@eagleoutice/flowr 2.8.3 → 2.8.5

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@eagleoutice/flowr",
-  "version": "2.8.3",
+  "version": "2.8.5",
   "description": "Static Dataflow Analyzer and Program Slicer for the R Programming Language",
   "types": "dist/src/index.d.ts",
   "repository": {

package/project/context/flowr-analyzer-files-context.d.ts

@@ -24,6 +24,7 @@ export type RoleBasedFiles = {
     [FileRole.Namespace]: FlowrNamespaceFile[];
     [FileRole.Vignette]: FlowrFileProvider[];
     [FileRole.Test]: FlowrFileProvider[];
+    [FileRole.License]: FlowrFileProvider[];
     [FileRole.Source]: FlowrFileProvider[];
     [FileRole.Data]: FlowrFileProvider[];
     [FileRole.Other]: FlowrFileProvider[];

package/project/context/flowr-file.d.ts

@@ -23,6 +23,8 @@ export declare enum FileRole {
     Test = "test",
     /** Data files, e.g., `R/sysdata.rda`, currently not specially supported. */
     Data = "data",
+    /** Signals separate license files, but please note, that DESCRIPTION files may contain license info too */
+    License = "license",
     /**
      * Catch-all for any file that provides usable R source code to incorporate into the analysis.
      * Please note, that the loading order/inclusion and even potential relevance of these source files

package/project/context/flowr-file.js

@@ -24,6 +24,8 @@ var FileRole;
     FileRole["Test"] = "test";
     /** Data files, e.g., `R/sysdata.rda`, currently not specially supported. */
     FileRole["Data"] = "data";
+    /** Signals separate license files, but please note, that DESCRIPTION files may contain license info too */
+    FileRole["License"] = "license";
     /**
      * Catch-all for any file that provides usable R source code to incorporate into the analysis.
      * Please note, that the loading order/inclusion and even potential relevance of these source files

package/project/plugins/file-plugins/flowr-analyzer-license-file-plugin.d.ts

@@ -0,0 +1,24 @@
+import { FlowrAnalyzerFilePlugin } from './flowr-analyzer-file-plugin';
+import { SemVer } from 'semver';
+import type { PathLike } from 'fs';
+import type { FlowrAnalyzerContext } from '../../context/flowr-analyzer-context';
+import type { FlowrFileProvider } from '../../context/flowr-file';
+/**
+ * This plugin provides supports for the identification of license files.
+ */
+export declare class FlowrAnalyzerLicenseFilePlugin extends FlowrAnalyzerFilePlugin {
+    readonly name = "flowr-analyzer-license-files-plugin";
+    readonly description = "This plugin provides support for loading license files.";
+    readonly version: SemVer;
+    private readonly pathPattern;
+    /**
+     * Creates a new instance of the TEST file plugin.
+     * @param pathPattern - The pathPattern to identify TEST files, see {@link FileNamePattern} for the default pathPattern.
+     */
+    constructor(pathPattern?: RegExp);
+    applies(file: PathLike): boolean;
+    /**
+     * Processes the given file, assigning it the {@link FileRole.License} role.
+     */
+    process(_ctx: FlowrAnalyzerContext, file: FlowrFileProvider): FlowrFileProvider;
+}

package/project/plugins/file-plugins/flowr-analyzer-license-file-plugin.js

@@ -0,0 +1,37 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.FlowrAnalyzerLicenseFilePlugin = void 0;
+const flowr_analyzer_file_plugin_1 = require("./flowr-analyzer-file-plugin");
+const semver_1 = require("semver");
+const flowr_file_1 = require("../../context/flowr-file");
+const built_in_source_1 = require("../../../dataflow/internal/process/functions/call/built-in/built-in-source");
+const FileNamePattern = /license(\.md|\.txt)?$/i;
+/**
+ * This plugin provides supports for the identification of license files.
+ */
+class FlowrAnalyzerLicenseFilePlugin extends flowr_analyzer_file_plugin_1.FlowrAnalyzerFilePlugin {
+    name = 'flowr-analyzer-license-files-plugin';
+    description = 'This plugin provides support for loading license files.';
+    version = new semver_1.SemVer('0.1.0');
+    pathPattern;
+    /**
+     * Creates a new instance of the TEST file plugin.
+     * @param pathPattern - The pathPattern to identify TEST files, see {@link FileNamePattern} for the default pathPattern.
+     */
+    constructor(pathPattern = FileNamePattern) {
+        super();
+        this.pathPattern = pathPattern;
+    }
+    applies(file) {
+        return this.pathPattern.test((0, built_in_source_1.platformBasename)(file.toString()));
+    }
+    /**
+     * Processes the given file, assigning it the {@link FileRole.License} role.
+     */
+    process(_ctx, file) {
+        file.assignRole(flowr_file_1.FileRole.License);
+        return file;
+    }
+}
+exports.FlowrAnalyzerLicenseFilePlugin = FlowrAnalyzerLicenseFilePlugin;
+//# sourceMappingURL=flowr-analyzer-license-file-plugin.js.map

package/project/plugins/flowr-analyzer-plugin-defaults.js

@@ -11,6 +11,7 @@ const flowr_analyzer_namespace_files_plugin_1 = require("./file-plugins/flowr-an
 const flowr_analyzer_news_file_plugin_1 = require("./file-plugins/flowr-analyzer-news-file-plugin");
 const flowr_analyzer_vignette_file_plugin_1 = require("./file-plugins/flowr-analyzer-vignette-file-plugin");
 const flowr_analyzer_test_file_plugin_1 = require("./file-plugins/flowr-analyzer-test-file-plugin");
+const flowr_analyzer_license_file_plugin_1 = require("./file-plugins/flowr-analyzer-license-file-plugin");
 /**
  * Provides the default set of Flowr Analyzer plugins.
  */
@@ -23,6 +24,7 @@ function FlowrAnalyzerPluginDefaults() {
         new flowr_analyzer_loading_order_description_file_plugin_1.FlowrAnalyzerLoadingOrderDescriptionFilePlugin(),
         new flowr_analyzer_rmd_file_plugin_1.FlowrAnalyzerRmdFilePlugin(),
         new flowr_analyzer_qmd_file_plugin_1.FlowrAnalyzerQmdFilePlugin(),
+        new flowr_analyzer_license_file_plugin_1.FlowrAnalyzerLicenseFilePlugin(),
         new flowr_analyzer_jupyter_file_plugin_1.FlowrAnalyzerJupyterFilePlugin(),
         new flowr_analyzer_namespace_files_plugin_1.FlowrAnalyzerNamespaceFilesPlugin(),
         new flowr_analyzer_news_file_plugin_1.FlowrAnalyzerNewsFilePlugin()

package/project/plugins/plugin-registry.d.ts

@@ -9,10 +9,11 @@ import { FlowrAnalyzerNamespaceFilesPlugin } from './file-plugins/flowr-analyzer
 import { FlowrAnalyzerNewsFilePlugin } from './file-plugins/flowr-analyzer-news-file-plugin';
 import { FlowrAnalyzerMetaVignetteFilesPlugin } from './file-plugins/flowr-analyzer-vignette-file-plugin';
 import { FlowrAnalyzerMetaTestFilesPlugin } from './file-plugins/flowr-analyzer-test-file-plugin';
+import { FlowrAnalyzerLicenseFilePlugin } from './file-plugins/flowr-analyzer-license-file-plugin';
 /**
  * The built-in Flowr Analyzer plugins that are always available.
  */
-export declare const BuiltInPlugins: [["file:description", typeof FlowrAnalyzerDescriptionFilePlugin], ["versions:description", typeof FlowrAnalyzerPackageVersionsDescriptionFilePlugin], ["loading-order:description", typeof FlowrAnalyzerLoadingOrderDescriptionFilePlugin], ["files:vignette", typeof FlowrAnalyzerMetaVignetteFilesPlugin], ["files:test", typeof FlowrAnalyzerMetaTestFilesPlugin], ["file:rmd", typeof FlowrAnalyzerRmdFilePlugin], ["file:qmd", typeof FlowrAnalyzerQmdFilePlugin], ["file:ipynb", typeof FlowrAnalyzerJupyterFilePlugin], ["file:namespace", typeof FlowrAnalyzerNamespaceFilesPlugin], ["file:news", typeof FlowrAnalyzerNewsFilePlugin]];
+export declare const BuiltInPlugins: [["file:description", typeof FlowrAnalyzerDescriptionFilePlugin], ["versions:description", typeof FlowrAnalyzerPackageVersionsDescriptionFilePlugin], ["loading-order:description", typeof FlowrAnalyzerLoadingOrderDescriptionFilePlugin], ["files:vignette", typeof FlowrAnalyzerMetaVignetteFilesPlugin], ["files:test", typeof FlowrAnalyzerMetaTestFilesPlugin], ["file:rmd", typeof FlowrAnalyzerRmdFilePlugin], ["file:qmd", typeof FlowrAnalyzerQmdFilePlugin], ["file:ipynb", typeof FlowrAnalyzerJupyterFilePlugin], ["file:namespace", typeof FlowrAnalyzerNamespaceFilesPlugin], ["file:news", typeof FlowrAnalyzerNewsFilePlugin], ["file:license", typeof FlowrAnalyzerLicenseFilePlugin]];
 export type BuiltInFlowrPluginName = typeof BuiltInPlugins[number][0];
 export type BuiltInFlowrPluginArgs<N extends BuiltInFlowrPluginName> = N extends typeof BuiltInPlugins[number][0] ? ConstructorParameters<Extract<typeof BuiltInPlugins[number], [N, PluginProducer]>[1]> : never;
 type PluginProducer = new (...args: never[]) => FlowrAnalyzerPlugin;

package/project/plugins/plugin-registry.js

@@ -15,6 +15,7 @@ const flowr_analyzer_namespace_files_plugin_1 = require("./file-plugins/flowr-an
 const flowr_analyzer_news_file_plugin_1 = require("./file-plugins/flowr-analyzer-news-file-plugin");
 const flowr_analyzer_vignette_file_plugin_1 = require("./file-plugins/flowr-analyzer-vignette-file-plugin");
 const flowr_analyzer_test_file_plugin_1 = require("./file-plugins/flowr-analyzer-test-file-plugin");
+const flowr_analyzer_license_file_plugin_1 = require("./file-plugins/flowr-analyzer-license-file-plugin");
 /**
  * The built-in Flowr Analyzer plugins that are always available.
  */
@@ -28,7 +29,8 @@ exports.BuiltInPlugins = [
     ['file:qmd', flowr_analyzer_qmd_file_plugin_1.FlowrAnalyzerQmdFilePlugin],
     ['file:ipynb', flowr_analyzer_jupyter_file_plugin_1.FlowrAnalyzerJupyterFilePlugin],
     ['file:namespace', flowr_analyzer_namespace_files_plugin_1.FlowrAnalyzerNamespaceFilesPlugin],
-    ['file:news', flowr_analyzer_news_file_plugin_1.FlowrAnalyzerNewsFilePlugin]
+    ['file:news', flowr_analyzer_news_file_plugin_1.FlowrAnalyzerNewsFilePlugin],
+    ['file:license', flowr_analyzer_license_file_plugin_1.FlowrAnalyzerLicenseFilePlugin]
 ];
 /**
  * The registry of built-in and user-registered Flowr Analyzer plugins.

package/project/plugins/project-discovery/flowr-analyzer-project-discovery-plugin.js

@@ -57,7 +57,6 @@ class DefaultFlowrAnalyzerProjectDiscoveryPlugin extends FlowrAnalyzerProjectDis
         const requests = [];
         /* the dummy approach of collecting all files, group R and Rmd files, and be done with it */
         for (const file of (0, files_1.getAllFilesSync)(args.content, /.*/, this.ignorePathsRegex)) {
-            console.log(`Discovered file: ${file}`);
             const relativePath = path_1.default.relative(args.content, file);
             if (this.supportedExtensions.test(relativePath) && (!this.onlyTraversePaths || this.onlyTraversePaths.test(relativePath)) && !this.excludePathsRegex.test((0, built_in_source_1.platformDirname)(relativePath))) {
                 requests.push({ content: file, request: 'file' });

package/queries/catalog/config-query/config-query-format.d.ts

@@ -4,7 +4,7 @@ import { type OutputFormatter } from '../../../util/text/ansi';
 import Joi from 'joi';
 import type { FlowrConfigOptions } from '../../../config';
 import type { DeepPartial } from 'ts-essentials';
-import type { ParsedQueryLine } from '../../query';
+import type { ParsedQueryLine, Query } from '../../query';
 import type { ReplOutput } from '../../../cli/repl/commands/repl-main';
 import type { CommandCompletions } from '../../../cli/repl/core';
 export interface ConfigQuery extends BaseQueryFormat {
@@ -18,7 +18,7 @@ declare function configReplCompleter(partialLine: readonly string[], _startingNe
 declare function configQueryLineParser(output: ReplOutput, line: readonly string[], _config: FlowrConfigOptions): ParsedQueryLine<'config'>;
 export declare const ConfigQueryDefinition: {
     readonly executor: typeof executeConfigQuery;
-    readonly asciiSummarizer: (formatter: OutputFormatter, _analyzer: unknown, queryResults: BaseQueryResult, result: string[]) => true;
+    readonly asciiSummarizer: (formatter: OutputFormatter, _analyzer: unknown, queryResults: BaseQueryResult, result: string[], queries: readonly Query[]) => true;
     readonly completer: typeof configReplCompleter;
     readonly fromLine: typeof configQueryLineParser;
     readonly schema: Joi.ObjectSchema<any>;

package/queries/catalog/config-query/config-query-format.js

@@ -74,12 +74,50 @@ function configQueryLineParser(output, line, _config) {
     return { query: [{ type: 'config' }]
     };
 }
+function collectKeysFromUpdate(update, prefix = '') {
+    // only collect leaf keys
+    const keys = [];
+    for (const [key, value] of Object.entries(update)) {
+        const fullKey = prefix ? `${prefix}.${key}` : key;
+        if (value && typeof value === 'object' && !Array.isArray(value)) {
+            keys.push(...collectKeysFromUpdate(value, fullKey));
+        }
+        else {
+            keys.push(fullKey);
+        }
+    }
+    return keys;
+}
+function getValueAtPath(obj, path) {
+    let current = obj;
+    for (const key of path) {
+        if (current && typeof current === 'object' && current[key] !== undefined) {
+            current = current[key];
+        }
+        else {
+            return undefined;
+        }
+    }
+    return current;
+}
 exports.ConfigQueryDefinition = {
     executor: config_query_executor_1.executeConfigQuery,
-    asciiSummarizer: (formatter, _analyzer, queryResults, result) => {
+    asciiSummarizer: (formatter, _analyzer, queryResults, result, queries) => {
         const out = queryResults;
         result.push(`Query: ${(0, ansi_1.bold)('config', formatter)} (${(0, time_1.printAsMs)(out['.meta'].timing, 0)})`);
-        result.push(`   ╰ Config:\n${JSON.stringify(out.config, json_1.jsonReplacer, 4)}`);
+        const configQueries = queries.filter(q => q.type === 'config');
+        if (configQueries.some(q => q.update)) {
+            const updatedKeys = configQueries.flatMap(q => q.update ? collectKeysFromUpdate(q.update) : []);
+            result.push('   ╰ Updated configuration:');
+            for (const key of updatedKeys) {
+                const path = key.split('.');
+                const newValue = getValueAtPath(out.config, path);
+                result.push(`       - ${key}: ${JSON.stringify(newValue, json_1.jsonReplacer)}`);
+            }
+        }
+        else {
+            result.push(`   ╰ Config:\n${JSON.stringify(out.config, json_1.jsonReplacer, 4)}`);
+        }
         return true;
     },
     completer: configReplCompleter,

package/queries/catalog/dependencies-query/function-info/read-functions.js

@@ -100,5 +100,13 @@ exports.ReadFunctions = [
     { package: 'DBI', name: 'dbReadTable', argIdx: 1, argName: 'name', resolveValue: true },
     { package: 'DBI', name: 'dbReadTableArrow', argIdx: 1, argName: 'name', resolveValue: true },
     { package: 'jsonlite', name: 'read_json', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'rpolars', name: 'pl_read_ipc', argIdx: 0, argName: 'source', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'rpolars', name: 'pl_read_csv', argIdx: 0, argName: 'source', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'rpolars', name: 'pl_read_ndjson', argIdx: 0, argName: 'source', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'rpolars', name: 'pl_read_parquet', argIdx: 0, argName: 'source', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'rpolars', name: 'pl_scan_csv', argIdx: 0, argName: 'source', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'rpolars', name: 'pl_scan_ipc', argIdx: 0, argName: 'source', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'rpolars', name: 'pl_scan_ndjson', argIdx: 0, argName: 'source', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'rpolars', name: 'pl_scan_parquet', argIdx: 0, argName: 'source', resolveValue: true, ignoreIf: 'arg-missing' },
 ];
 //# sourceMappingURL=read-functions.js.map

package/queries/catalog/dependencies-query/function-info/write-functions.js

@@ -106,5 +106,14 @@ exports.WriteFunctions = [
     { package: 'rasterpdf', name: 'agg_pdf', argIdx: 0, argName: 'filename', resolveValue: true },
     { package: 'highcharter', name: 'hc_exporting', argName: 'filename', resolveValue: true },
     { package: 'jsonlite', name: 'write_json', argIdx: 1, argName: 'path', resolveValue: true },
+    { package: 'rpolars', name: 'sink_ipc', argIdx: 0, argName: 'path', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'rpolars', name: 'sink_csv', argIdx: 0, argName: 'path', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'rpolars', name: 'sink_ndjson', argIdx: 0, argName: 'path', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'rpolars', name: 'sink_parquet', argIdx: 0, argName: 'path', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'rpolars', name: 'lazyframe__lazy_sink_csv', argIdx: 0, argName: 'path', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'rpolars', name: 'write_ipc', argIdx: 0, argName: 'file', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'rpolars', name: 'write_csv', argIdx: 0, argName: 'file', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'rpolars', name: 'write_ndjson', argIdx: 0, argName: 'file', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'rpolars', name: 'write_parquet', argIdx: 0, argName: 'file', resolveValue: true, ignoreIf: 'arg-missing' },
 ];
 //# sourceMappingURL=write-functions.js.map

package/queries/catalog/linter-query/linter-query-format.d.ts

@@ -31,6 +31,10 @@ export declare const LinterQueryDefinition: {
     readonly completer: typeof linterQueryCompleter;
     readonly fromLine: typeof linterQueryLineParser;
     readonly schema: Joi.ObjectSchema<any>;
-    readonly flattenInvolvedNodes: () => never[];
+    readonly flattenInvolvedNodes: (queryResults: BaseQueryResult) => ((string & {
+        __brand?: "node-id";
+    }) | (number & {
+        __brand?: "node-id";
+    }))[];
 };
 export {};

package/queries/catalog/linter-query/linter-query-format.js

@@ -105,7 +105,15 @@ exports.LinterQueryDefinition = {
             config: joi_1.default.object()
         })).description('The rules to lint for. If unset, all rules will be included.')
     }).description('The linter query lints for the given set of rules and returns the result.'),
-    flattenInvolvedNodes: () => []
+    flattenInvolvedNodes: (queryResults) => {
+        const out = queryResults;
+        return Object.values(out.results).flatMap(v => {
+            if ((0, linter_format_1.isLintingResultsError)(v)) {
+                return [];
+            }
+            return v.results.map(v => v.involvedId);
+        }).filter(assert_1.isNotUndefined);
+    }
 };
 function addLintingRuleResult(ruleName, results, result) {
     const rule = linter_rules_1.LintingRules[ruleName];

package/queries/query.d.ts

@@ -78,7 +78,7 @@ export declare const SupportedQueries: {
     };
     readonly config: {
         readonly executor: typeof import("./catalog/config-query/config-query-executor").executeConfigQuery;
-        readonly asciiSummarizer: (formatter: OutputFormatter, _analyzer: unknown, queryResults: BaseQueryResult, result: string[]) => true;
+        readonly asciiSummarizer: (formatter: OutputFormatter, _analyzer: unknown, queryResults: BaseQueryResult, result: string[], queries: readonly Query[]) => true;
         readonly completer: (partialLine: readonly string[], _startingNewArg: boolean, config: FlowrConfigOptions) => CommandCompletions;
         readonly fromLine: (output: ReplOutput, line: readonly string[], _config: FlowrConfigOptions) => ParsedQueryLine<"config">;
         readonly schema: Joi.ObjectSchema<any>;
@@ -228,7 +228,11 @@ export declare const SupportedQueries: {
         readonly completer: (line: readonly string[], startingNewArg: boolean, _config: FlowrConfigOptions) => CommandCompletions;
         readonly fromLine: (output: ReplOutput, line: readonly string[], _config: FlowrConfigOptions) => ParsedQueryLine<"linter">;
         readonly schema: Joi.ObjectSchema<any>;
-        readonly flattenInvolvedNodes: () => never[];
+        readonly flattenInvolvedNodes: (queryResults: BaseQueryResult) => ((string & {
+            __brand?: "node-id";
+        }) | (number & {
+            __brand?: "node-id";
+        }))[];
     };
 };
 export type SupportedQueryTypes = keyof typeof SupportedQueries;