@eagleoutice/flowr 2.4.8 → 2.5.0

package/README.md

@@ -24,7 +24,7 @@ It offers a wide variety of features, for example:
     
     ```shell
     $ docker run -it --rm eagleoutice/flowr # or npm run flowr 
-    flowR repl using flowR v2.4.7, R v4.5.0 (r-shell engine)
+    flowR repl using flowR v2.4.8, R v4.5.0 (r-shell engine)
     R> :query @linter "read.csv(\"/root/x.txt\")"
     ```
     
@@ -78,34 +78,34 @@ It offers a wide variety of features, for example:
     
     _Results (prettified and summarized):_
     
-    Query: **linter** (14 ms)\
+    Query: **linter** (15 ms)\
        ╰ **Deprecated Functions** (deprecated-functions):\
     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>{"totalDeprecatedCalls":0,"totalDeprecatedFunctionDefinitions":0,"searchTimeMs":2,"processTimeMs":0}</code>\
     &nbsp;&nbsp;&nbsp;╰ **File Path Validity** (file-path-validity):\
     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ certain:\
     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ Path `/root/x.txt` at 1.1-23\
-    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>{"totalReads":1,"totalUnknown":0,"totalWritesBeforeAlways":0,"totalValid":0,"searchTimeMs":4,"processTimeMs":1}</code>\
+    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>{"totalReads":1,"totalUnknown":0,"totalWritesBeforeAlways":0,"totalValid":0,"searchTimeMs":5,"processTimeMs":0}</code>\
     &nbsp;&nbsp;&nbsp;╰ **Seeded Randomness** (seeded-randomness):\
-    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>{"consumerCalls":0,"callsWithFunctionProducers":0,"callsWithAssignmentProducers":0,"callsWithNonConstantProducers":0,"searchTimeMs":0,"processTimeMs":1}</code>\
+    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>{"consumerCalls":0,"callsWithFunctionProducers":0,"callsWithAssignmentProducers":0,"callsWithNonConstantProducers":0,"searchTimeMs":1,"processTimeMs":0}</code>\
     &nbsp;&nbsp;&nbsp;╰ **Absolute Paths** (absolute-file-paths):\
     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ certain:\
     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ Path `/root/x.txt` at 1.1-23\
-    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>{"totalConsidered":1,"totalUnknown":0,"searchTimeMs":1,"processTimeMs":1}</code>\
+    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>{"totalConsidered":1,"totalUnknown":0,"searchTimeMs":2,"processTimeMs":0}</code>\
     &nbsp;&nbsp;&nbsp;╰ **Unused Definitions** (unused-definitions):\
     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>{"totalConsidered":0,"searchTimeMs":0,"processTimeMs":0}</code>\
     &nbsp;&nbsp;&nbsp;╰ **Naming Convention** (naming-convention):\
     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>{"numMatches":0,"numBreak":0,"searchTimeMs":0,"processTimeMs":0}</code>\
     &nbsp;&nbsp;&nbsp;╰ **Dataframe Access Validation** (dataframe-access-validation):\
-    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>{"numOperations":0,"numAccesses":0,"totalAccessed":0,"searchTimeMs":0,"processTimeMs":2}</code>\
+    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>{"numOperations":0,"numAccesses":0,"totalAccessed":0,"searchTimeMs":0,"processTimeMs":4}</code>\
     &nbsp;&nbsp;&nbsp;╰ **Dead Code** (dead-code):\
     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>{"consideredNodes":5,"searchTimeMs":1,"processTimeMs":0}</code>\
     &nbsp;&nbsp;&nbsp;╰ **Useless Loops** (useless-loop):\
-    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>{"numOfUselessLoops":0,"searchTimeMs":0,"processTimeMs":1}</code>\
-    _All queries together required ≈14 ms (1ms accuracy, total 216 ms)_
+    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>{"numOfUselessLoops":0,"searchTimeMs":0,"processTimeMs":0}</code>\
+    _All queries together required ≈16 ms (1ms accuracy, total 209 ms)_
     
     <details> <summary style="color:gray">Show Detailed Results as Json</summary>
     
-    The analysis required _215.9 ms_ (including parsing and normalization and the query) within the generation environment.	
+    The analysis required _209.2 ms_ (including parsing and normalization and the query) within the generation environment.	
     
     In general, the JSON contains the Ids of the nodes in question as they are present in the normalized AST or the dataflow graph of flowR.
     Please consult the [Interface](https://github.com/flowr-analysis/flowr/wiki/Interface) wiki page for more information on how to get those.
@@ -144,8 +144,8 @@ It offers a wide variety of features, for example:
               "totalUnknown": 0,
               "totalWritesBeforeAlways": 0,
               "totalValid": 0,
-              "searchTimeMs": 4,
-              "processTimeMs": 1
+              "searchTimeMs": 5,
+              "processTimeMs": 0
             }
           },
           "seeded-randomness": {
@@ -155,8 +155,8 @@ It offers a wide variety of features, for example:
               "callsWithFunctionProducers": 0,
               "callsWithAssignmentProducers": 0,
               "callsWithNonConstantProducers": 0,
-              "searchTimeMs": 0,
-              "processTimeMs": 1
+              "searchTimeMs": 1,
+              "processTimeMs": 0
             }
           },
           "absolute-file-paths": {
@@ -175,8 +175,8 @@ It offers a wide variety of features, for example:
             ".meta": {
               "totalConsidered": 1,
               "totalUnknown": 0,
-              "searchTimeMs": 1,
-              "processTimeMs": 1
+              "searchTimeMs": 2,
+              "processTimeMs": 0
             }
           },
           "unused-definitions": {
@@ -203,7 +203,7 @@ It offers a wide variety of features, for example:
               "numAccesses": 0,
               "totalAccessed": 0,
               "searchTimeMs": 0,
-              "processTimeMs": 2
+              "processTimeMs": 4
             }
           },
           "dead-code": {
@@ -219,16 +219,16 @@ It offers a wide variety of features, for example:
             ".meta": {
               "numOfUselessLoops": 0,
               "searchTimeMs": 0,
-              "processTimeMs": 1
+              "processTimeMs": 0
             }
           }
         },
         ".meta": {
-          "timing": 14
+          "timing": 15
         }
       },
       ".meta": {
-        "timing": 14
+        "timing": 16
       }
     }
     ```
@@ -295,7 +295,7 @@ It offers a wide variety of features, for example:
     
     ```shell
     $ docker run -it --rm eagleoutice/flowr # or npm run flowr 
-    flowR repl using flowR v2.4.7, R v4.5.0 (r-shell engine)
+    flowR repl using flowR v2.4.8, R v4.5.0 (r-shell engine)
     R> :slicer test/testfiles/example.R --criterion "11@sum"
     ```
     
@@ -378,7 +378,7 @@ It offers a wide variety of features, for example:
     
     ```shell
     $ docker run -it --rm eagleoutice/flowr # or npm run flowr 
-    flowR repl using flowR v2.4.7, R v4.5.0 (r-shell engine)
+    flowR repl using flowR v2.4.8, R v4.5.0 (r-shell engine)
     R> :dataflow* test/testfiles/example.R
     ```
     
@@ -683,7 +683,7 @@ It offers a wide variety of features, for example:
     ```
     
     	
-    (The analysis required _14.9 ms_ (including parse and normalize, using the [r-shell](https://github.com/flowr-analysis/flowr/wiki/Engines) engine) within the generation environment.)
+    (The analysis required _14.2 ms_ (including parse and normalize, using the [r-shell](https://github.com/flowr-analysis/flowr/wiki/Engines) engine) within the generation environment.)
     
     
     
@@ -728,6 +728,12 @@ You can enter <span title="Description (Repl Command): Show help information (al
 
 ![Example of a simple REPL session](wiki/gif/repl-demo-opt.gif)
 
+If you want to use the same commands:
+
+1. First this runs `docker run -it --rm eagleoutice/flowr` in a terminal to start the REPL.
+2. In the REPL, it runs `:slicer -c '11@prod' demo.R --diff` to slice the example file `demo.R` for the print statement in line 11.
+   Please note that the `11` refers to the 11th line number to slice for!
+
 </details>
 
 ## 📜 More Information

package/benchmark/slicer.js

@@ -9,7 +9,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BenchmarkSlicer = exports.benchmarkLogger = void 0;
 const stopwatch_1 = require("./stopwatch");
-const fs_1 = __importDefault(require("fs"));
 const seedrandom_1 = __importDefault(require("seedrandom"));
 const log_1 = require("../util/log");
 const assert_1 = require("../util/assert");
@@ -30,6 +29,7 @@ const extract_cfg_1 = require("../control-flow/extract-cfg");
 const absint_info_1 = require("../abstract-interpretation/data-frame/absint-info");
 const domain_1 = require("../abstract-interpretation/data-frame/domain");
 const shape_inference_1 = require("../abstract-interpretation/data-frame/shape-inference");
+const fs_1 = __importDefault(require("fs"));
 /**
  * The logger to be used for benchmarking as a global object.
  */

package/benchmark/summarizer/second-phase/graph.js

@@ -19,7 +19,7 @@ function writeGraphOutput(ultimate, outputGraphPath) {
                 name: pointName[0].toUpperCase() + pointName.slice(1),
                 unit: 'ms',
                 value: Number(measurement.mean / 1e6),
-                range: Number(measurement.std / 1e6),
+                range: String(Number(measurement.std / 1e6)),
                 extra: `median: ${(measurement.median / 1e6).toFixed(2)}ms`
             });
         }
@@ -51,7 +51,7 @@ function writeGraphOutput(ultimate, outputGraphPath) {
         name: 'memory (df-graph)',
         unit: 'KiB',
         value: ultimate.dataflow.sizeOfObject.mean / 1024,
-        range: ultimate.dataflow.sizeOfObject.std / 1024,
+        range: String(ultimate.dataflow.sizeOfObject.std / 1024),
         extra: `median: ${(ultimate.dataflow.sizeOfObject.median / 1024).toFixed(2)}`
     });
     // write the output file

package/cli/slicer-app.js

@@ -15,6 +15,7 @@ const print_1 = require("../benchmark/stats/print");
 const magic_comments_1 = require("../reconstruct/auto-select/magic-comments");
 const auto_select_defaults_1 = require("../reconstruct/auto-select/auto-select-defaults");
 const config_1 = require("../config");
+const adapter_1 = require("../util/formats/adapter");
 const options = (0, script_1.processCommandLineArgs)('slicer', ['input', 'criterion'], {
     subtitle: 'Slice R code based on a given slicing criterion',
     examples: [
@@ -32,7 +33,7 @@ async function getSlice() {
     const config = (0, config_1.getConfig)();
     await slicer.init(options['input-is-text']
         ? { request: 'text', content: options.input.replaceAll('\\n', '\n') }
-        : { request: 'file', content: options.input }, config, options['no-magic-comments'] ? auto_select_defaults_1.doNotAutoSelect : (0, magic_comments_1.makeMagicCommentHandler)(auto_select_defaults_1.doNotAutoSelect));
+        : (0, adapter_1.requestFromFile)(options.input), config, options['no-magic-comments'] ? auto_select_defaults_1.doNotAutoSelect : (0, magic_comments_1.makeMagicCommentHandler)(auto_select_defaults_1.doNotAutoSelect));
     let mappedSlices = [];
     let reconstruct = undefined;
     const doSlicing = options.criterion.trim() !== '';
@@ -74,7 +75,11 @@ async function getSlice() {
     }
     else {
         if (doSlicing && options.diff) {
-            const originalCode = options['input-is-text'] ? options.input : fs_1.default.readFileSync(options.input).toString();
+            let originalCode = options.input;
+            if (!options['input-is-text']) {
+                const request = (0, adapter_1.requestFromFile)(options.input);
+                originalCode = request.request === 'text' ? request.content : fs_1.default.readFileSync(request.content).toString();
+            }
             console.log((0, slice_diff_ansi_1.sliceDiffAnsi)(slice.result, normalize, new Set(mappedSlices.map(({ id }) => id)), originalCode));
         }
         if (options.stats) {

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

@@ -201,6 +201,10 @@ To get started, install the [vitest Extension](https://marketplace.visualstudio.
 #### Webstorm
 
 Please follow the official guide [here](https://www.jetbrains.com/help/webstorm/vitest.html).
+Note that the working directory has to be set to the project root directory, not the test subdirectory!
+Otherwise, the tests will not be instantiated.
+
+![Webstorm test configuration](img/testing-webstorm.png)
 
 <a id='ci-pipeline'></a>
 ## 🪈 CI Pipeline

package/documentation/print-readme.js

@@ -142,6 +142,12 @@ You can enter ${(0, doc_cli_option_1.getReplCommand)('help')} to gain more infor
 
 ![Example of a simple REPL session](wiki/gif/repl-demo-opt.gif)
 
+If you want to use the same commands:
+
+1. First this runs \`docker run -it --rm eagleoutice/flowr\` in a terminal to start the REPL.
+2. In the REPL, it runs \`:slicer -c '11@prod' demo.R --diff\` to slice the example file \`demo.R\` for the print statement in line 11.
+   Please note that the \`11\` refers to the 11th line number to slice for!
+
 </details>
 
 ## 📜 More Information

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@eagleoutice/flowr",
-  "version": "2.4.8",
+  "version": "2.5.0",
   "description": "Static Dataflow Analyzer and Program Slicer for the R Programming Language",
   "types": "dist/src/index.d.ts",
   "repository": {
@@ -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",

package/r-bridge/lang-4.x/tree-sitter/tree-sitter-executor.js

@@ -5,8 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.TreeSitterExecutor = exports.DEFAULT_TREE_SITTER_WASM_PATH = exports.DEFAULT_TREE_SITTER_R_WASM_PATH = void 0;
 const web_tree_sitter_1 = __importDefault(require("web-tree-sitter"));
-const fs_1 = __importDefault(require("fs"));
 const log_1 = require("../../../util/log");
+const fs_1 = __importDefault(require("fs"));
 exports.DEFAULT_TREE_SITTER_R_WASM_PATH = './node_modules/@eagleoutice/tree-sitter-r/tree-sitter-r.wasm';
 exports.DEFAULT_TREE_SITTER_WASM_PATH = './node_modules/web-tree-sitter/tree-sitter.wasm';
 const wasmLog = log_1.log.getSubLogger({ name: 'tree-sitter-wasm' });

package/r-bridge/retriever.d.ts

@@ -2,16 +2,24 @@ import { type RShell } from './shell';
 import type { AsyncOrSync } from 'ts-essentials';
 import { RShellExecutor } from './shell-executor';
 import type { NormalizedAst } from './lang-4.x/ast/model/processing/decorate';
+import type { SupportedFormats } from '../util/formats/adapter-format';
 export declare 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).
@@ -20,6 +28,10 @@ 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;
 }
 /**
  * A provider for an {@link RParseRequests} that can be used, for example, to override source file parsing behavior in tests

package/r-bridge/retriever.js

@@ -22,6 +22,7 @@ const decorate_1 = require("./lang-4.x/ast/model/processing/decorate");
 const type_1 = require("./lang-4.x/ast/model/type");
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
+const adapter_1 = require("../util/formats/adapter");
 exports.fileProtocol = 'file://';
 /**
  * Creates a {@link RParseRequests} from a given input.
@@ -35,10 +36,15 @@ function requestFromInput(input) {
     }
     const content = input;
     const file = content.startsWith(exports.fileProtocol);
-    return {
-        request: file ? 'file' : 'text',
-        content: file ? content.slice(7) : content
-    };
+    if (file) {
+        return (0, adapter_1.requestFromFile)(content.slice(7));
+    }
+    else {
+        return {
+            request: 'text',
+            content: content
+        };
+    }
 }
 function requestProviderFromFile() {
     return {

package/util/formats/adapter-format.d.ts

@@ -0,0 +1,6 @@
+import type { RParseRequest } from '../../r-bridge/retriever';
+export interface FileAdapter {
+    convertRequest(request: RParseRequest): RParseRequest;
+}
+export type SupportedFormats = 'R' | 'Rmd';
+export type SupportedDocumentTypes = '.r' | '.rmd';

package/util/formats/adapter-format.js

@@ -0,0 +1,3 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+//# sourceMappingURL=adapter-format.js.map

package/util/formats/adapter.d.ts

@@ -0,0 +1,16 @@
+import type { RParseRequest } from '../../r-bridge/retriever';
+export declare const FileAdapters: {
+    readonly R: {
+        convertRequest: (request: RParseRequest) => RParseRequest;
+    };
+    readonly Rmd: {
+        convertRequest: (request: RParseRequest) => import("../../r-bridge/retriever").RParseRequestFromText<import("./adapters/rmd-adapter").RmdInfo>;
+    };
+};
+export declare const DocumentTypeToFormat: {
+    readonly '.r': "R";
+    readonly '.rmd': "Rmd";
+};
+export type AdapterReturnTypes = ReturnType<typeof FileAdapters[keyof typeof FileAdapters]['convertRequest']>;
+export declare function requestFromFile(path: string): AdapterReturnTypes;
+export declare function inferFileType(request: RParseRequest): keyof typeof FileAdapters;

package/util/formats/adapter.js

@@ -0,0 +1,42 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.DocumentTypeToFormat = exports.FileAdapters = void 0;
+exports.requestFromFile = requestFromFile;
+exports.inferFileType = inferFileType;
+const r_adapter_1 = require("./adapters/r-adapter");
+const path_1 = __importDefault(require("path"));
+const rmd_adapter_1 = require("./adapters/rmd-adapter");
+exports.FileAdapters = {
+    'R': r_adapter_1.RAdapter,
+    'Rmd': rmd_adapter_1.RmdAdapter
+};
+exports.DocumentTypeToFormat = {
+    '.r': 'R',
+    '.rmd': 'Rmd'
+};
+function requestFromFile(path) {
+    const baseRequest = {
+        request: 'file',
+        content: path
+    };
+    const type = inferFileType(baseRequest);
+    return exports.FileAdapters[type].convertRequest(baseRequest);
+}
+function inferFileType(request) {
+    if (request.request === 'text') {
+        // For now we don't know what type the request is 
+        // and have to assume it is normal R Code
+        // In the future we could add a heuristic to guess the type
+        return 'R';
+    }
+    const type = path_1.default.extname(request.content).toLowerCase();
+    // Fallback to default if unknown
+    if (!Object.hasOwn(exports.DocumentTypeToFormat, type)) {
+        return 'R';
+    }
+    return exports.DocumentTypeToFormat[type];
+}
+//# sourceMappingURL=adapter.js.map

package/util/formats/adapters/r-adapter.d.ts

@@ -0,0 +1,4 @@
+import type { RParseRequest } from '../../../r-bridge/retriever';
+export declare const RAdapter: {
+    convertRequest: (request: RParseRequest) => RParseRequest;
+};

package/util/formats/adapters/r-adapter.js

@@ -0,0 +1,7 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.RAdapter = void 0;
+exports.RAdapter = {
+    convertRequest: (request) => request
+};
+//# sourceMappingURL=r-adapter.js.map

package/util/formats/adapters/rmd-adapter.d.ts

@@ -0,0 +1,26 @@
+import type { Node } from 'commonmark';
+import type { RParseRequest, RParseRequestFromText } from '../../../r-bridge/retriever';
+export interface CodeBlock {
+    options: string;
+    code: string;
+}
+export type CodeBlockEx = CodeBlock & {
+    startpos: {
+        line: number;
+        col: number;
+    };
+};
+export interface RmdInfo {
+    type: 'Rmd';
+    blocks: CodeBlock[];
+    options: object;
+}
+export declare const RmdAdapter: {
+    convertRequest: (request: RParseRequest) => RParseRequestFromText<RmdInfo>;
+};
+export declare function isRCodeBlock(node: Node): node is Node & {
+    literal: string;
+    info: string;
+};
+export declare function restoreBlocksWithoutMd(blocks: CodeBlockEx[], totalLines: number): string;
+export declare function parseCodeBlockOptions(header: string, content: string): string;

package/util/formats/adapters/rmd-adapter.js

@@ -0,0 +1,91 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.RmdAdapter = void 0;
+exports.isRCodeBlock = isRCodeBlock;
+exports.restoreBlocksWithoutMd = restoreBlocksWithoutMd;
+exports.parseCodeBlockOptions = parseCodeBlockOptions;
+const fs_1 = __importDefault(require("fs"));
+const commonmark_1 = require("commonmark");
+const gray_matter_1 = __importDefault(require("gray-matter"));
+const assert_1 = require("../../assert");
+exports.RmdAdapter = {
+    convertRequest: (request) => {
+        // Read and Parse Markdown
+        const raw = request.request === 'text'
+            ? request.content
+            : fs_1.default.readFileSync(request.content, 'utf-8').toString();
+        const parser = new commonmark_1.Parser();
+        const ast = parser.parse(raw);
+        // Parse Frontmatter
+        const frontmatter = (0, gray_matter_1.default)(raw);
+        // Parse Codeblocks
+        const walker = ast.walker();
+        const blocks = [];
+        let e;
+        while ((e = walker.next())) {
+            const node = e.node;
+            if (!isRCodeBlock(node)) {
+                continue;
+            }
+            blocks.push({
+                code: node.literal,
+                options: parseCodeBlockOptions(node.info, node.literal),
+                startpos: { line: node.sourcepos[0][0] + 1, col: 0 }
+            });
+        }
+        return {
+            request: 'text',
+            content: restoreBlocksWithoutMd(blocks, countNewlines(raw)),
+            info: {
+                // eslint-disable-next-line unused-imports/no-unused-vars
+                blocks: blocks.map(({ startpos, ...block }) => block),
+                options: frontmatter.data,
+                type: 'Rmd'
+            }
+        };
+    }
+};
+const RTagRegex = /{[rR](?:[\s,][^}]*)?}/;
+function isRCodeBlock(node) {
+    return node.type === 'code_block' && node.literal !== null && node.info !== null && RTagRegex.test(node.info);
+}
+const LineRegex = /\r\n|\r|\n/;
+function countNewlines(str) {
+    return str.split(LineRegex).length - 1;
+}
+function restoreBlocksWithoutMd(blocks, totalLines) {
+    let line = 1;
+    let output = '';
+    const goToLine = (n) => {
+        const diff = n - line;
+        (0, assert_1.guard)(diff >= 0);
+        line += diff;
+        output += '\n'.repeat(diff);
+    };
+    for (const block of blocks) {
+        goToLine(block.startpos.line);
+        output += block.code;
+        line += countNewlines(block.code);
+    }
+    // Add remainder of file 
+    goToLine(totalLines + 1);
+    return output;
+}
+function parseCodeBlockOptions(header, content) {
+    let opts = header.length === 3 // '{r}' => header.length=3 (no options in header)
+        ? ''
+        : header.substring(3, header.length - 1).trim();
+    const lines = content.split('\n');
+    for (const line of lines) {
+        if (!line.trim().startsWith('#|')) {
+            break;
+        }
+        const opt = line.substring(3);
+        opts += opts.length === 0 ? opt : `, ${opt}`;
+    }
+    return opts;
+}
+//# sourceMappingURL=rmd-adapter.js.map

package/util/version.js

@@ -3,7 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.flowrVersion = flowrVersion;
 const semver_1 = require("semver");
 // this is automatically replaced with the current version by release-it
-const version = '2.4.8';
+const version = '2.5.0';
 function flowrVersion() {
     return new semver_1.SemVer(version);
 }