@eagleoutice/flowr 2.2.12 → 2.2.14

package/documentation/print-linting-and-testing-wiki.js

@@ -22,32 +22,34 @@ function getText() {
 For the latest code coverage information, see [codecov.io](${doc_files_1.FlowrCodecovRef}), 
 for the latest benchmark results, see the [benchmark results](${doc_files_1.FlowrSiteBaseRef}/wiki/stats/benchmark) wiki page.
 
-- [Testing Suites](#testing-suites)
-  - [Functionality Tests](#functionality-tests)
-    - [Test Structure](#test-structure)
-    - [Writing a Test](#writing-a-test)
-    - [Running Only Some Tests](#running-only-some-tests)
-  - [System Tests](#system-tests)
-  - [Performance Tests](#performance-tests)
-  - [Oh no, the tests are slow](#oh-no-the-tests-are-slow)
-  - [Testing Within Your IDE](#testing-within-your-ide)
+- [🏨 Testing Suites](#testing-suites)
+  - [🧪 Functionality Tests](#functionality-tests)
+    - [🏗️ Test Structure](#test-structure)
+    - [🏷️ Test Labels](#test-labels)
+    - [🖋️ Writing a Test](#writing-a-test)
+    - [🤏 Running Only Some Tests](#running-only-some-tests)
+  - [💽 System Tests](#system-tests)
+  - [💃 Performance Tests](#performance-tests)
+  - [📝 Testing Within Your IDE](#testing-within-your-ide)
     - [VS Code](#vs-code)
     - [Webstorm](#webstorm)
-- [CI Pipeline](#ci-pipeline)
-- [Linting](#linting)
+- [🪈 CI Pipeline](#ci-pipeline)
+- [🧹 Linting](#linting)
   - [Oh no, the linter fails](#oh-no-the-linter-fails)
   - [License Checker](#license-checker)
-- [Debugging](#debugging)
+- [🐛 Debugging](#debugging)
   - [VS Code](#vs-code-1)
 
-## Testing Suites
+<a id='testing-suites'></a>
+## 🏨 Testing Suites
 
 Currently, flowR contains three testing suites: one for [functionality](#functionality-tests), 
 one for [system tests](#system-tests), and one for [performance](#performance-tests). We explain each of them in the following.
 In addition to running those tests, you can use the more generalized \`npm run checkup\`. 
 This command includes the construction of the docker image, the generation of the wiki pages, and the linter.
 
-### Functionality Tests
+<a id='functionality-tests'></a>
+### 🧪 Functionality Tests
 
 The functionality tests represent conventional unit (and depending on your terminology component/api) tests.
 We use [vitest](https://vitest.dev/) as our testing framework.
@@ -75,7 +77,8 @@ some tests may be skipped automatically as they do not apply to your current sys
 Each test can specify such requirements as part of the \`TestConfiguration\`, which is then used in the \`test.skipIf\` function of _vitest_.
 It is up to the [ci](#ci-pipeline) to run the tests on different systems to ensure that those tests run.
 
-#### Test Structure
+<a id='test-structure'></a>
+#### 🏗️ Test Structure
 
 All functionality tests are to be located under [test/functionality](${doc_files_1.RemoteFlowrFilePathBaseRef}/test/functionality).
 
@@ -94,15 +97,24 @@ to disable parallel execution for the respective test (otherwise, such tests are
 `
     })}
 
-#### Writing a Test
+<a id='test-labels'></a>
+#### 🏷️ Test Labels
 
-Currently, this is heavily dependent on what you want to test (normalization, dataflow, quad-export, …) 
-and it is probably best to have a look at existing tests in that area to get an idea of what comfort functionality is available.
+Generally, tests are [labeled](${doc_files_1.RemoteFlowrFilePathBaseRef}test/functionality/_helper/label.ts) according to the *flowR* capabilities they test. 
 
-Generally, tests should be [labeled](${doc_files_1.RemoteFlowrFilePathBaseRef}test/functionality/_helper/label.ts) according to the *flowR* capabilities they test. 
 The set of currently supported capabilities and their IDs can be found in ${(0, doc_files_1.getFilePathMd)('../r-bridge/data/data.ts')}. 
+
 The resulting labels are used in the test report that is generated as part of the test output. 
 They group tests by the capabilities they test and allow the report to display how many tests ensure that any given capability is properly supported.
+The report can be found on the wiki's [capabilities page](${doc_files_1.FlowrWikiBaseRef}/Capabilities).
+
+To add new labels, simply add them to the relevant section in ${(0, doc_files_1.getFilePathMd)('../r-bridge/data/data.ts')} as part of a pull request.
+
+<a id='writing-a-test'></a>
+#### 🖋️ Writing a Test
+
+Currently, this is heavily dependent on what you want to test (normalization, dataflow, quad-export, …) 
+and it is probably best to have a look at existing tests in that area to get an idea of what comfort functionality is available.
 
 Various helper functions are available to ease in writing tests with common behaviors, like testing for dataflow, slicing or query results. 
 These can be found in [the \`_helper\` subdirectory](${doc_files_1.RemoteFlowrFilePathBaseRef}test/functionality/_helper).
@@ -136,12 +148,14 @@ assertDataflow(label('without distractors', [...OperatorDatabase['<-'].capabilit
 );
 `)}
 
-#### Running Only Some Tests
+<a id='running-only-some-tests'></a>
+#### 🤏 Running Only Some Tests
 
 To run only some tests, vitest allows you to [filter](https://vitest.dev/guide/filtering.html) tests. 
 Besides, you can use the watch mode (with \`npm run test\`) to only run tests that are affected by your changes.
 
-### System Tests
+<a id='system-tests'></a>
+### 💽 System Tests
 
 In contrast to the [functionality tests](#functionality-tests), the system tests use runners like the \`npm\` scripts
 to test the behavior of the whole system, for example, by running the CLI or the server.
@@ -154,9 +168,8 @@ with the [functionality tests](#functionality-tests)).
 
 Have a look at the [test/system-tests](${doc_files_1.RemoteFlowrFilePathBaseRef}test/system-tests) folder for more information.
  
-
-
-### Performance Tests
+<a id='performance-tests'></a>
+### 💃 Performance Tests
 
 The performance test suite of *flowR* uses several suites to check for variations in the required times for certain steps.
 Although we measure wall time in the CI (which is subject to rather large variations), it should give a rough idea *flowR*'s performance.
@@ -167,8 +180,8 @@ ${(0, doc_code_1.codeBlock)('shell', 'npm run performance-test')}
 
 See [test/performance](${doc_files_1.RemoteFlowrFilePathBaseRef}test/performance) for more information on the suites, how to run them, and their results. If you are interested in the results of the benchmarks, see [here](${doc_files_1.FlowrSiteBaseRef}/wiki/stats/benchmark).
 
-
-### Testing Within Your IDE
+<a id='testing-within-your-ide'></a>
+### 📝 Testing Within Your IDE
 
 #### VS Code
 
@@ -188,8 +201,8 @@ To get started, install the [vitest Extension](https://marketplace.visualstudio.
 
 Please follow the official guide [here](https://www.jetbrains.com/help/webstorm/vitest.html).
 
-
-## CI Pipeline
+<a id='ci-pipeline'></a>
+## 🪈 CI Pipeline
 
 We have several workflows defined in [.github/workflows](${doc_files_1.RemoteFlowrFilePathBaseRef}/.github/workflows/).
 We explain the most important workflows in the following:
@@ -203,8 +216,9 @@ We explain the most important workflows in the following:
   - deploying the documentation to [GitHub Pages](${doc_files_1.FlowrSiteBaseRef}/doc/)
 - [release.yaml](${doc_files_1.RemoteFlowrFilePathBaseRef}/.github/workflows/release.yaml) is responsible for creating a new release, only to be run by repository owners. Furthermore, it adds the new docker image to [docker hub](${doc_files_1.FlowrDockerRef}).
 - [broken-links-and-wiki.yaml](${doc_files_1.RemoteFlowrFilePathBaseRef}/.github/workflows/broken-links-and-wiki.yaml) repeatedly tests that all links are not dead!
-
-## Linting
+ 
+<a id='linting'></a>
+## 🧹 Linting
 
 There are two linting scripts.
 The main one:
@@ -222,21 +236,23 @@ eslint can automatically fix several linting problems[](https://eslint.org/docs/
 So you may be fine by just running:
 
 ${(0, doc_code_1.codeBlock)('shell', 'npm run lint-local -- --fix')}
-
-### Oh no, the linter fails
+ 
+<a id='oh-no-the-linter-fails'></a>
+### 💥 Oh no, the linter fails
 
 By now, the rules should be rather stable and so, if the linter fails,
 it is usually best if you (when necessary) read the respective description and fix the respective problem.
 Rules in this project cover general JavaScript issues [using regular ESLint](https://eslint.org/docs/latest/rules), TypeScript-specific issues [using typescript-eslint](https://typescript-eslint.io/rules/), and code formatting [with ESLint Stylistic](https://eslint.style/packages/default#rules).
 
 However, in case you think that the linter is wrong, please do not hesitate to open a [new issue](${doc_files_1.FlowrGithubBaseRef}/flowr/issues/new/choose).
-
-### License Checker
+ 
+<a id='license-checker'></a>
+### 🪪 License Checker
 
 *flowR* is licensed under the [GPLv3 License](${doc_files_1.FlowrGithubBaseRef}/flowr/blob/main/LICENSE) requiring us to only rely on [compatible licenses](https://www.gnu.org/licenses/license-list.en.html). For now, this list is hardcoded as part of the npm [\`license-compat\`](${doc_files_1.RemoteFlowrFilePathBaseRef}/package.json) script so it can very well be that a new dependency you add causes the checker to fail &mdash; *even though it is compatible*. In that case, please either open a [new issue](${doc_files_1.FlowrGithubBaseRef}/flowr/issues/new/choose) or directly add the license to the list (including a reference to why it is compatible).
 
-
-## Debugging
+<a id='debugging'></a>
+## 🐛 Debugging
 ### VS Code
 When working with VS Code, you can attach a debugger to the REPL. This works automatically by running the \`Start Debugging\` command (\`F5\` by default).
 You can also set the \`Auto Attach Filter\` setting to automatically attach the debugger, when running \`npm run flowr\`.

package/documentation/print-normalized-ast-wiki.js

@@ -12,7 +12,7 @@ const doc_types_1 = require("./doc-util/doc-types");
 const path_1 = __importDefault(require("path"));
 const doc_files_1 = require("./doc-util/doc-files");
 const doc_cli_option_1 = require("./doc-util/doc-cli-option");
-const time_1 = require("../util/time");
+const time_1 = require("../util/text/time");
 const doc_structure_1 = require("./doc-util/doc-structure");
 const pipeline_executor_1 = require("../core/pipeline-executor");
 const retriever_1 = require("../r-bridge/retriever");

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

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

package/documentation/print-onboarding-wiki.js

@@ -0,0 +1,42 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const log_1 = require("../../test/functionality/_helper/log");
+const doc_files_1 = require("./doc-util/doc-files");
+const doc_code_1 = require("./doc-util/doc-code");
+const doc_auto_gen_1 = require("./doc-util/doc-auto-gen");
+function print() {
+    return `${(0, doc_auto_gen_1.autoGenHeader)({ filename: module.filename, purpose: 'developer onboarding process' })}	
+	
+To get started developing on *flowR*, we recommend carefully reading the following pages:
+- 💻 [Setting up the *flowR* development environment](${doc_files_1.FlowrWikiBaseRef}/Setup#%EF%B8%8F-building-from-scratch).\
+  This page explains how to install **R** and **Node.js**.  
+- 💖 [Contributing guidelines](${doc_files_1.FlowrGithubBaseRef}/flowr/tree/main/.github/CONTRIBUTING.md).\
+  This page also includes information about how to set up **git-lfs** and several **git hooks**.
+
+## ⌛ TL;DR
+
+The most important steps to get the *flowR* development environment set up (after installing **R** and **Node.js**) can be seen below. For convenience, they can be executed all at once using the following command:
+${(0, doc_code_1.codeBlock)('shell', 'npm run setup:dev')}
+
+If you want to execute the steps manually, please follow the instructions below:
+
+${(0, doc_code_1.codeBlock)('shell', `
+# Installing git-lfs for your current user (if you haven't already)
+git lfs install
+# Cloning the repository
+git clone https://github.com/flowr-analysis/flowr.git
+# Installing dependencies
+npm ci
+# Configuring git hooks
+git config --local core.hooksPath .githooks/
+# Test if the git hooks are working correctly
+# Running this command should lint the code
+git push --dry-run
+`)}
+    `.trim();
+}
+if (require.main === module) {
+    (0, log_1.setMinLevelOfAllLogs)(6 /* LogLevel.Fatal */);
+    console.log(print());
+}
+//# sourceMappingURL=print-onboarding-wiki.js.map

package/documentation/print-query-wiki.js

@@ -10,7 +10,7 @@ const query_1 = require("../queries/query");
 const doc_files_1 = require("./doc-util/doc-files");
 const doc_query_1 = require("./doc-util/doc-query");
 const schema_1 = require("../util/schema");
-const ansi_1 = require("../util/ansi");
+const ansi_1 = require("../util/text/ansi");
 const call_context_query_executor_1 = require("../queries/catalog/call-context-query/call-context-query-executor");
 const compound_query_1 = require("../queries/virtual-query/compound-query");
 const doc_auto_gen_1 = require("./doc-util/doc-auto-gen");
@@ -238,6 +238,26 @@ ${await (0, doc_query_1.showQuery)(shell, exampleCode, [{
 		`;
     }
 });
+(0, doc_query_1.registerQueryDocumentation)('origin', {
+    name: 'Origin Query',
+    type: 'active',
+    shortDescription: 'Retrieve the origin of a variable, function call, ...',
+    functionName: search_query_executor_1.executeSearch.name,
+    functionFile: '../queries/catalog/origin-query/origin-query-executor.ts',
+    buildExplanation: async (shell) => {
+        const exampleCode = 'x <- 1\nprint(x)';
+        return `
+With this query you can use flowR's origin tracking to find out the read origins of a variable,
+the functions called by a call, and more.
+
+Using the example code \`${exampleCode}\` (with the \`print(x)\` in the second line), the following query returns the origins of \`x\` in the code:
+${await (0, doc_query_1.showQuery)(shell, exampleCode, [{
+                type: 'origin',
+                criterion: '2@x'
+            }], { showCode: true })}
+		`;
+    }
+});
 (0, doc_query_1.registerQueryDocumentation)('search', {
     name: 'Search Query',
     type: 'active',

package/documentation/print-readme.js

@@ -23,9 +23,12 @@ async function getText(shell) {
 [![Docker Image Version (latest semver)](https://img.shields.io/docker/v/eagleoutice/flowr?logo=docker&logoColor=white&label=dockerhub)](${doc_files_1.FlowrDockerRef})
 [![latest tag](https://badgen.net/github/tag/flowr-analysis/flowr?label=latest&color=purple)](${doc_files_1.FlowrGithubBaseRef}/flowr/releases/latest)
 [![Marketplace](https://badgen.net/vs-marketplace/v/code-inspect.vscode-flowr)](${doc_files_1.FlowrVsCode})
+[![Marketplace](https://badgen.net/open-vsx/version/code-inspect/vscode-flowr?label=Positron/Open%20VSX)](${doc_files_1.FlowrPositron})
 [![DOI](https://zenodo.org/badge/624819038.svg)](https://zenodo.org/doi/10.5281/zenodo.13319290)
 
-_flowR_ is a sophisticated, static [dataflow analyzer](https://en.wikipedia.org/wiki/Data-flow_analysis) for the [R programming language](https://www.r-project.org/).
+_flowR_ is a sophisticated, static [dataflow analyzer](https://en.wikipedia.org/wiki/Data-flow_analysis) for the [R programming language](https://www.r-project.org/),
+available for [VSCode](${doc_files_1.FlowrVsCode}), [Positron](${doc_files_1.FlowrPositron}), [RStudio](${doc_files_1.FlowrGithubBaseRef}/rstudio-addin-flowr),
+and [Docker](${doc_files_1.FlowrDockerRef}).
 It offers a wide variety of features, for example:
 
 * 🍕 **program slicing**\\
@@ -90,12 +93,16 @@ ${await (0, doc_dfg_1.printDfGraphForCode)(shell, (0, doc_files_1.getFileContent
 
 If you want to use flowR and the features it provides, feel free to check out the:
 
-- [Visual Studio Code extension](${doc_files_1.FlowrVsCode}): provides access to flowR directly in VS Code (or [vscode.dev](https://vscode.dev/))
+- [Visual Studio Code](${doc_files_1.FlowrVsCode})/[Positron](${doc_files_1.FlowrPositron}): provides access to flowR directly in VS Code and Positron (or [vscode.dev](https://vscode.dev/))
 - [RStudio Addin](${doc_files_1.FlowrGithubBaseRef}/rstudio-addin-flowr): integrates flowR into [RStudio](https://posit.co/downloads/)
 - [R package](${doc_files_1.FlowrGithubBaseRef}/flowr-r-adapter): use flowR in your R scripts
 - [Docker image](${doc_files_1.FlowrDockerRef}): run flowR in a container, this also includes [flowR's server](${doc_files_1.FlowrWikiBaseRef}/Interface#communicating-with-the-server)
 - [NPM package](${doc_files_1.FlowrNpmRef}): include flowR in your TypeScript and JavaScript projects
  
+
+If you are already using flowR and want to give feedback, please consider filling out our [feedback form](https://docs.google.com/forms/d/e/1FAIpQLScKFhgnh9LGVU7QzqLvFwZe1oiv_5jNhkIO-G-zND0ppqsMxQ/viewform).
+
+ 
 ## ⭐ Getting Started
 
 To get started with _flowR_ and its features, please check out the [Overview](${doc_files_1.FlowrGithubBaseRef}/flowr/wiki/Overview) wiki page. 
@@ -121,7 +128,7 @@ as well as the deployed [code documentation](https://flowr-analysis.github.io/fl
 
 ## 🚀 Contributing
 
-We welcome every contribution! Please check out the [contributing guidelines](${doc_files_1.FlowrGithubBaseRef}/flowr/tree/main/.github/CONTRIBUTING.md) for more information.
+We welcome every contribution! Please check out the [developer onboarding](${doc_files_1.FlowrWikiBaseRef}/Onboarding) section in the wiki for all the information you will need.
 
 ### Contributors
 

package/linter/linter-executor.d.ts

@@ -0,0 +1,9 @@
+import type { LintingRuleConfig, LintingRuleNames } from './linter-rules';
+import type { NormalizedAst } from '../r-bridge/lang-4.x/ast/model/processing/decorate';
+import type { DataflowInformation } from '../dataflow/info';
+import type { LintingResults } from './linter-format';
+import type { DeepPartial } from 'ts-essentials';
+export declare function executeLintingRule<Name extends LintingRuleNames>(ruleName: Name, input: {
+    normalize: NormalizedAst;
+    dataflow: DataflowInformation;
+}, config?: DeepPartial<LintingRuleConfig<Name>>): LintingResults<Name>;

package/linter/linter-executor.js

@@ -0,0 +1,26 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+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 rule = linter_rules_1.LintingRules[ruleName];
+    const fullConfig = { ...rule.defaultConfig, ...config };
+    const ruleSearch = rule.createSearch(fullConfig, input);
+    const searchStart = Date.now();
+    const searchResult = (0, flowr_search_executor_1.runSearch)(ruleSearch, input);
+    const searchTime = Date.now() - searchStart;
+    const processStart = Date.now();
+    const result = rule.processSearchResult(new flowr_search_1.FlowrSearchElements(searchResult), fullConfig, input);
+    const processTime = Date.now() - processStart;
+    return {
+        ...result,
+        '.meta': {
+            ...result['.meta'],
+            searchTimeMs: searchTime,
+            processTimeMs: processTime
+        }
+    };
+}
+//# sourceMappingURL=linter-executor.js.map

package/linter/linter-format.d.ts

@@ -0,0 +1,65 @@
+import type { FlowrSearchLike } from '../search/flowr-search-builder';
+import type { FlowrSearchElement, FlowrSearchElements } from '../search/flowr-search';
+import type { MergeableRecord } from '../util/objects';
+import type { GeneratorNames } from '../search/search-executor/search-generators';
+import type { TransformerNames } from '../search/search-executor/search-transformer';
+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';
+/**
+ * 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}.
+ */
+export interface LintingRule<Result extends LintingResult, Metadata extends MergeableRecord, Config extends MergeableRecord = never, Info = ParentInformation, Elements extends FlowrSearchElement<Info>[] = FlowrSearchElement<Info>[]> {
+    /**
+     * Creates a flowR search that will then be executed and whose results will be passed to {@link processSearchResult}.
+     * In the future, additional optimizations and transformations may be applied to the search between this function and {@link processSearchResult}.
+     */
+    readonly createSearch: (config: Config, data: {
+        normalize: NormalizedAst;
+        dataflow: DataflowInformation;
+    }) => FlowrSearchLike<Info, GeneratorNames, TransformerNames[], FlowrSearchElements<Info, Elements>>;
+    /**
+     * Processes the search results of the search created through {@link createSearch}.
+     * This function is expected to return the linting results from this rule for the given search, ie usually the given script file.
+     */
+    readonly processSearchResult: (elements: FlowrSearchElements<Info, Elements>, config: Config, data: {
+        normalize: NormalizedAst;
+        dataflow: DataflowInformation;
+    }) => {
+        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.
+     */
+    readonly prettyPrint: (result: Result, metadata: Metadata) => string;
+    /**
+     * The default config for this linting rule.
+     * The default config is combined with the user config when executing the rule.
+     */
+    readonly defaultConfig: NoInfer<Config>;
+}
+/**
+ * A linting result for a single linting rule match.
+ */
+export interface LintingResult {
+    readonly certainty: LintingCertainty;
+}
+export interface ConfiguredLintingRule<Name extends LintingRuleNames = LintingRuleNames> {
+    readonly name: Name;
+    readonly config: DeepPartial<LintingRuleConfig<Name>>;
+}
+export interface LintingResults<Name extends LintingRuleNames> {
+    results: LintingRuleResult<Name>[];
+    '.meta': LintingRuleMetadata<Name> & {
+        readonly searchTimeMs: number;
+        readonly processTimeMs: number;
+    };
+}
+export declare enum LintingCertainty {
+    Maybe = "maybe",
+    Definitely = "definitely"
+}

package/linter/linter-format.js

@@ -0,0 +1,9 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.LintingCertainty = void 0;
+var LintingCertainty;
+(function (LintingCertainty) {
+    LintingCertainty["Maybe"] = "maybe";
+    LintingCertainty["Definitely"] = "definitely";
+})(LintingCertainty || (exports.LintingCertainty = LintingCertainty = {}));
+//# sourceMappingURL=linter-format.js.map

package/linter/linter-rules.d.ts

@@ -0,0 +1,42 @@
+import type { LintingRule } from './linter-format';
+/**
+ * The registry of currently supported linting rules.
+ * A linting rule can be executed on a dataflow pipeline result using {@link executeLintingRule}.
+ */
+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) => {
+            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;
+        };
+        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 '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: {
+            normalize: import("../r-bridge/lang-4.x/ast/model/processing/decorate").NormalizedAst;
+            dataflow: import("../dataflow/info").DataflowInformation;
+        }) => {
+            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;
+        };
+    };
+};
+export type LintingRuleNames = keyof typeof LintingRules;
+export type LintingRuleMetadata<Name extends LintingRuleNames> = typeof LintingRules[Name] extends LintingRule<infer _Result, infer Metadata, infer _Config, infer _Info, infer _Elements> ? Metadata : never;
+export type LintingRuleResult<Name extends LintingRuleNames> = typeof LintingRules[Name] extends LintingRule<infer Result, infer _Metadata, infer _Config, infer _Info, infer _Elements> ? Result : never;
+export type LintingRuleConfig<Name extends LintingRuleNames> = typeof LintingRules[Name] extends LintingRule<infer _Result, infer _Metadata, infer Config, infer _Info, infer _Elements> ? Config : never;

package/linter/linter-rules.js

@@ -0,0 +1,14 @@
+"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");
+/**
+ * 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
+};
+//# sourceMappingURL=linter-rules.js.map

package/linter/rules/1-deprecated-functions.d.ts

@@ -0,0 +1,34 @@
+import type { LintingResult } from '../linter-format';
+import { LintingCertainty } from '../linter-format';
+import type { MergeableRecord } from '../../util/objects';
+import type { SourceRange } from '../../util/range';
+import type { Identifier } from '../../dataflow/environments/identifier';
+export interface DeprecatedFunctionsResult extends LintingResult {
+    function: string;
+    range: SourceRange;
+}
+export interface DeprecatedFunctionsConfig extends MergeableRecord {
+    /**
+     * The list of function names that should be marked as deprecated.
+     */
+    deprecatedFunctions: string[];
+}
+export interface DeprecatedFunctionsMetadata extends MergeableRecord {
+    totalRelevant: number;
+    totalNotDeprecated: number;
+}
+export declare const R1_DEPRECATED_FUNCTIONS: {
+    readonly createSearch: (_config: 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: DeprecatedFunctionsConfig) => {
+        results: {
+            certainty: LintingCertainty.Definitely;
+            function: Identifier;
+            range: SourceRange;
+        }[];
+        '.meta': DeprecatedFunctionsMetadata;
+    };
+    readonly prettyPrint: (result: 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"];
+    };
+};

package/linter/rules/1-deprecated-functions.js

@@ -0,0 +1,54 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.R1_DEPRECATED_FUNCTIONS = void 0;
+const linter_format_1 = require("../linter-format");
+const flowr_search_builder_1 = require("../../search/flowr-search-builder");
+const dfg_1 = require("../../util/mermaid/dfg");
+const search_enrichers_1 = require("../../search/search-executor/search-enrichers");
+exports.R1_DEPRECATED_FUNCTIONS = {
+    createSearch: (_config) => flowr_search_builder_1.Q.all().with(search_enrichers_1.Enrichment.CallTargets),
+    processSearchResult: (elements, config) => {
+        const metadata = {
+            totalRelevant: 0,
+            totalNotDeprecated: 0
+        };
+        return {
+            results: elements.getElements()
+                .flatMap(element => {
+                const targets = (0, search_enrichers_1.enrichmentContent)(element, search_enrichers_1.Enrichment.CallTargets).targets;
+                // if there is a call target that is not built-in (ie a custom function), we don't want to mark it as deprecated
+                // eventually we'd want to solve this with an argument to the CallTargets enrichment like satisfiesCallTargets does!
+                if (targets.some(t => typeof t !== 'string')) {
+                    return [];
+                }
+                return targets.map(target => {
+                    metadata.totalRelevant++;
+                    return {
+                        range: element.node.info.fullRange,
+                        target: target
+                    };
+                });
+            })
+                .filter(element => {
+                if (config.deprecatedFunctions.includes(element.target)) {
+                    return true;
+                }
+                else {
+                    metadata.totalNotDeprecated++;
+                    return false;
+                }
+            })
+                .map(element => ({
+                certainty: linter_format_1.LintingCertainty.Definitely,
+                function: element.target,
+                range: element.range
+            })),
+            '.meta': metadata
+        };
+    },
+    prettyPrint: result => `Function ${result.function} at ${(0, dfg_1.formatRange)(result.range)}`,
+    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',]
+    }
+};
+//# sourceMappingURL=1-deprecated-functions.js.map