Add more testing

AGENTS.md

@@ -34,7 +34,7 @@ How you should interact with the codebase
 When working with the ReVISit codebase, work only with the source code files available to you. If you need an external library, please ask for approval first (and include how well used the library is). Make sure to follow best practices for React and TypeScript development, including proper state management, component structuring, and code documentation. Pay extra attention to lifecycle methods and hooks to ensure optimal performance and avoid memory leaks, including any updates to existing code. If you encounter any issues or have suggestions for improvements, feel free to bring them up for discussion. You can run git commands but don't run them unless asked to. Don't interact with GitHub directly. Always check package.json for the scripts available to you for building, testing, and running the project.
 
 Testing
-When adding a new feature or modifying code try to maximize unit test coverage. Unit tests should be colocated with the files they are testing, have the same names as the file with .spec., and use the vitest framework. Apply this to both UI/react code as well as non-UI code. For UI code, we use playwright for end-to-end testing. Try to add e2e tests for any new features that involve user interaction. E2E tests are located in the tests/ directory at the root of the project. Don't run `yarn test` directly; instead, describe the tests you want to run, and I'll handle executing them. You can run unittests locally using `yarn unittest`. Preferred commands are those listed in package.json (e.g., `yarn unittest`, `yarn lint`, `yarn typecheck`, `yarn serve`, `yarn build`).
+When adding a new feature or modifying code try to maximize unit test coverage. Unit tests should live in a sibling `tests/` folder near the code they are testing, keep the same base name as the tested file with `.spec.`, and use the vitest framework. For example, `src/store/hooks/useReplay.ts` should be tested in `src/store/hooks/tests/useReplay.spec.tsx`. Root-level app specs should live in `src/tests/`. Apply this to both UI/react code as well as non-UI code. For UI code, we use playwright for end-to-end testing. Try to add e2e tests for any new features that involve user interaction. E2E tests are located in the `tests/` directory at the repo root. Don't run `yarn test` directly; instead, describe the tests you want to run, and I'll handle executing them. You can run unittests locally using `yarn unittest`. Preferred commands are those listed in package.json (e.g., `yarn unittest`, `yarn lint`, `yarn typecheck`, `yarn serve`, `yarn build`).
 
 Parser
 When adding new features, sometimes it's required to update the parser and the associated types. The parser is located in src/parser/. The parser is responsible for validating and transforming the study config JSON files into a format that the application can use. When updating the parser, ensure that you also update the corresponding types in src/parser/types.ts to reflect any changes made to the study config schema. Make sure to add unit tests for any new parser functionality to ensure its correctness. Additionally, changes to the parser types will require updates to the generated JSON schema files located in src/schemas/. You can regenerate these schema files by running `yarn generate-schemas`.

LibraryDocGenerator.spec.ts

@@ -0,0 +1,124 @@
+import fs from 'fs';
+import os from 'os';
+import path from 'path';
+import { createRequire } from 'module';
+import {
+  afterEach,
+  describe,
+  expect,
+  it,
+} from 'vitest';
+
+const require = createRequire(import.meta.url);
+const { generateMd, generateLibraryDocs, getLibraries } = require('./libraryDocGenerator.cjs');
+
+describe('libraryDocGenerator', () => {
+  const tempDirs: string[] = [];
+
+  afterEach(() => {
+    tempDirs.forEach((dir) => {
+      if (fs.existsSync(dir)) {
+        fs.rmSync(dir, { recursive: true, force: true });
+      }
+    });
+    tempDirs.length = 0;
+  });
+
+  it('generateMd includes components, sequences, and reference sections', () => {
+    const md = generateMd('demo-lib', {
+      description: 'Demo description',
+      reference: 'Some reference',
+      doi: '10.1000/xyz',
+      externalLink: 'https://example.com',
+      components: { beta: {}, alpha: {} },
+      sequences: { second: {}, first: {} },
+      additionalDescription: 'Extra details',
+    }, true);
+
+    expect(md).toContain('# demo-lib');
+    expect(md).toContain('## Available Components');
+    expect(md).toContain('- alpha');
+    expect(md).toContain('- beta');
+    expect(md).toContain('## Available Sequences');
+    expect(md).toContain('- first');
+    expect(md).toContain('- second');
+    expect(md).toContain('## Reference');
+    expect(md).toContain('https://dx.doi.org/10.1000/xyz');
+    expect(md).toContain('## Additional Description');
+  });
+
+  it('generateMd handles example reference text and external-link-only docs links', () => {
+    const exampleMd = generateMd('demo-lib', {
+      description: 'Demo description',
+      reference: 'Some reference',
+      components: {},
+      sequences: {},
+    }, false);
+
+    expect(exampleMd).toContain('This is an example study of the library `demo-lib`.');
+    expect(exampleMd).toContain('Some reference');
+    expect(exampleMd).not.toContain(':::note[Reference]');
+
+    const docsMd = generateMd('demo-lib', {
+      description: 'Demo description',
+      externalLink: 'https://example.com',
+      components: {},
+      sequences: {},
+    }, true);
+
+    expect(docsMd).toContain('referenceLinks={[');
+    expect(docsMd).toContain('{name: "demo-lib", url: "https://example.com"}');
+    expect(docsMd).not.toContain('{name: "DOI"');
+
+    const docsWithDoiOnly = generateMd('demo-lib', {
+      description: 'Demo description',
+      doi: '10.1000/xyz',
+      components: {},
+      sequences: {},
+    }, true);
+
+    expect(docsWithDoiOnly).toContain('{name: "DOI", url: "https://dx.doi.org/10.1000/xyz"}');
+    expect(docsWithDoiOnly).not.toContain('{name: "demo-lib", url:');
+  });
+
+  it('getLibraries filters hidden entries and .DS_Store entries', () => {
+    const base = fs.mkdtempSync(path.join(os.tmpdir(), 'lib-doc-list-'));
+    tempDirs.push(base);
+    const libsPath = path.join(base, 'public', 'libraries');
+    fs.mkdirSync(libsPath, { recursive: true });
+    fs.mkdirSync(path.join(libsPath, 'alpha'));
+    fs.mkdirSync(path.join(libsPath, '.hidden'));
+    fs.writeFileSync(path.join(libsPath, '.DS_Store'), '');
+
+    expect(getLibraries(libsPath)).toEqual(['alpha']);
+  });
+
+  it('generateLibraryDocs writes docs and example markdown when assets folder exists', () => {
+    const base = fs.mkdtempSync(path.join(os.tmpdir(), 'lib-doc-run-'));
+    tempDirs.push(base);
+    const libraryName = 'alpha';
+    const librariesPath = path.join(base, 'public', 'libraries', libraryName);
+    const exampleAssetsPath = path.join(base, 'public', `library-${libraryName}`, 'assets');
+
+    fs.mkdirSync(librariesPath, { recursive: true });
+    fs.mkdirSync(exampleAssetsPath, { recursive: true });
+    fs.writeFileSync(
+      path.join(librariesPath, 'config.json'),
+      JSON.stringify({
+        description: 'Alpha description',
+        components: { compA: {} },
+        sequences: {},
+      }),
+    );
+
+    generateLibraryDocs(base);
+
+    const docsOut = path.join(base, 'docsLibraries', `${libraryName}.md`);
+    const exampleOut = path.join(exampleAssetsPath, `${libraryName}.md`);
+
+    expect(fs.existsSync(docsOut)).toBe(true);
+    expect(fs.existsSync(exampleOut)).toBe(true);
+    expect(fs.readFileSync(docsOut, 'utf8')).toContain('# alpha');
+    expect(fs.readFileSync(exampleOut, 'utf8')).toContain('This is an example study');
+  });
+});

LibraryExampleStudyGenerator.spec.ts

@@ -0,0 +1,88 @@
+import fs from 'fs';
+import os from 'os';
+import path from 'path';
+import { createRequire } from 'module';
+import {
+  afterEach,
+  describe,
+  expect,
+  it,
+  vi,
+} from 'vitest';
+
+const require = createRequire(import.meta.url);
+const {
+  createExampleConfig,
+  generateLibraryExamples,
+  getLibraries,
+} = require('./libraryExampleStudyGenerator.cjs');
+
+describe('libraryExampleStudyGenerator', () => {
+  const tempDirs: string[] = [];
+
+  afterEach(() => {
+    tempDirs.forEach((dir) => {
+      if (fs.existsSync(dir)) {
+        fs.rmSync(dir, { recursive: true, force: true });
+      }
+    });
+    tempDirs.length = 0;
+  });
+
+  it('createExampleConfig builds config with expected defaults', () => {
+    const config = createExampleConfig('my-lib');
+
+    expect(config.studyMetadata.title).toBe('my-lib Example Study');
+    expect(config.importedLibraries).toEqual(['my-lib']);
+    expect(config.components.introduction.path).toBe('library-my-lib/assets/my-lib.md');
+    expect(config.sequence.components).toEqual(['introduction']);
+  });
+
+  it('getLibraries filters hidden entries and .DS_Store entries', () => {
+    const base = fs.mkdtempSync(path.join(os.tmpdir(), 'lib-example-list-'));
+    tempDirs.push(base);
+    const libsPath = path.join(base, 'public', 'libraries');
+    fs.mkdirSync(libsPath, { recursive: true });
+    fs.mkdirSync(path.join(libsPath, 'alpha'));
+    fs.mkdirSync(path.join(libsPath, '.hidden'));
+    fs.writeFileSync(path.join(libsPath, '.DS_Store'), '');
+
+    expect(getLibraries(libsPath)).toEqual(['alpha']);
+  });
+
+  it('generateLibraryExamples creates missing example study and invokes doc generation command', () => {
+    const base = fs.mkdtempSync(path.join(os.tmpdir(), 'lib-example-run-'));
+    tempDirs.push(base);
+    const libraryName = 'alpha';
+    const librariesPath = path.join(base, 'public', 'libraries', libraryName);
+    fs.mkdirSync(librariesPath, { recursive: true });
+
+    const generateDocsFn = vi.fn();
+    generateLibraryExamples(base, generateDocsFn);
+
+    const examplePath = path.join(base, 'public', `library-${libraryName}`);
+    const configPath = path.join(examplePath, 'config.json');
+    const assetsPath = path.join(examplePath, 'assets');
+
+    expect(fs.existsSync(examplePath)).toBe(true);
+    expect(fs.existsSync(assetsPath)).toBe(true);
+    expect(fs.existsSync(configPath)).toBe(true);
+    expect(generateDocsFn).toHaveBeenCalledTimes(1);
+    expect(generateDocsFn).toHaveBeenCalledWith(base);
+  });
+
+  it('logs an error when doc generation throws', () => {
+    const base = fs.mkdtempSync(path.join(os.tmpdir(), 'lib-example-error-'));
+    tempDirs.push(base);
+    fs.mkdirSync(path.join(base, 'public', 'libraries', 'alpha'), { recursive: true });
+    const errorSpy = vi.spyOn(console, 'error').mockImplementation(() => undefined);
+    const generateDocsFn = vi.fn(() => {
+      throw new Error('test Error');
+    });
+
+    generateLibraryExamples(base, generateDocsFn);
+
+    expect(errorSpy).toHaveBeenCalledWith(expect.stringContaining('Error running libraryDocGenerator.cjs: Error: test Error'));
+    errorSpy.mockRestore();
+  });
+});

libraryDocGenerator.cjs

@@ -54,40 +54,50 @@ import StructuredLinks from '@site/src/components/StructuredLinks/StructuredLink
   />` : ''}
 `;
 
-const librariesPath = path.join(__dirname, './public/libraries');
-const docsLibrariesPath = path.join(__dirname, './docsLibraries');
-
-const libraries = fs.readdirSync(librariesPath)
+const getLibraries = (libsPath) => fs.readdirSync(libsPath)
   .filter((library) => !library.startsWith('.') && !library.endsWith('.DS_Store'));
 
-if (!fs.existsSync(docsLibrariesPath)) {
-  fs.mkdirSync(docsLibrariesPath);
-}
+const generateLibraryDocs = (base) => {
+  const librariesPath = path.join(base, 'public', 'libraries');
+  const docsLibrariesPath = path.join(base, 'docsLibraries');
 
-libraries.forEach((library) => {
-  const libraryPath = path.join(librariesPath, library, 'config.json');
-  const libraryConfig = JSON.parse(fs.readFileSync(libraryPath, 'utf8'));
+  const libraries = getLibraries(librariesPath);
 
-  const docsMd = generateMd(library, libraryConfig, true);
-  const exampleMd = generateMd(library, libraryConfig, false);
+  if (!fs.existsSync(docsLibrariesPath)) {
+    fs.mkdirSync(docsLibrariesPath);
+  }
 
-  // Save to docsLibraries folder
-  const docsLibraryPath = path.join(docsLibrariesPath, `${library}.md`);
-  fs.writeFileSync(docsLibraryPath, docsMd);
-  // eslint-disable-next-line no-console
-  console.log(`Documentation saved to ${docsLibraryPath}`);
+  libraries.forEach((library) => {
+    const libraryPath = path.join(librariesPath, library, 'config.json');
+    const libraryConfig = JSON.parse(fs.readFileSync(libraryPath, 'utf8'));
 
-  // Save to example study assets folder if assets folder exists
-  // Add a prefix to baseMarkdown when saving to example assets
-  const exampleAssetsPath = path.join(__dirname, 'public', `library-${library}`, 'assets');
-  if (fs.existsSync(exampleAssetsPath)) {
-    const exampleDocsPath = path.join(exampleAssetsPath, `${library}.md`);
-    fs.writeFileSync(exampleDocsPath, exampleMd);
+    const docsMd = generateMd(library, libraryConfig, true);
+    const exampleMd = generateMd(library, libraryConfig, false);
 
+    // Save to docsLibraries folder
+    const docsLibraryPath = path.join(docsLibrariesPath, `${library}.md`);
+    fs.writeFileSync(docsLibraryPath, docsMd);
     // eslint-disable-next-line no-console
-    console.log(`Documentation saved to ${exampleDocsPath}`);
-  }
-});
+    console.log(`Documentation saved to ${docsLibraryPath}`);
+
+    // Save to example study assets folder if assets folder exists
+    // Add a prefix to baseMarkdown when saving to example assets
+    const exampleAssetsPath = path.join(base, 'public', `library-${library}`, 'assets');
+    if (fs.existsSync(exampleAssetsPath)) {
+      const exampleDocsPath = path.join(exampleAssetsPath, `${library}.md`);
+      fs.writeFileSync(exampleDocsPath, exampleMd);
+
+      // eslint-disable-next-line no-console
+      console.log(`Documentation saved to ${exampleDocsPath}`);
+    }
+  });
+
+  // eslint-disable-next-line no-console
+  console.log('Library documentation generated');
+};
+
+if (require.main === module) {
+  generateLibraryDocs(__dirname);
+}
 
-// eslint-disable-next-line no-console
-console.log('Library documentation generated');
+module.exports = { generateMd, getLibraries, generateLibraryDocs };