chemicalml 0.1.0

data/lib/chemicalml/cml/bond_stereo.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::BondStereo.
+module Chemicalml
+  module Cml
+    remove_const(:BondStereo) if const_defined?(:BondStereo, false)
+    const_set(:BondStereo, Chemicalml::Cml::Schema3::BondStereo)
+  end
+end

data/lib/chemicalml/cml/cml_module.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::Module.
+module Chemicalml
+  module Cml
+    remove_const(:Module) if const_defined?(:Module, false)
+    const_set(:Module, Chemicalml::Cml::Schema3::Module)
+  end
+end

data/lib/chemicalml/cml/dictionary.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::Dictionary.
+module Chemicalml
+  module Cml
+    remove_const(:Dictionary) if const_defined?(:Dictionary, false)
+    const_set(:Dictionary, Chemicalml::Cml::Schema3::Dictionary)
+  end
+end

data/lib/chemicalml/cml/dictionary_entry.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::DictionaryEntry.
+module Chemicalml
+  module Cml
+    remove_const(:DictionaryEntry) if const_defined?(:DictionaryEntry, false)
+    const_set(:DictionaryEntry, Chemicalml::Cml::Schema3::DictionaryEntry)
+  end
+end

data/lib/chemicalml/cml/document.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::Document.
+module Chemicalml
+  module Cml
+    remove_const(:Document) if const_defined?(:Document, false)
+    const_set(:Document, Chemicalml::Cml::Schema3::Document)
+  end
+end

data/lib/chemicalml/cml/elements.rb

@@ -0,0 +1,58 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    # Single source of truth for the set of CML element wire classes
+    # each schema version must register. Adding a new CML element =
+    # adding one entry to `ALL`. Both `Schema3::Configuration` and
+    # `Schema24::Configuration` walk this list.
+    module Elements
+      # Maps the Ruby class name (Symbol, e.g. `:Atom`) to the XML
+      # element id used in the lutaml-model type registry
+      # (e.g. `:atom`, `:atomArray`).
+      ALL = {
+        Array:           :array,
+        Atom:            :atom,
+        AtomArray:       :atomArray,
+        AtomParity:      :atomParity,
+        Bond:            :bond,
+        BondArray:       :bondArray,
+        BondStereo:      :bondStereo,
+        Dictionary:      :dictionary,
+        DictionaryEntry: :entry,
+        Document:        :document,
+        Formula:         :formula,
+        Identifier:      :identifier,
+        Label:           :label,
+        List:            :list,
+        Matrix:          :matrix,
+        Metadata:        :metadata,
+        MetadataList:    :metadataList,
+        Module:          :module,
+        Molecule:        :molecule,
+        Name:            :name,
+        Parameter:       :parameter,
+        ParameterList:   :parameterList,
+        Product:         :product,
+        ProductList:     :productList,
+        Property:        :property,
+        PropertyList:    :propertyList,
+        Reaction:        :reaction,
+        ReactionList:    :reactionList,
+        Reactant:        :reactant,
+        ReactantList:    :reactantList,
+        Scalar:          :scalar,
+        Substance:       :substance,
+        Unit:            :unit,
+        UnitList:        :unitList,
+        UnitType:        :unitType,
+        UnitTypeList:    :unitTypeList,
+      }.freeze
+
+      # Elements that exist in Schema 3 but NOT in Schema 2.4. Used by
+      # `Schema24::Configuration` to skip registration of classes that
+      # don't exist for that version.
+      SCHEMA3_ONLY = %i[Module].freeze
+    end
+  end
+end

data/lib/chemicalml/cml/formula.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::Formula.
+module Chemicalml
+  module Cml
+    remove_const(:Formula) if const_defined?(:Formula, false)
+    const_set(:Formula, Chemicalml::Cml::Schema3::Formula)
+  end
+end

data/lib/chemicalml/cml/identifier.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::Identifier.
+module Chemicalml
+  module Cml
+    remove_const(:Identifier) if const_defined?(:Identifier, false)
+    const_set(:Identifier, Chemicalml::Cml::Schema3::Identifier)
+  end
+end

data/lib/chemicalml/cml/label.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::Label.
+module Chemicalml
+  module Cml
+    remove_const(:Label) if const_defined?(:Label, false)
+    const_set(:Label, Chemicalml::Cml::Schema3::Label)
+  end
+end

data/lib/chemicalml/cml/list.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::List.
+module Chemicalml
+  module Cml
+    remove_const(:List) if const_defined?(:List, false)
+    const_set(:List, Chemicalml::Cml::Schema3::List)
+  end
+end

data/lib/chemicalml/cml/matrix.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::Matrix.
+module Chemicalml
+  module Cml
+    remove_const(:Matrix) if const_defined?(:Matrix, false)
+    const_set(:Matrix, Chemicalml::Cml::Schema3::Matrix)
+  end
+end

data/lib/chemicalml/cml/metadata.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::Metadata.
+module Chemicalml
+  module Cml
+    remove_const(:Metadata) if const_defined?(:Metadata, false)
+    const_set(:Metadata, Chemicalml::Cml::Schema3::Metadata)
+  end
+end

data/lib/chemicalml/cml/metadata_list.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::MetadataList.
+module Chemicalml
+  module Cml
+    remove_const(:MetadataList) if const_defined?(:MetadataList, false)
+    const_set(:MetadataList, Chemicalml::Cml::Schema3::MetadataList)
+  end
+end

data/lib/chemicalml/cml/molecule.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::Molecule.
+module Chemicalml
+  module Cml
+    remove_const(:Molecule) if const_defined?(:Molecule, false)
+    const_set(:Molecule, Chemicalml::Cml::Schema3::Molecule)
+  end
+end

data/lib/chemicalml/cml/name.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::Name.
+module Chemicalml
+  module Cml
+    remove_const(:Name) if const_defined?(:Name, false)
+    const_set(:Name, Chemicalml::Cml::Schema3::Name)
+  end
+end

data/lib/chemicalml/cml/namespace.rb

@@ -0,0 +1,17 @@
+# frozen_string_literal: true
+
+
+module Chemicalml
+  module Cml
+    # The default CML XML namespace. CML itself doesn't actually
+    # declare a mandatory namespace URI on its root — most published
+    # CML files use the bare element names. We declare this for
+    # future schema-validation work and so consumers can request
+    # namespaced output via the `namespace:` serialisation option.
+    class Namespace < Lutaml::Xml::W3c::XmlNamespace
+      uri "http://www.xml-cml.org/schema"
+      prefix_default "cml"
+      element_form_default :unqualified
+    end
+  end
+end

data/lib/chemicalml/cml/parameter.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::Parameter.
+module Chemicalml
+  module Cml
+    remove_const(:Parameter) if const_defined?(:Parameter, false)
+    const_set(:Parameter, Chemicalml::Cml::Schema3::Parameter)
+  end
+end

data/lib/chemicalml/cml/parameter_list.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::ParameterList.
+module Chemicalml
+  module Cml
+    remove_const(:ParameterList) if const_defined?(:ParameterList, false)
+    const_set(:ParameterList, Chemicalml::Cml::Schema3::ParameterList)
+  end
+end

data/lib/chemicalml/cml/product.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::Product.
+module Chemicalml
+  module Cml
+    remove_const(:Product) if const_defined?(:Product, false)
+    const_set(:Product, Chemicalml::Cml::Schema3::Product)
+  end
+end

data/lib/chemicalml/cml/product_list.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::ProductList.
+module Chemicalml
+  module Cml
+    remove_const(:ProductList) if const_defined?(:ProductList, false)
+    const_set(:ProductList, Chemicalml::Cml::Schema3::ProductList)
+  end
+end

data/lib/chemicalml/cml/property.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::Property.
+module Chemicalml
+  module Cml
+    remove_const(:Property) if const_defined?(:Property, false)
+    const_set(:Property, Chemicalml::Cml::Schema3::Property)
+  end
+end

data/lib/chemicalml/cml/property_list.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::PropertyList.
+module Chemicalml
+  module Cml
+    remove_const(:PropertyList) if const_defined?(:PropertyList, false)
+    const_set(:PropertyList, Chemicalml::Cml::Schema3::PropertyList)
+  end
+end

data/lib/chemicalml/cml/reactant.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::Reactant.
+module Chemicalml
+  module Cml
+    remove_const(:Reactant) if const_defined?(:Reactant, false)
+    const_set(:Reactant, Chemicalml::Cml::Schema3::Reactant)
+  end
+end

data/lib/chemicalml/cml/reactant_list.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::ReactantList.
+module Chemicalml
+  module Cml
+    remove_const(:ReactantList) if const_defined?(:ReactantList, false)
+    const_set(:ReactantList, Chemicalml::Cml::Schema3::ReactantList)
+  end
+end

data/lib/chemicalml/cml/reaction.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::Reaction.
+module Chemicalml
+  module Cml
+    remove_const(:Reaction) if const_defined?(:Reaction, false)
+    const_set(:Reaction, Chemicalml::Cml::Schema3::Reaction)
+  end
+end

data/lib/chemicalml/cml/reaction_list.rb

@@ -0,0 +1,10 @@
+# frozen_string_literal: true
+
+# Backward-compatible alias. New code should reference the versioned
+# class directly: Chemicalml::Cml::Schema3::ReactionList.
+module Chemicalml
+  module Cml
+    remove_const(:ReactionList) if const_defined?(:ReactionList, false)
+    const_set(:ReactionList, Chemicalml::Cml::Schema3::ReactionList)
+  end
+end

data/lib/chemicalml/cml/role/array.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for any wire class implementing the CML
+      # <array> element, regardless of schema version.
+      # Included by Schema3::Array and Schema24::Array.
+      module Array
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/atom.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for any wire class implementing the CML
+      # <atom> element, regardless of schema version.
+      # Included by Schema3::Atom and Schema24::Atom.
+      module Atom
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/atom_array.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for any wire class implementing the CML
+      # <atomarray> element, regardless of schema version.
+      # Included by Schema3::AtomArray and Schema24::AtomArray.
+      module AtomArray
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/atom_parity.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for any wire class implementing the CML
+      # <atomparity> element, regardless of schema version.
+      # Included by Schema3::AtomParity and Schema24::AtomParity.
+      module AtomParity
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/bond.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for any wire class implementing the CML
+      # <bond> element, regardless of schema version.
+      # Included by Schema3::Bond and Schema24::Bond.
+      module Bond
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/bond_array.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for any wire class implementing the CML
+      # <bondarray> element, regardless of schema version.
+      # Included by Schema3::BondArray and Schema24::BondArray.
+      module BondArray
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/bond_stereo.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for any wire class implementing the CML
+      # <bondstereo> element, regardless of schema version.
+      # Included by Schema3::BondStereo and Schema24::BondStereo.
+      module BondStereo
+      end
+    end
+  end
+end

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

@@ -0,0 +1,14 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for any wire class implementing the CML
+      # <module> element. Included by Schema3::Module.
+      # (Schema24::Module does not exist - schema 2.4 lacks the
+      # generic <module> element.)
+      module Module
+      end
+    end
+  end
+end

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

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for any wire class implementing the CML
+      # <dictionary> element, regardless of schema version.
+      # Included by Schema3::Dictionary and Schema24::Dictionary.
+      module Dictionary
+      end
+    end
+  end
+end

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

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for any wire class implementing the CML
+      # <dictionaryentry> element, regardless of schema version.
+      # Included by Schema3::DictionaryEntry and Schema24::DictionaryEntry.
+      module DictionaryEntry
+      end
+    end
+  end
+end

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

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for any wire class implementing the CML
+      # <document> element, regardless of schema version.
+      # Included by Schema3::Document and Schema24::Document.
+      module Document
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/formula.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for any wire class implementing the CML
+      # <formula> element, regardless of schema version.
+      # Included by Schema3::Formula and Schema24::Formula.
+      module Formula
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/identifier.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for any wire class implementing the CML
+      # <identifier> element, regardless of schema version.
+      # Included by Schema3::Identifier and Schema24::Identifier.
+      module Identifier
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/label.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for any wire class implementing the CML
+      # <label> element, regardless of schema version.
+      # Included by Schema3::Label and Schema24::Label.
+      module Label
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/list.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for any wire class implementing the CML
+      # <list> element, regardless of schema version.
+      # Included by Schema3::List and Schema24::List.
+      module List
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/matrix.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for any wire class implementing the CML
+      # <matrix> element, regardless of schema version.
+      # Included by Schema3::Matrix and Schema24::Matrix.
+      module Matrix
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/metadata.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for any wire class implementing the CML
+      # <metadata> element, regardless of schema version.
+      # Included by Schema3::Metadata and Schema24::Metadata.
+      module Metadata
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/metadata_list.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for any wire class implementing the CML
+      # <metadatalist> element, regardless of schema version.
+      # Included by Schema3::MetadataList and Schema24::MetadataList.
+      module MetadataList
+      end
+    end
+  end
+end

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

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for any wire class implementing the CML
+      # <molecule> element, regardless of schema version.
+      # Included by Schema3::Molecule and Schema24::Molecule.
+      module Molecule
+      end
+    end
+  end
+end

data/lib/chemicalml/cml/role/name.rb

@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+module Chemicalml
+  module Cml
+    module Role
+      # Type marker for any wire class implementing the CML
+      # <name> element, regardless of schema version.
+      # Included by Schema3::Name and Schema24::Name.
+      module Name
+      end
+    end
+  end
+end