@eagleoutice/flowr 2.6.0 → 2.6.2

package/core/print/slice-diff-ansi.js

@@ -26,6 +26,9 @@ function highlight(s, selected) {
     const primary = ansi_1.ansiFormatter.format(s, { color: 3 /* Colors.Yellow */, effect: ansi_1.ColorEffect.Foreground, style: 1 /* FontStyles.Bold */ });
     return selected ? ansi_1.ansiFormatter.format(primary, { style: 4 /* FontStyles.Underline */ }) : primary;
 }
+/**
+ * Print a slice diff with ANSI colors
+ */
 function sliceDiffAnsi(slice, normalized, criteriaIds, originalCode) {
     let importantLocations = Array.from(normalized.idMap.entries())
         .filter(([id, { location }]) => slice.has(id) && (0, assert_1.isNotUndefined)(location))

package/core/steps/all/core/00-parse.d.ts

@@ -1,7 +1,7 @@
 import { internalPrinter } from '../../../print/print';
 import { PipelineStepStage } from '../../pipeline-step';
 import type { QuadSerializationConfiguration } from '../../../../util/quads';
-import type { ParseRequiredInput } from '../../../../r-bridge/parser';
+import { type ParseRequiredInput } from '../../../../r-bridge/parser';
 export declare const PARSE_WITH_R_SHELL_STEP: {
     readonly name: "parse";
     readonly humanReadableName: "parse with R shell";

package/core/steps/all/core/01-parse-tree-sitter.d.ts

@@ -1,17 +1,7 @@
 import { PipelineStepStage } from '../../pipeline-step';
 import { internalPrinter } from '../../../print/print';
 import type { Tree } from 'web-tree-sitter';
-import type { ParseRequiredInput } from '../../../../r-bridge/parser';
-export interface ParseStepOutputTS {
-    readonly parsed: Tree;
-}
-export interface TreeSitterParseJson {
-    readonly '.meta': {
-        readonly tokenCount: number;
-        readonly tokenCountNoComments: number;
-    };
-    readonly str: string;
-}
+import { type ParseRequiredInput } from '../../../../r-bridge/parser';
 export declare const PARSE_WITH_TREE_SITTER_STEP: {
     readonly name: "parse";
     readonly humanReadableName: "parse with tree-sitter";

package/core/steps/all/core/10-normalize.d.ts

@@ -12,6 +12,9 @@ export interface NormalizeRequiredInput {
     /** assume the input stems from a file and use the given path as the file path for the AST */
     readonly overwriteFilePath?: string;
 }
+/**
+ * Get the file attached to the current request, if any
+ */
 export declare function getCurrentRequestFile(request: RParseRequests | undefined): string | undefined;
 declare function processor(results: {
     parse?: ParseStepOutput<string>;

package/core/steps/all/core/10-normalize.js

@@ -5,6 +5,9 @@ exports.getCurrentRequestFile = getCurrentRequestFile;
 const print_1 = require("../../../print/print");
 const normalize_printer_1 = require("../../../print/normalize-printer");
 const parser_1 = require("../../../../r-bridge/lang-4.x/ast/parser/json/parser");
+/**
+ * Get the file attached to the current request, if any
+ */
 function getCurrentRequestFile(request) {
     if (request === undefined) {
         return undefined;

package/core/steps/all/core/11-normalize-tree-sitter.d.ts

@@ -1,11 +1,12 @@
 import { internalPrinter } from '../../../print/print';
 import { normalizedAstToJson, normalizedAstToQuads, printNormalizedAstToMermaid, printNormalizedAstToMermaidUrl } from '../../../print/normalize-printer';
 import { PipelineStepStage } from '../../pipeline-step';
-import type { NormalizeRequiredInput } from './10-normalize';
-import type { ParseStepOutputTS } from './01-parse-tree-sitter';
+import { type NormalizeRequiredInput } from './10-normalize';
 import type { FlowrConfigOptions } from '../../../../config';
+import type { ParseStepOutput } from '../../../../r-bridge/parser';
+import type { Tree } from 'web-tree-sitter';
 declare function processor(results: {
-    'parse'?: ParseStepOutputTS;
+    'parse'?: ParseStepOutput<Tree>;
 }, input: Partial<NormalizeRequiredInput>, config: FlowrConfigOptions): import("../../../../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst<import("../../../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, import("../../../../r-bridge/lang-4.x/ast/model/model").RNode<import("../../../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation>>;
 export declare const NORMALIZE_TREE_SITTER: {
     readonly name: "normalize";

package/core/steps/all/core/20-dataflow.d.ts

@@ -10,7 +10,9 @@ declare function processor(results: {
 }, input: {
     request?: RParseRequests;
     parser?: Parser<KnownParserType>;
-}, config: FlowrConfigOptions): import("../../../../dataflow/info").DataflowInformation;
+}, config: FlowrConfigOptions): import("../../../../dataflow/info").DataflowInformation & {
+    cfgQuick: import("../../../../control-flow/control-flow-graph").ControlFlowInformation | undefined;
+};
 export declare const STATIC_DATAFLOW: {
     readonly humanReadableName: "dataflow";
     readonly processor: typeof processor;

package/core/steps/pipeline/create-pipeline.d.ts

@@ -1,4 +1,4 @@
-import type { IPipelineStep } from '../pipeline-step';
+import { type IPipelineStep } from '../pipeline-step';
 import type { Pipeline } from './pipeline';
 /**
  * Given a set of {@link IPipelineStep|steps} with their dependencies, this function verifies all requirements of {@link createPipeline}.

package/core/steps/pipeline/default-pipelines.d.ts

@@ -61,7 +61,9 @@ export declare const DEFAULT_SLICING_PIPELINE: import("./pipeline").Pipeline<{
     }, input: {
         request?: import("../../../r-bridge/retriever").RParseRequests;
         parser?: Parser<import("../../../r-bridge/parser").KnownParserType>;
-    }, config: FlowrConfigOptions) => import("../../../dataflow/info").DataflowInformation;
+    }, config: FlowrConfigOptions) => import("../../../dataflow/info").DataflowInformation & {
+        cfgQuick: import("../../../control-flow/control-flow-graph").ControlFlowInformation | undefined;
+    };
     readonly requiredInput: {};
     readonly name: "dataflow";
     readonly description: "Construct the dataflow graph";
@@ -143,7 +145,9 @@ export declare const DEFAULT_SLICE_AND_RECONSTRUCT_PIPELINE: import("./pipeline"
     }, input: {
         request?: import("../../../r-bridge/retriever").RParseRequests;
         parser?: Parser<import("../../../r-bridge/parser").KnownParserType>;
-    }, config: FlowrConfigOptions) => import("../../../dataflow/info").DataflowInformation;
+    }, config: FlowrConfigOptions) => import("../../../dataflow/info").DataflowInformation & {
+        cfgQuick: import("../../../control-flow/control-flow-graph").ControlFlowInformation | undefined;
+    };
     readonly requiredInput: {};
     readonly name: "dataflow";
     readonly description: "Construct the dataflow graph";
@@ -225,7 +229,9 @@ export declare const DEFAULT_SLICE_WITHOUT_RECONSTRUCT_PIPELINE: import("./pipel
     }, input: {
         request?: import("../../../r-bridge/retriever").RParseRequests;
         parser?: Parser<import("../../../r-bridge/parser").KnownParserType>;
-    }, config: FlowrConfigOptions) => import("../../../dataflow/info").DataflowInformation;
+    }, config: FlowrConfigOptions) => import("../../../dataflow/info").DataflowInformation & {
+        cfgQuick: import("../../../control-flow/control-flow-graph").ControlFlowInformation | undefined;
+    };
     readonly requiredInput: {};
     readonly name: "dataflow";
     readonly description: "Construct the dataflow graph";
@@ -260,7 +266,9 @@ export declare const TREE_SITTER_SLICING_PIPELINE: import("./pipeline").Pipeline
     }, input: {
         request?: import("../../../r-bridge/retriever").RParseRequests;
         parser?: Parser<import("../../../r-bridge/parser").KnownParserType>;
-    }, config: FlowrConfigOptions) => import("../../../dataflow/info").DataflowInformation;
+    }, config: FlowrConfigOptions) => import("../../../dataflow/info").DataflowInformation & {
+        cfgQuick: import("../../../control-flow/control-flow-graph").ControlFlowInformation | undefined;
+    };
     readonly requiredInput: {};
     readonly name: "dataflow";
     readonly description: "Construct the dataflow graph";
@@ -307,7 +315,7 @@ export declare const TREE_SITTER_SLICING_PIPELINE: import("./pipeline").Pipeline
     readonly humanReadableName: "normalize tree-sitter tree";
     readonly description: "Normalize the AST to flowR's AST";
     readonly processor: (results: {
-        "parse"?: import("../all/core/01-parse-tree-sitter").ParseStepOutputTS;
+        "parse"?: import("../../../r-bridge/parser").ParseStepOutput<import("web-tree-sitter").Tree>;
     }, input: Partial<import("../all/core/10-normalize").NormalizeRequiredInput>, config: FlowrConfigOptions) => import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst<import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, import("../../../r-bridge/lang-4.x/ast/model/model").RNode<import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation>>;
     readonly executed: import("../pipeline-step").PipelineStepStage.OncePerFile;
     readonly printer: {
@@ -341,7 +349,9 @@ export declare const TREE_SITTER_SLICE_AND_RECONSTRUCT_PIPELINE: import("./pipel
     }, input: {
         request?: import("../../../r-bridge/retriever").RParseRequests;
         parser?: Parser<import("../../../r-bridge/parser").KnownParserType>;
-    }, config: FlowrConfigOptions) => import("../../../dataflow/info").DataflowInformation;
+    }, config: FlowrConfigOptions) => import("../../../dataflow/info").DataflowInformation & {
+        cfgQuick: import("../../../control-flow/control-flow-graph").ControlFlowInformation | undefined;
+    };
     readonly requiredInput: {};
     readonly name: "dataflow";
     readonly description: "Construct the dataflow graph";
@@ -388,7 +398,7 @@ export declare const TREE_SITTER_SLICE_AND_RECONSTRUCT_PIPELINE: import("./pipel
     readonly humanReadableName: "normalize tree-sitter tree";
     readonly description: "Normalize the AST to flowR's AST";
     readonly processor: (results: {
-        "parse"?: import("../all/core/01-parse-tree-sitter").ParseStepOutputTS;
+        "parse"?: import("../../../r-bridge/parser").ParseStepOutput<import("web-tree-sitter").Tree>;
     }, input: Partial<import("../all/core/10-normalize").NormalizeRequiredInput>, config: FlowrConfigOptions) => import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst<import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, import("../../../r-bridge/lang-4.x/ast/model/model").RNode<import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation>>;
     readonly executed: import("../pipeline-step").PipelineStepStage.OncePerFile;
     readonly printer: {
@@ -422,7 +432,9 @@ export declare const TREE_SITTER_SLICE_WITHOUT_RECONSTRUCT_PIPELINE: import("./p
     }, input: {
         request?: import("../../../r-bridge/retriever").RParseRequests;
         parser?: Parser<import("../../../r-bridge/parser").KnownParserType>;
-    }, config: FlowrConfigOptions) => import("../../../dataflow/info").DataflowInformation;
+    }, config: FlowrConfigOptions) => import("../../../dataflow/info").DataflowInformation & {
+        cfgQuick: import("../../../control-flow/control-flow-graph").ControlFlowInformation | undefined;
+    };
     readonly requiredInput: {};
     readonly name: "dataflow";
     readonly description: "Construct the dataflow graph";
@@ -455,7 +467,7 @@ export declare const TREE_SITTER_SLICE_WITHOUT_RECONSTRUCT_PIPELINE: import("./p
     readonly humanReadableName: "normalize tree-sitter tree";
     readonly description: "Normalize the AST to flowR's AST";
     readonly processor: (results: {
-        "parse"?: import("../all/core/01-parse-tree-sitter").ParseStepOutputTS;
+        "parse"?: import("../../../r-bridge/parser").ParseStepOutput<import("web-tree-sitter").Tree>;
     }, input: Partial<import("../all/core/10-normalize").NormalizeRequiredInput>, config: FlowrConfigOptions) => import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst<import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, import("../../../r-bridge/lang-4.x/ast/model/model").RNode<import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation>>;
     readonly executed: import("../pipeline-step").PipelineStepStage.OncePerFile;
     readonly printer: {
@@ -513,7 +525,9 @@ export declare const DEFAULT_DATAFLOW_PIPELINE: import("./pipeline").Pipeline<{
     }, input: {
         request?: import("../../../r-bridge/retriever").RParseRequests;
         parser?: Parser<import("../../../r-bridge/parser").KnownParserType>;
-    }, config: FlowrConfigOptions) => import("../../../dataflow/info").DataflowInformation;
+    }, config: FlowrConfigOptions) => import("../../../dataflow/info").DataflowInformation & {
+        cfgQuick: import("../../../control-flow/control-flow-graph").ControlFlowInformation | undefined;
+    };
     readonly requiredInput: {};
     readonly name: "dataflow";
     readonly description: "Construct the dataflow graph";
@@ -534,7 +548,9 @@ export declare const TREE_SITTER_DATAFLOW_PIPELINE: import("./pipeline").Pipelin
     }, input: {
         request?: import("../../../r-bridge/retriever").RParseRequests;
         parser?: Parser<import("../../../r-bridge/parser").KnownParserType>;
-    }, config: FlowrConfigOptions) => import("../../../dataflow/info").DataflowInformation;
+    }, config: FlowrConfigOptions) => import("../../../dataflow/info").DataflowInformation & {
+        cfgQuick: import("../../../control-flow/control-flow-graph").ControlFlowInformation | undefined;
+    };
     readonly requiredInput: {};
     readonly name: "dataflow";
     readonly description: "Construct the dataflow graph";
@@ -567,7 +583,7 @@ export declare const TREE_SITTER_DATAFLOW_PIPELINE: import("./pipeline").Pipelin
     readonly humanReadableName: "normalize tree-sitter tree";
     readonly description: "Normalize the AST to flowR's AST";
     readonly processor: (results: {
-        "parse"?: import("../all/core/01-parse-tree-sitter").ParseStepOutputTS;
+        "parse"?: import("../../../r-bridge/parser").ParseStepOutput<import("web-tree-sitter").Tree>;
     }, input: Partial<import("../all/core/10-normalize").NormalizeRequiredInput>, config: FlowrConfigOptions) => import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst<import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, import("../../../r-bridge/lang-4.x/ast/model/model").RNode<import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation>>;
     readonly executed: import("../pipeline-step").PipelineStepStage.OncePerFile;
     readonly printer: {
@@ -635,7 +651,7 @@ export declare const TREE_SITTER_NORMALIZE_PIPELINE: import("./pipeline").Pipeli
     readonly humanReadableName: "normalize tree-sitter tree";
     readonly description: "Normalize the AST to flowR's AST";
     readonly processor: (results: {
-        "parse"?: import("../all/core/01-parse-tree-sitter").ParseStepOutputTS;
+        "parse"?: import("../../../r-bridge/parser").ParseStepOutput<import("web-tree-sitter").Tree>;
     }, input: Partial<import("../all/core/10-normalize").NormalizeRequiredInput>, config: FlowrConfigOptions) => import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst<import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, import("../../../r-bridge/lang-4.x/ast/model/model").RNode<import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation>>;
     readonly executed: import("../pipeline-step").PipelineStepStage.OncePerFile;
     readonly printer: {

package/core/steps/pipeline/default-pipelines.js

@@ -35,7 +35,6 @@ exports.TREE_SITTER_PARSE_PIPELINE = (0, pipeline_1.createPipeline)(_01_parse_tr
 /**
  * **Please use {@link FlowrAnalyzer} instead of this directly unless you really know what you are doing.**
  * Returns either a {@link DEFAULT_PARSE_PIPELINE} or a {@link TREE_SITTER_PARSE_PIPELINE} depending on the parser used.
- *
  * @see {@link createNormalizePipeline}, {@link createDataflowPipeline}, {@link createSlicePipeline}
  */
 function createParsePipeline(parser, inputs, config) {
@@ -48,7 +47,6 @@ function createParsePipeline(parser, inputs, config) {
 /**
  * **Please use {@link FlowrAnalyzer} instead of this directly unless you really know what you are doing.**
  * Returns either a {@link DEFAULT_SLICING_PIPELINE} or a {@link TREE_SITTER_SLICING_PIPELINE} depending on the parser used.
- *
  * @see {@link createParsePipeline}, {@link createNormalizePipeline}, {@link createDataflowPipeline}
  */
 function createSlicePipeline(parser, inputs, config) {
@@ -61,7 +59,6 @@ function createSlicePipeline(parser, inputs, config) {
 /**
  * **Please use {@link FlowrAnalyzer} instead of this directly unless you really know what you are doing.**
  * Returns either a {@link DEFAULT_NORMALIZE_PIPELINE} or a {@link TREE_SITTER_NORMALIZE_PIPELINE} depending on the parser used.
- *
  * @see {@link createParsePipeline}, {@link createDataflowPipeline}, {@link createSlicePipeline}
  */
 function createNormalizePipeline(parser, inputs, config) {
@@ -74,7 +71,6 @@ function createNormalizePipeline(parser, inputs, config) {
 /**
  * **Please use {@link FlowrAnalyzer} instead of this directly unless you really know what you are doing.**
  * Returns either a {@link DEFAULT_DATAFLOW_PIPELINE} or a {@link TREE_SITTER_DATAFLOW_PIPELINE} depending on the parser used.
- *
  * @see {@link createParsePipeline}, {@link createNormalizePipeline}, {@link createSlicePipeline}
  */
 function createDataflowPipeline(parser, inputs, config) {

package/core/steps/pipeline/pipeline.d.ts

@@ -18,7 +18,6 @@ export interface Pipeline<T extends IPipelineStep = IPipelineStep> {
 }
 /**
  * Returns the types of all step names in the given pipeline.
- *
  * @see Pipeline for details
  */
 export type PipelineStepNames<P extends Pipeline> = PipelineStep<P>['name'];
@@ -47,7 +46,6 @@ export interface PipelinePerStepMetaInformation {
 }
 /**
  * Returns the step with the given name from the given pipeline.
- *
  * @example
  * ```ts
  * type Foo = PipelineStepWithName<typeof DEFAULT_DATAFLOW_PIPELINE, 'parse'>
@@ -67,7 +65,6 @@ export type PipelineStepProcessorWithName<P extends Pipeline, Name extends Pipel
 export type PipelineStepPrintersWithName<P extends Pipeline, Name extends PipelineStepName> = PipelineStepWithName<P, Name>['printer'];
 /**
  * Returns the output type of the step with the given name from the given pipeline.
- *
  * @example
  * ```ts
  * type Foo = PipelineStepOutputWithName<typeof DEFAULT_DATAFLOW_PIPELINE, 'parse'>
@@ -78,7 +75,6 @@ export type PipelineStepPrintersWithName<P extends Pipeline, Name extends Pipeli
 export type PipelineStepOutputWithName<P extends Pipeline, Name extends PipelineStepName> = Awaited<ReturnType<PipelineStepProcessorWithName<P, Name>>> & PipelinePerStepMetaInformation;
 /**
  * Returns a union type that represents the required inputs to be passed to the given pipeline.
- *
  * @example
  * ```ts
  * type Foo = PipelineInput<typeof DEFAULT_DATAFLOW_PIPELINE>
@@ -87,7 +83,6 @@ export type PipelineStepOutputWithName<P extends Pipeline, Name extends Pipeline
  *
  * In short, this can be useful whenever you want to describe _all_ inputs a complete
  * pipeline needs to run through (i.e., the union of all inputs required by the individual steps).
- *
  * @see {@link PipelineOutput}
  */
 export type PipelineInput<P extends Pipeline> = UnionToIntersection<PipelineStep<P>['requiredInput']>;
@@ -125,11 +120,9 @@ export type PipelineOutput<P extends Pipeline> = {
  * 4) the target of a {@link IPipelineStepOrder#decorates|step's decoration} exists
  * 5) if a {@link IPipelineStepOrder#decorates|decoration} applies, all of its {@link IPipelineStepOrder#dependencies|dependencies} are already in the pipeline
  * 6) in the resulting {@link Pipeline|pipeline}, there is a strict cut between {@link IPipelineStep|steps} that are executed
- * 		{@link PipelineStepStage#OncePerFile|once per file} and {@link PipelineStepStage#OncePerRequest|once per request}.
- *
+ * {@link PipelineStepStage#OncePerFile|once per file} and {@link PipelineStepStage#OncePerRequest|once per request}.
  * @returns The function will try to order your collection steps so that all the constraints hold.
  * If it succeeds it will return the resulting {@link Pipeline|pipeline}, otherwise it will throw an {@link InvalidPipelineError}.
- *
  * @throws InvalidPipelineError If any of the constraints listed above are not satisfied.
  */
 export declare function createPipeline<T extends readonly IPipelineStep[]>(...steps: T): Pipeline<T[number]>;

package/core/steps/pipeline/pipeline.js

@@ -14,11 +14,9 @@ const create_pipeline_1 = require("./create-pipeline");
  * 4) the target of a {@link IPipelineStepOrder#decorates|step's decoration} exists
  * 5) if a {@link IPipelineStepOrder#decorates|decoration} applies, all of its {@link IPipelineStepOrder#dependencies|dependencies} are already in the pipeline
  * 6) in the resulting {@link Pipeline|pipeline}, there is a strict cut between {@link IPipelineStep|steps} that are executed
- * 		{@link PipelineStepStage#OncePerFile|once per file} and {@link PipelineStepStage#OncePerRequest|once per request}.
- *
+ * {@link PipelineStepStage#OncePerFile|once per file} and {@link PipelineStepStage#OncePerRequest|once per request}.
  * @returns The function will try to order your collection steps so that all the constraints hold.
  * If it succeeds it will return the resulting {@link Pipeline|pipeline}, otherwise it will throw an {@link InvalidPipelineError}.
- *
  * @throws InvalidPipelineError If any of the constraints listed above are not satisfied.
  */
 function createPipeline(...steps) {

package/core/steps/pipeline-step.d.ts

@@ -1,6 +1,5 @@
 /**
  * Defines the {@link IPipelineStep} interface which specifies all data available for a single step.
- *
  * @module
  */
 import type { MergeableRecord } from '../../util/objects';

package/core/steps/pipeline-step.js

@@ -1,7 +1,6 @@
 "use strict";
 /**
  * Defines the {@link IPipelineStep} interface which specifies all data available for a single step.
- *
  * @module
  */
 Object.defineProperty(exports, "__esModule", { value: true });

package/dataflow/cluster.d.ts

@@ -17,4 +17,7 @@ export interface DataflowGraphCluster {
     /** If the cluster contains unknown side effects */
     readonly hasUnknownSideEffects: boolean;
 }
+/**
+ * Find all clusters in the given dataflow graph.
+ */
 export declare function findAllClusters(graph: DataflowGraph): DataflowGraphClusters;

package/dataflow/cluster.js

@@ -4,6 +4,9 @@ exports.findAllClusters = findAllClusters;
 const edge_1 = require("./graph/edge");
 const vertex_1 = require("./graph/vertex");
 const assert_1 = require("../util/assert");
+/**
+ * Find all clusters in the given dataflow graph.
+ */
 function findAllClusters(graph) {
     const clusters = [];
     // we reverse the vertices since dependencies usually point "backwards" from later nodes

package/dataflow/environments/append.d.ts

@@ -1,4 +1,4 @@
-import type { REnvironmentInformation } from './environment';
+import { type REnvironmentInformation } from './environment';
 /**
  * Adds all writes of `next` to `base` (i.e., the operations of `next` *might* happen).
  */

package/dataflow/environments/built-in-config.d.ts

@@ -1,5 +1,4 @@
-import type { BuiltInMappingName, ConfigOfBuiltInMappingName } from './built-in';
-import { BuiltIns } from './built-in';
+import { type BuiltInMappingName, type ConfigOfBuiltInMappingName, BuiltIns } from './built-in';
 import type { Identifier } from './identifier';
 export interface BaseBuiltInDefinition {
     /** The type of the built-in configuration */
@@ -11,7 +10,6 @@ export interface BaseBuiltInDefinition {
 }
 /**
  * Define a built-in constant (like `NULL` or `TRUE`) and the TS value it should have
- *
  * @template Value - The type of the constant value
  */
 export interface BuiltInConstantDefinition<Value> extends BaseBuiltInDefinition {
@@ -21,7 +19,6 @@ export interface BuiltInConstantDefinition<Value> extends BaseBuiltInDefinition
 }
 /**
  * Define a built-in function (like `print` or `c`) and the processor to use.
- *
  * @template BuiltInProcessor - The processor to use for this function
  */
 export interface BuiltInFunctionDefinition<BuiltInProcessor extends BuiltInMappingName> extends BaseBuiltInDefinition {
@@ -52,7 +49,6 @@ export type BuiltInDefinitions = BuiltInDefinition[];
 export declare function getDefaultBuiltInDefinitions(): BuiltIns;
 /**
  * Get the {@link BuiltIns#builtInMemory} and {@link BuiltIns#emptyBuiltInMemory} for the given list of built-in definitions.
- *
  * @param definitions - the list of built-in definitions
  * @param loadDefaults - whether to first add the {@link DefaultBuiltinConfig} before the given {@link definitions}
  */

package/dataflow/environments/built-in-config.js

@@ -16,7 +16,6 @@ function getDefaultBuiltInDefinitions() {
 }
 /**
  * Get the {@link BuiltIns#builtInMemory} and {@link BuiltIns#emptyBuiltInMemory} for the given list of built-in definitions.
- *
  * @param definitions - the list of built-in definitions
  * @param loadDefaults - whether to first add the {@link DefaultBuiltinConfig} before the given {@link definitions}
  */

package/dataflow/environments/built-in.d.ts

@@ -8,15 +8,14 @@ import { processPipe } from '../internal/process/functions/call/built-in/built-i
 import { processForLoop } from '../internal/process/functions/call/built-in/built-in-for-loop';
 import { processRepeatLoop } from '../internal/process/functions/call/built-in/built-in-repeat-loop';
 import { processWhileLoop } from '../internal/process/functions/call/built-in/built-in-while-loop';
-import type { Identifier, IdentifierDefinition, IdentifierReference } from './identifier';
-import { ReferenceType } from './identifier';
+import { type Identifier, type IdentifierDefinition, type IdentifierReference, ReferenceType } from './identifier';
 import { processReplacementFunction } from '../internal/process/functions/call/built-in/built-in-replacement';
 import { processQuote } from '../internal/process/functions/call/built-in/built-in-quote';
 import { processFunctionDefinition } from '../internal/process/functions/call/built-in/built-in-function-definition';
 import { processExpressionList } from '../internal/process/functions/call/built-in/built-in-expression-list';
 import { processGet } from '../internal/process/functions/call/built-in/built-in-get';
 import type { AstIdMap, ParentInformation, RNodeWithParent } from '../../r-bridge/lang-4.x/ast/model/processing/decorate';
-import type { RFunctionArgument } from '../../r-bridge/lang-4.x/ast/model/nodes/r-function-call';
+import { type RFunctionArgument } from '../../r-bridge/lang-4.x/ast/model/nodes/r-function-call';
 import type { RSymbol } from '../../r-bridge/lang-4.x/ast/model/nodes/r-symbol';
 import type { NodeId } from '../../r-bridge/lang-4.x/ast/model/processing/node-id';
 import { processLibrary } from '../internal/process/functions/call/built-in/built-in-library';
@@ -35,7 +34,13 @@ import type { DataflowGraph } from '../graph/graph';
 import type { VariableResolve } from '../../config';
 import type { BuiltInConstantDefinition, BuiltInDefinition, BuiltInFunctionDefinition, BuiltInReplacementDefinition } from './built-in-config';
 export type BuiltIn = `built-in:${string}`;
+/**
+ * Generate a built-in id for the given name
+ */
 export declare function builtInId(name: string): BuiltIn;
+/**
+ * Checks whether the given name is a built-in identifier
+ */
 export declare function isBuiltIn(name: NodeId | string): name is BuiltIn;
 export type BuiltInIdentifierProcessor = <OtherInfo>(name: RSymbol<OtherInfo & ParentInformation>, args: readonly RFunctionArgument<OtherInfo & ParentInformation>[], rootId: NodeId, data: DataflowProcessorInformation<OtherInfo & ParentInformation>) => DataflowInformation;
 export type BuiltInIdentifierProcessorWithConfig<Config> = <OtherInfo>(name: RSymbol<OtherInfo & ParentInformation>, args: readonly RFunctionArgument<OtherInfo & ParentInformation>[], rootId: NodeId, data: DataflowProcessorInformation<OtherInfo & ParentInformation>, config: Config) => DataflowInformation;
@@ -58,7 +63,8 @@ export interface DefaultBuiltInProcessorConfiguration extends ForceArguments {
     readonly hasUnknownSideEffects?: boolean | LinkTo<RegExp | string>;
     /** record mapping the actual function name called to the arguments that should be treated as function calls */
     readonly treatAsFnCall?: Record<string, readonly string[]>;
-    /** Name that should be used for the origin (useful when needing to differentiate between
+    /**
+     * Name that should be used for the origin (useful when needing to differentiate between
      * functions like 'return' that use the default builtin processor)
      */
     readonly useAsProcessor?: UseAsProcessors;
@@ -125,7 +131,6 @@ export declare class BuiltIns {
      * The twin of the {@link builtInMemory} but with less built ins defined for
      * cases in which we want some commonly overwritten variables to remain open.
      * If you do not know if you need the empty environment, you do not need the empty environment (right now).
-     *
      * @see {@link builtInMemory}
      */
     emptyBuiltInMemory: BuiltInMemory;

package/dataflow/environments/built-in.js

@@ -32,9 +32,15 @@ const vertex_1 = require("../graph/vertex");
 const type_1 = require("../../r-bridge/lang-4.x/ast/model/type");
 const unknown_side_effect_1 = require("../graph/unknown-side-effect");
 const resolve_1 = require("../eval/resolve/resolve");
+/**
+ * Generate a built-in id for the given name
+ */
 function builtInId(name) {
     return `built-in:${name}`;
 }
+/**
+ * Checks whether the given name is a built-in identifier
+ */
 function isBuiltIn(name) {
     return String(name).startsWith('built-in:');
 }
@@ -218,7 +224,6 @@ class BuiltIns {
      * The twin of the {@link builtInMemory} but with less built ins defined for
      * cases in which we want some commonly overwritten variables to remain open.
      * If you do not know if you need the empty environment, you do not need the empty environment (right now).
-     *
      * @see {@link builtInMemory}
      */
     emptyBuiltInMemory = new Map();

package/dataflow/environments/clone.d.ts

@@ -1,4 +1,4 @@
-import type { REnvironmentInformation } from './environment';
+import { type REnvironmentInformation } from './environment';
 /**
  * Produce a clone of the given environment information.
  * @param environment        - The environment information to clone.

package/dataflow/environments/default-builtin-config.d.ts

@@ -13,4 +13,7 @@ export declare const GgPlotAddons: string[];
  * Contains the built-in definitions recognized by flowR
  */
 export declare const DefaultBuiltinConfig: BuiltInDefinitions;
+/**
+ *
+ */
 export declare function getDefaultProcessor(name: string): BuiltInMappingName | 'unnamed' | undefined;

package/dataflow/environments/default-builtin-config.js

@@ -93,7 +93,7 @@ function toRegex(n) {
  * Contains the built-in definitions recognized by flowR
  */
 exports.DefaultBuiltinConfig = [
-    { type: 'constant', names: ['NULL', 'NA'], value: null, assumePrimitive: true },
+    { type: 'constant', names: ['NULL', 'NA', 'NaN', 'NA_integer_', 'NA_real_', 'NA_complex_', 'NA_character_'], value: null, assumePrimitive: true },
     { type: 'constant', names: ['TRUE', 'T'], value: true, assumePrimitive: true },
     { type: 'constant', names: ['FALSE', 'F'], value: false, assumePrimitive: true },
     {
@@ -212,6 +212,14 @@ exports.DefaultBuiltinConfig = [
     { type: 'function', names: ['('], processor: 'builtin:default', config: { returnsNthArgument: 0 }, assumePrimitive: true },
     { type: 'function', names: ['load', 'load_all', 'setwd', 'set.seed'], processor: 'builtin:default', config: { hasUnknownSideEffects: true, forceArgs: [true] }, assumePrimitive: false },
     { type: 'function', names: ['body', 'formals', 'environment'], processor: 'builtin:default', config: { hasUnknownSideEffects: true, forceArgs: [true] }, assumePrimitive: true },
+    { type: 'function', names: ['.Call', '.External', '.C', '.Fortran'], processor: 'builtin:default', config: { hasUnknownSideEffects: true, forceArgs: [true],
+            treatAsFnCall: {
+                '.Call': ['.NAME'],
+                '.External': ['.NAME'],
+                '.C': ['.NAME'],
+                '.Fortran': ['.NAME']
+            }
+        }, assumePrimitive: true },
     { type: 'function', names: ['eval'], processor: 'builtin:eval', config: { includeFunctionCall: true }, assumePrimitive: true },
     { type: 'function', names: ['cat'], processor: 'builtin:default', config: { forceArgs: 'all', hasUnknownSideEffects: { type: 'link-to-last-call', callName: /^sink$/ } }, assumePrimitive: false },
     { type: 'function', names: ['switch'], processor: 'builtin:default', config: { forceArgs: [true] }, assumePrimitive: false },
@@ -294,6 +302,9 @@ exports.DefaultBuiltinConfig = [
         }
     }
 ];
+/**
+ *
+ */
 function getDefaultProcessor(name) {
     if (name.startsWith(unnamed_call_handling_1.UnnamedFunctionCallPrefix)) {
         return 'unnamed';

package/dataflow/environments/diff.d.ts

@@ -1,6 +1,15 @@
-import type { GenericDifferenceInformation, WriteableDifferenceReport } from '../../util/diff';
-import type { IEnvironment, REnvironmentInformation } from './environment';
+import { type GenericDifferenceInformation, type WriteableDifferenceReport } from '../../util/diff';
+import { type IEnvironment, type REnvironmentInformation } from './environment';
 import type { IdentifierReference } from './identifier';
+/**
+ * Compares two identifier references and reports differences.
+ */
 export declare function diffIdentifierReferences<Report extends WriteableDifferenceReport>(a: IdentifierReference | undefined, b: IdentifierReference | undefined, info: GenericDifferenceInformation<Report>): void;
+/**
+ * Compares two environments and reports differences.
+ */
 export declare function diffEnvironment<Report extends WriteableDifferenceReport>(a: IEnvironment | undefined, b: IEnvironment | undefined, info: GenericDifferenceInformation<Report>, depth: number): void;
+/**
+ * Compares two REnvironmentInformation objects and reports differences.
+ */
 export declare function diffEnvironmentInformation<Report extends WriteableDifferenceReport>(a: REnvironmentInformation | undefined, b: REnvironmentInformation | undefined, info: GenericDifferenceInformation<Report>): void;

package/dataflow/environments/diff.js

@@ -7,6 +7,9 @@ const diff_1 = require("../../util/diff");
 const environment_1 = require("./environment");
 const json_1 = require("../../util/json");
 const info_1 = require("../info");
+/**
+ * Compares two identifier references and reports differences.
+ */
 function diffIdentifierReferences(a, b, info) {
     if (a === undefined || b === undefined) {
         if (a !== b) {
@@ -51,6 +54,9 @@ function diffMemory(a, b, info) {
         }
     }
 }
+/**
+ * Compares two environments and reports differences.
+ */
 function diffEnvironment(a, b, info, depth) {
     if (a === undefined || b === undefined) {
         if (a !== b) {
@@ -71,6 +77,9 @@ function diffEnvironment(a, b, info, depth) {
     diffMemory(a, b, { ...info, position: `${info.position}[at level: ${depth}] ` });
     diffEnvironment(a.parent, b.parent, { ...info, position: `${info.position}Parents of ${a.id} & ${b.id}. ` }, depth--);
 }
+/**
+ * Compares two REnvironmentInformation objects and reports differences.
+ */
 function diffEnvironmentInformation(a, b, info) {
     if (a === undefined || b === undefined) {
         if (a !== b) {

package/dataflow/environments/environment.d.ts

@@ -1,7 +1,6 @@
 /**
  * Provides an environment structure similar to R.
  * This allows the dataflow to hold current definition locations for variables, based on the current scope.
- *
  * @module
  */
 import type { IdentifierReference } from './identifier';
@@ -12,6 +11,9 @@ import type { BuiltInMemory } from './built-in';
  * Marks the reference as maybe (i.e., as controlled by a set of {@link IdentifierReference#controlDependencies|control dependencies}).
  */
 export declare function makeReferenceMaybe(ref: IdentifierReference, graph: DataflowGraph, environments: REnvironmentInformation, includeDefs: boolean, defaultCd?: ControlDependency | undefined): IdentifierReference;
+/**
+ *
+ */
 export declare function makeAllMaybe(references: readonly IdentifierReference[] | undefined, graph: DataflowGraph, environments: REnvironmentInformation, includeDefs: boolean, defaultCd?: ControlDependency | undefined): IdentifierReference[];
 /** A single entry/scope within an {@link REnvironmentInformation} */
 export interface IEnvironment {
@@ -55,8 +57,6 @@ export interface WorkingDirectoryReference {
  * One important environment is the {@link BuiltIns|BuiltInEnvironment} which contains the default definitions for R's built-in functions and constants.
  * Please use {@link initializeCleanEnvironments} to initialize the environments (which includes the built-ins).
  * During serialization, you may want to rely on the {@link builtInEnvJsonReplacer} to avoid the huge built-in environment.
- *
- *
  * @see {@link define} - to define a new {@link IdentifierDefinition|identifier definition} within an environment
  * @see {@link resolveByName} - to resolve an {@link Identifier|identifier/name} to its {@link IdentifierDefinition|definitions} within an environment
  * @see {@link makeReferenceMaybe} - to attach control dependencies to a reference