Support for rmd notebooks

package.json

@@ -183,6 +183,7 @@
     "@j-ulrich/release-it-regex-bumper": "^5.3.0",
     "@types/command-line-args": "^5.2.3",
     "@types/command-line-usage": "^5.0.4",
+    "@types/commonmark": "^0.27.10",
     "@types/n-readlines": "^1.0.6",
     "@types/n3": "^1.26.0",
     "@types/object-hash": "^3.0.6",
@@ -212,6 +213,8 @@
     "clipboardy": "^4.0.0",
     "command-line-args": "^6.0.1",
     "command-line-usage": "^7.0.3",
+    "commonmark": "^0.31.2",
+    "gray-matter": "^4.0.3",
     "joi": "^18.0.1",
     "lz-string": "^1.5.0",
     "n-readlines": "^1.0.1",

src/benchmark/slicer.ts

@@ -5,7 +5,6 @@
 
 import type { IStoppableStopwatch } from './stopwatch';
 import { Measurements } from './stopwatch';
-import fs from 'fs';
 import seedrandom from 'seedrandom';
 import { log, LogLevel } from '../util/log';
 import type { MergeableRecord } from '../util/objects';
@@ -29,8 +28,6 @@ import type { NormalizedAst, ParentInformation } from '../r-bridge/lang-4.x/ast/
 import type { SlicingCriteria } from '../slicing/criterion/parse';
 import type { DEFAULT_SLICING_PIPELINE, TREE_SITTER_SLICING_PIPELINE } from '../core/steps/pipeline/default-pipelines';
 import { createSlicePipeline } from '../core/steps/pipeline/default-pipelines';
-
-
 import type { RParseRequestFromFile, RParseRequestFromText } from '../r-bridge/retriever';
 import { retrieveNumberOfRTokensOfLastParse } from '../r-bridge/retriever';
 import type { PipelineStepNames, PipelineStepOutputWithName } from '../core/steps/pipeline/pipeline';
@@ -69,6 +66,7 @@ import {
 	IntervalTop
 } from '../abstract-interpretation/data-frame/domain';
 import { inferDataFrameShapes } from '../abstract-interpretation/data-frame/shape-inference';
+import fs from 'fs';
 
 /**
  * The logger to be used for benchmarking as a global object.

src/cli/slicer-app.ts

@@ -14,6 +14,7 @@ import { stats2string } from '../benchmark/stats/print';
 import { makeMagicCommentHandler } from '../reconstruct/auto-select/magic-comments';
 import { doNotAutoSelect } from '../reconstruct/auto-select/auto-select-defaults';
 import { getConfig, getEngineConfig } from '../config';
+import { requestFromFile } from '../util/formats/adapter';
 
 export interface SlicerCliOptions {
 	verbose:             boolean
@@ -50,7 +51,7 @@ async function getSlice() {
 	await slicer.init(
 		options['input-is-text']
 			? { request: 'text', content: options.input.replaceAll('\\n', '\n') }
-			: { request: 'file', content: options.input },
+			: requestFromFile(options.input),
 		config,
 		options['no-magic-comments'] ? doNotAutoSelect : makeMagicCommentHandler(doNotAutoSelect)
 	);
@@ -99,7 +100,11 @@ async function getSlice() {
 		console.log(JSON.stringify(output, jsonReplacer));
 	} else {
 		if(doSlicing && options.diff) {
-			const originalCode = options['input-is-text'] ? options.input : fs.readFileSync(options.input).toString();
+			let originalCode = options.input;
+			if(!options['input-is-text']) {
+				const request = requestFromFile(options.input);
+				originalCode = request.request === 'text' ? request.content : fs.readFileSync(request.content).toString(); 
+			}
 			console.log(sliceDiffAnsi((slice as SliceResult).result, normalize, new Set(mappedSlices.map(({ id }) => id)), originalCode));
 		}
 		if(options.stats) {

src/r-bridge/lang-4.x/tree-sitter/tree-sitter-executor.ts

@@ -1,10 +1,10 @@
 import Parser from 'web-tree-sitter';
 
 import type { RParseRequest } from '../../retriever';
-import fs from 'fs';
 import type { SyncParser } from '../../parser';
 import type { TreeSitterEngineConfig } from '../../../config';
 import { log } from '../../../util/log';
+import fs from 'fs';
 
 export const DEFAULT_TREE_SITTER_R_WASM_PATH = './node_modules/@eagleoutice/tree-sitter-r/tree-sitter-r.wasm';
 export const DEFAULT_TREE_SITTER_WASM_PATH = './node_modules/web-tree-sitter/tree-sitter.wasm';

src/r-bridge/retriever.ts

@@ -11,19 +11,31 @@ import { deterministicCountingIdGenerator } from './lang-4.x/ast/model/processin
 import { RawRType } from './lang-4.x/ast/model/type';
 import fs from 'fs';
 import path from 'path';
+import type { SupportedFormats } from '../util/formats/adapter-format';
+import { requestFromFile } from '../util/formats/adapter';
 
 export const fileProtocol = 'file://';
 
-export interface RParseRequestFromFile {
+export interface PraseRequestAdditionalInfoBase {
+	type: SupportedFormats
+}
+
+export interface RParseRequestFromFile<AdditionalInfo extends PraseRequestAdditionalInfoBase = PraseRequestAdditionalInfoBase> {
 	readonly request: 'file';
 	/**
 	 * The path to the file (an absolute path is probably best here).
 	 * See {@link RParseRequests} for multiple files.
 	 */
 	readonly content: string;
+
+	/**
+	 * Aditional info from different file formates like .Rmd
+	 */
+	readonly info?: AdditionalInfo;
+
 }
 
-export interface RParseRequestFromText {
+export interface RParseRequestFromText<AdditionalInfo extends PraseRequestAdditionalInfoBase = PraseRequestAdditionalInfoBase> {
 	readonly request: 'text'
 	/**
 	 * Source code to parse (not a file path).
@@ -32,6 +44,11 @@ export interface RParseRequestFromText {
 	 * or concatenate their contents to pass them with this request.
 	 */
 	readonly content: string
+
+	/**
+	 * Aditional info from different file formates like .Rmd
+	 */
+	readonly info?: AdditionalInfo;
 }
 
 /**
@@ -66,10 +83,15 @@ export function requestFromInput(input: `${typeof fileProtocol}${string}` | stri
 	}
 	const content = input as string;
 	const file = content.startsWith(fileProtocol);
-	return {
-		request: file ? 'file' : 'text',
-		content: file ? content.slice(7) : content
-	};
+
+	if(file) {
+		return requestFromFile(content.slice(7));
+	} else {
+		return {
+			request: 'text',
+			content: content
+		};
+	}
 }
 
 
@@ -135,6 +157,7 @@ export function retrieveParseDataFromRCode(request: RParseRequest, shell: RShell
 	if(isEmptyRequest(request)) {
 		return Promise.resolve('');
 	}
+
 	const suffix = request.request === 'file' ? ', encoding="utf-8"' : '';
 	/* call the function with the request */
 	const command =`flowr_get_ast(${request.request}=${JSON.stringify(

src/util/formats/adapter-format.ts

@@ -0,0 +1,9 @@
+import type { RParseRequest } from '../../r-bridge/retriever';
+
+export interface FileAdapter {
+    convertRequest(request: RParseRequest): RParseRequest
+}
+
+export type SupportedFormats = 'R' | 'Rmd';
+
+export type SupportedDocumentTypes = '.r' | '.rmd';