feat: Create snapshots when running notebooks

README.md

@@ -16,7 +16,6 @@ A powerful [Visual Studio Code](https://marketplace.visualstudio.com/items?itemN
 
 ![Deepnote Projects](./assets/deepnote-projects.png)
 
-
 Run Deepnote locally inside your IDE and unlock the next generation of data workflows:
 
 - **Rich block types:** Combine Python, Markdown, data visualizations, tables, and more — all in one place
@@ -66,6 +65,7 @@ Open the Command Palette (`Cmd+Shift+P` or `Ctrl+Shift+P`) and type `Deepnote` t
 | `Deepnote: Import Notebook`        | Import an existing notebook into your project      |
 | `Notebook: Select Notebook Kernel` | Select or switch kernels within your notebook      |
 | `Notebook: Change Cell Language`   | Change the language of the cell currently in focus |
+| `Deepnote: Enable Snapshots`       | Enable snapshot mode for the current workspace     |
 
 ### Database integrations
 
@@ -89,6 +89,24 @@ SELECT * FROM users WHERE created_at > '2024-01-01'
 
 Results are displayed as interactive tables that you can explore and export.
 
+### Snapshot mode
+
+Snapshot mode gives you a historical, portable record of all notebook executions without polluting your main project files. This makes it easier to work with Git since outputs are stored separately from your source code.
+
+**How it works:**
+
+- Execution outputs are saved to a `snapshots/` folder alongside your project
+- Your main `.deepnote` file stays clean (no outputs), making diffs readable
+- Each "Run All" execution creates a timestamped snapshot for historical tracking
+- Running individual cells updates only the latest snapshot
+
+**To enable:**
+
+1. Open Command Palette (`Cmd+Shift+P` or `Ctrl+Shift+P`)
+2. Run `Deepnote: Enable Snapshots`
+
+Once enabled, snapshots are automatically created when you execute notebooks. You can add the `snapshots/` folder to `.gitignore` to keep outputs local, or commit them to share execution history with your team.
+
 ## Need help?
 
 - Join our [Community](https://github.com/deepnote/deepnote/discussions)!

cspell.json

@@ -78,9 +78,14 @@
         "scikit",
         "scipy",
         "sklearn",
+        "slugification",
+        "slugified",
+        "slugifies",
+        "slugify",
         "sqlalchemy",
         "taskkill",
         "testdb",
+        "testproject",
         "toolsai",
         "trino",
         "Trino",

package.json

@@ -93,6 +93,16 @@
                 "category": "Deepnote",
                 "icon": "$(reveal)"
             },
+            {
+                "command": "deepnote.enableSnapshots",
+                "title": "%deepnote.commands.enableSnapshots.title%",
+                "category": "Deepnote"
+            },
+            {
+                "command": "deepnote.disableSnapshots",
+                "title": "%deepnote.commands.disableSnapshots.title%",
+                "category": "Deepnote"
+            },
             {
                 "command": "deepnote.environments.create",
                 "title": "%deepnote.commands.environments.create.title%",
@@ -1640,6 +1650,12 @@
                     "description": "Disable SSL certificate verification (for development only)",
                     "scope": "application"
                 },
+                "deepnote.snapshots.enabled": {
+                    "type": "boolean",
+                    "default": false,
+                    "description": "When enabled, outputs are saved to separate snapshot files in a 'snapshots' folder instead of the main .deepnote file.",
+                    "scope": "resource"
+                },
                 "deepnote.experiments.enabled": {
                     "type": "boolean",
                     "default": true,

package.nls.json

@@ -250,6 +250,8 @@
     "deepnote.commands.openNotebook.title": "Open Notebook",
     "deepnote.commands.openFile.title": "Open File",
     "deepnote.commands.revealInExplorer.title": "Reveal in Explorer",
+    "deepnote.commands.enableSnapshots.title": "Enable Snapshots",
+    "deepnote.commands.disableSnapshots.title": "Disable Snapshots",
     "deepnote.commands.manageIntegrations.title": "Manage Integrations",
     "deepnote.commands.newProject.title": "New Project",
     "deepnote.commands.importNotebook.title": "Import Notebook",

src/kernels/execution/cellExecutionQueue.ts

@@ -14,7 +14,8 @@ import { CodeExecution } from './codeExecution';
 import { once } from '../../platform/common/utils/events';
 import { getCellMetadata } from '../../platform/common/utils';
 import { NotebookCellExecutionState, notebookCellExecutions } from '../../platform/notebooks/cellExecutionStateService';
-import { ISnapshotMetadataService } from '../../platform/notebooks/deepnote/types';
+// eslint-disable-next-line import/no-restricted-paths
+import { ISnapshotMetadataService } from '../../notebooks/deepnote/snapshots/snapshotService';
 
 /**
  * A queue responsible for execution of cells.
@@ -324,5 +325,10 @@ export class CellExecutionQueue implements Disposable {
                 break;
             }
         }
+
+        // Notify listeners that execution queue is complete
+        if (this.notebook) {
+            notebookCellExecutions.notifyQueueComplete(this.notebook.uri.toString());
+        }
     }
 }

src/kernels/kernelExecution.ts

@@ -45,7 +45,7 @@ import {
 import { CodeExecution } from './execution/codeExecution';
 import type { ICodeExecution } from './execution/types';
 import { NotebookCellExecutionState, notebookCellExecutions } from '../platform/notebooks/cellExecutionStateService';
-import { ISnapshotMetadataService } from '../platform/notebooks/deepnote/types';
+import { ISnapshotMetadataService } from '../notebooks/deepnote/snapshots/snapshotService';
 
 /**
  * Everything in this classes gets disposed via the `onWillCancel` hook.

src/kernels/kernelProvider.node.ts

@@ -32,7 +32,8 @@ import { IReplNotebookTrackerService } from '../platform/notebooks/replNotebookT
 import { logger } from '../platform/logging';
 import { getDisplayPath } from '../platform/common/platform/fs-paths.node';
 import { IRawNotebookSupportedService } from './raw/types';
-import { ISnapshotMetadataService } from '../platform/notebooks/deepnote/types';
+// eslint-disable-next-line import/no-restricted-paths
+import { ISnapshotMetadataService } from '../notebooks/deepnote/snapshots/snapshotService';
 
 /**
  * Node version of a kernel provider. Needed in order to create the node version of a kernel.

src/notebooks/deepnote/deepnoteActivationService.ts

@@ -9,7 +9,7 @@ import { DeepnoteNotebookSerializer } from './deepnoteSerializer';
 import { DeepnoteExplorerView } from './deepnoteExplorerView';
 import { IIntegrationManager } from './integrations/types';
 import { DeepnoteInputBlockEditProtection } from './deepnoteInputBlockEditProtection';
-import { ISnapshotMetadataService, ISnapshotMetadataServiceFull } from './snapshotMetadataService';
+import { SnapshotService } from './snapshots/snapshotService';
 
 /**
  * Service responsible for activating and configuring Deepnote notebook support in VS Code.
@@ -30,7 +30,7 @@ export class DeepnoteActivationService implements IExtensionSyncActivationServic
         @inject(IDeepnoteNotebookManager) private readonly notebookManager: IDeepnoteNotebookManager,
         @inject(IIntegrationManager) integrationManager: IIntegrationManager,
         @inject(ILogger) private readonly logger: ILogger,
-        @inject(ISnapshotMetadataService) @optional() private readonly snapshotService?: ISnapshotMetadataServiceFull
+        @inject(SnapshotService) @optional() private readonly snapshotService?: SnapshotService
     ) {
         this.integrationManager = integrationManager;
     }

src/notebooks/deepnote/deepnoteDataConverter.ts

@@ -95,6 +95,8 @@ export class DeepnoteDataConverter {
             cell.metadata = {
                 ...block.metadata,
                 id: block.id,
+                // Store a backup of the ID under a different key in case VS Code modifies 'id'
+                __deepnoteBlockId: block.id,
                 type: block.type,
                 sortingKey: block.sortingKey,
                 ...(blockWithOptionalFields.blockGroup && { blockGroup: blockWithOptionalFields.blockGroup }),

src/notebooks/deepnote/deepnoteNotebookCommandListener.ts

@@ -1,6 +1,7 @@
 import { injectable, inject } from 'inversify';
 import {
     commands,
+    ConfigurationTarget,
     window,
     NotebookCellData,
     NotebookCellKind,
@@ -16,7 +17,7 @@ import z from 'zod';
 
 import { logger } from '../../platform/logging';
 import { IExtensionSyncActivationService } from '../../platform/activation/types';
-import { IDisposableRegistry } from '../../platform/common/types';
+import { IConfigurationService, IDisposableRegistry } from '../../platform/common/types';
 import { Commands } from '../../platform/common/constants';
 import { notebookUpdaterUtils } from '../../kernels/execution/notebookUpdater';
 import { WrappedError } from '../../platform/errors/types';
@@ -149,7 +150,10 @@ export function getNextDeepnoteVariableName(cells: NotebookCell[], prefix: 'df'
  */
 @injectable()
 export class DeepnoteNotebookCommandListener implements IExtensionSyncActivationService {
-    constructor(@inject(IDisposableRegistry) private readonly disposableRegistry: IDisposableRegistry) {}
+    constructor(
+        @inject(IConfigurationService) private readonly configurationService: IConfigurationService,
+        @inject(IDisposableRegistry) private readonly disposableRegistry: IDisposableRegistry
+    ) {}
 
     /**
      * Activates the service by registering Deepnote-specific commands.
@@ -217,6 +221,10 @@ export class DeepnoteNotebookCommandListener implements IExtensionSyncActivation
                 this.addTextBlockCommandHandler({ textBlockType: 'text-cell-p' })
             )
         );
+        this.disposableRegistry.push(commands.registerCommand(Commands.EnableSnapshots, () => this.enableSnapshots()));
+        this.disposableRegistry.push(
+            commands.registerCommand(Commands.DisableSnapshots, () => this.disableSnapshots())
+        );
     }
 
     public async addSqlBlock(): Promise<void> {
@@ -537,4 +545,34 @@ export class DeepnoteNotebookCommandListener implements IExtensionSyncActivation
         // Enter edit mode on the new cell
         await commands.executeCommand('notebook.cell.edit');
     }
+
+    private async disableSnapshots(): Promise<void> {
+        try {
+            await this.configurationService.updateSetting(
+                'snapshots.enabled',
+                false,
+                undefined,
+                ConfigurationTarget.Workspace
+            );
+            void window.showInformationMessage(l10n.t('Snapshots disabled for this workspace.'));
+        } catch (error) {
+            logger.error('Failed to disable snapshots', error);
+            void window.showErrorMessage(l10n.t('Failed to disable snapshots.'));
+        }
+    }
+
+    private async enableSnapshots(): Promise<void> {
+        try {
+            await this.configurationService.updateSetting(
+                'snapshots.enabled',
+                true,
+                undefined,
+                ConfigurationTarget.Workspace
+            );
+            void window.showInformationMessage(l10n.t('Snapshots enabled for this workspace.'));
+        } catch (error) {
+            logger.error('Failed to enable snapshots', error);
+            void window.showErrorMessage(l10n.t('Failed to enable snapshots.'));
+        }
+    }
 }

src/notebooks/deepnote/deepnoteNotebookCommandListener.unit.test.ts

@@ -18,7 +18,7 @@ import {
     InputBlockType
 } from './deepnoteNotebookCommandListener';
 import { formatInputBlockCellContent, getInputBlockLanguage } from './inputBlockContentFormatter';
-import { IDisposable } from '../../platform/common/types';
+import { IConfigurationService, IDisposable } from '../../platform/common/types';
 import * as notebookUpdater from '../../kernels/execution/notebookUpdater';
 import { createMockedNotebookDocument } from '../../test/datascience/editor-integration/helpers';
 import { WrappedError } from '../../platform/errors/types';
@@ -29,11 +29,21 @@ suite('DeepnoteNotebookCommandListener', () => {
     let commandListener: DeepnoteNotebookCommandListener;
     let disposables: IDisposable[];
     let sandbox: sinon.SinonSandbox;
+    let mockConfigService: IConfigurationService;
+
+    function createMockConfigService(): IConfigurationService {
+        return {
+            getSettings: sinon.stub().returns({}),
+            updateSetting: sinon.stub().resolves(),
+            updateSectionSetting: sinon.stub().resolves()
+        } as unknown as IConfigurationService;
+    }
 
     setup(() => {
         sandbox = sinon.createSandbox();
         disposables = [];
-        commandListener = new DeepnoteNotebookCommandListener(disposables);
+        mockConfigService = createMockConfigService();
+        commandListener = new DeepnoteNotebookCommandListener(mockConfigService, disposables);
     });
 
     teardown(() => {
@@ -78,7 +88,7 @@ suite('DeepnoteNotebookCommandListener', () => {
 
             // Create new instance and activate again
             const disposables2: IDisposable[] = [];
-            const commandListener2 = new DeepnoteNotebookCommandListener(disposables2);
+            const commandListener2 = new DeepnoteNotebookCommandListener(createMockConfigService(), disposables2);
             commandListener2.activate();
 
             // Both should register the same number of commands

src/notebooks/deepnote/deepnoteNotebookManager.ts

@@ -11,8 +11,8 @@ import type { DeepnoteProject } from '../../platform/deepnote/deepnoteTypes';
 export class DeepnoteNotebookManager implements IDeepnoteNotebookManager {
     private readonly currentNotebookId = new Map<string, string>();
     private readonly originalProjects = new Map<string, DeepnoteProject>();
-    private readonly selectedNotebookByProject = new Map<string, string>();
     private readonly projectsWithInitNotebookRun = new Set<string>();
+    private readonly selectedNotebookByProject = new Map<string, string>();
 
     /**
      * Gets the currently selected notebook ID for a project.
@@ -61,7 +61,13 @@ export class DeepnoteNotebookManager implements IDeepnoteNotebookManager {
      * @param notebookId Initial notebook ID to set as current
      */
     storeOriginalProject(projectId: string, project: DeepnoteProject, notebookId: string): void {
-        this.originalProjects.set(projectId, project);
+        // Deep clone to prevent mutations from affecting stored state
+        // This is critical for multi-notebook projects where multiple notebooks
+        // share the same stored project reference
+        // Using structuredClone to handle circular references (e.g., in output metadata)
+        const clonedProject = structuredClone(project);
+
+        this.originalProjects.set(projectId, clonedProject);
         this.currentNotebookId.set(projectId, notebookId);
     }
 
@@ -90,7 +96,7 @@ export class DeepnoteNotebookManager implements IDeepnoteNotebookManager {
             return false;
         }
 
-        const updatedProject = JSON.parse(JSON.stringify(project)) as DeepnoteProject;
+        const updatedProject = structuredClone(project);
         updatedProject.project.integrations = integrations;
 
         const currentNotebookId = this.currentNotebookId.get(projectId);