@eagleoutice/flowr 2.2.15 → 2.2.16

package/documentation/print-readme.js

@@ -14,6 +14,7 @@ const doc_repl_1 = require("./doc-util/doc-repl");
 const doc_auto_gen_1 = require("./doc-util/doc-auto-gen");
 const doc_general_1 = require("./doc-util/doc-general");
 const doc_dfg_1 = require("./doc-util/doc-dfg");
+const doc_query_1 = require("./doc-util/doc-query");
 async function getText(shell) {
     const dateOptions = { year: 'numeric', month: 'short', day: 'numeric' };
     return `
@@ -31,6 +32,28 @@ available for [VSCode](${doc_files_1.FlowrVsCode}), [Positron](${doc_files_1.Flo
 and [Docker](${doc_files_1.FlowrDockerRef}).
 It offers a wide variety of features, for example:
 
+* 🐞 **code linting**\\
+   Analyze your R scripts for common issues and potential bugs (see the [wiki page](${doc_files_1.FlowrGithubBaseRef}/flowr/wiki/Linter) for more information on the currently supported linters).
+
+	${(0, doc_general_1.prefixLines)((0, doc_structure_1.details)('Example: Linting code with flowR', `To lint your code, you can use the [REPL](${doc_files_1.FlowrWikiBaseRef}/Interface#using-the-repl) or the [Visual Studio Code extension](${doc_files_1.FlowrVsCode}) (see [vscode-flowr#283](https://github.com/flowr-analysis/vscode-flowr/pull/283)).
+	
+${await (async () => {
+        const code = 'read.csv("/root/x.txt")';
+        const res = await (0, doc_query_1.showQuery)(shell, code, [{ type: 'linter' }], { showCode: false, collapseQuery: true, collapseResult: false });
+        return await (0, doc_repl_1.documentReplSession)(shell, [{
+                command: `:query @linter ${JSON.stringify(code)}`,
+                description: `
+The linter will analyze the code and return any issues found.
+Formatted more nicely, this returns:
+
+${res}
+		`
+            }]);
+    })()}
+	   
+	   `), '    ')}
+
+
 * 🍕 **program slicing**\\
    Given a point of interest like the visualization of a plot, _flowR_ reduces the program to just the parts which are relevant
    for the computation of the point of interest.
@@ -117,7 +140,7 @@ You can enter ${(0, doc_cli_option_1.getReplCommand)('help')} to gain more infor
 
 <summary>Example REPL session</summary>
 
-![Example of a simple REPL session](wiki/gif/repl-demo.gif)
+![Example of a simple REPL session](wiki/gif/repl-demo-opt.gif)
 
 </details>
 

package/documentation/print-search-wiki.js

@@ -15,9 +15,8 @@ const path_1 = __importDefault(require("path"));
 const flowr_search_executor_1 = require("../search/flowr-search-executor");
 async function getText(shell) {
     const rversion = (await shell.usedRVersion())?.format() ?? 'unknown';
-    const types = (0, doc_types_1.getTypesFromFolderAsMermaid)({
+    const types = (0, doc_types_1.getTypesFromFolder)({
         rootFolder: path_1.default.resolve('./src/search/'),
-        typeName: 'FlowrSearchGenerator',
         inlineTypes: doc_types_1.mermaidHide
     });
     return `${(0, doc_auto_gen_1.autoGenHeader)({ filename: module.filename, purpose: 'search API', rVersion: rversion })}

package/linter/linter-executor.d.ts

@@ -3,7 +3,9 @@ import type { NormalizedAst } from '../r-bridge/lang-4.x/ast/model/processing/de
 import type { DataflowInformation } from '../dataflow/info';
 import type { LintingResults } from './linter-format';
 import type { DeepPartial } from 'ts-essentials';
+import type { FlowrConfigOptions } from '../config';
 export declare function executeLintingRule<Name extends LintingRuleNames>(ruleName: Name, input: {
     normalize: NormalizedAst;
     dataflow: DataflowInformation;
-}, config?: DeepPartial<LintingRuleConfig<Name>>): LintingResults<Name>;
+    config: FlowrConfigOptions;
+}, lintingRuleConfig?: DeepPartial<LintingRuleConfig<Name>>): LintingResults<Name>;

package/linter/linter-executor.js

@@ -4,9 +4,10 @@ exports.executeLintingRule = executeLintingRule;
 const linter_rules_1 = require("./linter-rules");
 const flowr_search_executor_1 = require("../search/flowr-search-executor");
 const flowr_search_1 = require("../search/flowr-search");
-function executeLintingRule(ruleName, input, config) {
+const objects_1 = require("../util/objects");
+function executeLintingRule(ruleName, input, lintingRuleConfig) {
     const rule = linter_rules_1.LintingRules[ruleName];
-    const fullConfig = { ...rule.defaultConfig, ...config };
+    const fullConfig = (0, objects_1.deepMergeObject)(rule.info.defaultConfig, lintingRuleConfig);
     const ruleSearch = rule.createSearch(fullConfig, input);
     const searchStart = Date.now();
     const searchResult = (0, flowr_search_executor_1.runSearch)(ruleSearch, input);

package/linter/linter-format.d.ts

@@ -6,7 +6,28 @@ import type { TransformerNames } from '../search/search-executor/search-transfor
 import type { NormalizedAst, ParentInformation } from '../r-bridge/lang-4.x/ast/model/processing/decorate';
 import type { LintingRuleConfig, LintingRuleMetadata, LintingRuleNames, LintingRuleResult } from './linter-rules';
 import type { DataflowInformation } from '../dataflow/info';
-import type { DeepPartial } from 'ts-essentials';
+import type { FlowrConfigOptions } from '../config';
+import type { DeepPartial, DeepReadonly } from 'ts-essentials';
+import type { LintingRuleTag } from './linter-tags';
+import type { SourceRange } from '../util/range';
+export interface LinterRuleInformation<Config extends MergeableRecord = never> {
+    /** Human-Readable name of the linting rule. */
+    readonly name: string;
+    /**
+     * The default config for this linting rule.
+     * This config is combined with the user config when executing the rule.
+     */
+    readonly defaultConfig: NoInfer<DeepReadonly<Config>>;
+    /**
+     * A short list of tags that describe and categorize the linting rule.
+     */
+    readonly tags: readonly LintingRuleTag[];
+    /**
+     * A short description of the linting rule.
+     * This is used to display the rule in the UI and to provide a brief overview of what the rule does.
+     */
+    readonly description: string;
+}
 /**
  * The base interface for a linting rule, which contains all of its relevant settings.
  * The registry of valid linting rules is stored in {@link LintingRules}.
@@ -27,26 +48,54 @@ export interface LintingRule<Result extends LintingResult, Metadata extends Merg
     readonly processSearchResult: (elements: FlowrSearchElements<Info, Elements>, config: Config, data: {
         normalize: NormalizedAst;
         dataflow: DataflowInformation;
+        config: FlowrConfigOptions;
     }) => {
         results: Result[];
         '.meta': Metadata;
     };
     /**
-     * A function used to pretty-print the given linting result.
-     * By default, the {@link LintingResult#certainty} is automatically printed alongside this information.
+     * A set of functions used to pretty-print the given linting result.
+     * By default, the {@link LintingResult#certainty} and whether any {@link LintingResult#quickFix} values are available is automatically printed alongside this information.
+     */
+    readonly prettyPrint: {
+        [C in LintingPrettyPrintContext]: (result: Result, metadata: Metadata) => string;
+    };
+    readonly info: LinterRuleInformation<NoInfer<Config>>;
+}
+interface BaseQuickFix {
+    /**
+     * The type of the quick fix.
      */
-    readonly prettyPrint: (result: Result, metadata: Metadata) => string;
+    readonly type: string;
     /**
-     * The default config for this linting rule.
-     * The default config is combined with the user config when executing the rule.
+     * A short, human-readable description of the quick fix.
      */
-    readonly defaultConfig: NoInfer<Config>;
+    readonly description: string;
+    /**
+     * The range of the text that should be replaced.
+     */
+    readonly range: SourceRange;
 }
+export interface LintQuickFixReplacement extends BaseQuickFix {
+    readonly type: 'replace';
+    /**
+     * The text that should replace the given range.
+     */
+    readonly replacement: string;
+}
+export interface LintQuickFixRemove extends BaseQuickFix {
+    readonly type: 'remove';
+}
+export type LintQuickFix = LintQuickFixReplacement | LintQuickFixRemove;
 /**
  * A linting result for a single linting rule match.
  */
 export interface LintingResult {
     readonly certainty: LintingCertainty;
+    /**
+     * If available, what to do to fix the linting result.
+     */
+    readonly quickFix?: LintQuickFix[];
 }
 export interface ConfiguredLintingRule<Name extends LintingRuleNames = LintingRuleNames> {
     readonly name: Name;
@@ -60,6 +109,17 @@ export interface LintingResults<Name extends LintingRuleNames> {
     };
 }
 export declare enum LintingCertainty {
+    /**
+     * The linting rule cannot say for sure whether the result is correct or not.
+     */
     Maybe = "maybe",
+    /**
+     * The linting rule is certain that the reported lint is real.
+     */
     Definitely = "definitely"
 }
+export declare enum LintingPrettyPrintContext {
+    Query = "query",
+    Full = "full"
+}
+export {};

package/linter/linter-format.js

@@ -1,9 +1,20 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.LintingCertainty = void 0;
+exports.LintingPrettyPrintContext = exports.LintingCertainty = void 0;
 var LintingCertainty;
 (function (LintingCertainty) {
+    /**
+     * The linting rule cannot say for sure whether the result is correct or not.
+     */
     LintingCertainty["Maybe"] = "maybe";
+    /**
+     * The linting rule is certain that the reported lint is real.
+     */
     LintingCertainty["Definitely"] = "definitely";
 })(LintingCertainty || (exports.LintingCertainty = LintingCertainty = {}));
+var LintingPrettyPrintContext;
+(function (LintingPrettyPrintContext) {
+    LintingPrettyPrintContext["Query"] = "query";
+    LintingPrettyPrintContext["Full"] = "full";
+})(LintingPrettyPrintContext || (exports.LintingPrettyPrintContext = LintingPrettyPrintContext = {}));
 //# sourceMappingURL=linter-format.js.map

package/linter/linter-rules.d.ts

@@ -5,34 +5,173 @@ import type { LintingRule } from './linter-format';
  */
 export declare const LintingRules: {
     readonly 'deprecated-functions': {
-        readonly createSearch: (_config: import("./rules/1-deprecated-functions").DeprecatedFunctionsConfig) => 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/search-executor/search-enrichers").EnrichedFlowrSearchElement<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: import("./rules/1-deprecated-functions").DeprecatedFunctionsConfig) => {
+        readonly createSearch: (config: import("./rules/deprecated-functions").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: import("./linter-format").LintingCertainty.Definitely;
                 function: import("../dataflow/environments/identifier").Identifier;
                 range: import("../util/range").SourceRange;
             }[];
-            '.meta': import("./rules/1-deprecated-functions").DeprecatedFunctionsMetadata;
+            '.meta': import("./rules/deprecated-functions").DeprecatedFunctionsMetadata;
         };
-        readonly prettyPrint: (result: import("./rules/1-deprecated-functions").DeprecatedFunctionsResult) => string;
-        readonly defaultConfig: {
-            readonly 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"];
+        readonly prettyPrint: {
+            readonly query: (result: import("./rules/deprecated-functions").DeprecatedFunctionsResult) => string;
+            readonly full: (result: import("./rules/deprecated-functions").DeprecatedFunctionsResult) => string;
+        };
+        readonly info: {
+            readonly name: "Deprecated Functions";
+            readonly tags: readonly [import("./linter-tags").LintingRuleTag.Deprecated, import("./linter-tags").LintingRuleTag.Smell, import("./linter-tags").LintingRuleTag.Usability, import("./linter-tags").LintingRuleTag.Reproducibility];
+            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"];
+            };
         };
     };
     readonly 'file-path-validity': {
-        readonly createSearch: (config: import("./rules/2-file-path-validity").FilePathValidityConfig) => import("../search/flowr-search-builder").FlowrSearchBuilder<"from-query", [], 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").FlowrSearchElementFromQuery<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").FlowrSearchElementFromQuery<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation>[]>, config: import("./rules/2-file-path-validity").FilePathValidityConfig, data: {
+        readonly createSearch: (config: import("./rules/file-path-validity").FilePathValidityConfig) => import("../search/flowr-search-builder").FlowrSearchBuilder<"from-query", [], 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").FlowrSearchElementFromQuery<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").FlowrSearchElementFromQuery<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation>[]>, config: import("./rules/file-path-validity").FilePathValidityConfig, data: {
+            normalize: import("../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst;
+            dataflow: import("../dataflow/info").DataflowInformation;
+            config: import("../config").FlowrConfigOptions;
+        }) => {
+            results: import("./rules/file-path-validity").FilePathValidityResult[];
+            ".meta": import("./rules/file-path-validity").FilePathValidityMetadata;
+        };
+        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 tags: readonly [import("./linter-tags").LintingRuleTag.Robustness, import("./linter-tags").LintingRuleTag.Reproducibility, import("./linter-tags").LintingRuleTag.Bug];
+            readonly defaultConfig: {
+                readonly additionalReadFunctions: readonly [];
+                readonly additionalWriteFunctions: readonly [];
+                readonly includeUnknown: false;
+            };
+        };
+        readonly prettyPrint: {
+            readonly query: (result: import("./rules/file-path-validity").FilePathValidityResult) => string;
+            readonly full: (result: import("./rules/file-path-validity").FilePathValidityResult) => string;
+        };
+    };
+    readonly 'seeded-randomness': {
+        readonly createSearch: (config: import("./rules/seeded-randomness").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 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: import("./rules/seeded-randomness").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: import("./linter-format").LintingCertainty.Definitely;
+                function: import("../dataflow/environments/identifier").Identifier;
+                range: import("../util/range").SourceRange;
+            }[];
+            '.meta': import("./rules/seeded-randomness").SeededRandomnessMeta;
+        };
+        readonly info: {
+            readonly defaultConfig: {
+                readonly randomnessProducers: readonly [{
+                    readonly type: "function";
+                    readonly name: "set.seed";
+                }, {
+                    readonly type: "assignment";
+                    readonly name: ".Random.seed";
+                }];
+                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 [import("./linter-tags").LintingRuleTag.Robustness, import("./linter-tags").LintingRuleTag.Reproducibility];
+            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`.";
+        };
+        readonly prettyPrint: {
+            readonly query: (result: import("./rules/seeded-randomness").SeededRandomnessResult, _meta: import("./rules/seeded-randomness").SeededRandomnessMeta) => string;
+            readonly full: (result: import("./rules/seeded-randomness").SeededRandomnessResult, _meta: import("./rules/seeded-randomness").SeededRandomnessMeta) => string;
+        };
+    };
+    readonly 'absolute-file-paths': {
+        readonly createSearch: (config: import("./rules/absolute-path").AbsoluteFilePathConfig) => import("../search/flowr-search-builder").FlowrSearchBuilder<"from-query", ["unique"], 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, {
+            readonly query?: "config" | "origin" | "dataflow" | "search" | "call-context" | "control-flow" | "dataflow-lens" | "normalized-ast" | "id-map" | "dataflow-cluster" | "static-slice" | "lineage" | "dependencies" | "location-map" | "happens-before" | "resolve-value" | "project" | "linter" | undefined;
+            readonly queryResult?: import("../queries/base-query-format").BaseQueryResult | undefined;
+            readonly node: import("../r-bridge/lang-4.x/ast/model/nodes/r-expression-list").RExpressionList<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation> | import("../r-bridge/lang-4.x/ast/model/nodes/r-function-definition").RFunctionDefinition<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation> | import("../r-bridge/lang-4.x/ast/model/nodes/r-function-call").RNamedFunctionCall<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation> | import("../r-bridge/lang-4.x/ast/model/nodes/r-function-call").RUnnamedFunctionCall<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation> | import("../r-bridge/lang-4.x/ast/model/nodes/r-parameter").RParameter<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation> | import("../r-bridge/lang-4.x/ast/model/nodes/r-argument").RArgument<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation> | import("../r-bridge/lang-4.x/ast/model/nodes/r-comment").RComment<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation> | import("../r-bridge/lang-4.x/ast/model/nodes/r-line-directive").RLineDirective<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation> | import("../r-bridge/lang-4.x/ast/model/nodes/r-for-loop").RForLoop<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation> | import("../r-bridge/lang-4.x/ast/model/nodes/r-repeat-loop").RRepeatLoop<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation> | import("../r-bridge/lang-4.x/ast/model/nodes/r-while-loop").RWhileLoop<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation> | import("../r-bridge/lang-4.x/ast/model/nodes/r-if-then-else").RIfThenElse<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation> | import("../r-bridge/lang-4.x/ast/model/nodes/r-access").RNamedAccess<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation> | import("../r-bridge/lang-4.x/ast/model/nodes/r-access").RIndexAccess<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation> | import("../r-bridge/lang-4.x/ast/model/nodes/r-unary-op").RUnaryOp<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation> | import("../r-bridge/lang-4.x/ast/model/nodes/r-binary-op").RBinaryOp<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation> | import("../r-bridge/lang-4.x/ast/model/nodes/r-symbol").RSymbol<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation, string> | import("../r-bridge/lang-4.x/ast/model/nodes/r-number").RNumber<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation> | import("../r-bridge/lang-4.x/ast/model/nodes/r-string").RString<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation> | import("../r-bridge/lang-4.x/ast/model/nodes/r-logical").RLogical<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation> | import("../r-bridge/lang-4.x/ast/model/nodes/r-break").RBreak<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation> | import("../r-bridge/lang-4.x/ast/model/nodes/r-next").RNext<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation> | import("../r-bridge/lang-4.x/ast/model/nodes/r-pipe").RPipe<import("../r-bridge/lang-4.x/ast/model/processing/decorate").ParentInformation>;
+        }[]>, config: import("./rules/absolute-path").AbsoluteFilePathConfig, data: {
             normalize: import("../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst;
             dataflow: import("../dataflow/info").DataflowInformation;
+            config: import("../config").FlowrConfigOptions;
         }) => {
-            results: import("./rules/2-file-path-validity").FilePathValidityResult[];
-            ".meta": import("./rules/2-file-path-validity").FilePathValidityMetadata;
-        };
-        readonly prettyPrint: (result: import("./rules/2-file-path-validity").FilePathValidityResult) => string;
-        readonly defaultConfig: {
-            readonly additionalReadFunctions: [];
-            readonly additionalWriteFunctions: [];
-            readonly includeUnknown: false;
+            results: import("./rules/absolute-path").AbsoluteFilePathResult[];
+            ".meta": import("./rules/absolute-path").AbsoluteFilePathMetadata;
+        };
+        readonly prettyPrint: {
+            readonly query: (result: import("./rules/absolute-path").AbsoluteFilePathResult) => string;
+            readonly full: (result: import("./rules/absolute-path").AbsoluteFilePathResult) => string;
+        };
+        readonly info: {
+            readonly name: "Absolute Paths";
+            readonly description: "Checks whether file paths are absolute.";
+            readonly tags: readonly [import("./linter-tags").LintingRuleTag.Robustness, import("./linter-tags").LintingRuleTag.Reproducibility, import("./linter-tags").LintingRuleTag.Smell, import("./linter-tags").LintingRuleTag.QuickFix];
+            readonly defaultConfig: {
+                readonly include: {
+                    readonly constructed: true;
+                    readonly allStrings: false;
+                };
+                readonly additionalPathFunctions: readonly [];
+                readonly absolutePathRegex: undefined;
+                readonly useAsWd: "@script";
+            };
+        };
+    };
+    readonly 'unused-definitions': {
+        readonly createSearch: (config: import("./rules/unused-definition").UnusedDefinitionConfig) => import("../search/flowr-search-builder").FlowrSearchBuilder<"all", ["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>[]>, config: import("./rules/unused-definition").UnusedDefinitionConfig, data: {
+            normalize: import("../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst;
+            dataflow: import("../dataflow/info").DataflowInformation;
+            config: import("../config").FlowrConfigOptions;
+        }) => {
+            results: import("./rules/unused-definition").UnusedDefinitionResult[];
+            ".meta": import("./rules/unused-definition").UnusedDefinitionMetadata;
+        };
+        readonly prettyPrint: {
+            readonly query: (result: import("./rules/unused-definition").UnusedDefinitionResult) => string;
+            readonly full: (result: import("./rules/unused-definition").UnusedDefinitionResult) => string;
+        };
+        readonly info: {
+            readonly name: "Unused Definitions";
+            readonly description: "Checks for unused definitions.";
+            readonly tags: readonly [import("./linter-tags").LintingRuleTag.Readability, import("./linter-tags").LintingRuleTag.Smell, import("./linter-tags").LintingRuleTag.QuickFix];
+            readonly defaultConfig: {
+                readonly includeFunctionDefinitions: true;
+            };
+        };
+    };
+    readonly 'naming-convention': {
+        readonly createSearch: (_config: import("./rules/naming-convention").NamingConventionConfig) => import("../search/flowr-search-builder").FlowrSearchBuilder<"all", ["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>[]>, config: import("./rules/naming-convention").NamingConventionConfig, data: {
+            normalize: import("../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst;
+            dataflow: import("../dataflow/info").DataflowInformation;
+            config: import("../config").FlowrConfigOptions;
+        }) => {
+            results: {
+                quickFix: import("./linter-format").LintQuickFixReplacement[] | undefined;
+                certainty: import("./linter-format").LintingCertainty;
+                detectedCasing: import("./rules/naming-convention").CasingConvention;
+                name: string;
+                range: import("../util/range").SourceRange;
+            }[];
+            '.meta': {
+                numMatches: number;
+                numBreak: number;
+            };
+        };
+        readonly prettyPrint: {
+            readonly query: (result: import("./rules/naming-convention").NamingConventionResult) => string;
+            readonly full: (result: import("./rules/naming-convention").NamingConventionResult) => string;
+        };
+        readonly info: {
+            readonly name: "Naming Convention";
+            readonly description: "Checks wether the symbols conform to a certain naming convention";
+            readonly tags: readonly [import("./linter-tags").LintingRuleTag.Style, import("./linter-tags").LintingRuleTag.QuickFix];
+            readonly defaultConfig: {
+                readonly caseing: import("./rules/naming-convention").CasingConvention.PascalCase;
+            };
         };
     };
 };

package/linter/linter-rules.js

@@ -1,14 +1,22 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.LintingRules = void 0;
-const _1_deprecated_functions_1 = require("./rules/1-deprecated-functions");
-const _2_file_path_validity_1 = require("./rules/2-file-path-validity");
+const deprecated_functions_1 = require("./rules/deprecated-functions");
+const file_path_validity_1 = require("./rules/file-path-validity");
+const absolute_path_1 = require("./rules/absolute-path");
+const unused_definition_1 = require("./rules/unused-definition");
+const seeded_randomness_1 = require("./rules/seeded-randomness");
+const naming_convention_1 = require("./rules/naming-convention");
 /**
  * The registry of currently supported linting rules.
  * A linting rule can be executed on a dataflow pipeline result using {@link executeLintingRule}.
  */
 exports.LintingRules = {
-    'deprecated-functions': _1_deprecated_functions_1.R1_DEPRECATED_FUNCTIONS,
-    'file-path-validity': _2_file_path_validity_1.R2_FILE_PATH_VALIDITY
+    'deprecated-functions': deprecated_functions_1.DEPRECATED_FUNCTIONS,
+    'file-path-validity': file_path_validity_1.FILE_PATH_VALIDITY,
+    'seeded-randomness': seeded_randomness_1.SEEDED_RANDOMNESS,
+    'absolute-file-paths': absolute_path_1.ABSOLUTE_PATH,
+    'unused-definitions': unused_definition_1.UNUSED_DEFINITION,
+    'naming-convention': naming_convention_1.NAMING_CONVENTION
 };
 //# sourceMappingURL=linter-rules.js.map

package/linter/linter-tags.d.ts

@@ -0,0 +1,80 @@
+/**
+ * Specify the tags for the linter rules.
+ */
+export declare enum LintingRuleTag {
+    /**
+     * This rule is used to detect bugs in the code.
+     * Everything that affects the semantics of the code, such as incorrect function calls, wrong arguments, etc.
+     * is to be considered a bug. Otherwise, it may be a smell or a style issue.
+     */
+    Bug = "bug",
+    /**
+     * This signals the use of deprecated functions or features.
+     */
+    Deprecated = "deprecated",
+    /**
+     * This rule is used to detect issues that are related to the documentation of the code.
+     * For example, missing or misleading comments.
+     */
+    Documentation = "documentation",
+    /**
+     * This marks rules which are currently considered experimental, _not_ that they detect experimental code.
+     */
+    Experimental = "experimental",
+    /**
+     * This rule is used to detect issues that are related to the performance of the code.
+     * For example, inefficient algorithms, unnecessary computations, or unoptimized data structures.
+     */
+    Performance = "performance",
+    /**
+     * This rule is used to detect issues that are related to the portability of the code.
+     * For example, platform-specific code, or code that relies on specific R versions or packages.
+     */
+    Robustness = "robustness",
+    /**
+     * The rule is specific to R version 3.x.
+     */
+    Rver3 = "rver3",
+    /**
+     * The rule is specific to R version 4.x.
+     */
+    Rver4 = "rver4",
+    /**
+     * This rule is used to detect issues that are related to the readability of the code.
+     * For example, complex expressions, long lines, or inconsistent formatting.
+     */
+    Readability = "readability",
+    /**
+     * This rule is used to detect issues that are related to the reproducibility of the code.
+     * For example, missing or incorrect random seeds, or missing data.
+     */
+    Reproducibility = "reproducibility",
+    /**
+     * This rule is used to detect security-critical.
+     * For example, missing input validation.
+     */
+    Security = "security",
+    /**
+     * This rule is used to detect issues that are related to the shiny framework.
+     */
+    Shiny = "shiny",
+    /**
+     * This rule is used to detect issues that do not directly affect the semantics of the code,
+     * but are still considered bad practice.
+     */
+    Smell = "smell",
+    /**
+     * This rule is used to detect issues that are related to the style of the code.
+     * For example, inconsistent naming conventions, or missing or incorrect formatting.
+     */
+    Style = "style",
+    /**
+     * This rule is used to detect issues that are related to the (re-)usability of the code.
+     * For example, missing or incorrect error handling, or missing or incorrect user interface elements.
+     */
+    Usability = "usability",
+    /**
+     * This rule may provide quickfixes to automatically fix the issues it detects.
+     */
+    QuickFix = "quickfix"
+}

package/linter/linter-tags.js

@@ -0,0 +1,85 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.LintingRuleTag = void 0;
+/**
+ * Specify the tags for the linter rules.
+ */
+var LintingRuleTag;
+(function (LintingRuleTag) {
+    /**
+     * This rule is used to detect bugs in the code.
+     * Everything that affects the semantics of the code, such as incorrect function calls, wrong arguments, etc.
+     * is to be considered a bug. Otherwise, it may be a smell or a style issue.
+     */
+    LintingRuleTag["Bug"] = "bug";
+    /**
+     * This signals the use of deprecated functions or features.
+     */
+    LintingRuleTag["Deprecated"] = "deprecated";
+    /**
+     * This rule is used to detect issues that are related to the documentation of the code.
+     * For example, missing or misleading comments.
+     */
+    LintingRuleTag["Documentation"] = "documentation";
+    /**
+     * This marks rules which are currently considered experimental, _not_ that they detect experimental code.
+     */
+    LintingRuleTag["Experimental"] = "experimental";
+    /**
+     * This rule is used to detect issues that are related to the performance of the code.
+     * For example, inefficient algorithms, unnecessary computations, or unoptimized data structures.
+     */
+    LintingRuleTag["Performance"] = "performance";
+    /**
+     * This rule is used to detect issues that are related to the portability of the code.
+     * For example, platform-specific code, or code that relies on specific R versions or packages.
+     */
+    LintingRuleTag["Robustness"] = "robustness";
+    /**
+     * The rule is specific to R version 3.x.
+     */
+    LintingRuleTag["Rver3"] = "rver3";
+    /**
+     * The rule is specific to R version 4.x.
+     */
+    LintingRuleTag["Rver4"] = "rver4";
+    /**
+     * This rule is used to detect issues that are related to the readability of the code.
+     * For example, complex expressions, long lines, or inconsistent formatting.
+     */
+    LintingRuleTag["Readability"] = "readability";
+    /**
+     * This rule is used to detect issues that are related to the reproducibility of the code.
+     * For example, missing or incorrect random seeds, or missing data.
+     */
+    LintingRuleTag["Reproducibility"] = "reproducibility";
+    /**
+     * This rule is used to detect security-critical.
+     * For example, missing input validation.
+     */
+    LintingRuleTag["Security"] = "security";
+    /**
+     * This rule is used to detect issues that are related to the shiny framework.
+     */
+    LintingRuleTag["Shiny"] = "shiny";
+    /**
+     * This rule is used to detect issues that do not directly affect the semantics of the code,
+     * but are still considered bad practice.
+     */
+    LintingRuleTag["Smell"] = "smell";
+    /**
+     * This rule is used to detect issues that are related to the style of the code.
+     * For example, inconsistent naming conventions, or missing or incorrect formatting.
+     */
+    LintingRuleTag["Style"] = "style";
+    /**
+     * This rule is used to detect issues that are related to the (re-)usability of the code.
+     * For example, missing or incorrect error handling, or missing or incorrect user interface elements.
+     */
+    LintingRuleTag["Usability"] = "usability";
+    /**
+     * This rule may provide quickfixes to automatically fix the issues it detects.
+     */
+    LintingRuleTag["QuickFix"] = "quickfix";
+})(LintingRuleTag || (exports.LintingRuleTag = LintingRuleTag = {}));
+//# sourceMappingURL=linter-tags.js.map