@eagleoutice/flowr 2.5.0 → 2.6.0

package/cli/slicer-app.js

@@ -32,7 +32,7 @@ async function getSlice() {
     (0, assert_1.guard)(options.criterion !== undefined, 'a slicing criterion must be given');
     const config = (0, config_1.getConfig)();
     await slicer.init(options['input-is-text']
-        ? { request: 'text', content: options.input.replaceAll('\\n', '\n') }
+        ? (0, adapter_1.requestFromText)(options.input.replaceAll('\\n', '\n'))
         : (0, adapter_1.requestFromFile)(options.input), config, options['no-magic-comments'] ? auto_select_defaults_1.doNotAutoSelect : (0, magic_comments_1.makeMagicCommentHandler)(auto_select_defaults_1.doNotAutoSelect));
     let mappedSlices = [];
     let reconstruct = undefined;

package/config.d.ts

@@ -209,7 +209,7 @@ export declare function parseConfig(jsonString: string): FlowrConfigOptions | un
 /**
  * Creates a new flowr config that has the updated values.
  */
-export declare function amendConfig(config: FlowrConfigOptions, amendmentFunc: (config: DeepWritable<FlowrConfigOptions>) => FlowrConfigOptions): FlowrConfigOptions;
+export declare function amendConfig(config: FlowrConfigOptions, amendmentFunc: (config: DeepWritable<FlowrConfigOptions>) => FlowrConfigOptions | void): FlowrConfigOptions;
 export declare function cloneConfig(config: FlowrConfigOptions): FlowrConfigOptions;
 export declare function getConfig(configFile?: string, configWorkingDirectory?: string): FlowrConfigOptions;
 export declare function getEngineConfig<T extends EngineConfig['type']>(config: FlowrConfigOptions, engine: T): EngineConfig & {

package/config.js

@@ -162,8 +162,11 @@ function parseConfig(jsonString) {
 /**
  * Creates a new flowr config that has the updated values.
  */
+// eslint-disable-next-line @typescript-eslint/no-invalid-void-type
 function amendConfig(config, amendmentFunc) {
-    return amendmentFunc(cloneConfig(config));
+    const newConfig = cloneConfig(config);
+    amendmentFunc(newConfig);
+    return newConfig;
 }
 function cloneConfig(config) {
     return JSON.parse(JSON.stringify(config));

package/control-flow/extract-cfg.d.ts

@@ -18,7 +18,7 @@ import type { FlowrConfigOptions } from '../config';
  */
 export declare function extractCfg<Info = ParentInformation>(ast: NormalizedAst<Info & ParentInformation>, config: FlowrConfigOptions, graph?: DataflowGraph, simplifications?: readonly CfgSimplificationPassName[]): ControlFlowInformation;
 /**
- * A version of {@link extractCfg} that is much quicker and does not apply any simplifciations or dataflow information.
+ * A version of {@link extractCfg} that is much quicker and does not apply any simplifications or dataflow information.
  */
 export declare function extractCfgQuick<Info = ParentInformation>(ast: NormalizedAst<Info>): ControlFlowInformation<import("./control-flow-graph").CfgSimpleVertex>;
 export declare const ResolvedCallSuffix = "-resolved-call-exit";

package/control-flow/extract-cfg.js

@@ -67,7 +67,7 @@ function extractCfg(ast, config, graph, simplifications) {
     return (0, cfg_simplification_1.simplifyControlFlowInformation)((0, fold_1.foldAst)(ast.ast, graph ? dataflowCfgFolds(graph) : cfgFolds), { ast, dfg: graph, config }, simplifications);
 }
 /**
- * A version of {@link extractCfg} that is much quicker and does not apply any simplifciations or dataflow information.
+ * A version of {@link extractCfg} that is much quicker and does not apply any simplifications or dataflow information.
  */
 function extractCfgQuick(ast) {
     return (0, fold_1.foldAst)(ast.ast, cfgFolds);

package/core/pipeline-executor.d.ts

@@ -3,6 +3,10 @@ import { PipelineStepStage } from './steps/pipeline-step';
 import type { Pipeline, PipelineInput, PipelineOutput, PipelinePerRequestInput, PipelineStepOutputWithName } from './steps/pipeline/pipeline';
 import type { FlowrConfigOptions } from '../config';
 /**
+ * **Please note:** The {@link PipelineExecutor} is now considered to be a rather low-level API for flowR. While it still works
+ * and is the basis for all other layers, we strongly recommend using the {@link FlowrAnalyzer} and its {@link FlowrAnalyzerBuilder|builder}
+ * to create and use an analyzer instance that is pre-configured for your use-case.
+ *
  * The pipeline executor allows to execute arbitrary {@link Pipeline|pipelines} in a step-by-step fashion.
  * If you are not yet in the possession of a {@link Pipeline|pipeline}, you can use the {@link createPipeline} function
  * to create one for yourself, based on the steps that you want to execute.
@@ -98,6 +102,7 @@ export declare class PipelineExecutor<P extends Pipeline> {
      * The required additional input is specified by the {@link IPipelineStep#requiredInput|required input configuration} of each step in the `pipeline`.
      *
      * Please see {@link createDataflowPipeline} and friends for engine agnostic shortcuts to create a pipeline executor.
+     * And in general, please prefer using the {@link FlowrAnalyzer} and its {@link FlowrAnalyzerBuilder|builder} to create and use an analyzer instance.
      *
      * @param pipeline - The {@link Pipeline} to execute, probably created with {@link createPipeline}.
      * @param input    - External {@link PipelineInput|configuration and input} required to execute the given pipeline.

package/core/pipeline-executor.js

@@ -3,6 +3,10 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.PipelineExecutor = void 0;
 const assert_1 = require("../util/assert");
 /**
+ * **Please note:** The {@link PipelineExecutor} is now considered to be a rather low-level API for flowR. While it still works
+ * and is the basis for all other layers, we strongly recommend using the {@link FlowrAnalyzer} and its {@link FlowrAnalyzerBuilder|builder}
+ * to create and use an analyzer instance that is pre-configured for your use-case.
+ *
  * The pipeline executor allows to execute arbitrary {@link Pipeline|pipelines} in a step-by-step fashion.
  * If you are not yet in the possession of a {@link Pipeline|pipeline}, you can use the {@link createPipeline} function
  * to create one for yourself, based on the steps that you want to execute.
@@ -98,6 +102,7 @@ class PipelineExecutor {
      * The required additional input is specified by the {@link IPipelineStep#requiredInput|required input configuration} of each step in the `pipeline`.
      *
      * Please see {@link createDataflowPipeline} and friends for engine agnostic shortcuts to create a pipeline executor.
+     * And in general, please prefer using the {@link FlowrAnalyzer} and its {@link FlowrAnalyzerBuilder|builder} to create and use an analyzer instance.
      *
      * @param pipeline - The {@link Pipeline} to execute, probably created with {@link createPipeline}.
      * @param input    - External {@link PipelineInput|configuration and input} required to execute the given pipeline.

package/core/steps/pipeline/create-pipeline.js

@@ -27,7 +27,7 @@ function verifyAndBuildPipeline(steps) {
     // now, we do the same for the per-request steps, keeping the per-file steps known
     initializeSteps(perRequestSteps, perRequestStepMap, initsPerRequest, visited);
     const sortedPerRequest = topologicalSort(initsPerRequest, perRequestStepMap, visited);
-    const sorted = [...sortedPerFile, ...sortedPerRequest];
+    const sorted = sortedPerFile.concat(sortedPerRequest);
     validateStepOutput(sorted, perRequestStepMap, steps);
     return {
         steps: perRequestStepMap,

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

@@ -8,20 +8,6 @@ import type { RShell } from '../../../r-bridge/shell';
 import type { TreeSitterExecutor } from '../../../r-bridge/lang-4.x/tree-sitter/tree-sitter-executor';
 import type { FlowrConfigOptions } from '../../../config';
 export declare const DEFAULT_SLICING_PIPELINE: import("./pipeline").Pipeline<{
-    readonly name: "slice";
-    readonly humanReadableName: "static slice";
-    readonly description: "Calculate the actual static slice from the dataflow graph and the given slicing criteria";
-    readonly processor: (results: {
-        dataflow?: import("../../../dataflow/info").DataflowInformation;
-        normalize?: import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst;
-    }, input: Partial<import("../all/static-slicing/00-slice").SliceRequiredInput>, _config: FlowrConfigOptions) => Readonly<import("../../../slicing/static/slicer-types").SliceResult>;
-    readonly executed: import("../pipeline-step").PipelineStepStage.OncePerRequest;
-    readonly printer: {
-        readonly 0: typeof import("../../print/print").internalPrinter;
-    };
-    readonly dependencies: readonly ["dataflow"];
-    readonly requiredInput: import("../all/static-slicing/00-slice").SliceRequiredInput;
-} | {
     readonly name: "parse";
     readonly humanReadableName: "parse with R shell";
     readonly description: "Parse the given R code into an AST";
@@ -54,6 +40,20 @@ export declare const DEFAULT_SLICING_PIPELINE: import("./pipeline").Pipeline<{
     };
     readonly dependencies: readonly ["parse"];
     readonly requiredInput: import("../all/core/10-normalize").NormalizeRequiredInput;
+} | {
+    readonly name: "slice";
+    readonly humanReadableName: "static slice";
+    readonly description: "Calculate the actual static slice from the dataflow graph and the given slicing criteria";
+    readonly processor: (results: {
+        dataflow?: import("../../../dataflow/info").DataflowInformation;
+        normalize?: import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst;
+    }, input: Partial<import("../all/static-slicing/00-slice").SliceRequiredInput>, _config: FlowrConfigOptions) => Readonly<import("../../../slicing/static/slicer-types").SliceResult>;
+    readonly executed: import("../pipeline-step").PipelineStepStage.OncePerRequest;
+    readonly printer: {
+        readonly 0: typeof import("../../print/print").internalPrinter;
+    };
+    readonly dependencies: readonly ["dataflow"];
+    readonly requiredInput: import("../all/static-slicing/00-slice").SliceRequiredInput;
 } | {
     readonly humanReadableName: "dataflow";
     readonly processor: (results: {
@@ -90,20 +90,6 @@ export declare const DEFAULT_SLICING_PIPELINE: import("./pipeline").Pipeline<{
     readonly requiredInput: import("../all/static-slicing/10-reconstruct").ReconstructRequiredInput;
 }>;
 export declare const DEFAULT_SLICE_AND_RECONSTRUCT_PIPELINE: import("./pipeline").Pipeline<{
-    readonly name: "slice";
-    readonly humanReadableName: "static slice";
-    readonly description: "Calculate the actual static slice from the dataflow graph and the given slicing criteria";
-    readonly processor: (results: {
-        dataflow?: import("../../../dataflow/info").DataflowInformation;
-        normalize?: import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst;
-    }, input: Partial<import("../all/static-slicing/00-slice").SliceRequiredInput>, _config: FlowrConfigOptions) => Readonly<import("../../../slicing/static/slicer-types").SliceResult>;
-    readonly executed: import("../pipeline-step").PipelineStepStage.OncePerRequest;
-    readonly printer: {
-        readonly 0: typeof import("../../print/print").internalPrinter;
-    };
-    readonly dependencies: readonly ["dataflow"];
-    readonly requiredInput: import("../all/static-slicing/00-slice").SliceRequiredInput;
-} | {
     readonly name: "parse";
     readonly humanReadableName: "parse with R shell";
     readonly description: "Parse the given R code into an AST";
@@ -136,6 +122,20 @@ export declare const DEFAULT_SLICE_AND_RECONSTRUCT_PIPELINE: import("./pipeline"
     };
     readonly dependencies: readonly ["parse"];
     readonly requiredInput: import("../all/core/10-normalize").NormalizeRequiredInput;
+} | {
+    readonly name: "slice";
+    readonly humanReadableName: "static slice";
+    readonly description: "Calculate the actual static slice from the dataflow graph and the given slicing criteria";
+    readonly processor: (results: {
+        dataflow?: import("../../../dataflow/info").DataflowInformation;
+        normalize?: import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst;
+    }, input: Partial<import("../all/static-slicing/00-slice").SliceRequiredInput>, _config: FlowrConfigOptions) => Readonly<import("../../../slicing/static/slicer-types").SliceResult>;
+    readonly executed: import("../pipeline-step").PipelineStepStage.OncePerRequest;
+    readonly printer: {
+        readonly 0: typeof import("../../print/print").internalPrinter;
+    };
+    readonly dependencies: readonly ["dataflow"];
+    readonly requiredInput: import("../all/static-slicing/00-slice").SliceRequiredInput;
 } | {
     readonly humanReadableName: "dataflow";
     readonly processor: (results: {
@@ -172,20 +172,6 @@ export declare const DEFAULT_SLICE_AND_RECONSTRUCT_PIPELINE: import("./pipeline"
     readonly requiredInput: import("../all/static-slicing/10-reconstruct").ReconstructRequiredInput;
 }>;
 export declare const DEFAULT_SLICE_WITHOUT_RECONSTRUCT_PIPELINE: import("./pipeline").Pipeline<{
-    readonly name: "slice";
-    readonly humanReadableName: "static slice";
-    readonly description: "Calculate the actual static slice from the dataflow graph and the given slicing criteria";
-    readonly processor: (results: {
-        dataflow?: import("../../../dataflow/info").DataflowInformation;
-        normalize?: import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst;
-    }, input: Partial<import("../all/static-slicing/00-slice").SliceRequiredInput>, _config: FlowrConfigOptions) => Readonly<import("../../../slicing/static/slicer-types").SliceResult>;
-    readonly executed: import("../pipeline-step").PipelineStepStage.OncePerRequest;
-    readonly printer: {
-        readonly 0: typeof import("../../print/print").internalPrinter;
-    };
-    readonly dependencies: readonly ["dataflow"];
-    readonly requiredInput: import("../all/static-slicing/00-slice").SliceRequiredInput;
-} | {
     readonly name: "parse";
     readonly humanReadableName: "parse with R shell";
     readonly description: "Parse the given R code into an AST";
@@ -218,6 +204,20 @@ export declare const DEFAULT_SLICE_WITHOUT_RECONSTRUCT_PIPELINE: import("./pipel
     };
     readonly dependencies: readonly ["parse"];
     readonly requiredInput: import("../all/core/10-normalize").NormalizeRequiredInput;
+} | {
+    readonly name: "slice";
+    readonly humanReadableName: "static slice";
+    readonly description: "Calculate the actual static slice from the dataflow graph and the given slicing criteria";
+    readonly processor: (results: {
+        dataflow?: import("../../../dataflow/info").DataflowInformation;
+        normalize?: import("../../../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst;
+    }, input: Partial<import("../all/static-slicing/00-slice").SliceRequiredInput>, _config: FlowrConfigOptions) => Readonly<import("../../../slicing/static/slicer-types").SliceResult>;
+    readonly executed: import("../pipeline-step").PipelineStepStage.OncePerRequest;
+    readonly printer: {
+        readonly 0: typeof import("../../print/print").internalPrinter;
+    };
+    readonly dependencies: readonly ["dataflow"];
+    readonly requiredInput: import("../all/static-slicing/00-slice").SliceRequiredInput;
 } | {
     readonly humanReadableName: "dataflow";
     readonly processor: (results: {

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

@@ -33,6 +33,7 @@ exports.TREE_SITTER_NORMALIZE_PIPELINE = (0, pipeline_1.createPipeline)(_01_pars
 exports.DEFAULT_PARSE_PIPELINE = (0, pipeline_1.createPipeline)(_00_parse_1.PARSE_WITH_R_SHELL_STEP);
 exports.TREE_SITTER_PARSE_PIPELINE = (0, pipeline_1.createPipeline)(_01_parse_tree_sitter_1.PARSE_WITH_TREE_SITTER_STEP);
 /**
+ * **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}
@@ -45,6 +46,7 @@ function createParsePipeline(parser, inputs, config) {
     }, 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}
@@ -57,6 +59,7 @@ function createSlicePipeline(parser, inputs, config) {
     }, 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}
@@ -69,10 +72,10 @@ function createNormalizePipeline(parser, inputs, config) {
     }, 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) {
     const base = parser.name === 'tree-sitter' ? exports.TREE_SITTER_DATAFLOW_PIPELINE : exports.DEFAULT_DATAFLOW_PIPELINE;

package/dataflow/graph/dataflowgraph-builder.d.ts

@@ -7,8 +7,7 @@ import type { DataflowGraphVertexAstLink, DataflowGraphVertexUse, FunctionOrigin
 import type { ControlDependency } from '../info';
 import type { LinkTo } from '../../queries/catalog/call-context-query/call-context-query-format';
 import type { FlowrSearchLike } from '../../search/flowr-search-builder';
-import type { Pipeline } from '../../core/steps/pipeline/pipeline';
-import type { FlowrSearchInput } from '../../search/flowr-search';
+import type { FlowrAnalysisProvider } from '../../project/flowr-analyzer';
 export declare function emptyGraph(idMap?: AstIdMap): DataflowGraphBuilder;
 export type DataflowGraphEdgeTarget = NodeId | (readonly NodeId[]);
 /**
@@ -103,9 +102,9 @@ export declare class DataflowGraphBuilder extends DataflowGraph {
      *
      * @param from - Either a node id or a query to find the node id.
      * @param to - Either a node id or a query to find the node id.
-     * @param data - The data to search in i.e. the dataflow graph.
+     * @param input - The input to search in i.e. the dataflow graph.
      */
-    readsQuery<P extends Pipeline>(from: FromQueryParam, to: ToQueryParam, data: FlowrSearchInput<P>): this;
+    readsQuery(from: FromQueryParam, to: ToQueryParam, input: FlowrAnalysisProvider): Promise<this>;
     /**
      * Adds a **defined-by edge** with from as defined variable, and to
      * as a variable/function contributing to its definition.
@@ -118,7 +117,7 @@ export declare class DataflowGraphBuilder extends DataflowGraph {
      *
      * @see {@link DataflowGraphBuilder#readsQuery|readsQuery} for parameters.
      */
-    definedByQuery<P extends Pipeline>(from: FromQueryParam, to: ToQueryParam, data: FlowrSearchInput<P>): this;
+    definedByQuery(from: FromQueryParam, to: ToQueryParam, data: FlowrAnalysisProvider): Promise<this>;
     /**
      * Adds a **call edge** with from as caller, and to as callee.
      *
@@ -130,7 +129,7 @@ export declare class DataflowGraphBuilder extends DataflowGraph {
      *
      * @see {@link DataflowGraphBuilder#readsQuery|readsQuery} for parameters.
      */
-    callsQuery<P extends Pipeline>(from: FromQueryParam, to: ToQueryParam, data: FlowrSearchInput<P>): this;
+    callsQuery(from: FromQueryParam, to: ToQueryParam, data: FlowrAnalysisProvider): Promise<this>;
     /**
      * Adds a **return edge** with from as function, and to as exit point.
      *
@@ -142,7 +141,7 @@ export declare class DataflowGraphBuilder extends DataflowGraph {
      *
      * @see {@link DataflowGraphBuilder#readsQuery|readsQuery} for parameters.
      */
-    returnsQuery<P extends Pipeline>(from: FromQueryParam, to: ToQueryParam, data: FlowrSearchInput<P>): this;
+    returnsQuery(from: FromQueryParam, to: ToQueryParam, data: FlowrAnalysisProvider): Promise<this>;
     /**
      * Adds a **defines-on-call edge** with from as variable, and to as its definition
      *
@@ -154,7 +153,7 @@ export declare class DataflowGraphBuilder extends DataflowGraph {
      *
      * @see {@link DataflowGraphBuilder#readsQuery|readsQuery} for parameters.
      */
-    definesOnCallQuery<P extends Pipeline>(from: FromQueryParam, to: ToQueryParam, data: FlowrSearchInput<P>): this;
+    definesOnCallQuery(from: FromQueryParam, to: ToQueryParam, data: FlowrAnalysisProvider): Promise<this>;
     /**
      * Adds a **defined-by-on-call edge** with from as definition, and to as variable.
      *
@@ -166,7 +165,7 @@ export declare class DataflowGraphBuilder extends DataflowGraph {
      *
      * @see {@link DataflowGraphBuilder#readsQuery|readsQuery} for parameters.
      */
-    definedByOnCallQuery<P extends Pipeline>(from: FromQueryParam, to: ToQueryParam, data: FlowrSearchInput<P>): this;
+    definedByOnCallQuery(from: FromQueryParam, to: ToQueryParam, data: FlowrAnalysisProvider): Promise<this>;
     /**
      * Adds an **argument edge** with from as function call, and to as argument.
      *
@@ -178,7 +177,7 @@ export declare class DataflowGraphBuilder extends DataflowGraph {
      *
      * @see {@link DataflowGraphBuilder#readsQuery|readsQuery} for parameters.
      */
-    argumentQuery<P extends Pipeline>(from: FromQueryParam, to: ToQueryParam, data: FlowrSearchInput<P>): this;
+    argumentQuery(from: FromQueryParam, to: ToQueryParam, data: FlowrAnalysisProvider): Promise<this>;
     /**
      * Adds a **non-standard evaluation edge** with from as vertex, and to as vertex.
      *
@@ -190,7 +189,7 @@ export declare class DataflowGraphBuilder extends DataflowGraph {
      *
      * @see {@link DataflowGraphBuilder#readsQuery|readsQuery} for parameters.
      */
-    nseQuery<P extends Pipeline>(from: FromQueryParam, to: ToQueryParam, data: FlowrSearchInput<P>): this;
+    nseQuery(from: FromQueryParam, to: ToQueryParam, data: FlowrAnalysisProvider): Promise<this>;
     /**
      * Adds a **side-effect-on-call edge** with from as vertex, and to as vertex.
      *
@@ -202,7 +201,7 @@ export declare class DataflowGraphBuilder extends DataflowGraph {
      *
      * @see {@link DataflowGraphBuilder#readsQuery|readsQuery} for parameters.
      */
-    sideEffectOnCallQuery<P extends Pipeline>(from: FromQueryParam, to: ToQueryParam, data: FlowrSearchInput<P>): this;
+    sideEffectOnCallQuery(from: FromQueryParam, to: ToQueryParam, data: FlowrAnalysisProvider): Promise<this>;
     /**
      * explicitly overwrite the root ids of the graph,
      * this is just an easier variant in case you working with a lot of functions this saves you a lot of `false` flags.

package/dataflow/graph/dataflowgraph-builder.js

@@ -174,13 +174,13 @@ class DataflowGraphBuilder extends graph_1.DataflowGraph {
         }
         return this.addEdge((0, node_id_1.normalizeIdToNumberIfPossible)(from), (0, node_id_1.normalizeIdToNumberIfPossible)(to), type);
     }
-    queryHelper(from, to, data, type) {
+    async queryHelper(from, to, data, type) {
         let fromId;
         if ('nodeId' in from) {
             fromId = from.nodeId;
         }
         else {
-            const result = (0, flowr_search_executor_1.runSearch)(from.query, data).getElements();
+            const result = (await (0, flowr_search_executor_1.runSearch)(from.query, data)).getElements();
             (0, assert_1.guard)(result.length === 1, `from query result should yield exactly one node, but yielded ${result.length}`);
             fromId = result[0].node.info.id;
         }
@@ -189,7 +189,7 @@ class DataflowGraphBuilder extends graph_1.DataflowGraph {
             toIds = to.target;
         }
         else {
-            const result = (0, flowr_search_executor_1.runSearch)(to.query, data).getElements();
+            const result = (await (0, flowr_search_executor_1.runSearch)(to.query, data)).getElements();
             toIds = result.map(r => r.node.info.id);
         }
         return this.edgeHelper(fromId, toIds, type);
@@ -209,10 +209,10 @@ class DataflowGraphBuilder extends graph_1.DataflowGraph {
      *
      * @param from - Either a node id or a query to find the node id.
      * @param to - Either a node id or a query to find the node id.
-     * @param data - The data to search in i.e. the dataflow graph.
+     * @param input - The input to search in i.e. the dataflow graph.
      */
-    readsQuery(from, to, data) {
-        return this.queryHelper(from, to, data, edge_1.EdgeType.Reads);
+    readsQuery(from, to, input) {
+        return this.queryHelper(from, to, input, edge_1.EdgeType.Reads);
     }
     /**
      * Adds a **defined-by edge** with from as defined variable, and to

package/documentation/doc-util/doc-query.d.ts

@@ -1,16 +1,13 @@
 import type { RShell } from '../../r-bridge/shell';
-import type { Queries, QueryResults, SupportedQueryTypes } from '../../queries/query';
-import { DEFAULT_DATAFLOW_PIPELINE } from '../../core/steps/pipeline/default-pipelines';
+import type { Queries, SupportedQueryTypes } from '../../queries/query';
 import type { SupportedVirtualQueryTypes } from '../../queries/virtual-query/virtual-queries';
 import type { VirtualCompoundConstraint } from '../../queries/virtual-query/compound-query';
-import type { PipelineOutput } from '../../core/steps/pipeline/pipeline';
-export interface ShowQueryOptions<Base extends SupportedQueryTypes> {
+export interface ShowQueryOptions {
     readonly showCode?: boolean;
     readonly collapseResult?: boolean;
     readonly collapseQuery?: boolean;
-    readonly addOutput?: (result: QueryResults<Base>, pipeline: PipelineOutput<typeof DEFAULT_DATAFLOW_PIPELINE>) => string;
 }
-export declare function showQuery<Base extends SupportedQueryTypes, VirtualArguments extends VirtualCompoundConstraint<Base> = VirtualCompoundConstraint<Base>>(shell: RShell, code: string, queries: Queries<Base, VirtualArguments>, { showCode, collapseResult, collapseQuery, addOutput }?: ShowQueryOptions<Base>): Promise<string>;
+export declare function showQuery<Base extends SupportedQueryTypes, VirtualArguments extends VirtualCompoundConstraint<Base> = VirtualCompoundConstraint<Base>>(shell: RShell, code: string, queries: Queries<Base, VirtualArguments>, { showCode, collapseResult, collapseQuery }?: ShowQueryOptions): Promise<string>;
 export interface QueryDocumentation {
     readonly name: string;
     readonly type: 'virtual' | 'active';

package/documentation/doc-util/doc-query.js

@@ -6,9 +6,6 @@ exports.registerQueryDocumentation = registerQueryDocumentation;
 exports.linkToQueryOfName = linkToQueryOfName;
 exports.tocForQueryType = tocForQueryType;
 exports.explainQueries = explainQueries;
-const query_1 = require("../../queries/query");
-const pipeline_executor_1 = require("../../core/pipeline-executor");
-const default_pipelines_1 = require("../../core/steps/pipeline/default-pipelines");
 const retriever_1 = require("../../r-bridge/retriever");
 const json_1 = require("../../util/json");
 const ansi_1 = require("../../util/text/ansi");
@@ -17,19 +14,12 @@ const doc_dfg_1 = require("./doc-dfg");
 const doc_code_1 = require("./doc-code");
 const time_1 = require("../../util/text/time");
 const query_print_1 = require("../../queries/query-print");
+const flowr_analyzer_builder_1 = require("../../project/flowr-analyzer-builder");
 const doc_cli_option_1 = require("./doc-cli-option");
-const config_1 = require("../../config");
-async function showQuery(shell, code, queries, { showCode, collapseResult, collapseQuery, addOutput = () => '' } = {}) {
+async function showQuery(shell, code, queries, { showCode, collapseResult, collapseQuery } = {}) {
     const now = performance.now();
-    const analysis = await new pipeline_executor_1.PipelineExecutor(default_pipelines_1.DEFAULT_DATAFLOW_PIPELINE, {
-        parser: shell,
-        request: (0, retriever_1.requestFromInput)(code)
-    }, config_1.defaultConfigOptions).allRemainingSteps();
-    const results = await Promise.resolve((0, query_1.executeQueries)({
-        dataflow: analysis.dataflow,
-        ast: analysis.normalize,
-        config: (0, config_1.cloneConfig)(config_1.defaultConfigOptions)
-    }, queries));
+    const analyzer = await new flowr_analyzer_builder_1.FlowrAnalyzerBuilder((0, retriever_1.requestFromInput)(code)).setParser(shell).build();
+    const results = await analyzer.query(queries);
     const duration = performance.now() - now;
     const metaInfo = `
 The analysis required _${(0, time_1.printAsMs)(duration)}_ (including parsing and normalization and the query) within the generation environment.
@@ -52,7 +42,7 @@ ${collapseResult ? ' <details> <summary style="color:gray">Show Results</summary
 
 _Results (prettified and summarized):_
 
-${(0, query_print_1.asciiSummaryOfQueryResult)(ansi_1.markdownFormatter, duration, results, analysis, queries)}
+${await (0, query_print_1.asciiSummaryOfQueryResult)(ansi_1.markdownFormatter, duration, results, analyzer, queries)}
 
 <details> <summary style="color:gray">Show Detailed Results as Json</summary>
 
@@ -75,8 +65,6 @@ ${await (0, doc_dfg_1.printDfGraphForCode)(shell, code, { switchCodeAndGraph: tr
 
 ${collapseResult ? '</details>' : ''}
 
-${addOutput(results, analysis)}
-
 	`;
 }
 exports.RegisteredQueries = {

package/documentation/doc-util/doc-search.js

@@ -6,29 +6,26 @@ exports.registerQueryDocumentation = registerQueryDocumentation;
 exports.linkToQueryOfName = linkToQueryOfName;
 exports.tocForQueryType = tocForQueryType;
 exports.explainQueries = explainQueries;
-const pipeline_executor_1 = require("../../core/pipeline-executor");
-const default_pipelines_1 = require("../../core/steps/pipeline/default-pipelines");
 const retriever_1 = require("../../r-bridge/retriever");
 const doc_files_1 = require("./doc-files");
 const doc_dfg_1 = require("./doc-dfg");
 const doc_code_1 = require("./doc-code");
 const time_1 = require("../../util/text/time");
-const flowr_search_executor_1 = require("../../search/flowr-search-executor");
 const flowr_search_printer_1 = require("../../search/flowr-search-printer");
 const node_id_1 = require("../../r-bridge/lang-4.x/ast/model/processing/node-id");
 const dfg_1 = require("../../util/mermaid/dfg");
-const config_1 = require("../../config");
+const flowr_analyzer_builder_1 = require("../../project/flowr-analyzer-builder");
 async function showSearch(shell, code, search, { collapseResult = true } = {}) {
     const now = performance.now();
-    const analysis = await new pipeline_executor_1.PipelineExecutor(default_pipelines_1.DEFAULT_DATAFLOW_PIPELINE, {
-        parser: shell,
-        request: (0, retriever_1.requestFromInput)(code)
-    }, config_1.defaultConfigOptions).allRemainingSteps();
-    const result = (0, flowr_search_executor_1.runSearch)(search, { ...analysis, config: config_1.defaultConfigOptions });
+    const analyzer = await new flowr_analyzer_builder_1.FlowrAnalyzerBuilder((0, retriever_1.requestFromInput)(code))
+        .setParser(shell)
+        .build();
+    const result = await analyzer.runSearch(search);
     const duration = performance.now() - now;
     const metaInfo = `
 The search required _${(0, time_1.printAsMs)(duration)}_ (including parsing and normalization and the query) within the generation environment.
 	`.trim();
+    const dataflow = await analyzer.dataflow();
     return `
 
 ${(0, doc_code_1.codeBlock)('ts', (0, flowr_search_printer_1.flowrSearchToCode)(search))}
@@ -53,7 +50,7 @@ ${(0, doc_code_1.codeBlock)('json', JSON.stringify(search, null, 2))}
 ${collapseResult ? ' <details> <summary style="color:gray">Show Results</summary>' : ''}
 
 The query returns the following vetices (all references to \`x\` in the code):
-${result.getElements().map(({ node }) => `<b>${node.info.id} ('${(0, node_id_1.recoverContent)(node.info.id, analysis.dataflow.graph)}')</b> at L${(0, dfg_1.formatRange)(node.location)}`).join(', ')}
+${result.getElements().map(({ node }) => `<b>${node.info.id} ('${(0, node_id_1.recoverContent)(node.info.id, dataflow.graph)}')</b> at L${(0, dfg_1.formatRange)(node.location)}`).join(', ')}
 
 ${metaInfo}	
 

package/documentation/doc-util/doc-structure.d.ts

@@ -11,3 +11,7 @@ export interface BlockOptions {
 }
 export declare function block({ type, content }: BlockOptions): string;
 export declare function section(title: string, depth?: 1 | 2 | 3 | 4 | 5 | 6, anchor?: string): string;
+/**
+ * Supported pattern: `Name@link`
+ */
+export declare function collapsibleToc(content: Record<string, Record<string, Record<string, undefined> | undefined> | undefined>): string;

package/documentation/doc-util/doc-structure.js

@@ -3,8 +3,10 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.details = details;
 exports.block = block;
 exports.section = section;
+exports.collapsibleToc = collapsibleToc;
 const doc_general_1 = require("./doc-general");
 const mermaid_1 = require("../../util/mermaid/mermaid");
+const strings_1 = require("../../util/text/strings");
 function details(title, content, { color, open = false, hideIfEmpty = true, prefixInit = '' } = {}) {
     return hideIfEmpty && content.trim().length === 0 ? '' : `
 ${prefixInit}<details${open ? ' open' : ''}><summary style="${color ? 'color:' + color : ''}">${title}</summary>
@@ -23,4 +25,30 @@ ${(0, doc_general_1.prefixLines)(content, '> ')}
 function section(title, depth = 2, anchor = (0, mermaid_1.escapeId)(title)) {
     return `<h${depth} id="${anchor}">${title}</h${depth}>`;
 }
+function strToLink(str) {
+    const match = str.match(/^(.*?)@(.*)$/);
+    if (match) {
+        const [, name, link] = match;
+        return `[${name}](${link})`;
+    }
+    return `[${str}](#${(0, mermaid_1.escapeId)(str)})`;
+}
+/**
+ * Supported pattern: `Name@link`
+ */
+function collapsibleToc(content) {
+    let output = '';
+    for (const [section, subsections] of Object.entries(content)) {
+        output += `- ${strToLink(section)}\n`;
+        if (subsections) {
+            for (const [subsection, items] of Object.entries(subsections)) {
+                output += `  - ${strToLink(subsection)}  \n`;
+                if (items) {
+                    output += `    ${(0, strings_1.joinWithLast)(Object.keys(items).map(strToLink))}\n`;
+                }
+            }
+        }
+    }
+    return output;
+}
 //# sourceMappingURL=doc-structure.js.map

package/documentation/doc-util/doc-types.d.ts

@@ -62,8 +62,12 @@ export declare function printHierarchy({ program, info, root, collapseFromNestin
 interface FnInfo {
     info: TypeElementInSource[];
     program: ts.Program;
+    dropLinesStart?: number;
+    dropLinesEnd?: number;
+    doNotAutoGobble?: boolean;
+    hideDefinedAt?: boolean;
 }
-export declare function printCodeOfElement({ program, info }: FnInfo, name: string): string;
+export declare function printCodeOfElement({ program, info, dropLinesEnd, dropLinesStart, doNotAutoGobble, hideDefinedAt }: FnInfo, name: string): string;
 /**
  * Create a short link to a type in the documentation
  * @param name      - The name of the type, e.g. `MyType`, may include a container, e.g.,`MyContainer::MyType` (this works with function nestings too)

package/documentation/doc-util/doc-types.js

@@ -387,14 +387,40 @@ function printHierarchy({ program, info, root, collapseFromNesting = 1, initialN
         return thisLine + (out ? '\n' + out : '');
     }
 }
-function printCodeOfElement({ program, info }, name) {
+function printCodeOfElement({ program, info, dropLinesEnd = 0, dropLinesStart = 0, doNotAutoGobble, hideDefinedAt }, name) {
     const node = info.find(e => e.name === name);
     if (!node) {
         console.error(`Could not find node ${name} when resolving function!`);
         return '';
     }
-    const code = node.node.getFullText(program.getSourceFile(node.node.getSourceFile().fileName));
-    return `${(0, doc_code_1.codeBlock)('ts', code)}\n<i>Defined at <a href="${getTypePathLink(node)}">${getTypePathLink(node, '.')}</a></i>\n`;
+    let code = node.node.getFullText(program.getSourceFile(node.node.getSourceFile().fileName)).trim();
+    if (dropLinesStart > 0 || dropLinesEnd > 0) {
+        const lines = code.split(/\n/g);
+        if (dropLinesStart + dropLinesEnd >= lines.length) {
+            return '';
+        }
+        code = lines.slice(dropLinesStart, lines.length - dropLinesEnd).join('\n');
+    }
+    if (!doNotAutoGobble) {
+        // gobble leading spaces
+        const lines = code.replaceAll('\t', '    ').split(/\n/g);
+        let gobble = Number.POSITIVE_INFINITY;
+        for (const line of lines) {
+            const match = line.match(/^(\s+)\S+/);
+            if (match) {
+                gobble = Math.min(gobble, match[1].length);
+            }
+        }
+        if (gobble !== Number.POSITIVE_INFINITY && gobble > 0) {
+            code = lines.map(line => line.startsWith(' '.repeat(gobble)) ? line.slice(gobble) : line).join('\n');
+        }
+    }
+    if (hideDefinedAt) {
+        return (0, doc_code_1.codeBlock)('ts', code);
+    }
+    else {
+        return `${(0, doc_code_1.codeBlock)('ts', code)}\n<i>Defined at <a href="${getTypePathLink(node)}">${getTypePathLink(node, '.')}</a></i>\n`;
+    }
 }
 function fuzzyCompare(a, b) {
     const aStr = a.toLowerCase().replace(/[^a-z0-9]/g, '-').trim();

package/documentation/print-analyzer-wiki.d.ts

@@ -0,0 +1 @@
+export {};