Code change:
<ins> /*--------------------------------------------------------------------------------------------- *  Copyright (c) Microsoft Corporation. All rights reserved. *  Licensed under the MIT License. See License.txt in the project root for license information. *--------------------------------------------------------------------------------------------*/ import { ExtensionContext, NotebookCellKind, NotebookDocument, NotebookDocumentChangeEvent, NotebookEdit, workspace, WorkspaceEdit, type NotebookCell, type NotebookDocumentWillSaveEvent } from 'vscode'; import { getCellMetadata, getVSCodeCellLanguageId, removeVSCodeCellLanguageId, setVSCodeCellLanguageId } from './serializers'; import { CellMetadata } from './common'; import { getNotebookMetadata } from './notebookSerializer'; import type * as nbformat from '@jupyterlab/nbformat'; const noop = () => { // }; /** * Code here is used to ensure the Notebook Model is in sync the the ipynb JSON file. * E.g. assume you add a new cell, this new cell will not have any metadata at all. * However when we save the ipynb, the metadata will be an empty object `{}`. * Now thats completely different from the metadata os being `empty/undefined` in the model. * As a result, when looking at things like diff view or accessing metadata, we'll see differences. * * This code ensures that the model is in sync with the ipynb file. */ export const pendingNotebookCellModelUpdates = new WeakMap<NotebookDocument, Set<Thenable<void>>>(); export function activate(context: ExtensionContext) { workspace.onDidChangeNotebookDocument(onDidChangeNotebookCells, undefined, context.subscriptions); workspace.onWillSaveNotebookDocument(waitForPendingModelUpdates, undefined, context.subscriptions); } function isSupportedNotebook(notebook: NotebookDocument) { return notebook.notebookType === 'jupyter-notebook' || notebook.notebookType === 'interactive'; } function waitForPendingModelUpdates(e: NotebookDocumentWillSaveEvent) { if (!isSupportedNotebook(e.notebook)) { return; } const promises = pendingNotebookCellModelUpdates.get(e.notebook); if (!promises) { return; } e.waitUntil(Promise.all(promises)); } function cleanup(notebook: NotebookDocument, promise: PromiseLike<void>) { const pendingUpdates = pendingNotebookCellModelUpdates.get(notebook); if (pendingUpdates) { pendingUpdates.delete(promise); if (!pendingUpdates.size) { pendingNotebookCellModelUpdates.delete(notebook); } } } function trackAndUpdateCellMetadata(notebook: NotebookDocument, cell: NotebookCell, metadata: CellMetadata & { vscode?: { languageId: string } }) { const pendingUpdates = pendingNotebookCellModelUpdates.get(notebook) ?? new Set<Thenable<void>>(); pendingNotebookCellModelUpdates.set(notebook, pendingUpdates); const edit = new WorkspaceEdit(); edit.set(cell.notebook.uri, [NotebookEdit.updateCellMetadata(cell.index, { ...(cell.metadata), custom: metadata })]); const promise = workspace.applyEdit(edit).then(noop, noop); pendingUpdates.add(promise); const clean = () => cleanup(notebook, promise); promise.then(clean, clean); } function onDidChangeNotebookCells(e: NotebookDocumentChangeEvent) { if (!isSupportedNotebook(e.notebook)) { return; } const notebook = e.notebook; const notebookMetadata = getNotebookMetadata(e.notebook); // use the preferred language from document metadata or the first cell language as the notebook preferred cell language const preferredCellLanguage = notebookMetadata.metadata?.language_info?.name; // When we change the language of a cell, // Ensure the metadata in the notebook cell has been updated as well, // Else model will be out of sync with ipynb https://github.com/microsoft/vscode/issues/207968#issuecomment-2002858596 e.cellChanges.forEach(e => { if (!preferredCellLanguage || e.cell.kind !== NotebookCellKind.Code) { return; } const languageIdInMetadata = getVSCodeCellLanguageId(getCellMetadata(e.cell)); if (e.cell.document.languageId !== preferredCellLanguage && e.cell.document.languageId !== languageIdInMetadata) { const metadata: CellMetadata = JSON.parse(JSON.stringify(getCellMetadata(e.cell))); metadata.metadata = metadata.metadata || {}; setVSCodeCellLanguageId(metadata, e.cell.document.languageId); trackAndUpdateCellMetadata(notebook, e.cell, metadata); } else if (e.cell.document.languageId === preferredCellLanguage && languageIdInMetadata) { const metadata: CellMetadata = JSON.parse(JSON.stringify(getCellMetadata(e.cell))); metadata.metadata = metadata.metadata || {}; removeVSCodeCellLanguageId(metadata); trackAndUpdateCellMetadata(notebook, e.cell, metadata); } else if (e.cell.document.languageId === preferredCellLanguage && e.cell.document.languageId === languageIdInMetadata) { const metadata: CellMetadata = JSON.parse(JSON.stringify(getCellMetadata(e.cell))); metadata.metadata = metadata.metadata || {}; removeVSCodeCellLanguageId(metadata); trackAndUpdateCellMetadata(notebook, e.cell, metadata); } }); // Ensure all new cells in notebooks with nbformat >= 4.5 have an id. // Details of the spec can be found here https://jupyter.org/enhancement-proposals/62-cell-id/cell-id.html# e.contentChanges.forEach(change => { change.addedCells.forEach(cell => { // When ever a cell is added, always update the metadata // as metadata is always an empty `{}` in ipynb JSON file const cellMetadata = getCellMetadata(cell); // Avoid updating the metadata if it's not required. if (cellMetadata.metadata) { if (!isCellIdRequired(notebookMetadata)) { return; } if (isCellIdRequired(notebookMetadata) && cellMetadata?.id) { return; } } // Don't edit the metadata directly, always get a clone (prevents accidental singletons and directly editing the objects). const metadata: CellMetadata = { ...JSON.parse(JSON.stringify(cellMetadata || {})) }; metadata.metadata = metadata.metadata || {}; if (isCellIdRequired(notebookMetadata) && !cellMetadata?.id) { metadata.id = generateCellId(e.notebook); } trackAndUpdateCellMetadata(notebook, cell, metadata); }); }); } /** * Cell ids are required in notebooks only in notebooks with nbformat >= 4.5 */ function isCellIdRequired(metadata: Pick<Partial<nbformat.INotebookContent>, 'nbformat' | 'nbformat_minor'>) { if ((metadata.nbformat || 0) >= 5) { return true; } if ((metadata.nbformat || 0) === 4 && (metadata.nbformat_minor || 0) >= 5) { return true; } return false; } function generateCellId(notebook: NotebookDocument) { while (true) { // Details of the id can be found here https://jupyter.org/enhancement-proposals/62-cell-id/cell-id.html#adding-an-id-field, // & here https://jupyter.org/enhancement-proposals/62-cell-id/cell-id.html#updating-older-formats const id = generateUuid().replace(/-/g, '').substring(0, 8); let duplicate = false; for (let index = 0; index < notebook.cellCount; index++) { const cell = notebook.cellAt(index); const existingId = getCellMetadata(cell)?.id; if (!existingId) { continue; } if (existingId === id) { duplicate = true; break; } } if (!duplicate) { return id; } } } /** * Copied from src/vs/base/common/uuid.ts */ function generateUuid() { // use `randomValues` if possible function getRandomValues(bucket: Uint8Array): Uint8Array { for (let i = 0; i < bucket.length; i++) { bucket[i] = Math.floor(Math.random() * 256); } return bucket; } // prep-work const _data = new Uint8Array(16); const _hex: string[] = []; for (let i = 0; i < 256; i++) { _hex.push(i.toString(16).padStart(2, '0')); } // get data getRandomValues(_data); // set version bits _data[6] = (_data[6] & 0x0f) | 0x40; _data[8] = (_data[8] & 0x3f) | 0x80; // print as string let i = 0; let result = ''; result += _hex[_data[i++]]; result += _hex[_data[i++]]; result += _hex[_data[i++]]; result += _hex[_data[i++]]; result += '-'; result += _hex[_data[i++]]; result += _hex[_data[i++]]; result += '-'; result += _hex[_data[i++]]; result += _hex[_data[i++]]; result += '-'; result += _hex[_data[i++]]; result += _hex[_data[i++]]; result += '-'; result += _hex[_data[i++]]; result += _hex[_data[i++]]; result += _hex[_data[i++]]; result += _hex[_data[i++]]; result += _hex[_data[i++]]; result += _hex[_data[i++]]; return result; } </ins>

Related discussion:
text: Create an ipynb file (with one Python cell) Save this Verify the entry exists in time line Change the language of the cell to Save this Verify we have an entry Click that item Bug On the left we need On the right there's no such entry in metadata This is incorrect. The ipynb has the above metadata. What seems to be happening is When the language changes, We serialize the ipynb and JSon contains the metadata However the model is not updated with corresponding changes to the ipynb file I.e. model change triggered =ipynb serialize to JSON =Json contains new metadtaa not in model =Missing step is to update the model again If we implement the last step, we could always end up in an infinite loop, Perhaps we should first update the model with metadata when ever we detect chagnes in the model before the save event. E.g. as part of pre-Save (onDidChangeNotebookDocument &/or onWillSaveNotebookDocument) This way, model will always be accurate and upto date when ipynb is serialized.
Easier way to explain the bug Create an ipynb file (with one Python cell) Save this Change the language of the cell to Save this The cell metadata will not contain the new metadata that exists in the ipynb JSON file. (model is not in sync with ipynb json)
Suggested Solution Perform model updates when we're about to save (or when we detect changes to model) When saving, ensure we save the metadata as is, without generating any new content I.e. JSON.stringify the metadata.
/cc
Considering that a serialize operation should not have side effects (ideally), enforcing a "save participant" from ipynb extension makes very good sense to me. We can leverage which support additional async operations, like how we handle attachment clearnup
For such critical metadata change, we might want to handle both auto save and manual save as we want the json and model to be always in sync.
Another simple repro step Create a notebook, and save this Add a new cell The latest entry in timeline will be However there's a difference, one has and the other (current model state) does not have any Again, model does not contain metadta (as this is a new cell) and ipynb JSON contains metadata when serialized.