@eagleoutice/flowr 2.2.16 → 2.4.0

package/linter/rules/absolute-path.js

@@ -87,7 +87,7 @@ exports.ABSOLUTE_PATH = {
         }
         if (config.include.constructed) {
             q = q.merge(flowr_search_builder_1.Q.all().filter(vertex_1.VertexType.FunctionCall).with(search_enrichers_1.Enrichment.CallTargets));
-            /* in the future we want to directly check whether this is one of the supported functions */
+            /* in the future, we want to directly check whether this is one of the supported functions */
         }
         return q.unique();
     },
@@ -96,6 +96,7 @@ exports.ABSOLUTE_PATH = {
             totalConsidered: 0,
             totalUnknown: 0
         };
+        const queryResults = elements.enrichmentContent(search_enrichers_1.Enrichment.QueryData)?.queries;
         const regex = config.absolutePathRegex ? new RegExp(config.absolutePathRegex) : undefined;
         return {
             results: elements.getElements().flatMap(element => {
@@ -105,7 +106,7 @@ exports.ABSOLUTE_PATH = {
                 if ((0, r_string_1.isRString)(node)) {
                     if (node.content.str.length >= 3 && (0, strings_1.isAbsolutePath)(node.content.str, regex)) {
                         return [{
-                                certainty: linter_format_1.LintingCertainty.Maybe,
+                                certainty: linter_format_1.LintingResultCertainty.Uncertain,
                                 filePath: node.content.str,
                                 range: node.info.fullRange ?? node.location,
                                 quickFix: buildQuickFix(node, node.content.str, wd)
@@ -115,12 +116,12 @@ exports.ABSOLUTE_PATH = {
                         return [];
                     }
                 }
-                else if (element.queryResult) {
-                    const result = element.queryResult;
+                else if ((0, search_enrichers_1.enrichmentContent)(element, search_enrichers_1.Enrichment.QueryData)) {
+                    const result = queryResults[(0, search_enrichers_1.enrichmentContent)(element, search_enrichers_1.Enrichment.QueryData).query];
                     const mappedStrings = result.readData.filter(r => r.source !== dependencies_query_format_1.Unknown && (0, strings_1.isAbsolutePath)(r.source, regex)).map(r => {
                         const elem = data.normalize.idMap.get(r.nodeId);
                         return {
-                            certainty: linter_format_1.LintingCertainty.Definitely,
+                            certainty: linter_format_1.LintingResultCertainty.Certain,
                             filePath: r.source,
                             range: elem?.info.fullRange ?? elem?.location ?? (0, range_1.rangeFrom)(-1, -1, -1, -1),
                             quickFix: buildQuickFix(elem, r.source, wd)
@@ -141,7 +142,7 @@ exports.ABSOLUTE_PATH = {
                         const strings = handler ? handler(data.dataflow.graph, dfNode, data.config) : [];
                         if (strings) {
                             return strings.filter(s => (0, strings_1.isAbsolutePath)(s, regex)).map(str => ({
-                                certainty: linter_format_1.LintingCertainty.Maybe,
+                                certainty: linter_format_1.LintingResultCertainty.Uncertain,
                                 filePath: str,
                                 range: node.info.fullRange ?? node.location ?? (0, range_1.rangeFrom)(-1, -1, -1, -1)
                             }));
@@ -163,6 +164,8 @@ exports.ABSOLUTE_PATH = {
         name: 'Absolute Paths',
         description: 'Checks whether file paths are absolute.',
         tags: [linter_tags_1.LintingRuleTag.Robustness, linter_tags_1.LintingRuleTag.Reproducibility, linter_tags_1.LintingRuleTag.Smell, linter_tags_1.LintingRuleTag.QuickFix],
+        // checks all found paths for whether they're absolute to ensure correctness, but doesn't handle non-constant paths so not all will be returned
+        certainty: linter_format_1.LintingRuleCertainty.BestEffort,
         defaultConfig: {
             include: {
                 constructed: true,

package/linter/rules/dataframe-access-validation.d.ts

@@ -0,0 +1,55 @@
+import type { ParentInformation } from '../../r-bridge/lang-4.x/ast/model/processing/decorate';
+import type { FlowrSearchElements } from '../../search/flowr-search';
+import { type MergeableRecord } from '../../util/objects';
+import { type SourceRange } from '../../util/range';
+import type { LintingResult } from '../linter-format';
+import { LintingRuleCertainty } from '../linter-format';
+import { LintingRuleTag } from '../linter-tags';
+export interface DataFrameAccessValidationResult extends LintingResult {
+    /** The type of the data frame access ("column" or "row") */
+    type: 'column' | 'row';
+    /** The name or index of the column or row being accessed in the data frame */
+    accessed: string | number;
+    /** The name of the function/operation used for the access (e.g. `$`, `[`, `[[`, but also `filter`, `select`, ...) */
+    access: string;
+    /** The variable/symbol name of the accessed data frame operand (`undefined` if operand is no symbol) */
+    operand?: string;
+    /** The source range in the code where the access occurs */
+    range: SourceRange;
+}
+export interface DataFrameAccessValidationConfig extends MergeableRecord {
+    /** Whether data frame shapes should be extracted from loaded external data files, such as CSV files (defaults to the option in the flowR config if `undefined`) */
+    readLoadedData?: boolean;
+}
+export interface DataFrameAccessValidationMetadata extends MergeableRecord {
+    /** The number of data frame functions and operations containing inferred column or row accesses */
+    numOperations: number;
+    /** The number of inferred abstract column or row access operations */
+    numAccesses: number;
+    /** The total number of inferred accessed columns and rows */
+    totalAccessed: number;
+}
+export declare const DATA_FRAME_ACCESS_VALIDATION: {
+    readonly createSearch: () => import("../../search/flowr-search-builder").FlowrSearchBuilder<"all", ["with"], ParentInformation, FlowrSearchElements<ParentInformation, import("../../search/flowr-search").FlowrSearchElement<ParentInformation>[]>>;
+    readonly processSearchResult: (elements: FlowrSearchElements<ParentInformation, import("../../search/flowr-search").FlowrSearchElement<ParentInformation>[]>, config: DataFrameAccessValidationConfig, data: {
+        normalize: import("../../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst;
+        dataflow: import("../../dataflow/info").DataflowInformation;
+        config: import("../../config").FlowrConfigOptions;
+    }) => {
+        results: DataFrameAccessValidationResult[];
+        '.meta': DataFrameAccessValidationMetadata;
+    };
+    readonly prettyPrint: {
+        readonly query: (result: DataFrameAccessValidationResult) => string;
+        readonly full: (result: DataFrameAccessValidationResult) => string;
+    };
+    readonly info: {
+        readonly name: "Dataframe Access Validation";
+        readonly tags: readonly [LintingRuleTag.Bug, LintingRuleTag.Usability, LintingRuleTag.Reproducibility];
+        readonly certainty: LintingRuleCertainty.BestEffort;
+        readonly description: "Validates the existance of accessed columns and rows of dataframes.";
+        readonly defaultConfig: {
+            readonly readLoadedData: false;
+        };
+    };
+};

package/linter/rules/dataframe-access-validation.js

@@ -0,0 +1,118 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.DATA_FRAME_ACCESS_VALIDATION = void 0;
+const absint_info_1 = require("../../abstract-interpretation/data-frame/absint-info");
+const domain_1 = require("../../abstract-interpretation/data-frame/domain");
+const shape_inference_1 = require("../../abstract-interpretation/data-frame/shape-inference");
+const config_1 = require("../../config");
+const extract_cfg_1 = require("../../control-flow/extract-cfg");
+const type_1 = require("../../r-bridge/lang-4.x/ast/model/type");
+const flowr_search_builder_1 = require("../../search/flowr-search-builder");
+const search_enrichers_1 = require("../../search/search-executor/search-enrichers");
+const dfg_1 = require("../../util/mermaid/dfg");
+const range_1 = require("../../util/range");
+const linter_format_1 = require("../linter-format");
+const linter_tags_1 = require("../linter-tags");
+;
+;
+exports.DATA_FRAME_ACCESS_VALIDATION = {
+    createSearch: () => flowr_search_builder_1.Q.all().with(search_enrichers_1.Enrichment.CallTargets, { onlyBuiltin: true }),
+    processSearchResult: (elements, config, data) => {
+        const flowrConfig = (0, config_1.amendConfig)(data.config, flowrConfig => {
+            if (config.readLoadedData !== undefined) {
+                flowrConfig.abstractInterpretation.dataFrame.readLoadedData.readExternalFiles = config.readLoadedData;
+            }
+            return flowrConfig;
+        });
+        const cfg = (0, extract_cfg_1.extractCfg)(data.normalize, flowrConfig, data.dataflow.graph);
+        (0, shape_inference_1.inferDataFrameShapes)(cfg, data.dataflow.graph, data.normalize, flowrConfig);
+        const accessOperations = getAccessOperations(elements);
+        const accesses = [];
+        for (const [nodeId, operations] of accessOperations) {
+            const access = { nodeId };
+            for (const operation of operations) {
+                access.operand ??= operation.operand;
+                access.operandShape ??= (0, shape_inference_1.resolveIdToDataFrameShape)(operation.operand, data.dataflow.graph);
+                if (operation.operation === 'accessCols' && operation.columns !== undefined) {
+                    access.accessedCols ??= [];
+                    access.accessedCols.push(...operation.columns);
+                }
+                else if (operation.operation === 'accessRows' && operation.rows !== undefined) {
+                    access.accessedRows ??= [];
+                    access.accessedRows.push(...operation.rows);
+                }
+            }
+            accesses.push(access);
+        }
+        const operations = accessOperations.entries().flatMap(([, operations]) => operations).toArray();
+        const metadata = {
+            numOperations: accessOperations.size,
+            numAccesses: operations.length,
+            totalAccessed: operations
+                .map(operation => operation.operation === 'accessCols' ? operation.columns?.length ?? 0 : operation.rows?.length ?? 0)
+                .reduce((a, b) => a + b, 0)
+        };
+        const results = accesses
+            .flatMap(access => findInvalidDataFrameAccesses(access)
+            .map(accessed => ({ nodeId: access.nodeId, operand: access.operand, ...accessed })))
+            .map(({ nodeId, operand, ...accessed }) => ({
+            ...accessed,
+            node: data.normalize.idMap.get(nodeId),
+            operand: operand !== undefined ? data.normalize.idMap.get(operand) : undefined,
+        }))
+            .map(({ node, operand, ...accessed }) => ({
+            ...accessed,
+            access: node?.lexeme ?? '???',
+            ...(operand?.type === type_1.RType.Symbol ? { operand: operand.content } : {}),
+            range: node?.info.fullRange ?? node?.location ?? (0, range_1.rangeFrom)(-1, -1, -1, -1),
+            certainty: linter_format_1.LintingResultCertainty.Certain
+        }));
+        return { results, '.meta': metadata };
+    },
+    prettyPrint: {
+        [linter_format_1.LintingPrettyPrintContext.Query]: result => `Access of ${result.type} ` +
+            (typeof result.accessed === 'string' ? `"${result.accessed}"` : result.accessed) + ' ' +
+            (result.operand !== undefined ? `of \`${result.operand}\`` : `at \`${result.access}\``) + ` at ${(0, dfg_1.formatRange)(result.range)}`,
+        [linter_format_1.LintingPrettyPrintContext.Full]: result => `Accessed ${result.type} ` +
+            (typeof result.accessed === 'string' ? `"${result.accessed}"` : result.accessed) + ' does not exist ' +
+            (result.operand !== undefined ? `in \`${result.operand}\`` : `at \`${result.access}\``) + ` at ${(0, dfg_1.formatRange)(result.range)}`
+    },
+    info: {
+        name: 'Dataframe Access Validation',
+        tags: [linter_tags_1.LintingRuleTag.Bug, linter_tags_1.LintingRuleTag.Usability, linter_tags_1.LintingRuleTag.Reproducibility],
+        // this rule is unable to detect all cases of dataframe access, but sufficiently ensures returned results are valid
+        certainty: linter_format_1.LintingRuleCertainty.BestEffort,
+        description: 'Validates the existance of accessed columns and rows of dataframes.',
+        defaultConfig: { readLoadedData: false }
+    }
+};
+function getAccessOperations(elements) {
+    return new Map(elements.getElements()
+        .map(element => element.node)
+        .filter(absint_info_1.hasDataFrameExpressionInfo)
+        .map(node => [node.info.id, node.info.dataFrame.operations
+            .filter(({ operation }) => operation === 'accessCols' || operation === 'accessRows')
+            .map(({ operation, operand, type: _type, options: _options, ...args }) => ({ operation, operand, ...args }))
+    ])
+        .filter(([, operations]) => operations.length > 0));
+}
+function findInvalidDataFrameAccesses({ operandShape, accessedCols, accessedRows }) {
+    const invalidAccesses = [];
+    if (operandShape !== undefined) {
+        for (const row of accessedRows ?? []) {
+            if (!(0, domain_1.satisfiesLeqInterval)(operandShape.rows, row)) {
+                invalidAccesses.push({ type: 'row', accessed: row });
+            }
+        }
+        for (const col of accessedCols ?? []) {
+            if (typeof col === 'string' && !(0, domain_1.satisfiesColsNames)(operandShape.colnames, col)) {
+                invalidAccesses.push({ type: 'column', accessed: col });
+            }
+            else if (typeof col === 'number' && !(0, domain_1.satisfiesLeqInterval)(operandShape.cols, col)) {
+                invalidAccesses.push({ type: 'column', accessed: col });
+            }
+        }
+    }
+    return invalidAccesses;
+}
+//# sourceMappingURL=dataframe-access-validation.js.map

package/linter/rules/dead-code.d.ts

@@ -0,0 +1,43 @@
+import { LintingResultCertainty, type LintingResult, LintingRuleCertainty } from '../linter-format';
+import type { SourceRange } from '../../util/range';
+import type { MergeableRecord } from '../../util/objects';
+import { LintingRuleTag } from '../linter-tags';
+import { type CfgSimplificationPassName } from '../../control-flow/cfg-simplification';
+export interface DeadCodeResult extends LintingResult {
+    range: SourceRange;
+}
+export interface DeadCodeConfig extends MergeableRecord {
+    /**
+     * The simplification passes that should be run on the extracted CFG.
+     * Defaults to the entries of {@link DefaultCfgSimplificationOrder} and `analyze-dead-code`.
+     */
+    simplificationPasses?: CfgSimplificationPassName[];
+}
+export interface DeadCodeMetadata extends MergeableRecord {
+    consideredNodes: number;
+}
+export declare const DEAD_CODE: {
+    readonly createSearch: (config: DeadCodeConfig) => import("../../search/flowr-search-builder").FlowrSearchBuilder<"all", ["with"], import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, import("../../search/flowr-search").FlowrSearchElements<import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, import("../../search/flowr-search").FlowrSearchElement<import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation>[]>>;
+    readonly processSearchResult: (elements: import("../../search/flowr-search").FlowrSearchElements<import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, import("../../search/flowr-search").FlowrSearchElement<import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation>[]>, _config: DeadCodeConfig, _data: {
+        normalize: import("../../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst;
+        dataflow: import("../../dataflow/info").DataflowInformation;
+        config: import("../../config").FlowrConfigOptions;
+    }) => {
+        results: {
+            certainty: LintingResultCertainty.Certain;
+            range: SourceRange;
+        }[];
+        '.meta': DeadCodeMetadata;
+    };
+    readonly prettyPrint: {
+        readonly query: (result: DeadCodeResult) => string;
+        readonly full: (result: DeadCodeResult) => string;
+    };
+    readonly info: {
+        readonly name: "Dead Code";
+        readonly tags: readonly [LintingRuleTag.Smell, LintingRuleTag.Usability, LintingRuleTag.Reproducibility];
+        readonly certainty: LintingRuleCertainty.BestEffort;
+        readonly description: "Marks areas of code that are never reached during execution.";
+        readonly defaultConfig: {};
+    };
+};

package/linter/rules/dead-code.js

@@ -0,0 +1,50 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.DEAD_CODE = void 0;
+const linter_format_1 = require("../linter-format");
+const range_1 = require("../../util/range");
+const flowr_search_builder_1 = require("../../search/flowr-search-builder");
+const dfg_1 = require("../../util/mermaid/dfg");
+const linter_tags_1 = require("../linter-tags");
+const search_enrichers_1 = require("../../search/search-executor/search-enrichers");
+const assert_1 = require("../../util/assert");
+const cfg_simplification_1 = require("../../control-flow/cfg-simplification");
+exports.DEAD_CODE = {
+    createSearch: (config) => flowr_search_builder_1.Q.all().with(search_enrichers_1.Enrichment.CfgInformation, {
+        checkReachable: true,
+        simplificationPasses: config.simplificationPasses ?? [...cfg_simplification_1.DefaultCfgSimplificationOrder, 'analyze-dead-code']
+    }),
+    processSearchResult: (elements, _config, _data) => {
+        const meta = {
+            consideredNodes: 0
+        };
+        return {
+            results: (0, range_1.combineRanges)(...new Set(elements.getElements()
+                .filter(element => {
+                meta.consideredNodes++;
+                const cfgInformation = (0, search_enrichers_1.enrichmentContent)(element, search_enrichers_1.Enrichment.CfgInformation);
+                return cfgInformation.isRoot && !cfgInformation.isReachable;
+            })
+                .map(element => element.node.info.fullRange ?? element.node.location)
+                .filter(assert_1.isNotUndefined)))
+                .map(range => ({
+                certainty: linter_format_1.LintingResultCertainty.Certain,
+                range
+            })),
+            '.meta': meta
+        };
+    },
+    prettyPrint: {
+        [linter_format_1.LintingPrettyPrintContext.Query]: result => `Code at ${(0, dfg_1.formatRange)(result.range)}`,
+        [linter_format_1.LintingPrettyPrintContext.Full]: result => `Code at ${(0, dfg_1.formatRange)(result.range)} can never be executed`,
+    },
+    info: {
+        name: 'Dead Code',
+        tags: [linter_tags_1.LintingRuleTag.Smell, linter_tags_1.LintingRuleTag.Usability, linter_tags_1.LintingRuleTag.Reproducibility],
+        // our limited dead code analysis causes complex cases of dead code not to be included in the linting result, but deadness is properly investigated for returned results
+        certainty: linter_format_1.LintingRuleCertainty.BestEffort,
+        description: 'Marks areas of code that are never reached during execution.',
+        defaultConfig: {}
+    }
+};
+//# sourceMappingURL=dead-code.js.map

package/linter/rules/deprecated-functions.d.ts

@@ -1,5 +1,5 @@
 import type { LintingResult } from '../linter-format';
-import { LintingCertainty } from '../linter-format';
+import { LintingResultCertainty, LintingRuleCertainty } from '../linter-format';
 import type { MergeableRecord } from '../../util/objects';
 import type { SourceRange } from '../../util/range';
 import type { Identifier } from '../../dataflow/environments/identifier';
@@ -22,7 +22,7 @@ export declare const DEPRECATED_FUNCTIONS: {
     readonly createSearch: (config: DeprecatedFunctionsConfig) => import("../../search/flowr-search-builder").FlowrSearchBuilder<"all", ["with", "filter"], import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, import("../../search/flowr-search").FlowrSearchElements<import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, [] | import("../../search/flowr-search").FlowrSearchElement<import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation>[]>>;
     readonly processSearchResult: (elements: import("../../search/flowr-search").FlowrSearchElements<import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, import("../../search/flowr-search").FlowrSearchElement<import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation>[]>) => {
         results: {
-            certainty: LintingCertainty.Definitely;
+            certainty: LintingResultCertainty.Certain;
             function: Identifier;
             range: SourceRange;
         }[];
@@ -35,6 +35,7 @@ export declare const DEPRECATED_FUNCTIONS: {
     readonly info: {
         readonly name: "Deprecated Functions";
         readonly tags: readonly [LintingRuleTag.Deprecated, LintingRuleTag.Smell, LintingRuleTag.Usability, LintingRuleTag.Reproducibility];
+        readonly certainty: LintingRuleCertainty.BestEffort;
         readonly description: "Marks deprecated functions that should not be used anymore.";
         readonly defaultConfig: {
             readonly deprecatedFunctions: readonly ["all_equal", "arrange_all", "distinct_all", "filter_all", "group_by_all", "summarise_all", "mutate_all", "select_all", "vars", "all_vars", "id", "failwith", "select_vars", "rename_vars", "select_var", "current_vars", "bench_tbls", "compare_tbls", "compare_tbls2", "eval_tbls", "eval_tbls2", "location", "changes", "combine", "do", "funs", "add_count_", "add_tally_", "arrange_", "count_", "distinct_", "do_", "filter_", "funs_", "group_by_", "group_indices_", "mutate_", "tally_", "transmute_", "rename_", "rename_vars_", "select_", "select_vars_", "slice_", "summarise_", "summarize_", "summarise_each", "src_local", "tbl_df", "add_rownames", "group_nest", "group_split", "with_groups", "nest_by", "progress_estimated", "recode", "sample_n", "top_n", "transmute", "fct_explicit_na", "aes_", "aes_auto", "annotation_logticks", "is.Coord", "coord_flip", "coord_map", "is.facet", "fortify", "is.ggproto", "guide_train", "is.ggplot", "qplot", "is.theme", "gg_dep", "liply", "isplit2", "list_along", "cross", "invoke", "at_depth", "prepend", "rerun", "splice", "`%@%`", "rbernoulli", "rdunif", "when", "update_list", "map_raw", "accumulate", "reduce_right", "flatten", "map_dfr", "as_vector", "transpose", "melt_delim", "melt_fwf", "melt_table", "read_table2", "str_interp", "as_tibble", "data_frame", "tibble_", "data_frame_", "lst_", "as_data_frame", "as.tibble", "frame_data", "trunc_mat", "is.tibble", "tidy_names", "set_tidy_names", "repair_names", "extract_numeric", "complete_", "drop_na_", "expand_", "crossing_", "nesting_", "extract_", "fill_", "gather_", "nest_", "separate_rows_", "separate_", "spread_", "unite_", "unnest_", "extract", "gather", "nest_legacy", "separate_rows", "separate", "spread"];

package/linter/rules/deprecated-functions.js

@@ -35,7 +35,7 @@ exports.DEPRECATED_FUNCTIONS = {
                 });
             })
                 .map(element => ({
-                certainty: linter_format_1.LintingCertainty.Definitely,
+                certainty: linter_format_1.LintingResultCertainty.Certain,
                 function: element.target,
                 range: element.range
             })),
@@ -49,6 +49,8 @@ exports.DEPRECATED_FUNCTIONS = {
     info: {
         name: 'Deprecated Functions',
         tags: [linter_tags_1.LintingRuleTag.Deprecated, linter_tags_1.LintingRuleTag.Smell, linter_tags_1.LintingRuleTag.Usability, linter_tags_1.LintingRuleTag.Reproducibility],
+        // ensures all deprecated functions found are actually deprecated through its limited config, but doesn't find all deprecated functions since the config is pre-crawled
+        certainty: linter_format_1.LintingRuleCertainty.BestEffort,
         description: 'Marks deprecated functions that should not be used anymore.',
         defaultConfig: {
             deprecatedFunctions: ['all_equal', 'arrange_all', 'distinct_all', 'filter_all', 'group_by_all', 'summarise_all', 'mutate_all', 'select_all', 'vars', 'all_vars', 'id', 'failwith', 'select_vars', 'rename_vars', 'select_var', 'current_vars', 'bench_tbls', 'compare_tbls', 'compare_tbls2', 'eval_tbls', 'eval_tbls2', 'location', 'changes', 'combine', 'do', 'funs', 'add_count_', 'add_tally_', 'arrange_', 'count_', 'distinct_', 'do_', 'filter_', 'funs_', 'group_by_', 'group_indices_', 'mutate_', 'tally_', 'transmute_', 'rename_', 'rename_vars_', 'select_', 'select_vars_', 'slice_', 'summarise_', 'summarize_', 'summarise_each', 'src_local', 'tbl_df', 'add_rownames', 'group_nest', 'group_split', 'with_groups', 'nest_by', 'progress_estimated', 'recode', 'sample_n', 'top_n', 'transmute', 'fct_explicit_na', 'aes_', 'aes_auto', 'annotation_logticks', 'is.Coord', 'coord_flip', 'coord_map', 'is.facet', 'fortify', 'is.ggproto', 'guide_train', 'is.ggplot', 'qplot', 'is.theme', 'gg_dep', 'liply', 'isplit2', 'list_along', 'cross', 'invoke', 'at_depth', 'prepend', 'rerun', 'splice', '`%@%`', 'rbernoulli', 'rdunif', 'when', 'update_list', 'map_raw', 'accumulate', 'reduce_right', 'flatten', 'map_dfr', 'as_vector', 'transpose', 'melt_delim', 'melt_fwf', 'melt_table', 'read_table2', 'str_interp', 'as_tibble', 'data_frame', 'tibble_', 'data_frame_', 'lst_', 'as_data_frame', 'as.tibble', 'frame_data', 'trunc_mat', 'is.tibble', 'tidy_names', 'set_tidy_names', 'repair_names', 'extract_numeric', 'complete_', 'drop_na_', 'expand_', 'crossing_', 'nesting_', 'extract_', 'fill_', 'gather_', 'nest_', 'separate_rows_', 'separate_', 'spread_', 'unite_', 'unnest_', 'extract', 'gather', 'nest_legacy', 'separate_rows', 'separate', 'spread',]

package/linter/rules/file-path-validity.d.ts

@@ -1,8 +1,7 @@
 import type { LintingResult } from '../linter-format';
+import { LintingRuleCertainty } from '../linter-format';
 import type { MergeableRecord } from '../../util/objects';
 import type { SourceRange } from '../../util/range';
-import type { ParentInformation } from '../../r-bridge/lang-4.x/ast/model/processing/decorate';
-import type { FlowrSearchElementFromQuery } from '../../search/flowr-search';
 import type { FunctionInfo } from '../../queries/catalog/dependencies-query/function-info/function-info';
 import { LintingRuleTag } from '../linter-tags';
 export interface FilePathValidityResult extends LintingResult {
@@ -32,8 +31,8 @@ export interface FilePathValidityMetadata extends MergeableRecord {
     totalValid: number;
 }
 export declare const FILE_PATH_VALIDITY: {
-    readonly createSearch: (config: FilePathValidityConfig) => import("../../search/flowr-search-builder").FlowrSearchBuilder<"from-query", [], ParentInformation, import("../../search/flowr-search").FlowrSearchElements<ParentInformation, FlowrSearchElementFromQuery<ParentInformation>[]>>;
-    readonly processSearchResult: (elements: import("../../search/flowr-search").FlowrSearchElements<ParentInformation, FlowrSearchElementFromQuery<ParentInformation>[]>, config: FilePathValidityConfig, data: {
+    readonly createSearch: (config: FilePathValidityConfig) => import("../../search/flowr-search-builder").FlowrSearchBuilder<"from-query", ["with"], import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, import("../../search/flowr-search").FlowrSearchElements<import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, import("../../search/flowr-search").FlowrSearchElement<import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation>[]>>;
+    readonly processSearchResult: (elements: import("../../search/flowr-search").FlowrSearchElements<import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, import("../../search/flowr-search").FlowrSearchElement<import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation>[]>, config: FilePathValidityConfig, data: {
         normalize: import("../../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst;
         dataflow: import("../../dataflow/info").DataflowInformation;
         config: import("../../config").FlowrConfigOptions;
@@ -44,6 +43,7 @@ export declare const FILE_PATH_VALIDITY: {
     readonly info: {
         readonly name: "File Path Validity";
         readonly description: "Checks whether file paths used in read and write operations are valid and point to existing files.";
+        readonly certainty: LintingRuleCertainty.BestEffort;
         readonly tags: readonly [LintingRuleTag.Robustness, LintingRuleTag.Reproducibility, LintingRuleTag.Bug];
         readonly defaultConfig: {
             readonly additionalReadFunctions: readonly [];

package/linter/rules/file-path-validity.js

@@ -10,9 +10,9 @@ const logic_1 = require("../../util/logic");
 const retriever_1 = require("../../r-bridge/retriever");
 const read_functions_1 = require("../../queries/catalog/dependencies-query/function-info/read-functions");
 const write_functions_1 = require("../../queries/catalog/dependencies-query/function-info/write-functions");
-const extract_cfg_1 = require("../../control-flow/extract-cfg");
 const happens_before_1 = require("../../control-flow/happens-before");
 const linter_tags_1 = require("../linter-tags");
+const search_enrichers_1 = require("../../search/search-executor/search-enrichers");
 exports.FILE_PATH_VALIDITY = {
     createSearch: (config) => flowr_search_builder_1.Q.fromQuery({
         type: 'dependencies',
@@ -20,9 +20,9 @@ exports.FILE_PATH_VALIDITY = {
         ignoreDefaultFunctions: true,
         readFunctions: read_functions_1.ReadFunctions.concat(config.additionalReadFunctions),
         writeFunctions: write_functions_1.WriteFunctions.concat(config.additionalWriteFunctions)
-    }),
+    }).with(search_enrichers_1.Enrichment.CfgInformation),
     processSearchResult: (elements, config, data) => {
-        const cfg = (0, extract_cfg_1.extractSimpleCfg)(data.normalize).graph;
+        const cfg = elements.enrichmentContent(search_enrichers_1.Enrichment.CfgInformation).cfg.graph;
         const metadata = {
             totalReads: 0,
             totalUnknown: 0,
@@ -31,7 +31,7 @@ exports.FILE_PATH_VALIDITY = {
         };
         return {
             results: elements.getElements().flatMap(element => {
-                const results = element.queryResult;
+                const results = elements.enrichmentContent(search_enrichers_1.Enrichment.QueryData).queries['dependencies'];
                 const matchingRead = results.readData.find(r => r.nodeId == element.node.info.id);
                 if (!matchingRead) {
                     return [];
@@ -45,7 +45,7 @@ exports.FILE_PATH_VALIDITY = {
                         return [{
                                 range,
                                 filePath: dependencies_query_format_1.Unknown,
-                                certainty: linter_format_1.LintingCertainty.Maybe
+                                certainty: linter_format_1.LintingResultCertainty.Uncertain
                             }];
                     }
                     else {
@@ -70,7 +70,7 @@ exports.FILE_PATH_VALIDITY = {
                 return [{
                         range,
                         filePath: matchingRead.source,
-                        certainty: writesBefore && writesBefore.length && writesBefore.every(w => w === logic_1.Ternary.Maybe) ? linter_format_1.LintingCertainty.Maybe : linter_format_1.LintingCertainty.Definitely
+                        certainty: writesBefore && writesBefore.length && writesBefore.every(w => w === logic_1.Ternary.Maybe) ? linter_format_1.LintingResultCertainty.Uncertain : linter_format_1.LintingResultCertainty.Certain
                     }];
             }),
             '.meta': metadata
@@ -79,6 +79,8 @@ exports.FILE_PATH_VALIDITY = {
     info: {
         name: 'File Path Validity',
         description: 'Checks whether file paths used in read and write operations are valid and point to existing files.',
+        // checks all found paths for whether they're valid to ensure correctness, but doesn't handle non-constant paths so not all will be returned
+        certainty: linter_format_1.LintingRuleCertainty.BestEffort,
         tags: [linter_tags_1.LintingRuleTag.Robustness, linter_tags_1.LintingRuleTag.Reproducibility, linter_tags_1.LintingRuleTag.Bug],
         defaultConfig: {
             additionalReadFunctions: [],

package/linter/rules/naming-convention.d.ts

@@ -2,8 +2,8 @@ import type { DataflowGraph } from '../../dataflow/graph/graph';
 import type { NodeId } from '../../r-bridge/lang-4.x/ast/model/processing/node-id';
 import type { MergeableRecord } from '../../util/objects';
 import type { SourceRange } from '../../util/range';
-import type { LintQuickFixReplacement, LintingResult } from '../linter-format';
-import { LintingCertainty } from '../linter-format';
+import type { LintingResult, LintQuickFixReplacement } from '../linter-format';
+import { LintingResultCertainty, LintingRuleCertainty } from '../linter-format';
 import { LintingRuleTag } from '../linter-tags';
 export declare enum CasingConvention {
     CamelCase = "camelCase",
@@ -46,7 +46,7 @@ export declare const NAMING_CONVENTION: {
     }) => {
         results: {
             quickFix: LintQuickFixReplacement[] | undefined;
-            certainty: LintingCertainty;
+            certainty: LintingResultCertainty;
             detectedCasing: CasingConvention;
             name: string;
             range: SourceRange;
@@ -62,10 +62,11 @@ export declare const NAMING_CONVENTION: {
     };
     readonly info: {
         readonly name: "Naming Convention";
+        readonly certainty: LintingRuleCertainty.OverApproximative;
         readonly description: "Checks wether the symbols conform to a certain naming convention";
         readonly tags: readonly [LintingRuleTag.Style, LintingRuleTag.QuickFix];
         readonly defaultConfig: {
-            readonly caseing: CasingConvention.PascalCase;
+            readonly caseing: "auto";
         };
     };
 };

package/linter/rules/naming-convention.js

@@ -66,11 +66,15 @@ function detectCasing(identifier) {
     return CasingConvention.Unknown;
 }
 function getMostUsedCasing(symbols) {
+    if (symbols.length === 0) {
+        return CasingConvention.Unknown;
+    }
     const map = new Map();
     for (const symbol of symbols) {
         const o = map.get(symbol.detectedCasing) ?? 0;
         map.set(symbol.detectedCasing, o + 1);
     }
+    // Return element with most occurances 
     return [...map].reduce((p, c) => p[1] > c[1] ? p : c)[0];
 }
 function fixCasing(identifier, convention) {
@@ -128,7 +132,7 @@ exports.NAMING_CONVENTION = {
     processSearchResult: (elements, config, data) => {
         const symbols = elements.getElements()
             .map(m => ({
-            certainty: linter_format_1.LintingCertainty.Definitely,
+            certainty: linter_format_1.LintingResultCertainty.Certain,
             detectedCasing: detectCasing(m.node.lexeme),
             name: m.node.lexeme,
             range: m.node.info.fullRange,
@@ -154,10 +158,12 @@ exports.NAMING_CONVENTION = {
     },
     info: {
         name: 'Naming Convention',
+        // detects casing heuristically so correctness is not ensured using default config, but checks all identifiers in the code for naming convention match
+        certainty: linter_format_1.LintingRuleCertainty.OverApproximative,
         description: 'Checks wether the symbols conform to a certain naming convention',
         tags: [linter_tags_1.LintingRuleTag.Style, linter_tags_1.LintingRuleTag.QuickFix],
         defaultConfig: {
-            caseing: CasingConvention.PascalCase
+            caseing: 'auto'
         }
     }
 };

package/linter/rules/seeded-randomness.d.ts

@@ -1,5 +1,5 @@
 import type { LintingResult } from '../linter-format';
-import { LintingCertainty } from '../linter-format';
+import { LintingResultCertainty, LintingRuleCertainty } from '../linter-format';
 import type { SourceRange } from '../../util/range';
 import type { MergeableRecord } from '../../util/objects';
 import type { Identifier } from '../../dataflow/environments/identifier';
@@ -30,14 +30,14 @@ export interface SeededRandomnessMeta extends MergeableRecord {
     callsWithNonConstantProducers: number;
 }
 export declare const SEEDED_RANDOMNESS: {
-    readonly createSearch: (config: SeededRandomnessConfig) => import("../../search/flowr-search-builder").FlowrSearchBuilder<"all", ["with", "filter", "with"], import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, import("../../search/flowr-search").FlowrSearchElements<import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, import("../../search/search-executor/search-enrichers").EnrichedFlowrSearchElement<import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation>[]>>;
+    readonly createSearch: (config: SeededRandomnessConfig) => import("../../search/flowr-search-builder").FlowrSearchBuilder<"all", ["with", "filter", "with"], import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, import("../../search/flowr-search").FlowrSearchElements<import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, import("../../search/flowr-search").FlowrSearchElement<import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation>[]>>;
     readonly processSearchResult: (elements: import("../../search/flowr-search").FlowrSearchElements<import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, import("../../search/flowr-search").FlowrSearchElement<import("../../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation>[]>, config: SeededRandomnessConfig, { dataflow }: {
         normalize: import("../../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst;
         dataflow: import("../../dataflow/info").DataflowInformation;
         config: import("../../config").FlowrConfigOptions;
     }) => {
         results: {
-            certainty: LintingCertainty.Definitely;
+            certainty: LintingResultCertainty.Certain;
             function: Identifier;
             range: SourceRange;
         }[];
@@ -55,6 +55,7 @@ export declare const SEEDED_RANDOMNESS: {
             readonly randomnessConsumers: readonly ["jitter", "sample", "sample.int", "arima.sim", "kmeans", "princomp", "rcauchy", "rchisq", "rexp", "rgamma", "rgeom", "rlnorm", "rlogis", "rmultinom", "rnbinom", "rnorm", "rpois", "runif", "pointLabel", "some", "rbernoulli", "rdunif", "generateSeedVectors"];
         };
         readonly tags: readonly [LintingRuleTag.Robustness, LintingRuleTag.Reproducibility];
+        readonly certainty: LintingRuleCertainty.BestEffort;
         readonly name: "Seeded Randomness";
         readonly description: "Checks whether randomness-based function calls are preceded by a random seed generation function. For consistent reproducibility, functions that use randomness should only be called after a constant random seed is set using a function like `set.seed`.";
     };

package/linter/rules/seeded-randomness.js

@@ -86,7 +86,7 @@ exports.SEEDED_RANDOMNESS = {
                 return true;
             })
                 .map(element => ({
-                certainty: linter_format_1.LintingCertainty.Definitely,
+                certainty: linter_format_1.LintingResultCertainty.Certain,
                 function: element.target,
                 range: element.range
             })),
@@ -99,6 +99,8 @@ exports.SEEDED_RANDOMNESS = {
             randomnessConsumers: ['jitter', 'sample', 'sample.int', 'arima.sim', 'kmeans', 'princomp', 'rcauchy', 'rchisq', 'rexp', 'rgamma', 'rgeom', 'rlnorm', 'rlogis', 'rmultinom', 'rnbinom', 'rnorm', 'rpois', 'runif', 'pointLabel', 'some', 'rbernoulli', 'rdunif', 'generateSeedVectors'],
         },
         tags: [linter_tags_1.LintingRuleTag.Robustness, linter_tags_1.LintingRuleTag.Reproducibility],
+        // only finds proper randomness producers and consumers due to its config, but will not find all producers/consumers since not all existing deprecated functions will be in the config
+        certainty: linter_format_1.LintingRuleCertainty.BestEffort,
         name: 'Seeded Randomness',
         description: 'Checks whether randomness-based function calls are preceded by a random seed generation function. For consistent reproducibility, functions that use randomness should only be called after a constant random seed is set using a function like `set.seed`.'
     },

package/linter/rules/unused-definition.d.ts

@@ -1,4 +1,5 @@
 import type { LintingResult } from '../linter-format';
+import { LintingRuleCertainty } from '../linter-format';
 import type { MergeableRecord } from '../../util/objects';
 import type { SourceRange } from '../../util/range';
 import { LintingRuleTag } from '../linter-tags';
@@ -34,6 +35,7 @@ export declare const UNUSED_DEFINITION: {
         readonly name: "Unused Definitions";
         readonly description: "Checks for unused definitions.";
         readonly tags: readonly [LintingRuleTag.Readability, LintingRuleTag.Smell, LintingRuleTag.QuickFix];
+        readonly certainty: LintingRuleCertainty.BestEffort;
         readonly defaultConfig: {
             readonly includeFunctionDefinitions: true;
         };