@eagleoutice/flowr 2.6.2 → 2.7.0

package/project/flowr-analyzer.js

@@ -4,6 +4,8 @@ exports.FlowrAnalyzer = void 0;
 const query_1 = require("../queries/query");
 const flowr_search_executor_1 = require("../search/flowr-search-executor");
 const cfg_kind_1 = require("./cfg-kind");
+const retriever_1 = require("../r-bridge/retriever");
+const files_1 = require("../util/files");
 /**
  * Central class for conducting analyses with FlowR.
  * Use the {@link FlowrAnalyzerBuilder} to create a new instance.
@@ -11,9 +13,9 @@ const cfg_kind_1 = require("./cfg-kind");
  * If you want the original pattern of creating a pipeline and running all steps, you can still do this with {@link FlowrAnalyzer#runFull}.
  *
  * To inspect the context of the analyzer, use {@link FlowrAnalyzer#inspectContext} (if you are a plugin and need to modify it, use {@link FlowrAnalyzer#context} instead).
+ * @see https://github.com/flowr-analysis/flowr/wiki/Analyzer
  */
 class FlowrAnalyzer {
-    flowrConfig;
     /** The parser and engine backend */
     parser;
     /** The cache used for storing analysis results */
@@ -23,17 +25,18 @@ class FlowrAnalyzer {
     /**
      * Create a new analyzer instance.
      * **Prefer the use of the {@link FlowrAnalyzerBuilder} instead of calling this constructor directly.**
-     * @param config - The FlowR config to use for the analyses
      * @param parser - The parser to use for parsing the given request.
      * @param ctx    - The context to use for the analyses.
      * @param cache  - The caching layer to use for storing analysis results.
      */
-    constructor(config, parser, ctx, cache) {
-        this.flowrConfig = config;
+    constructor(parser, ctx, cache) {
         this.parser = parser;
         this.ctx = ctx;
         this.cache = cache;
     }
+    get flowrConfig() {
+        return this.ctx.config;
+    }
     context() {
         return this.ctx;
     }
@@ -48,21 +51,60 @@ class FlowrAnalyzer {
         this.ctx.reset();
         this.cache.reset();
     }
-    addRequests(requests) {
-        this.ctx.addRequests(requests);
+    addRequest(...request) {
+        for (const r of request) {
+            if (typeof r === 'string') {
+                const trimmed = r.substring(retriever_1.fileProtocol.length);
+                if (r.startsWith(retriever_1.fileProtocol) && !(0, files_1.isFilePath)(trimmed)) {
+                    this.addAnalysisRequest({ request: 'project', content: trimmed });
+                }
+                else {
+                    this.addRequestFromInput(r);
+                }
+            }
+            else {
+                this.addAnalysisRequest(r);
+            }
+        }
+        return this;
+    }
+    addFile(...f) {
+        this.ctx.addFiles(f);
+        return this;
     }
-    addRequest(request) {
-        this.ctx.addRequest(request);
+    /**
+     * Add a request created from the given input.
+     * This is a convenience method that uses {@link requestFromInput} internally.
+     */
+    addRequestFromInput(input) {
+        this.addAnalysisRequest((0, retriever_1.requestFromInput)(input));
+        return this;
+    }
+    /**
+     * Add one or multiple requests to analyze the builder.
+     */
+    addAnalysisRequest(request) {
+        this.ctx.addRequests((Array.isArray(request) ? request : [request]));
+        return this;
     }
     async parse(force) {
         return this.cache.parse(force);
     }
+    peekParse() {
+        return this.cache.peekParse();
+    }
     async normalize(force) {
         return this.cache.normalize(force);
     }
+    peekNormalize() {
+        return this.cache.peekNormalize();
+    }
     async dataflow(force) {
         return this.cache.dataflow(force);
     }
+    peekDataflow() {
+        return this.cache.peekDataflow();
+    }
     async runFull(force) {
         await this.dataflow(force);
         return;
@@ -70,6 +112,9 @@ class FlowrAnalyzer {
     async controlflow(simplifications, kind, force) {
         return this.cache.controlflow(force, kind ?? cfg_kind_1.CfgKind.NoDataflow, simplifications);
     }
+    peekControlflow(simplifications, kind) {
+        return this.cache.peekControlflow(kind ?? cfg_kind_1.CfgKind.NoDataflow, simplifications);
+    }
     async query(query) {
         return (0, query_1.executeQueries)({ analyzer: this }, query);
     }

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

@@ -12,6 +12,12 @@ export declare class FlowrAnalyzerDescriptionFilePlugin extends FlowrAnalyzerFil
     readonly name = "flowr-analyzer-description-file-plugin";
     readonly description = "This plugin provides support for DESCRIPTION files and extracts their content into key-value(s) pairs.";
     readonly version: SemVer;
+    private readonly pattern;
+    /**
+     * Creates a new instance of the DESCRIPTION file plugin.
+     * @param filePattern - The pattern to identify DESCRIPTION files, see {@link DescriptionFilePattern} for the default pattern.
+     */
+    constructor(filePattern?: RegExp);
     applies(file: PathLike): boolean;
-    process(_ctx: FlowrAnalyzerContext, file: FlowrFileProvider<string>): FlowrDescriptionFile;
+    process(_ctx: FlowrAnalyzerContext, file: FlowrFileProvider): FlowrDescriptionFile;
 }

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

@@ -6,7 +6,9 @@ const semver_1 = require("semver");
 const log_1 = require("../../../util/log");
 const flowr_description_file_1 = require("./flowr-description-file");
 const flowr_file_1 = require("../../context/flowr-file");
+const built_in_source_1 = require("../../../dataflow/internal/process/functions/call/built-in/built-in-source");
 exports.descriptionFileLog = log_1.log.getSubLogger({ name: 'flowr-analyzer-loading-order-description-file-plugin' });
+const DescriptionFilePattern = /^(DESCRIPTION|DESCRIPTION\.txt)$/i;
 /**
  * This plugin provides support for R `DESCRIPTION` files.
  */
@@ -14,14 +16,20 @@ class FlowrAnalyzerDescriptionFilePlugin extends flowr_analyzer_file_plugin_1.Fl
     name = 'flowr-analyzer-description-file-plugin';
     description = 'This plugin provides support for DESCRIPTION files and extracts their content into key-value(s) pairs.';
     version = new semver_1.SemVer('0.1.0');
+    pattern;
+    /**
+     * Creates a new instance of the DESCRIPTION file plugin.
+     * @param filePattern - The pattern to identify DESCRIPTION files, see {@link DescriptionFilePattern} for the default pattern.
+     */
+    constructor(filePattern = DescriptionFilePattern) {
+        super();
+        this.pattern = filePattern;
+    }
     applies(file) {
-        return /^(DESCRIPTION|DESCRIPTION\.txt)$/i.test(file.toString().split(/[/\\]/).pop() ?? '');
+        return this.pattern.test((0, built_in_source_1.platformBasename)(file.toString()));
     }
     process(_ctx, file) {
-        const f = flowr_description_file_1.FlowrDescriptionFile.from(file, flowr_file_1.SpecialFileRole.Description);
-        // already load it here
-        f.content();
-        return f;
+        return flowr_description_file_1.FlowrDescriptionFile.from(file, flowr_file_1.FileRole.Description);
     }
 }
 exports.FlowrAnalyzerDescriptionFilePlugin = FlowrAnalyzerDescriptionFilePlugin;

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

@@ -4,14 +4,14 @@ import type { FlowrFileProvider } from '../../context/flowr-file';
 /**
  * This is the base class for all plugins that load and possibly transform files when they are loaded.
  * Different from other plugins, these plugins trigger for each file that is loaded (if they {@link applies} to the file).
- * See the {@link FlowrAnalyzerFilesContext.addFile} for more information on how files are loaded and managed.
+ * See the {@link FlowrAnalyzer.addFile} for more information on how files are loaded and managed.
  *
- * It is upt to the construction to ensure that no two file plugins {@link applies} to the same file, otherwise, the loading order
+ * It is up to the construction to ensure that no two file plugins {@link applies} to the same file, otherwise, the loading order
  * of these plugins will determine which plugin gets to process the file.
  *
  * See {@link DefaultFlowrAnalyzerFilePlugin} for the no-op default implementation.
  */
-export declare abstract class FlowrAnalyzerFilePlugin extends FlowrAnalyzerPlugin<FlowrFileProvider<string>, FlowrFileProvider> {
+export declare abstract class FlowrAnalyzerFilePlugin extends FlowrAnalyzerPlugin<FlowrFileProvider, FlowrFileProvider> {
     readonly type = PluginType.FileLoad;
     /**
      * Determine whether this plugin applies to the given file.

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

@@ -2,13 +2,14 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.FlowrAnalyzerFilePlugin = void 0;
 const flowr_analyzer_plugin_1 = require("../flowr-analyzer-plugin");
+const flowr_file_1 = require("../../context/flowr-file");
 const semver_1 = require("semver");
 /**
  * This is the base class for all plugins that load and possibly transform files when they are loaded.
  * Different from other plugins, these plugins trigger for each file that is loaded (if they {@link applies} to the file).
- * See the {@link FlowrAnalyzerFilesContext.addFile} for more information on how files are loaded and managed.
+ * See the {@link FlowrAnalyzer.addFile} for more information on how files are loaded and managed.
  *
- * It is upt to the construction to ensure that no two file plugins {@link applies} to the same file, otherwise, the loading order
+ * It is up to the construction to ensure that no two file plugins {@link applies} to the same file, otherwise, the loading order
  * of these plugins will determine which plugin gets to process the file.
  *
  * See {@link DefaultFlowrAnalyzerFilePlugin} for the no-op default implementation.
@@ -22,13 +23,18 @@ class FlowrAnalyzerFilePlugin extends flowr_analyzer_plugin_1.FlowrAnalyzerPlugi
 exports.FlowrAnalyzerFilePlugin = FlowrAnalyzerFilePlugin;
 class DefaultFlowrAnalyzerFilePlugin extends FlowrAnalyzerFilePlugin {
     name = 'default-file-plugin';
-    description = 'This is the default file plugin that does nothing.';
+    description = 'This is the default file plugin that does nothing (but assigning default .r/.R files).';
     version = new semver_1.SemVer('0.0.0');
     applies() {
         return true;
     }
-    process(_context, args) {
-        return args;
+    process(_ctx, arg) {
+        const path = arg.path().toString();
+        if (/\.r$/i.test(path)) {
+            // we just assign the role :D
+            arg.assignRole(flowr_file_1.FileRole.Source);
+        }
+        return arg;
     }
 }
 //# sourceMappingURL=flowr-analyzer-file-plugin.js.map

package/project/plugins/file-plugins/flowr-description-file.d.ts

@@ -1,4 +1,4 @@
-import { type FlowrFileProvider, type SpecialFileRole, FlowrFile } from '../../context/flowr-file';
+import { type FlowrFileProvider, type FileRole, FlowrFile } from '../../context/flowr-file';
 export type DCF = Map<string, string[]>;
 /**
  * This decorates a text file and provides access to its content as a DCF (Debian Control File)-like structure.
@@ -9,7 +9,7 @@ export declare class FlowrDescriptionFile extends FlowrFile<DCF> {
      * Prefer the static {@link FlowrDescriptionFile.from} method to create instances of this class as it will not re-create if already a description file
      * and handle role assignments.
      */
-    constructor(file: FlowrFileProvider<string>);
+    constructor(file: FlowrFileProvider);
     /**
      * Loads and parses the content of the wrapped file as a DCF structure.
      * @see {@link parseDCF} for details on the parsing logic.
@@ -18,5 +18,5 @@ export declare class FlowrDescriptionFile extends FlowrFile<DCF> {
     /**
      * Description file lifter, this does not re-create if already a description file
      */
-    static from(file: FlowrFileProvider<string> | FlowrDescriptionFile, role?: SpecialFileRole): FlowrDescriptionFile;
+    static from(file: FlowrFileProvider | FlowrDescriptionFile, role?: FileRole): FlowrDescriptionFile;
 }

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

@@ -0,0 +1,22 @@
+import type { PathLike } from 'fs';
+import { SemVer } from 'semver';
+import type { FlowrAnalyzerContext } from '../../../context/flowr-analyzer-context';
+import type { FlowrFileProvider } from '../../../context/flowr-file';
+import { FlowrAnalyzerFilePlugin } from '../flowr-analyzer-file-plugin';
+import { FlowrJupyterFile } from './flowr-jupyter-file';
+/**
+ * The plugin provides support for Jupyter (`.ipynb`) files
+ */
+export declare class FlowrAnalyzerJupyterFilePlugin extends FlowrAnalyzerFilePlugin {
+    readonly name = "ipynb-file-plugin";
+    readonly description = "Parses Jupyter files";
+    readonly version: SemVer;
+    private readonly pattern;
+    /**
+     * Creates a new instance of the Jupyter file plugin.
+     * @param filePattern - The pattern to identify Jupyter files, see {@link IpynbPattern} for the default pattern.
+     */
+    constructor(filePattern?: RegExp);
+    applies(file: PathLike): boolean;
+    protected process(_ctx: FlowrAnalyzerContext, arg: FlowrFileProvider<string>): FlowrJupyterFile;
+}

package/project/plugins/file-plugins/notebooks/flowr-analyzer-jupyter-file-plugin.js

@@ -0,0 +1,33 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.FlowrAnalyzerJupyterFilePlugin = void 0;
+const semver_1 = require("semver");
+const flowr_analyzer_file_plugin_1 = require("../flowr-analyzer-file-plugin");
+const built_in_source_1 = require("../../../../dataflow/internal/process/functions/call/built-in/built-in-source");
+const flowr_jupyter_file_1 = require("./flowr-jupyter-file");
+const IpynbPattern = /\.ipynb$/i;
+/**
+ * The plugin provides support for Jupyter (`.ipynb`) files
+ */
+class FlowrAnalyzerJupyterFilePlugin extends flowr_analyzer_file_plugin_1.FlowrAnalyzerFilePlugin {
+    name = 'ipynb-file-plugin';
+    description = 'Parses Jupyter files';
+    version = new semver_1.SemVer('0.1.0');
+    pattern;
+    /**
+     * Creates a new instance of the Jupyter file plugin.
+     * @param filePattern - The pattern to identify Jupyter files, see {@link IpynbPattern} for the default pattern.
+     */
+    constructor(filePattern = IpynbPattern) {
+        super();
+        this.pattern = filePattern;
+    }
+    applies(file) {
+        return this.pattern.test((0, built_in_source_1.platformBasename)(file.toString()));
+    }
+    process(_ctx, arg) {
+        return flowr_jupyter_file_1.FlowrJupyterFile.from(arg);
+    }
+}
+exports.FlowrAnalyzerJupyterFilePlugin = FlowrAnalyzerJupyterFilePlugin;
+//# sourceMappingURL=flowr-analyzer-jupyter-file-plugin.js.map

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

@@ -0,0 +1,22 @@
+import type { PathLike } from 'fs';
+import { SemVer } from 'semver';
+import type { FlowrAnalyzerContext } from '../../../context/flowr-analyzer-context';
+import type { FlowrFileProvider } from '../../../context/flowr-file';
+import { FlowrAnalyzerFilePlugin } from '../flowr-analyzer-file-plugin';
+import { FlowrRMarkdownFile } from './flowr-rmarkdown-file';
+/**
+ * The plugin provides support for Quarto R Markdown (`.qmd`) files
+ */
+export declare class FlowrAnalyzerQmdFilePlugin extends FlowrAnalyzerFilePlugin {
+    readonly name = "qmd-file-plugin";
+    readonly description = "Parses Quarto R Markdown files";
+    readonly version: SemVer;
+    private readonly pattern;
+    /**
+     * Creates a new instance of the Quarto R Markdown file plugin.
+     * @param filePattern - The pattern to identify Quarto R Markdown files, see {@link QmdPattern} for the default pattern.
+     */
+    constructor(filePattern?: RegExp);
+    applies(file: PathLike): boolean;
+    protected process(_ctx: FlowrAnalyzerContext, arg: FlowrFileProvider<string>): FlowrRMarkdownFile;
+}

package/project/plugins/file-plugins/notebooks/flowr-analyzer-qmd-file-plugin.js

@@ -0,0 +1,33 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.FlowrAnalyzerQmdFilePlugin = void 0;
+const semver_1 = require("semver");
+const flowr_analyzer_file_plugin_1 = require("../flowr-analyzer-file-plugin");
+const flowr_rmarkdown_file_1 = require("./flowr-rmarkdown-file");
+const built_in_source_1 = require("../../../../dataflow/internal/process/functions/call/built-in/built-in-source");
+const QmdPattern = /\.qmd$/i;
+/**
+ * The plugin provides support for Quarto R Markdown (`.qmd`) files
+ */
+class FlowrAnalyzerQmdFilePlugin extends flowr_analyzer_file_plugin_1.FlowrAnalyzerFilePlugin {
+    name = 'qmd-file-plugin';
+    description = 'Parses Quarto R Markdown files';
+    version = new semver_1.SemVer('0.1.0');
+    pattern;
+    /**
+     * Creates a new instance of the Quarto R Markdown file plugin.
+     * @param filePattern - The pattern to identify Quarto R Markdown files, see {@link QmdPattern} for the default pattern.
+     */
+    constructor(filePattern = QmdPattern) {
+        super();
+        this.pattern = filePattern;
+    }
+    applies(file) {
+        return this.pattern.test((0, built_in_source_1.platformBasename)(file.toString()));
+    }
+    process(_ctx, arg) {
+        return flowr_rmarkdown_file_1.FlowrRMarkdownFile.from(arg);
+    }
+}
+exports.FlowrAnalyzerQmdFilePlugin = FlowrAnalyzerQmdFilePlugin;
+//# sourceMappingURL=flowr-analyzer-qmd-file-plugin.js.map

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

@@ -0,0 +1,22 @@
+import type { PathLike } from 'fs';
+import { SemVer } from 'semver';
+import type { FlowrAnalyzerContext } from '../../../context/flowr-analyzer-context';
+import { type FlowrFileProvider } from '../../../context/flowr-file';
+import { FlowrAnalyzerFilePlugin } from '../flowr-analyzer-file-plugin';
+import { FlowrRMarkdownFile } from './flowr-rmarkdown-file';
+/**
+ * The plugin provides support for R Markdown (`.rmd`) files
+ */
+export declare class FlowrAnalyzerRmdFilePlugin extends FlowrAnalyzerFilePlugin {
+    readonly name = "rmd-file-plugin";
+    readonly description = "Parses R Markdown files";
+    readonly version: SemVer;
+    private readonly pattern;
+    /**
+     * Creates a new instance of the R Markdown file plugin.
+     * @param filePattern - The pattern to identify R Markdown files, see {@link RmdPattern} for the default pattern.
+     */
+    constructor(filePattern?: RegExp);
+    applies(file: PathLike): boolean;
+    protected process(_ctx: FlowrAnalyzerContext, arg: FlowrFileProvider<string>): FlowrRMarkdownFile;
+}

package/project/plugins/file-plugins/notebooks/flowr-analyzer-rmd-file-plugin.js

@@ -0,0 +1,33 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.FlowrAnalyzerRmdFilePlugin = void 0;
+const semver_1 = require("semver");
+const flowr_analyzer_file_plugin_1 = require("../flowr-analyzer-file-plugin");
+const flowr_rmarkdown_file_1 = require("./flowr-rmarkdown-file");
+const built_in_source_1 = require("../../../../dataflow/internal/process/functions/call/built-in/built-in-source");
+const RmdPattern = /\.rmd$/i;
+/**
+ * The plugin provides support for R Markdown (`.rmd`) files
+ */
+class FlowrAnalyzerRmdFilePlugin extends flowr_analyzer_file_plugin_1.FlowrAnalyzerFilePlugin {
+    name = 'rmd-file-plugin';
+    description = 'Parses R Markdown files';
+    version = new semver_1.SemVer('0.1.0');
+    pattern;
+    /**
+     * Creates a new instance of the R Markdown file plugin.
+     * @param filePattern - The pattern to identify R Markdown files, see {@link RmdPattern} for the default pattern.
+     */
+    constructor(filePattern = RmdPattern) {
+        super();
+        this.pattern = filePattern;
+    }
+    applies(file) {
+        return this.pattern.test((0, built_in_source_1.platformBasename)(file.toString()));
+    }
+    process(_ctx, arg) {
+        return flowr_rmarkdown_file_1.FlowrRMarkdownFile.from(arg);
+    }
+}
+exports.FlowrAnalyzerRmdFilePlugin = FlowrAnalyzerRmdFilePlugin;
+//# sourceMappingURL=flowr-analyzer-rmd-file-plugin.js.map

package/project/plugins/file-plugins/notebooks/flowr-jupyter-file.d.ts

@@ -0,0 +1,20 @@
+import type { FlowrFileProvider } from '../../../context/flowr-file';
+import { FlowrFile } from '../../../context/flowr-file';
+/**
+ * This decorates a text file and parses its contents as a Jupyter file.
+ * Finnaly, it provides access to the single cells, and all cells fused together as one R file.
+ */
+export declare class FlowrJupyterFile extends FlowrFile<string> {
+    private readonly wrapped;
+    /**
+     * Prefer the static {@link FlowrRMarkdownFile.from} method
+     * @param file - the file to load as R Markdown
+     */
+    constructor(file: FlowrFileProvider<string>);
+    /**
+     * Loads and parses the content of the wrapped file.
+     * @returns RmdInfo
+     */
+    protected loadContent(): string;
+    static from(file: FlowrFileProvider<string> | FlowrJupyterFile): FlowrJupyterFile;
+}

package/project/plugins/file-plugins/notebooks/flowr-jupyter-file.js

@@ -0,0 +1,42 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.FlowrJupyterFile = void 0;
+const flowr_file_1 = require("../../../context/flowr-file");
+/**
+ * This decorates a text file and parses its contents as a Jupyter file.
+ * Finnaly, it provides access to the single cells, and all cells fused together as one R file.
+ */
+class FlowrJupyterFile extends flowr_file_1.FlowrFile {
+    wrapped;
+    /**
+     * Prefer the static {@link FlowrRMarkdownFile.from} method
+     * @param file - the file to load as R Markdown
+     */
+    constructor(file) {
+        super(file.path(), flowr_file_1.FileRole.Source);
+        this.wrapped = file;
+    }
+    /**
+     * Loads and parses the content of the wrapped file.
+     * @returns RmdInfo
+     */
+    loadContent() {
+        return loadJupyter(this.wrapped.content());
+    }
+    static from(file) {
+        return file instanceof FlowrJupyterFile ? file : new FlowrJupyterFile(file);
+    }
+}
+exports.FlowrJupyterFile = FlowrJupyterFile;
+function loadJupyter(content) {
+    const nb = JSON.parse(content);
+    return nb.cells.map(cell => {
+        if (cell.cell_type === 'code') {
+            return typeof cell.source === 'object' ? cell.source.join('') : cell.source;
+        }
+        else {
+            return typeof cell.source === 'object' ? cell.source.map(s => `# ${s}`).join('') : `# ${cell.source}`;
+        }
+    }).join('\n');
+}
+//# sourceMappingURL=flowr-jupyter-file.js.map

package/project/plugins/file-plugins/notebooks/flowr-rmarkdown-file.d.ts

@@ -0,0 +1,59 @@
+import type { FlowrFileProvider } from '../../../context/flowr-file';
+import { FlowrFile } from '../../../context/flowr-file';
+import { type Node } from 'commonmark';
+/**
+ * This decorates a text file and parses its contents as a R Markdown file.
+ * Finnaly, it provides access to the single cells, and all cells fused together as one R file.
+ */
+export declare class FlowrRMarkdownFile extends FlowrFile<string> {
+    private data?;
+    private readonly wrapped;
+    /**
+     * Prefer the static {@link FlowrRMarkdownFile.from} method
+     * @param file - the file to load as R Markdown
+     */
+    constructor(file: FlowrFileProvider<string>);
+    get rmd(): RmdInfo;
+    /**
+     * Loads and parses the content of the wrapped file.
+     * @returns RmdInfo
+     */
+    protected loadContent(): string;
+    static from(file: FlowrFileProvider<string> | FlowrRMarkdownFile): FlowrRMarkdownFile;
+}
+export interface CodeBlock {
+    options: string;
+    code: string;
+}
+export type CodeBlockEx = CodeBlock & {
+    startpos: {
+        line: number;
+        col: number;
+    };
+};
+export interface RmdInfo {
+    content: string;
+    blocks: CodeBlock[];
+    options: object;
+}
+/**
+ * Parse the contents of a RMarkdown file into complete code and blocks
+ * @param raw - the raw file content
+ * @returns Rmd Info
+ */
+export declare function parseRMarkdownFile(raw: string): RmdInfo;
+/**
+ * Checks whether a CommonMark node is an R code block
+ */
+export declare function isRCodeBlock(node: Node): node is Node & {
+    literal: string;
+    info: string;
+};
+/**
+ * Restores an Rmd file from code blocks, filling non-code lines with empty lines
+ */
+export declare function restoreBlocksWithoutMd(blocks: CodeBlockEx[], totalLines: number): string;
+/**
+ * Parses the options of an R code block from its header and content
+ */
+export declare function parseCodeBlockOptions(header: string, content: string): string;