suma 0.1.23 → 0.1.24

checksums.yaml

@@ -1,7 +1,7 @@
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data/.rubocop_todo.yml

@@ -1,6 +1,6 @@
 # This configuration was generated by
 # `rubocop --auto-gen-config`
-# on 2025-10-05 11:55:30 UTC using RuboCop version 1.81.1.
+# on 2025-10-12 09:15:38 UTC using RuboCop version 1.81.1.
 # The point is for the user to remove these configuration records
 # one by one as the offenses are removed from the code base.
 # Note that changes in the inspected code, or installation of new
@@ -18,23 +18,51 @@ Gemspec/RequiredRubyVersion:
   Exclude:
     - 'suma.gemspec'
 
-# Offense count: 70
+# Offense count: 2
+# This cop supports safe autocorrection (--autocorrect).
+# Configuration parameters: EnforcedStyle, IndentationWidth.
+# SupportedStyles: with_first_argument, with_fixed_indentation
+Layout/ArgumentAlignment:
+  Exclude:
+    - 'spec/suma/cli/export_spec.rb'
+
+# Offense count: 1
+# This cop supports safe autocorrection (--autocorrect).
+# Configuration parameters: EnforcedStyleAlignWith.
+# SupportedStylesAlignWith: either, start_of_block, start_of_line
+Layout/BlockAlignment:
+  Exclude:
+    - 'spec/suma/cli/export_spec.rb'
+
+# Offense count: 1
+# This cop supports safe autocorrection (--autocorrect).
+Layout/BlockEndNewline:
+  Exclude:
+    - 'spec/suma/cli/export_spec.rb'
+
+# Offense count: 2
+# This cop supports safe autocorrection (--autocorrect).
+# Configuration parameters: Width, AllowedPatterns.
+Layout/IndentationWidth:
+  Exclude:
+    - 'spec/suma/cli/export_spec.rb'
+
+# Offense count: 74
 # This cop supports safe autocorrection (--autocorrect).
 # Configuration parameters: Max, AllowHeredoc, AllowURI, AllowQualifiedName, URISchemes, IgnoreCopDirectives, AllowedPatterns, SplitStrings.
 # URISchemes: http, https
 Layout/LineLength:
   Exclude:
-    - 'lib/suma/cli.rb'
     - 'lib/suma/cli/build.rb'
-    - 'lib/suma/cli/export.rb'
     - 'lib/suma/cli/validate.rb'
+    - 'lib/suma/collection_manifest.rb'
     - 'lib/suma/jsdai/figure.rb'
     - 'lib/suma/jsdai/figure_image.rb'
     - 'lib/suma/processor.rb'
     - 'lib/suma/schema_attachment.rb'
-    - 'lib/suma/schema_collection.rb'
     - 'lib/suma/schema_document.rb'
     - 'lib/suma/thor_ext.rb'
+    - 'spec/suma/cli/export_spec.rb'
     - 'spec/suma/cli/extract_terms_spec.rb'
     - 'spec/suma/cli/validate_ascii_spec.rb'
     - 'spec/suma/jsdai/figure_spec.rb'
@@ -74,11 +102,6 @@ Metrics/CyclomaticComplexity:
     - 'lib/suma/jsdai/figure_image.rb'
     - 'lib/suma/thor_ext.rb'
 
-# Offense count: 4
-# Configuration parameters: CountComments, CountAsOne, AllowedMethods, AllowedPatterns.
-Metrics/MethodLength:
-  Max: 13
-
 # Offense count: 1
 # Configuration parameters: AllowedMethods, AllowedPatterns, Max.
 Metrics/PerceivedComplexity:
@@ -94,20 +117,21 @@ Naming/VariableNumber:
     - 'spec/suma/cli/export_spec.rb'
     - 'spec/suma/cli/validate_ascii_spec.rb'
 
-# Offense count: 1
+# Offense count: 2
 # Configuration parameters: MinSize.
 Performance/CollectionLiteralInLoop:
   Exclude:
+    - 'spec/suma/cli/export_spec.rb'
     - 'spec/suma/cli_spec.rb'
 
-# Offense count: 1
+# Offense count: 2
 # Configuration parameters: Prefixes, AllowedPatterns.
 # Prefixes: when, with, without
 RSpec/ContextWording:
   Exclude:
     - 'spec/suma/cli/export_spec.rb'
 
-# Offense count: 32
+# Offense count: 37
 # Configuration parameters: CountAsOne.
 RSpec/ExampleLength:
   Max: 44
@@ -118,6 +142,24 @@ RSpec/IndexedLet:
   Exclude:
     - 'spec/suma/cli/export_spec.rb'
 
-# Offense count: 28
+# Offense count: 33
 RSpec/MultipleExpectations:
   Max: 12
+
+# Offense count: 1
+# Configuration parameters: CustomTransform, IgnoreMethods, IgnoreMetadata.
+RSpec/SpecFilePathFormat:
+  Exclude:
+    - '**/spec/routing/**/*'
+    - 'spec/suma/cli/expressir_spec.rb'
+
+# Offense count: 1
+# This cop supports safe autocorrection (--autocorrect).
+# Configuration parameters: EnforcedStyle, ProceduralMethods, FunctionalMethods, AllowedMethods, AllowedPatterns, AllowBracesOnProceduralOneLiners, BracesRequiredMethods.
+# SupportedStyles: line_count_based, semantic, braces_for_chaining, always_braces
+# ProceduralMethods: benchmark, bm, bmbm, create, each_with_object, measure, new, realtime, tap, with_object
+# FunctionalMethods: let, let!, subject, watch
+# AllowedMethods: lambda, proc, it
+Style/BlockDelimiters:
+  Exclude:
+    - 'spec/suma/cli/export_spec.rb'

data/README.adoc

@@ -138,8 +138,9 @@ $ suma validate SUBCOMMAND [options]
 ----
 
 Subcommands:
-- `links` - Validate EXPRESS links
-- `ascii` - Check for non-ASCII characters in EXPRESS files
+
+`links`:: Validate EXPRESS links
+`ascii`:: Check for non-ASCII characters in EXPRESS files
 
 ==== Links subcommand
 
@@ -552,38 +553,50 @@ list
 
 ==== General
 
-The `suma export` command exports EXPRESS schemas from a manifest file to a
-specified output directory. This command is useful for extracting plain or
-annotated EXPRESS schemas for distribution or further processing.
+The `suma export` command exports EXPRESS schemas from manifest files and/or
+standalone EXPRESS files to a specified output directory.
+
+This command is useful for extracting plain or annotated EXPRESS schemas for
+distribution or further processing.
 
 [source,sh]
 ----
-$ suma export MANIFEST_FILE [options]
+$ suma export -o OUTPUT_DIR FILE1 [FILE2 FILE3 ...]
 ----
 
 Parameters:
 
-`MANIFEST_FILE`:: Path to the EXPRESS schema manifest file (e.g., "schemas-srl.yml")
+`FILE1 [FILE2 FILE3 ...]`:: One or more files to export. Each file can be:
+
+An EXPRESS schema manifest file (`.yml`, `.yaml`)::: schemas listed in the
+manifest will be exported
+
+An standalone EXPRESS file (`.exp`)::: the schema will be exported directly
 
 Options:
 
 `--output=PATH`, `-o PATH`:: (required) Output directory path
 
-`--additional=PATH`, `-a PATH`:: Additional schemas manifest file to merge
-
 `--[no-]annotations`:: Include annotations (remarks/comments) in exported schemas (default: false)
 
 `--[no-]zip`:: Create ZIP archive of exported schemas (default: false)
 
 ==== Behavior
 
-The command exports schemas while preserving the directory structure from the
-manifest file paths:
+The command exports schemas based on the input file types:
+
+**For EXPRESS schema manifest files:**
 
+* Schemas are exported while preserving the directory structure from the manifest file paths
 * Schemas under `resources/` are exported to `OUTPUT/resources/`
 * Schemas under `modules/` are exported to `OUTPUT/modules/`
 * Other categories (`business_object_models/`, `core_model/`) follow the same pattern
 
+**For standalone EXPRESS files:**
+
+* Schemas are exported directly to the output directory root
+* Output filename format: `{schema_id}.exp`
+
 By default, schemas are exported without annotations (plain EXPRESS). Use the
 `--annotations` flag to include remarks and comments.
 
@@ -591,7 +604,7 @@ The `--zip` flag creates a ZIP archive in addition to the directory output,
 named `OUTPUT.zip`.
 
 [example]
-.To export schemas without annotations
+.To export schemas from a manifest file
 [source,sh]
 ----
 $ bundle exec suma export -o express-files schemas-srl.yml
@@ -599,52 +612,54 @@ $ bundle exec suma export -o express-files schemas-srl.yml
 ----
 
 [example]
-.To export schemas with annotations
+.To export a single plain schema
 [source,sh]
 ----
-$ bundle exec suma export -o express-files --annotations schemas-srl.yml
-# => generates express-files/ directory with annotated EXPRESS schemas
+$ bundle exec suma export -o express-files geometry_schema.exp
+# => generates express-files/geometry_schema.exp
 ----
 
 [example]
-.To export and create ZIP archive
+.To export multiple plain schemas
 [source,sh]
 ----
-$ bundle exec suma export -o express-files --zip schemas-srl.yml
-# => generates both:
-#    - express-files/ directory
-#    - express-files.zip archive
+$ bundle exec suma export -o express-files schema1.exp schema2.exp schema3.exp
+# => generates express-files/{schema1,schema2,schema3}.exp
 ----
 
 [example]
-.To merge additional schemas and export
+.To export from multiple manifest files
 [source,sh]
 ----
-$ bundle exec suma export -o express-files \
-    -a additional-schemas.yml \
-    schemas-srl.yml
+$ bundle exec suma export -o express-files schemas-srl.yml additional-schemas.yml
 # => exports schemas from both manifest files
 ----
 
 [example]
-.To merge multiple additional schemas
+.To export mix of manifest and plain schemas
 [source,sh]
 ----
-$ bundle exec suma export -o express-files \
-    -a additional-schemas-1.yml \
-    -a additional-schemas-2.yml \
-    schemas-srl.yml
-# => exports schemas from primary manifest and all additional manifests
+$ bundle exec suma export -o express-files schemas-srl.yml geometry_schema.exp
+# => exports schemas from manifest with directory structure
+#    plus geometry_schema.exp at the root
 ----
 
 [example]
-.To export with all options
+.To export schemas with annotations
 [source,sh]
 ----
-$ bundle exec suma export -o express-files \
-    -a additional-schemas.yml \
-    schemas-srl.yml
-# => exports schemas from both manifest files
+$ bundle exec suma export -o express-files --annotations schemas-srl.yml
+# => generates express-files/ directory with annotated EXPRESS schemas
+----
+
+[example]
+.To export and create ZIP archive
+[source,sh]
+----
+$ bundle exec suma export -o express-files --zip schemas-srl.yml
+# => generates both:
+#    - express-files/ directory
+#    - express-files.zip archive
 ----
 
 [example]
@@ -654,35 +669,197 @@ $ bundle exec suma export -o express-files \
 $ bundle exec suma export -o express-files \
     --annotations \
     --zip \
-    -a additional-schemas.yml \
-    schemas-srl.yml
-# => generates annotated schemas in both directory and ZIP format,
-#    including schemas from both manifest files
+    schemas-srl.yml geometry_schema.exp
+# => generates annotated schemas in both directory and ZIP format
 ----
 
 ==== Output structure
 
-The exported directory structure mirrors the schema paths in the manifest:
+The exported directory structure depends on the input file types:
 
 [source]
 ----
 express-files/
-├── resources/
+├── geometry_schema.exp          # standalone EXPRESS file (at root)
+├── topology_schema.exp          # standalone EXPRESS file (at root)
+├── resources/                   # from manifest files
 │   ├── action_schema/
 │   │   └── action_schema.exp
 │   └── ...
-├── modules/
+├── modules/                     # from manifest files
 │   ├── activity/
 │   │   ├── arm.exp
 │   │   └── mim.exp
 │   └── ...
-├── business_object_models/
+├── business_object_models/      # from manifest files
 │   └── ...
-└── core_model/
+└── core_model/                  # from manifest files
     └── ...
 ----
 
 
+=== Expressir command
+
+==== General
+
+The `suma expressir` command provides access to all Expressir commands for
+working with EXPRESS schemas. This includes documentation coverage analysis,
+schema formatting, validation, and other EXPRESS-related operations.
+
+Expressir is a comprehensive toolkit for EXPRESS schema processing that Suma
+integrates to provide additional functionality beyond Suma's core features.
+
+[source,sh]
+----
+$ suma expressir SUBCOMMAND ...ARGS [options]
+----
+
+Available subcommands:
+
+`coverage`:: Check documentation coverage of EXPRESS schemas
+`format`:: Pretty print EXPRESS schemas
+`clean`:: Strip remarks and prettify EXPRESS schemas
+`validate`:: Validate EXPRESS schemas
+`benchmark`:: Benchmark schema loading performance
+`version`:: Display expressir version
+
+==== Coverage subcommand
+
+The `coverage` subcommand analyzes EXPRESS schemas to determine documentation
+coverage, reporting how many EXPRESS objects (entities, constants, functions,
+types, etc.) have been documented with Annotated EXPRESS.
+
+This addresses the need to measure and improve documentation quality in EXPRESS
+schema collections.
+
+[source,sh]
+----
+$ suma expressir coverage PATH [PATH...] [options]
+----
+
+Parameters:
+
+`PATH`:: One or more paths to analyze. Each path can be:
++
+--
+* An EXPRESS schema manifest file (`.yml`, `.yaml`)
+* A single EXPRESS file (`.exp`)
+* A directory containing EXPRESS files
+--
+
+Options:
+
+`--format=FORMAT`:: Output format: `text` (default), `json`, or `yaml`
+`--output=FILE`:: Output file path for JSON/YAML formats (defaults to
+`coverage_report.json` or `coverage_report.yaml`)
+`--exclude=TYPES`:: Comma-separated list of EXPRESS entity types to exclude
+from coverage analysis (e.g., `TYPE,CONSTANT,TYPE:SELECT`)
+`--ignore-files=FILE`:: Path to YAML file containing array of file patterns
+to ignore from overall coverage calculation
+
+[example]
+.To analyze documentation coverage of a schema collection
+[source,sh]
+----
+$ suma expressir coverage schemas-srl.yml
+----
+
+.To analyze coverage and export as JSON
+[source,sh]
+----
+$ suma expressir coverage schemas-srl.yml --format=json --output=coverage.json
+----
+
+.To analyze with exclusions
+[source,sh]
+----
+$ suma expressir coverage schemas/ --exclude=TYPE:ENUMERATION,PARAMETER
+----
+
+.To analyze multiple sources
+[source,sh]
+----
+$ suma expressir coverage schemas-srl.yml additional-schemas.yml
+----
+
+The coverage report includes:
+
+* Overall coverage statistics (total entities, documented entities, percentage)
+* Per-file coverage details
+* Per-directory coverage summaries
+* List of undocumented entities by type and name
+
+==== Format subcommand
+
+The `format` subcommand pretty-prints EXPRESS schemas.
+
+[source,sh]
+----
+$ suma expressir format PATH
+----
+
+Parameters:
+
+`PATH`:: Path to the EXPRESS schema file to format
+
+[example]
+.To format an EXPRESS schema
+[source,sh]
+----
+$ suma expressir format schema.exp
+----
+
+==== Clean subcommand
+
+The `clean` subcommand strips remarks and prettifies EXPRESS schemas.
+
+[source,sh]
+----
+$ suma expressir clean PATH [options]
+----
+
+Parameters:
+
+`PATH`:: Path to the EXPRESS schema file to clean
+
+Options:
+
+`--output=FILE`:: Output file path (defaults to stdout)
+
+[example]
+.To clean an EXPRESS schema and save to file
+[source,sh]
+----
+$ suma expressir clean schema.exp --output=cleaned_schema.exp
+----
+
+==== Validate subcommand
+
+The `validate` subcommand validates EXPRESS schemas for syntactic correctness.
+
+[source,sh]
+----
+$ suma expressir validate PATH [PATH...]
+----
+
+Parameters:
+
+`PATH`:: One or more paths to EXPRESS schema files or directories to validate
+
+[example]
+.To validate EXPRESS schemas
+[source,sh]
+----
+$ suma expressir validate schema.exp
+$ suma expressir validate schemas/
+----
+
+==== Additional information
+
+For complete documentation of all Expressir commands and options, see the
+https://github.com/lutaml/expressir[Expressir documentation].
+
+
 == Usage: Ruby
 
 === General

data/lib/suma/cli/export.rb

@@ -7,37 +7,44 @@ module Suma
   module Cli
     # Export command for exporting EXPRESS schemas from a manifest
     class Export < Thor
-      desc "export MANIFEST_FILE",
-           "Export EXPRESS schemas from manifest"
+      desc "export *FILES",
+           "Export EXPRESS schemas from manifest files or " \
+           "standalone EXPRESS files"
       option :output, type: :string, aliases: "-o", required: true,
                       desc: "Output directory path"
-      option :additional, type: :array, aliases: "-a",
-                          desc: "Additional schemas manifest files to merge (can be specified multiple times)"
       option :annotations, type: :boolean, default: false,
                            desc: "Include annotations (remarks/comments)"
       option :zip, type: :boolean, default: false,
                    desc: "Create ZIP archive of exported schemas"
 
-      def export(manifest_file)
+      def export(*files)
         require_relative "../schema_exporter"
         require_relative "../utils"
         require "expressir"
 
-        unless File.exist?(manifest_file)
-          raise Errno::ENOENT, "Specified manifest file " \
-                               "`#{manifest_file}` not found."
-        end
-
-        run(manifest_file, options)
+        validate_files(files)
+        run(files, options)
       end
 
       private
 
-      def run(manifest_file, options)
-        config = load_and_merge_configs(manifest_file, options[:additional])
+      def validate_files(files)
+        if files.empty?
+          raise ArgumentError, "At least one file must be specified"
+        end
+
+        files.each do |file|
+          unless File.exist?(file)
+            raise Errno::ENOENT, "Specified file `#{file}` not found."
+          end
+        end
+      end
+
+      def run(files, options)
+        schemas = load_schemas_from_files(files)
 
         exporter = SchemaExporter.new(
-          config: config,
+          schemas: schemas,
           output_path: options[:output],
           options: {
             annotations: options[:annotations],
@@ -48,39 +55,53 @@ module Suma
         exporter.export
       end
 
-      # rubocop:disable Metrics/MethodLength
-      def load_and_merge_configs(primary_path, additional_paths)
-        primary_config = Expressir::SchemaManifest.from_file(primary_path)
-        return primary_config unless additional_paths && !additional_paths.empty?
+      def load_schemas_from_files(files)
+        all_schemas = []
 
-        # Load all additional manifests
-        additional_configs = additional_paths.map do |path|
-          unless File.exist?(path)
-            raise Errno::ENOENT, "Specified additional manifest file " \
-                                 "`#{path}` not found."
-          end
-          Expressir::SchemaManifest.from_file(path)
+        files.each do |file|
+          all_schemas += process_file(file)
         end
 
-        # Merge all configs into the primary
-        merge_all_configs(primary_config, additional_configs)
+        all_schemas
       end
-      # rubocop:enable Metrics/MethodLength
 
-      def merge_all_configs(primary, additional_configs)
-        # Collect all schemas from primary and all additional manifests
-        all_schemas = primary.schemas.dup
-
-        additional_configs.each do |config|
-          all_schemas += config.schemas
+      def process_file(file)
+        case File.extname(file).downcase
+        when ".yml", ".yaml"
+          load_manifest_schemas(file)
+        when ".exp"
+          [create_schema_from_exp_file(file)]
+        else
+          raise ArgumentError, "Unsupported file type: #{file}. " \
+                               "Only .yml, .yaml, and .exp files are " \
+                               "supported."
         end
+      end
+
+      def load_manifest_schemas(file)
+        manifest = Expressir::SchemaManifest.from_file(file)
+        manifest.schemas
+      end
 
-        Expressir::SchemaManifest.new(
-          path: primary.path,
-          schemas: all_schemas,
+      def create_schema_from_exp_file(exp_file)
+        # Create a schema object from a standalone EXPRESS file
+        # The id will be determined during parsing
+        StandaloneSchema.new(
+          id: nil,
+          path: File.expand_path(exp_file),
         )
       end
 
+      # Simple schema class for standalone EXPRESS files
+      class StandaloneSchema
+        attr_accessor :id, :path
+
+        def initialize(id:, path:)
+          @id = id
+          @path = path
+        end
+      end
+
       def self.exit_on_failure?
         true
       end

data/lib/suma/cli.rb

@@ -3,6 +3,7 @@
 require "thor"
 require_relative "thor_ext"
 require_relative "cli/validate"
+require "expressir/cli"
 
 module Suma
   module Cli
@@ -15,10 +16,9 @@ module Suma
       option :compile, type: :boolean, default: true,
                        desc: "Compile or skip compile of collection"
       option :schemas_all_path, type: :string, aliases: "-s",
-                                desc: "Generate file that contains all schemas in the collection."
+                                desc: "Generate file that contains all " \
+                                      "schemas in the collection."
       def build(_site_manifest)
-        # # If no arguments, add an empty array to ensure the default command is triggered
-        # args = [] if args.empty?
         require_relative "cli/build"
         Cli::Build.start
       end
@@ -60,17 +60,16 @@ module Suma
         Cli::ConvertJsdai.start
       end
 
-      desc "export MANIFEST_FILE",
-           "Export EXPRESS schemas from manifest"
+      desc "export *FILES",
+           "Export EXPRESS schemas from manifest files or " \
+           "standalone EXPRESS files"
       option :output, type: :string, aliases: "-o", required: true,
                       desc: "Output directory path"
-      option :additional, type: :array, aliases: "-a",
-                          desc: "Additional schemas manifest files to merge (can be specified multiple times)"
       option :annotations, type: :boolean, default: false,
                            desc: "Include annotations (remarks/comments)"
       option :zip, type: :boolean, default: false,
                    desc: "Create ZIP archive of exported schemas"
-      def export(_manifest_file)
+      def export(*_files)
         require_relative "cli/export"
         Cli::Export.start
       end
@@ -78,6 +77,9 @@ module Suma
       desc "validate SUBCOMMAND ...ARGS", "Validate express documents"
       subcommand "validate", Cli::Validate
 
+      desc "expressir SUBCOMMAND ...ARGS", "Expressir commands"
+      subcommand "expressir", Expressir::Cli
+
       def self.exit_on_failure?
         true
       end

data/lib/suma/collection_manifest.rb

@@ -36,12 +36,25 @@ module Suma
       model.entry = CollectionManifest.from_yaml(value.to_yaml)
     end
 
+    # Recursively exports schema configuration by traversing collection manifests.
+    #
+    # This method builds an EXPRESS Schema Manifest (Expressir::SchemaManifest) by:
+    # 1. Starting with an empty or existing Expressir::SchemaManifest
+    # 2. Recursively traversing child entries to collect schemas
+    # 3. Using Expressir::SchemaManifest#concat to combine manifests
+    #
+    # The actual schema manifest operations (creation, concatenation, serialization)
+    # are handled by Expressir's SchemaManifest class, keeping the logic DRY.
+    #
+    # @param path [String] Base path for resolving relative schema paths
+    # @return [Expressir::SchemaManifest] Combined schema manifest
     def export_schema_config(path)
       export_config = @schema_config || Expressir::SchemaManifest.new
       return export_config unless entry
 
       entry.each do |x|
         child_config = x.export_schema_config(path)
+        # Use Expressir's concat method to combine schema manifests
         export_config.concat(child_config) if child_config
       end
 

data/lib/suma/express_schema.rb

@@ -6,19 +6,20 @@ require "expressir"
 
 module Suma
   class ExpressSchema
-    attr_accessor :path, :id, :parsed, :output_path
+    attr_accessor :path, :id, :parsed, :output_path, :is_standalone_file
 
-    def initialize(id:, path:, output_path:)
+    def initialize(id:, path:, output_path:, is_standalone_file: false)
       @path = Pathname.new(path).expand_path
       @id = id
       @output_path = output_path
+      @is_standalone_file = is_standalone_file
     end
 
     def type
-      case @path.to_s
-      when %r{.*/resources/.*}
+      path_str = @path.to_s
+      if path_str.include?("/resources/")
         "resources"
-      when %r{.*/modules/.*}
+      elsif path_str.include?("/modules/")
         "modules"
       else
         "unknown_type"
@@ -39,7 +40,23 @@ module Suma
     end
 
     def filename_plain
-      File.join(@output_path, type, id, File.basename(@path))
+      ensure_id_loaded
+      build_output_filename
+    end
+
+    def ensure_id_loaded
+      parsed unless @id
+    end
+
+    def build_output_filename
+      if @is_standalone_file
+        # For standalone files, output directly to output_path
+        File.join(@output_path, "#{@id}.exp")
+      else
+        # For manifest schemas, preserve directory structure
+        # Note: @output_path already contains the category (resources/modules)
+        File.join(@output_path, @id, File.basename(@path))
+      end
     end
 
     def save_exp(with_annotations: false)

data/lib/suma/processor.rb

@@ -15,12 +15,15 @@ module Suma
       def run(metanorma_yaml_path:, schemas_all_path:, compile:,
 output_directory: "_site")
         Utils.log "Current directory: #{Dir.getwd}, writing #{schemas_all_path}..."
+
+        # Generate EXPRESS Schema Manifest by traversing Metanorma Site Manifest
+        # This uses Expressir::SchemaManifest for all manifest operations
         collection_config = export_schema_config(metanorma_yaml_path,
                                                  schemas_all_path)
 
         unless compile
           Utils.log "No compile option set. Skipping schema compilation."
-          nil
+          return nil
         end
 
         Utils.log "Compiling schema collection..."
@@ -33,6 +36,18 @@ output_directory: "_site")
 
       private
 
+      # Generates EXPRESS Schema Manifest from Metanorma Site Manifest structure.
+      #
+      # This method:
+      # 1. Reads the Metanorma site manifest to discover collection files
+      # 2. Traverses collection manifests to find individual schemas.yaml files
+      # 3. Uses Expressir::SchemaManifest to aggregate and manage schema entries
+      # 4. Saves the unified schema manifest using Expressir's to_file method
+      #
+      # @param metanorma_yaml_path [String] Path to Metanorma site manifest
+      # @param schemas_all_path [String] Output path for unified schema manifest
+      # @return [CollectionConfig] The loaded collection configuration
+      # rubocop:disable Metrics/MethodLength
       def export_schema_config(metanorma_yaml_path, schemas_all_path)
         # This reads the metanorma.yml file
         site_config = Suma::SiteConfig::Config.from_file(metanorma_yaml_path)
@@ -43,13 +58,17 @@ output_directory: "_site")
         collection_config.path = collection_config_path
         collection_config.manifest.expand_schemas_only("schema_docs")
 
+        # Recursively traverse collection manifests to build unified schema manifest
+        # Uses Expressir::SchemaManifest methods (concat, to_file) for operations
         exported_schema_config = collection_config.manifest.export_schema_config(schemas_all_path)
         exported_schema_config.path = schemas_all_path
 
+        # Save using Expressir's SchemaManifest#to_file method
         exported_schema_config.to_file
 
         collection_config
       end
+      # rubocop:enable Metrics/MethodLength
 
       def compile_schema(schemas_all_path, collection_config)
         # now get rid of the source documents for schema sources

data/lib/suma/schema_collection.rb

@@ -9,8 +9,8 @@ require_relative "utils"
 
 module Suma
   class SchemaCollection
-    attr_accessor :config, :schemas, :docs, :output_path_docs, :output_path_schemas,
-                  :manifest
+    attr_accessor :config, :schemas, :docs, :output_path_docs,
+                  :output_path_schemas, :manifest
 
     def initialize(config: nil, config_yaml: nil, output_path_docs: nil,
                    output_path_schemas: nil, manifest: nil)
@@ -18,7 +18,9 @@ module Suma
       @docs = {}
       @schema_name_to_docs = {}
       @output_path_docs = Pathname.new(output_path_docs || Dir.pwd).expand_path
-      @output_path_schemas = Pathname.new(output_path_schemas || Dir.pwd).expand_path
+      @output_path_schemas = Pathname.new(
+        output_path_schemas || Dir.pwd,
+      ).expand_path
       @config = config
       @config ||= config_yaml && Expressir::SchemaManifest.from_file(config_yaml)
       @manifest = manifest
@@ -69,7 +71,7 @@ module Suma
 
       # Use SchemaExporter for schema export
       exporter = SchemaExporter.new(
-        config: @config,
+        schemas: @config.schemas,
         output_path: @output_path_schemas,
         options: { annotations: false },
       )

data/lib/suma/schema_exporter.rb

@@ -8,10 +8,10 @@ module Suma
   # SchemaExporter exports EXPRESS schemas from a manifest
   # with configurable options for annotations and ZIP packaging
   class SchemaExporter
-    attr_reader :config, :output_path, :options
+    attr_reader :schemas, :output_path, :options
 
-    def initialize(config:, output_path:, options: {})
-      @config = config
+    def initialize(schemas:, output_path:, options: {})
+      @schemas = schemas
       @output_path = Pathname.new(output_path).expand_path
       @options = default_options.merge(options)
     end
@@ -19,7 +19,6 @@ module Suma
     def export
       Utils.log "Exporting schemas to: #{output_path}"
 
-      schemas = config.schemas
       export_to_directory(schemas)
       create_zip_archive if options[:create_zip]
 
@@ -43,22 +42,37 @@ module Suma
     end
 
     def export_single_schema(schema)
-      category = categorize_schema(schema)
-      schema_output_path = output_path.join(category).to_s
+      # Check if this is a standalone EXPRESS file
+      # (not from a manifest structure)
+      is_standalone_file = schema.is_a?(Cli::Export::StandaloneSchema)
+      schema_output_path = determine_output_path(schema, is_standalone_file)
 
       express_schema = ExpressSchema.new(
         id: schema.id,
         path: schema.path.to_s,
         output_path: schema_output_path,
+        is_standalone_file: is_standalone_file,
       )
 
       express_schema.save_exp(with_annotations: options[:annotations])
     end
 
+    def determine_output_path(schema, is_standalone_file)
+      if is_standalone_file
+        # For standalone files, output directly to the root
+        output_path.to_s
+      else
+        # For manifest schemas, preserve directory structure
+        category = categorize_schema(schema)
+        output_path.join(category).to_s
+      end
+    end
+
     # rubocop:disable Metrics/MethodLength
     def categorize_schema(schema)
       path = schema.path.to_s
 
+      # Check if this is from a manifest structure or a standalone EXPRESS file
       case path
       when %r{/resources/}
         "resources"
@@ -69,7 +83,8 @@ module Suma
       when %r{/core_model/}
         "core_model"
       else
-        "other"
+        # standalone EXPRESS file not from a manifest structure
+        "standalone"
       end
     end
     # rubocop:enable Metrics/MethodLength

data/lib/suma/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Suma
-  VERSION = "0.1.23"
+  VERSION = "0.1.24"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: suma
 version: !ruby/object:Gem::Version
-  version: 0.1.23
+  version: 0.1.24
 platform: ruby
 authors:
 - Ribose Inc.
 autorequire:
 bindir: exe
 cert_chain: []
-date: 2025-10-06 00:00:00.000000000 Z
+date: 2025-10-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: expressir