Merge branch 'alpha' into health-checks-pilot

# Conflicts:
#	apps/smart-forms-app/.env

Author: Sean Fong

.github/workflows/build_test_lint.yml

@@ -60,7 +60,11 @@ jobs:
         run: npm ci
 
       - name: Build workspace packages
-        run: npm run build -w packages/sdc-template-extract
+        run: |
+          npm run build -w packages/sdc-assemble
+          npm run build -w packages/sdc-populate
+          npm run build -w packages/sdc-template-extract
+          npm run build -w packages/smart-forms-renderer
 
       - name: Run jest tests
         run: npm run test -w apps/smart-forms-app
@@ -73,17 +77,33 @@ jobs:
     if: github.actor != 'dependabot[bot]'
     steps:
       - uses: actions/checkout@v4
+
       - name: Use Node.js 20.x
         uses: actions/setup-node@v4
         with:
           node-version: 20
           cache: npm
+
       - name: Install dependencies
         run: npm ci
+
+      #  sdc-populate is a dependency of the renderer so we need to build it
+      - name: Build workspace packages
+        run: |
+          npm run build -w packages/sdc-populate
+
       - name: Run jest tests
         run: npm run test -w packages/smart-forms-renderer
       - uses: codecov/codecov-action@v4
 
+      - name: Upload smart-forms-renderer coverage report to GitHub
+        uses: actions/upload-artifact@v4
+        if: ${{ !cancelled() }}
+        with:
+          name: smart-forms-renderer-coverage-report
+          path: packages/smart-forms-renderer/coverage
+          retention-days: 30
+
   jest-populate-tests:
     name: Jest Tests - Populate
     runs-on: ubuntu-latest
@@ -113,6 +133,35 @@ jobs:
           path: packages/sdc-populate/coverage
           retention-days: 30
 
+  jest-assemble-tests:
+    name: Jest Tests - Assemble
+    runs-on: ubuntu-latest
+    # Conditional logic to skip if workflow is triggered by Dependabot
+    if: github.actor != 'dependabot[bot]'
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Use Node.js 20.x
+        uses: actions/setup-node@v4
+        with:
+          node-version: 20
+          cache: npm
+
+      - name: Install dependencies
+        run: npm ci
+
+      - name: Run jest tests
+        run: npm run test -w packages/sdc-assemble
+      - uses: codecov/codecov-action@v4
+
+      - name: Upload sdc-assemble coverage report to GitHub
+        uses: actions/upload-artifact@v4
+        if: ${{ !cancelled() }}
+        with:
+          name: sdc-assemble-coverage-report
+          path: packages/sdc-assemble/coverage
+          retention-days: 30
+
   jest-extract-tests:
     name: Jest Tests - Template-Based Extract
     runs-on: ubuntu-latest

.github/workflows/publish_container.yaml

@@ -52,8 +52,9 @@ jobs:
       - name: Build and push Docker image
         uses: docker/build-push-action@v5
         with:
-          context: apps/smart-forms-app
-          file: ./Dockerfile
+          context: ./apps/smart-forms-app
+          file: ./apps/smart-forms-app/Dockerfile
           push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
+          platforms: linux/amd64,linux/arm64

.gitignore

@@ -1,5 +1,9 @@
 node_modules
 coverage
 changelog_guide.md
+
 #Mac OS .DS_STORE
 .DS_STORE
+
+# GitHub copilot instructions
+.github/copilot-instructions.md

.prettierignore

@@ -4,7 +4,6 @@ coverage
 build
 storybook-static
 *.md
-*.stories.*
 *.cjs
 *.js
 *.config.*

CHANGELOG.alpha.md

@@ -7,6 +7,69 @@ This changelog only includes changes from version 1.0.0-alpha.1 onwards. For sta
 
 WARNING: Alpha releases are not stable and may contain breaking changes. Changes are also most likely to be undocumented.
 
+## [1.0.0-alpha.97] - 2025-09-04
+#### Changed
+- Changed item-level repopulate button custom extension to the below. See https://chat.fhir.org/#narrow/channel/179255-questionnaire/topic/Granular.20Repopulate.20button/with/533937578 for more details.
+```json
+{
+  "url": "https://smartforms.csiro.au/ig/StructureDefinition/questionnaire-initialExpression-repopulatable",
+  "valueCode": "manual"
+}
+```
+
+## [1.0.0-alpha.96] - 2025-09-04
+#### Added
+- Added support for an item-level repopulate button via a custom extension 'https://smartforms.csiro.au/ig/StructureDefinition/questionnaire-initialExpression-showRepopulateButton'. This button can only be used on string, text, integer and decimal fields, and cannot be used in repeating items or groups.
+
+## sdc-template-extract [1.0.8] - 2025-08-29
+#### Added
+- Fix $extract filtering logic when comparing extracted resource with comparison resource (for modified-only usage). Fixed https://github.com/aehrc/smart-forms/issues/1507.
+
+## [1.0.0-alpha.95] - 2025-08-20
+#### Fixed
+- Various TypeScript-related bug fixes.
+- In the autocomplete component, when the input is less than 2 characters, an info icon will be displayed at the right end.
+
+## [1.0.0-alpha.94] - 2025-08-20
+#### Fixed
+- Add enableColorScheme at ScopedCssBaseline for native light/dark alignment with parent app i.e. native scrollbars, native focus rings, etc.
+  Note that this doesn't provide you with dark mode. for that, you need to wrap `<BaseRenderer>` with your own light/dark-mode enabled `<ThemeProvider>`. See https://mui.com/material-ui/customization/theming/ for more details.
+
+## [1.0.0-alpha.93] - 2025-08-19
+#### Changed
+- Remove MUI GlobalStyles (which overrides the parent app) with ScopedCssBaseline in RendererThemeProvider. This sets a baseline for the renderer's MUI styles without affecting the parent app's styles.
+
+## [1.0.0-alpha.92] - 2025-08-15
+#### Changed
+- Changed "questionnaire-item-text-hidden" custom extension to use the "https://smartforms.csiro.au/ig/StructureDefinition/<extension_name>" convention. Affected extensions:
+
+| Old Extension URL                                                                 | New Extension URL                                                                                                                                                 |
+|-----------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| https://smartforms.csiro.au/docs/custom-extension/questionnaire-item-text-hidden             | https://smartforms.csiro.au/ig/StructureDefinition/QuestionnaireItemTextHidden (or https://smartforms.csiro.au/docs/custom-extension/QuestionnaireItemTextHidden) |
+
+- Added backwards compatibility for custom extensions defined in Smart Forms.
+  Both URLs "https://smartforms.csiro.au/ig/StructureDefinition/<extension_name>" and "https://smartforms.csiro.au/docs/custom-extension/<extension_name>" will work for the custom extensions listed below.
+
+| Extension URLs                                                              |
+|-----------------------------------------------------------------------------|
+| https://smartforms.csiro.au/docs/custom-extension/minValue-feedback         |
+| https://smartforms.csiro.au/docs/custom-extension/maxValue-feedback         |
+| https://smartforms.csiro.au/docs/custom-extension/required-feedback         |
+| https://smartforms.csiro.au/docs/custom-extension/minQuantityValue-feedback |
+| https://smartforms.csiro.au/docs/custom-extension/maxQuantityValue-feedback |
+| https://smartforms.csiro.au/docs/custom-extension/QuestionnaireItemTextHidden |
+| https://smartforms.csiro.au/docs/custom-extension/GroupHideAddItemButton |
+
+## sdc-assemble [2.0.2] - 2025-08-15
+#### Fixed
+- Handle axios-based FetchResourceCallback calls correctly, for both happy and sad paths (res.data).
+- Fix TypeScript issues in type predicates.
+- When resolving subquestionnaire canonical URLs, enforce in the root questionnaire (returns OperationOutcome if not present), otherwise if it's a recursive resolution within subquestionnaires (for sub-subquestionnaires), be more lenient by returning an empty array.
+
+## [1.0.0-alpha.91] - 2025-08-11
+#### Changed
+- Remove Iconify dependency and replaced them with MUI icons. This affects the next/previous tab and page buttons.
+
 ## sdc-template-extract [1.0.7] - 2025-08-11
 #### Added
 - Allow handling of non-Error exceptions when evaluating FHIRPath expressions. Reason: fhirpath.js might not type exceptions as Error objects correctly.
@@ -75,7 +138,7 @@ _(WARNING: Possible breaking changes with QuestionnaireStore.itemTypes)_
 - Due to space constraints for textfield-based items in gtables/grids, expression update animations for textfield-based items are now changed to a faint green glow. Animations are unchanged for radio and checkbox items.
 
 ## [1.0.0-alpha.80] - 2025-07-15
-_(WARNING: Possible breaking changes with Questionnaires definitions)_
+_(WARNING: Possible breaking changes with Questionnaire definitions)_
 #### Changed
 - Changed all instances of custom extensions to use the "https://smartforms.csiro.au/docs/custom-extension/*" convention. Affected extensions:
 

LICENSE

@@ -1489,18 +1489,6 @@ separate files distributed with the Software.
 │  ├─ publisher: Nicholas C. Zakas
 │  ├─ path: node_modules/@humanwhocodes/object-schema
 │  └─ licenseFile: node_modules/@humanwhocodes/object-schema/LICENSE
-├─ @iconify/react@4.1.0
-│  ├─ licenses: MIT
-│  ├─ repository: https://github.com/iconify/iconify
-│  ├─ publisher: Vjacheslav Trushkin
-│  ├─ path: node_modules/@iconify/react
-│  └─ licenseFile: node_modules/@iconify/react/license.txt
-├─ @iconify/types@2.0.0
-│  ├─ licenses: MIT
-│  ├─ repository: https://github.com/iconify/iconify
-│  ├─ publisher: Vjacheslav Trushkin
-│  ├─ path: node_modules/@iconify/types
-│  └─ licenseFile: node_modules/@iconify/types/license.txt
 ├─ @istanbuljs/load-nyc-config@1.1.0
 │  ├─ licenses: ISC
 │  ├─ repository: https://github.com/istanbuljs/load-nyc-config
@@ -13645,4 +13633,4 @@ separate files distributed with the Software.
    ├─ path: node_modules/yui-lint
    └─ licenseFile: node_modules/yui-lint/LICENSE
 
-Generated by license-checker v25.0.1 https://www.npmjs.com/package/license-checker
+Generated by license-checker v25.0.1 https://www.npmjs.com/package/license-checker

LOCAL_DEVELOPMENT.md

@@ -50,7 +50,7 @@ However, it has its own set of complexities to watch out for, such as dependenci
 
 2. Duplicate .env and rename it to .env.local. This file will be used to store your local environment variables.
 
-3. Change VITE_PRESERVE_SYM_LINKS=true to VITE_PRESERVE_SYM_LINKS=false in .env.local. This will allow `tsc -w` to watch for changes properly in the smart-forms-renderer component.
+3. Change VITE_PRESERVE_SYM_LINKS=true to VITE_PRESERVE_SYM_LINKS=false in .env.local or add it if it does not exist. This will allow `tsc -w` to watch for changes properly in the smart-forms-renderer component.
 
 
 ## Running the Smart Forms and Storybook Locally on Docker with Live Code Reload
@@ -66,11 +66,9 @@ docker-compose --env-file ./apps/smart-forms-app/.env.local build
 ```sh
 docker-compose --env-file ./apps/smart-forms-app/.env.local up  
 ```
-4. Press CTRL+C to stop the container. 
+4. Go to [http://localhost:5173/](http://localhost:5173/) for Smart Forms App 
 
-5. Go to [http://localhost:5173/](http://localhost:5173/) for Smart Forms App 
-
-6. Go to [http://localhost:6006/](http://localhost:6006/) for Story Book App
+5. Go to [http://localhost:6006/](http://localhost:6006/) for Story Book App
 
 NOTE: In the Docker setup, the current source code folder is shared as a volume to the Docker container. This allows the live code reload to work.
 
@@ -80,9 +78,18 @@ TODO: We have experienced some issues with "Type Error: styled_default is not de
 
 
 ## Running the Smart Forms app locally
-1. Ensure you are in the directory containing the Smart Forms app.
+1. In order to prepare all packages for use, you need to run the build script in each package located in the /packages directory.
+
+  cd packages/<package-name>
+  npm run build
+
+Repeat this for each package in /packages 
+
+2. Ensure you are in the directory containing the Smart Forms app.
+
+  cd apps/smart-forms-app
 
-2. Start the app on localhost. It defaults to port 5173.
+3. Start the app on localhost. It defaults to port 5173.
     ```sh
     npm start
     ```

apps/smart-forms-app/Dockerfile

@@ -1,14 +1,21 @@
 # Dockerfile
 
 # Step 1: Use a Node.js image to build the app
-FROM node:18 AS builder
+FROM --platform=$BUILDPLATFORM node:18 AS builder
 
 # Set working directory inside the container
 WORKDIR /app
 
 # Copy package.json and package-lock.json
 COPY package*.json ./
 
+# Install build tools for native dependencies
+RUN apt-get update && apt-get install -y python3 build-essential && rm -rf /var/lib/apt/lists/*
+
+# Set npm config for python and permissions (use ENV for cross-platform compatibility)
+ENV npm_config_python=python3 \
+    npm_config_unsafe_perm=true
+
 # Install dependencies
 RUN npm install
 
@@ -20,7 +27,7 @@ RUN npm run build
 
 
 # Step 2: Use an Nginx image to serve the static files
-FROM nginx:alpine
+FROM --platform=$BUILDPLATFORM nginx:alpine
 
 # Copy the build files from the builder stage to the Nginx web directory
 COPY --from=builder /app/dist /usr/share/nginx/html

apps/smart-forms-app/__mocks__/emptyModule.js

@@ -0,0 +1,2 @@
+// Mock for CSS/font imports
+module.exports = {};

apps/smart-forms-app/jest.config.ts

@@ -19,14 +19,53 @@ import type { Config } from 'jest';
 
 const config: Config = {
   verbose: true,
-  roots: ['<rootDir>'],
+  roots: ['src'],
+  preset: 'ts-jest',
+  testEnvironment: 'jsdom',
+  setupFilesAfterEnv: ['./src/setup-jest.ts'],
   transform: {
-    '^.+\\.ts?$': 'ts-jest'
+    '^.+\\.(ts|tsx)$': ['ts-jest', {
+      useESM: true,
+      isolatedModules: true,
+    }]
+  },
+  transformIgnorePatterns: [
+    '/node_modules/(?!(@aehrc|@fontsource)/)'
+  ],
+  moduleNameMapper: {
+    '^@fontsource/(.*)$': '<rootDir>/__mocks__/emptyModule.js'
   },
   // Exclude "spec" folder
-  testRegex: '(/__tests__/.*|(\\.|/)(test))\\.ts?$',
-  moduleFileExtensions: ['ts', 'js', 'json', 'node'],
+  testRegex: '(/__tests__/.*|(\\.|/)(test))\\.(ts|tsx)?$',
+  moduleFileExtensions: ['ts', 'tsx', 'js', 'json', 'node'],
   collectCoverage: true,
+  collectCoverageFrom: [
+    '**/api/*.{ts,tsx}',
+    '**/hooks/*.{ts,tsx}',
+    '**/utils/*.{ts,tsx}',
+    '**/contexts/*.{ts,tsx}',
+    '!**/*.config.{ts,tsx,js,jsx}',  // exclude config files
+    '!**/*.test.{ts,tsx}',           // exclude test files
+    '!**/*.spec.{ts,tsx}',           // exclude spec files
+    '!**/*.styles.{ts,tsx}',         // exclude style files
+    '!**/*.interface.{ts,tsx}',      // exclude interface files
+    '!**/*.d.ts',                    // exclude declaration files
+    '!**/e2e/**',                    // exclude e2e files
+    '!src/test/data-shared/**',      // explicitly exclude src/test/data-shared
+    '!src/features/standalone/**',    // explicitly exclude src/features/standalone
+    '!src/theme/**',                 // explicitly exclude src/theme
+    '!src/globals.ts',               // explicitly exclude src/globals.ts
+    '!src/utils/dayjsExtend.ts',     // explicitly exclude src/utils/dayjsExtend.ts
+    '!src/stores/selector.ts',       // explicitly exclude src/stores/selector.ts
+  ],
+  coverageThreshold: {
+    "global": {
+      "statements": 80,
+      "branches": 75,
+      "functions": 80,
+      "lines": 80
+    }
+  },
   clearMocks: true,
   coverageDirectory: 'coverage'
 };