Merge branch 'main' into user-testing-1

NeurodataWithoutBorders · Sep 25, 2023 · 1f85f8e · 1f85f8e
2 parents e79a7b3 + f86da5d
commit 1f85f8e
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diff --git a/.github/workflows/Build-and-deploy-mac.yml b/.github/workflows/Build-and-deploy-mac.yml
@@ -37,25 +37,14 @@ jobs:
 
       - uses: apple-actions/import-codesign-certs@v1
         with:
-          # https://developer.apple.com/account/resources/certificates/add
-          # Sign up for an Apple Developer account (annual fee)
-          # Create a new certificate for Mac development at website above (max 1 certificate)
-          # Create a Certificate Signing Request (CSR) on your Mac --
-          # see https://developer.apple.com/help/account/create-certificates/create-a-certificate-signing-request
-          # Keychain Access > Certificate Assistant > Request a Certificate from a Certificate Authority...
-          # Enter email address, common name
-          # Download the new certificate (.cer file)
-          # Double click the .cer file to install in Keychain Access
-          # Use Keychain Access to export the certificate as a .p12
-          # base64 -i cent.p12 -o base64.txt
-          # Open base64.txt and copy the contents to the nwb-guide repository secret for MACOS_CERTIFICATE
-          # Currently this is set up to use Ryan's account and certificate
+          # Currently this is set to Ryan's Developer ID certificate
           p12-file-base64: ${{ secrets.MACOS_CERTIFICATE }}
           p12-password: ${{ secrets.MACOS_CERTIFICATE_PWD }}
 
       - name: Build and deploy on MAC
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          appleId: ${{ secrets.APPLE_ID }}  # currently this is set to Ryan's Apple ID and password
+          # Currently this is set to Ryan's Apple ID and app-specific password
+          appleId: ${{ secrets.APPLE_ID }}
           appleIdPassword: ${{ secrets.APPLE_PASSWORD }}
         run: npm run deploy:mac
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -9,7 +9,7 @@ concurrency:  # Cancel previous workflows on the same pull request
   cancel-in-progress: true
 
 env:
-  CACHE_NUMBER: 1  # increase to reset cache manually
+  CACHE_NUMBER: 2  # increase to reset cache manually
 
 jobs:
   testing:
@@ -24,20 +24,14 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
         include:
-          - python-version: "3.9"
-            os: ubuntu-latest
+          - os: ubuntu-latest
             label: environments/environment-Linux.yml
-            prefix: /usr/share/miniconda3/envs/env-electron-python
 
-          - python-version: "3.10"
-            os: macos-latest
+          - os: macos-latest
             label: environments/environment-Mac.yml
-            prefix: /Users/runner/miniconda3/envs/env-electron-python
 
-          - python-version: "3.9"
-            os: windows-latest
+          - os: windows-latest
             label: environments/environment-Windows.yml
-            prefix: C:\Miniconda3\envs\env-electron-python
 
 
     steps:
@@ -50,7 +44,7 @@ jobs:
         with:
           miniforge-variant: Mambaforge
           miniforge-version: latest
-          activate-environment: env-electron-python
+          activate-environment: nwb-guide
           use-mamba: true
 
       - name: Set cache date
@@ -62,17 +56,12 @@ jobs:
         uses: actions/cache@v2
         with:
           path: ${{ env.CONDA }}/envs
-          key:
-            conda-${{ runner.os }}-${{ runner.arch }}-${{steps.get-date.outputs.today }}-${{ hashFiles(matrix.label) }}-${{ env.CACHE_NUMBER }}
-        env:
-          # Increase this value to reset cache if environment file has not changed
-          CACHE_NUMBER: 0
+          key: conda-${{ runner.os }}-${{ runner.arch }}-${{steps.get-date.outputs.today }}-${{ hashFiles(matrix.label) }}-${{ env.CACHE_NUMBER }}
         id: cache
 
-      - name: Update environment
-        run:
-          mamba env update -n env-electron-python -f ${{ matrix.label }}
-        if: steps.cache.outputs.cache-hit != 'true'
+      - if: steps.cache.outputs.cache-hit != 'true'
+        name: Create and activate environment
+        run: mamba env update -n nwb-guide -f ${{ matrix.label }}
 
       - name: Use Node.js 18
         uses: actions/setup-node@v3

diff --git a/docs/developer_guide.rst b/docs/developer_guide.rst
@@ -125,3 +125,49 @@ Pre-Commit
 We use an automated pre-commit bot to enforce these on the main repo, but contributions from external forks would either have to grant bot permissions on their own fork (via :pre-commit-bot:`the pre-commit bot website <>`) or run pre-commit manually.
 
 For instructions to install pre-commit, as well as some other minor coding styles we follow, refer to the :neuroconv-coding-style:`NeuroConv style guide <>`.
+
+Code signing on Mac OS
+---------------------------
+
+1. Sign up for an Apple Developer account (99 USD annual fee).
+
+2. Follow steps in https://developer.apple.com/help/account/create-certificates/create-developer-id-certificates/
+    a. Browse current Certificates at https://developer.apple.com/account/resources/certificates/list.
+    b. Click Certificates in the sidebar. On the top left, click the add button (+).
+    c. Under Software, select Developer ID Application.
+    d. Select Profile Type: G2 Sub-CA (Xcode 11.4.1 or later).
+    e. Create a certificate signing request (CSR) by following the steps in https://developer.apple.com/help/account/create-certificates/create-a-certificate-signing-request
+        i. Open Keychain Access.
+        ii. Choose Keychain Access > Certificate Assistant > Request a Certificate from a Certificate Authority.
+        iii. In the Certificate Assistant dialog, enter an email address in the User Email Address field.
+        iv. In the Common Name field, enter a name for the key (for example, John Doe Dev Key). Ryan entered "Ryan Ly".
+        v. Leave the CA Email Address field empty.
+        vi. Choose “Saved to disk”, and click Continue.
+        vii. Save the certificate request file to disk.
+    f. Select the certificate request file (a file with a .certSigningRequest file extension), then click Choose.
+    g. Click Continue, click Download - The certificate file (.cer file) appears in your Downloads folder.
+    h. To install the certificate in your keychain, double-click the downloaded certificate file.
+    i. The certificate appears in the My Certificates category in Keychain Access, but may not be trusted.
+    j. For local development, download the appropriate Apple Intermediate Certificate.
+    k. from https://www.apple.com/certificateauthority/ to make certificate trusted/valid.
+    l. For this, it is Developer ID - G2 (Expiring 09/17/2031 00:00:00 UTC).
+    m. Double-click the downloaded file.
+    n. Confirm that the certificate now shows up as trusted in Keychain Access.
+
+3. Provide a p12 file for notarizing via GitHub Action.
+    a. Open Keychain Access.
+    b. Select the Developer ID Application certificate.
+    c. Choose Keychain Access > Export Items...
+    d. Export the certificate to a file with a password.
+    e. Get a base64 version of the certificate by running: base64 -i Certificate.p12 -o base64.txt
+    f. Open base64.txt and copy the contents to the nwb-guide repository secret MACOS_CERTIFICATE.
+    g. Set the password for the certificate in the nwb-guide repository secret MACOS_CERTIFICATE_PASSWORD.
+
+4. Create an app-specific password for building locally and via the GitHub Action.
+    a. Go to https://appleid.apple.com/account/manage.
+    b. Follow the steps to create an App-Specific Password.
+    c. Use that for local building and in the secrets.APPLE_PASSWORD repository secret.
+
+5. Review and agree to any pending agreements.
+    a. Go to https://appstoreconnect.apple.com/agreements/#/ and agree to pending agreements for Free Apps.
+    b. Review and agree to the Apple Developer Program License Agreement, which updates periodically.
diff --git a/package.json b/package.json
@@ -77,8 +77,20 @@
     "mac": {
       "asar": true,
       "target": [
-        "dmg",
-        "zip"
+        {
+          "target": "dmg",
+          "arch": [
+            "x64",
+            "arm64"
+          ]
+        },
+        {
+          "target": "zip",
+          "arch": [
+            "x64",
+            "arm64"
+          ]
+        }
       ],
       "icon": "src/renderer/assets/img/logo-guide-draft.png",
       "darkModeSupport": false,

diff --git a/prepare_pyinstaller_spec.py b/prepare_pyinstaller_spec.py
@@ -20,9 +20,11 @@
 lines[data_line_index] = "datas = [('./paths.config.json', '.'), ('./package.json', '.')]\n"
 
 # Another platform specific difference is the app.py location
-app_py_line_index = next(index for index, line in enumerate(lines) if "app.py" in line)
-app_py_line = "    [f\"{Path('pyflask') / 'app.py'}\"],\n"
-lines[app_py_line_index] = app_py_line
+app_py_line_index, app_py_line = next((index, line) for index, line in enumerate(lines) if "app.py" in line)
+pyflask_start = app_py_line.find("pyflask")  # Can change on certain systems
+injected_app_py_line_base = app_py_line[: (pyflask_start - 1)]
+injected_app_py_line = injected_app_py_line_base + "f\"{Path('pyflask') / 'app.py'}\"],\n"
+lines[app_py_line_index] = injected_app_py_line
 
 with open(file=Path(__file__).parent / "nwb-guide.spec", mode="w") as io:
     io.writelines(lines)

diff --git a/src/main/main.ts b/src/main/main.ts
@@ -125,7 +125,7 @@ const pythonIsClosed = (err = globals.python.latestError) => {
  * @returns {boolean} True if the app is packaged, false if it is running from a dev version.
  */
 const getPackagedPath = () => {
-  const scriptPath = isWindows ? path.join(__dirname, PY_FLASK_DIST_FOLDER, PYFLASK_BUILD_SUBFOLDER_NAME, `${PYINSTALLER_NAME}.exe`) : path.join(process.resourcesPath, PYFLASK_BUILD_SUBFOLDER_NAME, PYINSTALLER_NAME)
+  const scriptPath = isWindows ? path.join(__dirname, PY_FLASK_DIST_FOLDER, PYINSTALLER_NAME, `${PYINSTALLER_NAME}.exe`) : path.join(process.resourcesPath, PYFLASK_BUILD_SUBFOLDER_NAME, PYINSTALLER_NAME)
   if (fs.existsSync(scriptPath)) return scriptPath;
 };
 
@@ -190,7 +190,7 @@ const exitPyProc = async () => {
     "/t",
   ])  // Windows does not properly shut off the python server process. This ensures it is killed.
 
-  else pyflaskProcess.kill()
+  pyflaskProcess.kill() // Try killing twice on Windows
 
   pyflaskProcess = null;
 };
@@ -223,6 +223,8 @@ let hasBeenOpened = false;
 
 function initialize() {
 
+  if (globals.mainWindow) return // Do not re-initialize if the main window is already declared
+
   makeSingleInstance();
 
   function createWindow() {
@@ -254,42 +256,39 @@ function initialize() {
             })
             .then((responseObject) => {
               let { response } = responseObject;
-              if (response === 0) quit_app()
+              if (response === 0) app.quit();
               else globals.mainWindowReady = true
             });
         }
       } else {
-        await exitPyProc();
-        app.exit();
+        app.quit();
       }
     });
   }
 
-  const quit_app = () => {
-    globals.mainWindow.close();
-    if (!globals.mainWindow.closed) globals.mainWindow.destroy()
-  };
-
   function onAppReady () {
 
-    const promise = createPyProc();
-
-    // Listen after first load
-    promise.then(() => {
-      const chokidar = require('chokidar');
-      chokidar.watch(path.join(__dirname, "../../pyflask"), {
-        ignored:  ['**/__pycache__/**']
-      }).on('all', async (event: string) => {
-        if (event === 'change' && !globals.python.restart) {
-          globals.python.restart = true
-          await exitPyProc();
-          setTimeout(async () => {
-            await createPyProc();
-            globals.python.restart = false
-          }, 1000)
-        }
-      });
-    })
+    // Only create one python process
+    if (!pyflaskProcess) {
+      const promise = createPyProc();
+
+      // Listen after first load
+      promise.then(() => {
+        const chokidar = require('chokidar');
+        chokidar.watch(path.join(__dirname, "../../pyflask"), {
+          ignored:  ['**/__pycache__/**']
+        }).on('all', async (event: string) => {
+          if (event === 'change' && !globals.python.restart) {
+            globals.python.restart = true
+            await exitPyProc();
+            setTimeout(async () => {
+              await createPyProc();
+              globals.python.restart = false
+            }, 1000)
+          }
+        });
+      })
+    }
 
     const windowOptions = {
       minWidth: 1121,
@@ -394,13 +393,22 @@ app.on('activate', () => {
   if (BrowserWindow.getAllWindows().length === 0) initialize()
 })
 
-app.on("window-all-closed", async () => {
-  if (process.platform != 'darwin') {
-    await exitPyProc();
-    app.quit();
+app.on('will-quit', async () => {
+  try {
+    await exitPyProc()
+    if (globals.mainWindow) {
+      globals.mainWindow.close();
+      if (!globals.mainWindow.closed) globals.mainWindow.destroy()
+    }
+  } catch (err) {
+    console.error(err);
   }
 });
 
+app.on("window-all-closed", async () => {
+  if (process.platform != 'darwin') app.quit();
+});
+
 // app.on("will-quit", () => app.quit());
 
 app.on("open-file", onFileOpened)

diff --git a/src/renderer/src/progress/index.js b/src/renderer/src/progress/index.js
@@ -14,6 +14,8 @@ import { merge } from "../stories/pages/utils.js";
 import { updateAppProgress, updateFile } from "./update.js";
 import { updateURLParams } from "../../utils/url.js";
 
+import * as operations from "./operations";
+
 export * from "./update";
 
 class GlobalAppConfig {
@@ -122,24 +124,7 @@ export const remove = async (name) => {
         focusCancel: true,
     });
 
-    if (result.isConfirmed) {
-        //Get the path of the progress file to delete
-        const progressFilePathToDelete = joinPath(guidedProgressFilePath, name + ".json");
-
-        //delete the progress file
-        if (fs) fs.unlinkSync(progressFilePathToDelete);
-        else localStorage.removeItem(progressFilePathToDelete);
-
-        if (fs) {
-            // delete default stub location
-            fs.rmSync(joinPath(stubSaveFolderPath, name), { recursive: true, force: true });
-
-            // delete default conversion location
-            fs.rmSync(joinPath(conversionSaveFolderPath, name), { recursive: true, force: true });
-        }
-
-        return true;
-    }
+    if (result.isConfirmed) return operations.remove(name);
 
     return false;
 };

diff --git a/src/renderer/src/progress/operations.js b/src/renderer/src/progress/operations.js
@@ -0,0 +1,22 @@
+import { joinPath } from "../globals";
+import { conversionSaveFolderPath, guidedProgressFilePath, stubSaveFolderPath } from "../dependencies/simple";
+import { fs } from "../electron";
+
+export const remove = (name) => {
+    //Get the path of the progress file to delete
+    const progressFilePathToDelete = joinPath(guidedProgressFilePath, name + ".json");
+
+    //delete the progress file
+    if (fs) fs.unlinkSync(progressFilePathToDelete);
+    else localStorage.removeItem(progressFilePathToDelete);
+
+    if (fs) {
+        // delete default stub location
+        fs.rmSync(joinPath(stubSaveFolderPath, name), { recursive: true, force: true });
+
+        // delete default conversion location
+        fs.rmSync(joinPath(conversionSaveFolderPath, name), { recursive: true, force: true });
+    }
+
+    return true;
+};
diff --git a/src/renderer/src/progress/update.js b/src/renderer/src/progress/update.js
@@ -2,15 +2,15 @@ import { updateURLParams } from "../../utils/url.js";
 import { guidedProgressFilePath } from "../dependencies/simple.js";
 import { fs } from "../electron/index.js";
 import { joinPath } from "../globals.js";
-import { get } from "./index.js";
+import { get, hasEntry } from "./index.js";
 
-export const update = (newDatasetName, previousDatasetName) => {
-    //If updataing the dataset, update the old banner image path with a new one
+export const rename = (newDatasetName, previousDatasetName) => {
+    //If updating the dataset, update the old banner image path with a new one
     if (previousDatasetName) {
-        if (previousDatasetName === newDatasetName) return "No changes made to dataset name";
+        if (previousDatasetName === newDatasetName) return;
 
         if (hasEntry(newDatasetName))
-            throw new Error("An existing progress file already exists with that name. Please choose a different name.");
+            throw new Error("An existing project already exists with that name. Please choose a different name.");
 
         // update old progress file with new dataset name
         const oldProgressFilePath = `${guidedProgressFilePath}/${previousDatasetName}.json`;
@@ -20,10 +20,9 @@ export const update = (newDatasetName, previousDatasetName) => {
             localStorage.setItem(newProgressFilePath, localStorage.getItem(oldProgressFilePath));
             localStorage.removeItem(oldProgressFilePath);
         }
-
-        return "Dataset name updated";
-    } else throw new Error("No previous dataset name provided");
+    } else throw new Error("No previous project name provided");
 };
+
 export const updateAppProgress = (
     pageId,
     dataOrProjectName = {},