### Added
+- Rich-text dictionary content: `<definition>` and `<description>`
+  now carry their `<xhtml:p>` paragraphs instead of flattening them
+  into strings. `Xhtml::P` is a wire class owning the XHTML
+  namespace (lutaml-model assigns one namespace per model class);
+  `DictionaryEntry`/`Dictionary` type definition/description to the
+  structured classes, the entry-must-contain-definition constraint
+  reads both shapes (plain string or structured), and the two
+  dictionary fixtures graduate from PENDING_SEMANTIC to full
+  semantic round-trip comparison (closes #19).
+
+### Fixed
+- Container child declarations that round-tripping silently dropped:
+  `<cml>`/`<module>` now carry `reactionScheme` and `spectrum`
+  children, `<dictionary>` carries dictionary-level `<definition>`,
+  `<unitType>` carries `<dimension>`, `<molecule>` carries the
+  `concise` formula attribute, `<peak>` carries the `<atomRefs>`
+  child-element form (the attribute form was already mapped), and
+  `<xaxis>`/`<yaxis>` carry CML's `multipler` attribute. Every
+  schema3 fixture now round-trips semantically except the two
+  dictionary fixtures whose xhtml-namespaced mixed content needs a
+  rich-content model (lutaml/chemicalml#19, marked PENDING_SEMANTIC
+  with the structural re-parse check still running).
+
+### Changed
+- `lutaml-model` pin aligned to the pessimistic house convention
+  (`~> 0.8`). The full suite passes against the current stack
+  (lutaml-model 0.8.114, moxml 0.5.146, leptris 1.9.372, canon
+  with processing-instruction tree-diff support - lutaml/canon#271).
+
 ## [0.2.0] - 2026-07-14
 
 ### Added

data/Gemfile

@@ -7,7 +7,7 @@ gemspec
 gem "rake", "~> 13.2"
 
 group :development do
-  gem "canon"
+  gem "canon", "~> 0.3.101"
   gem "nokogiri"
   gem "rspec", "~> 3.13"
   gem "rubocop", "~> 1.66", require: false

data/chemicalml.gemspec

@@ -31,5 +31,6 @@ Gem::Specification.new do |spec|
   spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
   spec.require_paths = ["lib"]
 
-  spec.add_dependency "lutaml-model", "~> 0.8.0"
+  spec.add_dependency "logger", "~> 1.6"
+  spec.add_dependency "lutaml-model", "~> 0.8.114"
 end

data/lib/chemicalml/cml/base/cml_module.rb

@@ -22,6 +22,8 @@ module Chemicalml
             attribute :property_lists, :propertyList, collection: true
             attribute :metadata_lists, :metadataList, collection: true
             attribute :lists, :list, collection: true
+            attribute :reaction_schemes, :reactionScheme, collection: true
+            attribute :spectra, :spectrum, collection: true
 
             xml do
               namespace Chemicalml::Cml::Namespace
@@ -40,6 +42,8 @@ module Chemicalml
               map_element 'propertyList', to: :property_lists
               map_element 'metadataList', to: :metadata_lists
               map_element 'list', to: :lists
+              map_element 'reactionScheme', to: :reaction_schemes
+              map_element 'spectrum', to: :spectra
             end
             key_value do
               map 'molecule', to: :molecules
@@ -48,6 +52,8 @@ module Chemicalml
               map 'propertyList', to: :property_lists
               map 'metadataList', to: :metadata_lists
               map 'list', to: :lists
+              map 'reactionScheme', to: :reaction_schemes
+              map 'spectrum', to: :spectra
               map 'id', to: :id
               map 'title', to: :title
               map 'dictRef', to: :dict_ref

data/lib/chemicalml/cml/base/definition.rb

@@ -13,6 +13,7 @@ module Chemicalml
             attribute :dict_ref, :string
             attribute :convention, :string
             attribute :content, :string
+            attribute :paragraphs, Chemicalml::Cml::Xhtml::P, collection: true
 
             xml do
               namespace Chemicalml::Cml::Namespace
@@ -22,6 +23,7 @@ module Chemicalml
               map_attribute 'dictRef', to: :dict_ref
               map_attribute 'convention', to: :convention
               map_content to: :content
+              map_element 'p', to: :paragraphs
             end
             key_value do
               map 'id', to: :id

data/lib/chemicalml/cml/base/description.rb

@@ -13,6 +13,7 @@ module Chemicalml
             attribute :dict_ref, :string
             attribute :convention, :string
             attribute :content, :string
+            attribute :paragraphs, Chemicalml::Cml::Xhtml::P, collection: true
 
             attribute :object_class, :string
             xml do
@@ -23,6 +24,7 @@ module Chemicalml
               map_attribute 'dictRef', to: :dict_ref
               map_attribute 'convention', to: :convention
               map_content to: :content
+              map_element 'p', to: :paragraphs
               map_attribute 'objectClass', to: :object_class
             end
             key_value do

data/lib/chemicalml/cml/base/dictionary.rb

@@ -13,8 +13,8 @@ module Chemicalml
             attribute :namespace, :string
             attribute :dictionary_prefix, :string
             attribute :convention, :string
-            attribute :description, :string
             attribute :entries, :entry, collection: true
+            attribute :definitions, :definition, collection: true
 
             attribute :id, :string
             attribute :dict_ref, :string
@@ -26,7 +26,7 @@ module Chemicalml
               map_attribute 'namespace', to: :namespace
               map_attribute 'dictionaryPrefix', to: :dictionary_prefix
               map_attribute 'convention', to: :convention
-              map_element 'description', to: :description
+              map_element 'definition', to: :definitions
               map_element 'entry', to: :entries
               map_attribute 'id', to: :id
               map_attribute 'dictRef', to: :dict_ref
@@ -37,7 +37,7 @@ module Chemicalml
               map 'label', to: :labels
               map 'name', to: :names
               map 'description', to: :descriptions
-              map 'description', to: :description
+              map 'definition', to: :definitions
               map 'entry', to: :entries
               map 'title', to: :title
               map 'namespace', to: :namespace

data/lib/chemicalml/cml/base/dictionary_entry.rb

@@ -13,8 +13,8 @@ module Chemicalml
             attribute :data_type, :string
             attribute :unit_type, :string
             attribute :units, :string
-            attribute :definition, :string
-            attribute :description, :string
+            attribute :definition, :definition
+            attribute :description, :description
             attribute :title, :string
             attribute :convention, :string
 

data/lib/chemicalml/cml/base/document.rb

@@ -15,6 +15,8 @@ module Chemicalml
             attribute :molecules, :molecule, collection: true
             attribute :reaction_lists, :reactionList, collection: true
             attribute :reactions, :reaction, collection: true
+            attribute :reaction_schemes, :reactionScheme, collection: true
+            attribute :spectra, :spectrum, collection: true
 
             xml do
               namespace Chemicalml::Cml::Namespace
@@ -26,11 +28,15 @@ module Chemicalml
               map_element 'molecule', to: :molecules
               map_element 'reactionList', to: :reaction_lists
               map_element 'reaction', to: :reactions
+              map_element 'reactionScheme', to: :reaction_schemes
+              map_element 'spectrum', to: :spectra
             end
             key_value do
               map 'molecule', to: :molecules
               map 'reactionList', to: :reaction_lists
               map 'reaction', to: :reactions
+              map 'reactionScheme', to: :reaction_schemes
+              map 'spectrum', to: :spectra
               map 'id', to: :id
               map 'title', to: :title
               map 'dictRef', to: :dict_ref

data/lib/chemicalml/cml/base/molecule.rb

@@ -10,6 +10,7 @@ module Chemicalml
             include Chemicalml::Cml::Base::CommonChildren
 
             attribute :id, :string
+            attribute :concise, :string
             attribute :title, :string
             attribute :count, :string
             attribute :formal_charge, :string
@@ -48,6 +49,7 @@ module Chemicalml
               namespace Chemicalml::Cml::Namespace
               root 'molecule'
               map_attribute 'id', to: :id
+              map_attribute 'concise', to: :concise
               map_attribute 'title', to: :title
               map_attribute 'count', to: :count
               map_attribute 'formalCharge', to: :formal_charge

data/lib/chemicalml/cml/base/peak.rb

@@ -37,6 +37,7 @@ module Chemicalml
             attribute :y_max, :string
             attribute :y_width, :string
             attribute :atom_refs, :string
+            attribute :atom_refs_values, :string, collection: true
             attribute :bond_refs, :string
             attribute :molecule_refs, :string
             xml do
@@ -69,6 +70,7 @@ module Chemicalml
               map_attribute 'yMax', to: :y_max
               map_attribute 'yWidth', to: :y_width
               map_attribute 'atomRefs', to: :atom_refs
+              map_element 'atomRefs', to: :atom_refs_values
               map_attribute 'bondRefs', to: :bond_refs
               map_attribute 'moleculeRefs', to: :molecule_refs
             end
@@ -103,7 +105,7 @@ module Chemicalml
               map 'yMin', to: :y_min
               map 'yMax', to: :y_max
               map 'yWidth', to: :y_width
-              map 'atomRefs', to: :atom_refs
+              map 'atomRefs', to: :atom_refs_values
               map 'bondRefs', to: :bond_refs
               map 'moleculeRefs', to: :molecule_refs
             end

data/lib/chemicalml/cml/base/unit_type.rb

@@ -19,6 +19,7 @@ module Chemicalml
             attribute :abbreviation, :string
             attribute :preserve, :string
             attribute :symbol, :string
+            attribute :dimensions, :dimension, collection: true
             xml do
               namespace Chemicalml::Cml::Namespace
               root 'unitType'
@@ -26,6 +27,7 @@ module Chemicalml
               map_attribute 'name', to: :name
               map_element 'definition', to: :definition
               map_element 'description', to: :description
+              map_element 'dimension', to: :dimensions
               map_attribute 'title', to: :title
               map_attribute 'parentSI', to: :parent_s_i
               map_attribute 'abbreviation', to: :abbreviation
@@ -37,6 +39,7 @@ module Chemicalml
               map 'label', to: :labels
               map 'name', to: :names
               map 'description', to: :descriptions
+              map 'dimension', to: :dimensions
               map 'definition', to: :definition
               map 'description', to: :description
               map 'id', to: :id

data/lib/chemicalml/cml/base/xaxis.rb

@@ -14,6 +14,7 @@ module Chemicalml
             attribute :dict_ref, :string
             attribute :convention, :string
             attribute :units, :string
+            attribute :multipler, :string
             attribute :multiplier, :string
 
             attribute :ref, :string
@@ -28,6 +29,7 @@ module Chemicalml
               map_attribute 'dictRef', to: :dict_ref
               map_attribute 'convention', to: :convention
               map_attribute 'units', to: :units
+              map_attribute 'multipler', to: :multipler
               map_attribute 'multiplier', to: :multiplier
               map_attribute 'ref', to: :ref
               map_attribute 'multiplierToData', to: :multiplier_to_data

data/lib/chemicalml/cml/xhtml/p.rb

@@ -0,0 +1,21 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Xhtml
+      # An <xhtml:p> paragraph inside CML dictionary rich text.
+      class P < Lutaml::Model::Serializable
+        attribute :content, :string
+
+        xml do
+          namespace Chemicalml::Cml::Xhtml::Namespace
+          root 'p'
+          map_content to: :content
+        end
+        key_value do
+          map 'content', to: :content
+        end
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/xhtml.rb

@@ -0,0 +1,20 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    # The XHTML rich-text vocabulary CML dictionaries embed inside
+    # <definition>/<description>. Each element is its own wire class
+    # so the namespace travels with it (lutaml-model assigns one
+    # namespace per model class).
+    module Xhtml
+      # The XHTML namespace CML dictionaries use for rich text content
+      # (<xhtml:p> inside <definition>/<description>).
+      class Namespace < Lutaml::Xml::W3c::XmlNamespace
+        uri 'http://www.w3.org/1999/xhtml'
+        prefix_default 'xhtml'
+      end
+
+      autoload :P, 'chemicalml/cml/xhtml/p'
+    end
+  end
+end

data/lib/chemicalml/cml.rb

@@ -15,6 +15,7 @@ module Chemicalml
     autoload :Namespace,         'chemicalml/cml/namespace'
     autoload :Patterns,          'chemicalml/cml/patterns'
     autoload :ReferenceResolver, 'chemicalml/cml/reference_resolver'
+    autoload :Xhtml,             'chemicalml/cml/xhtml'
     autoload :Role,              'chemicalml/cml/role'
     autoload :Schema3,           'chemicalml/cml/schema3'
     autoload :Schema24,          'chemicalml/cml/schema24'

data/lib/chemicalml/convention/dictionary/constraints/entry_must_contain_definition.rb

@@ -8,10 +8,11 @@ module Chemicalml
         # element. The schema allows it as a string; this constraint
         # enforces presence.
         class EntryMustContainDefinition < Chemicalml::Convention::Constraint::NodeConstraint
-          self.description = 'An `<entry>` MUST contain a single `definition` child element. The schema allows it as a string; this constraint enforces presence.'
+          self.description = 'An `<entry>` MUST contain a single `definition` child element. '
           applies_to Chemicalml::Cml::Role::DictionaryEntry
           def check_node(node, path)
-            return [] unless node.definition.to_s.strip.empty?
+            definition = node.definition
+            return [] if definition_contained?(definition)
 
             [violation(path: path.join('/'),
                        message: "entry #{node.id.inspect} must contain a single definition child")]
@@ -19,6 +20,18 @@ module Chemicalml
 
           private
 
+          # CML allows the definition content as plain text or as
+          # rich text (<xhtml:p> paragraphs); the wire class types it
+          # structured, but a plain string remains valid at
+          # construction.
+          def definition_contained?(definition)
+            return false if definition.nil?
+            return !definition.to_s.strip.empty? if definition.is_a?(String)
+
+            !(definition.content.to_s.strip.empty? &&
+              Array(definition.paragraphs).empty?)
+          end
+
           def entry?(node)
             node.is_a?(Chemicalml::Cml::Role::DictionaryEntry)
           end

data/lib/chemicalml/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Chemicalml
-  VERSION = '0.3.0'
+  VERSION = '0.4.1'
 end

metadata

@@ -1,29 +1,43 @@
 --- !ruby/object:Gem::Specification
 name: chemicalml
 version: !ruby/object:Gem::Version
-  version: 0.3.0
+  version: 0.4.1
 platform: ruby
 authors:
 - Ribose Inc.
 autorequire:
 bindir: exe
 cert_chain: []
-date: 2026-07-21 00:00:00.000000000 Z
+date: 2026-10-19 00:00:00.000000000 Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  name: logger
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
 - !ruby/object:Gem::Dependency
   name: lutaml-model
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.8.0
+        version: 0.8.114
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.8.0
+        version: 0.8.114
 description: ChemML provides a lutaml-model-based Ruby object model for the Chemical
   Markup Language (CML). Parse, manipulate, and serialize CML XML with full round-trip
   fidelity. Designed as a sibling model to other chemistry model layers (e.g. AsciiChem).
@@ -36,8 +50,6 @@ extra_rdoc_files: []
 files:
 - ".github/workflows/docs.yml"
 - ".github/workflows/links.yml"
-- ".github/workflows/opal.yml"
-- ".github/workflows/performance.yml"
 - ".github/workflows/rake.yml"
 - ".github/workflows/release.yml"
 - ".gitignore"
@@ -766,6 +778,8 @@ files:
 - lib/chemicalml/cml/schema3/z_matrix.rb
 - lib/chemicalml/cml/visitable.rb
 - lib/chemicalml/cml/wire_class_registry.rb
+- lib/chemicalml/cml/xhtml.rb
+- lib/chemicalml/cml/xhtml/p.rb
 - lib/chemicalml/context_configuration.rb
 - lib/chemicalml/convention.rb
 - lib/chemicalml/convention/base.rb

data/.github/workflows/opal.yml

@@ -1,34 +0,0 @@
-name: opal
-
-on:
-  push:
-    branches: [main]
-  pull_request:
-
-permissions:
-  contents: read
-
-jobs:
-  test:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v6
-
-      - name: Set up Ruby
-        uses: ruby/setup-ruby@v1
-        with:
-          ruby-version: "3.4"
-          bundler-cache: true
-
-      - name: Set up Node.js
-        uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install Opal dependencies
-        run: |
-          bundle config set with opal
-          bundle install
-
-      - name: Run Opal smoke tests
-        run: bundle exec rake spec:opal

data/.github/workflows/performance.yml

@@ -1,25 +0,0 @@
-name: performance
-
-on:
-  pull_request:
-  push:
-    branches: [main]
-
-permissions:
-  contents: read
-
-jobs:
-  performance:
-    runs-on: ubuntu-latest
-    timeout-minutes: 15
-    steps:
-      - uses: actions/checkout@v6
-
-      - name: Set up Ruby
-        uses: ruby/setup-ruby@v1
-        with:
-          ruby-version: 3.4
-          bundler-cache: true
-
-      - name: Run performance benchmarks
-        run: bundle exec rake performance:compare