Merge pull request #166 from brainlife/hotfix/resolve-pet-path-issues

fix: added smoke test, fixed PET paths, improved UI

Author: nicoalee

.github/workflows/desktop-smoke-test.yml

@@ -0,0 +1,60 @@
+name: Desktop pack smoke test
+
+on:
+    push:
+        tags:
+            - 'v*'
+    workflow_dispatch:
+
+permissions:
+    contents: read
+
+jobs:
+    smoke-test:
+        name: Pack and verify binaries (${{ matrix.platform }}-${{ matrix.arch }})
+        runs-on: ${{ matrix.os }}
+        strategy:
+            fail-fast: false
+            matrix:
+                include:
+                    - os: macos-latest
+                      platform: darwin
+                      arch: arm64
+                    - os: ubuntu-latest
+                      platform: linux
+                      arch: amd64
+                    - os: windows-latest
+                      platform: windows
+                      arch: amd64
+
+        defaults:
+            run:
+                shell: bash
+
+        env:
+            npm_config_script_shell: bash
+            EZBIDS_PLATFORM: ${{ matrix.platform }}
+            EZBIDS_ARCH: ${{ matrix.arch }}
+
+        steps:
+            - name: Checkout
+              uses: actions/checkout@v4
+              with:
+                  submodules: recursive
+
+            - name: Setup Node.js
+              uses: actions/setup-node@v4
+              with:
+                  node-version: '20'
+                  cache: npm
+
+            - name: Install dependencies
+              run: npm ci
+
+            - name: Fetch binaries
+              run: ./fetch-binaries.sh ${{ matrix.platform }} ${{ matrix.arch }}
+              env:
+                  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+            - name: Pack test app and smoke test binaries
+              run: npm run electron:pack-test && npm run electron:smoke-test

README.md

@@ -115,7 +115,7 @@ Electron build and packaging logic is split between root workspace scripts (`pac
 -   **`npm run fetch-binaries:macos`** -> `./fetch-binaries.sh darwin arm64`
 -   **`npm run fetch-binaries:linux`** -> `./fetch-binaries.sh linux amd64`
 -   **`npm run fetch-binaries:windows`** -> `./fetch-binaries.sh windows amd64`
--   **`npm run electron:pack-test`** -> fetch binaries, run Electron build, then `electron-builder --dir` (unsigned/unpacked app output for testing packaging contents)
+-   **`npm run electron:pack-test`** -> run Electron build, then `electron-builder --dir` (unsigned/unpacked app output for testing packaging contents; run a `fetch-binaries:*` script first if `handler/bin` is missing)
 -   **`npm run electron:pack`** -> full build + `electron-builder` distributables (DMG/EXE/AppImage/DEB depending on platform/target)
 
 Note: packaging/signing keys (for example Apple certificate/API key variables) are only needed for signed release workflows, not for local desktop development.

electron/build/afterSign.js

@@ -15,7 +15,7 @@
         "build:electron-main": "esbuild main.ts --bundle --platform=node --format=cjs --target=es2020 --outfile=dist/main.cjs --external:electron --external:electron-store --external:ts-node-dev",
         "build:electron-preload": "mkdir -p dist && esbuild preload/preload.ts --bundle --platform=node --format=cjs --target=es6 --outfile=preload/preload.js --external:electron --external:electron-store --external:ts-node-dev && cp preload/preload.js dist/preload.js",
         "build:electron": "rm -rf dist && npm run build:electron-api && npm run build:electron-handler && npm run build:electron-handler-scripts && npm run build:electron-python && npm run build:electron-templates && npm run build:electron-bids-spec && npm run build:electron-frontend && npm run build:electron-main && npm run build:electron-preload",
-        "app:dir": "CSC_IDENTITY_AUTO_DISCOVERY=false env -u APPLE_API_KEY -u APPLE_API_KEY_ID -u APPLE_API_ISSUER electron-builder --dir",
+        "app:dir": "CSC_IDENTITY_AUTO_DISCOVERY=false env -u APPLE_API_KEY -u APPLE_API_KEY_ID -u APPLE_API_ISSUER electron-builder --dir -c.mac.identity=null",
         "app:dist": "electron-builder",
         "app:build-dist": "npm run build:electron && npm run app:dist"
     },

electron/package.json

@@ -83,7 +83,7 @@ async function runDcm2niix(itemPath: string): Promise<{ status: number; stderr:
 /** Run dcm2niix4pet for one path; appends to pet2bids.done on success. Uses shipped Python interpreter. */
 async function runDcm2niix4Pet(itemPath: string): Promise<{ status: number; stderr: string }> {
     log(`----------------------- dcm2niix4pet: ${itemPath} ------------------------`);
-    const r = await runPython(['-m', 'dcm2niix4pet', '--silent', itemPath], {
+    const r = await runPython(['-m', 'pypet2bids.dcm2niix4pet', '--silent', itemPath], {
         cwd: resolvedRoot,
         timeout: CMD_TIMEOUT_MS,
         reject: true,
@@ -97,7 +97,7 @@ async function runDcm2niix4Pet(itemPath: string): Promise<{ status: number; stde
 /** Run ecatpet2bids for one path; appends to pet2bids.done on success. Uses shipped Python interpreter. */
 async function runEcatPet2Bids(itemPath: string): Promise<{ status: number; stderr: string }> {
     log(`----------------------- ecatpet2bids: ${itemPath} ------------------------`);
-    const r = await runPython(['-m', 'ecatpet2bids', itemPath, '--convert'], {
+    const r = await runPython(['-m', 'pypet2bids.ecat_cli', itemPath, '--convert'], {
         cwd: resolvedRoot,
         timeout: CMD_TIMEOUT_MS,
     });

handler/preprocess.ts

@@ -23,7 +23,8 @@
         "ui:dev": "npm run dev -w ui",
         "ui:build": "npm run build -w ui",
         "electron:start-dev": "npm run start-dev -w ezbids-electron",
-        "electron:pack-test": "npm run fetch-binaries && npm run build:electron -w ezbids-electron && npm run app:dir -w ezbids-electron",
+        "electron:pack-test": "npm run build:electron -w ezbids-electron && npm run app:dir -w ezbids-electron",
+        "electron:smoke-test": "./test/smoke-test-packaged-binaries.sh",
         "electron:pack": "npm run app:build-dist -w ezbids-electron",
         "fetch-binaries:macos": "./fetch-binaries.sh darwin arm64",
         "fetch-binaries:linux": "./fetch-binaries.sh linux amd64",