[WIP] rework GroveHealthKitFHIR

.gitattributes

@@ -0,0 +1,11 @@
+#
+# This source file is part of the Grove open-source project
+#
+# SPDX-FileCopyrightText: 2026 Stanford University and the project authors (see CONTRIBUTORS.md)
+#
+# SPDX-License-Identifier: MIT
+#
+
+# The HealthKit content corpus is recorded by its tests (see ContentCorpusStore): review a regeneration through the
+# content-corpus.changes.txt it writes beside the corpus, not through this file's one-line-per-vector diff.
+Tests/GroveHealthKitFHIRTests/Resources/ContentCorpus/content-corpus.jsonl linguist-generated=true

.github/workflows/tests.yml

@@ -18,7 +18,7 @@
       grove_fhir_ref:
         description: grove-fhir commit carrying the Grove FHIR Implementation Guides contract.
         type: string
-        default: eff5af8f58cdd99bb8988c237f2996e9e1de75ff
+        default: c078136f12b4713ceee19619b1bcd2ff96186ecc
       fhir_only:
         description: Run only producer conformance against the selected grove-fhir contract.
         type: boolean
@@ -32,7 +32,7 @@
       grove_fhir_ref:
         description: grove-fhir commit carrying the Grove FHIR Implementation Guides contract.
         type: string
-        default: eff5af8f58cdd99bb8988c237f2996e9e1de75ff
+        default: c078136f12b4713ceee19619b1bcd2ff96186ecc
 
 concurrency:
   group: tests-${{ github.ref }}
@@ -124,7 +124,7 @@
         # Every source change is resolved through the graph, so the head revision is always dumped.
         run: swift package --manifest-cache none dump-package > "$RUNNER_TEMP/head-package.json"
       - name: Evaluate the base package graph and configuration
         if: steps.changes.outputs.manifest_changed == 'true' || steps.changes.outputs.packages_changed == 'true' || steps.changes.outputs.ui_test_projects_changed == 'true'
         env:
           BASE_SHA: ${{ steps.changes.outputs.base_sha }}
         run: |
@@ -203,7 +203,7 @@
     # self-hosted label set (matrix.selfHostedLabels) is ["self-hosted","macOS"] plus any
     # per-package `extra_runner_labels` from packages.toml, computed by
     # Scripts/affected-test-matrix.py.
     runs-on: ${{ matrix.platform == 'Linux' && 'ubuntu-latest' || (matrix.selfHosted && fromJson(matrix.selfHostedLabels) || fromJson('["macos-latest"]')) }}
     strategy:
       fail-fast: false
       matrix: ${{ fromJSON(needs.detect.outputs.matrix) }}
@@ -280,17 +280,17 @@
         with:
           repository: SchmiedmayerLab/grove-fhir
           path: .fhir/grove-fhir
-          ref: ${{ inputs.grove_fhir_ref || 'eff5af8f58cdd99bb8988c237f2996e9e1de75ff' }}
+          ref: ${{ inputs.grove_fhir_ref || 'c078136f12b4713ceee19619b1bcd2ff96186ecc' }}
           persist-credentials: false
       - name: Record grove-fhir contract revision
         working-directory: .fhir/grove-fhir
         run: |
-          echo "grove-fhir ref: ${{ inputs.grove_fhir_ref || 'eff5af8f58cdd99bb8988c237f2996e9e1de75ff' }}"
+          echo "grove-fhir ref: ${{ inputs.grove_fhir_ref || 'c078136f12b4713ceee19619b1bcd2ff96186ecc' }}"
           echo "grove-fhir SHA: $(git rev-parse HEAD)"
       - name: Pin the implementation-guide cache key
         run: |
           RESOLVED_GROVE_FHIR_SHA="$(git -C .fhir/grove-fhir rev-parse HEAD)"
           echo "GROVE_FHIR_GUIDE_CACHE_KEY=grove-fhir-validation-${{ runner.os }}-$RESOLVED_GROVE_FHIR_SHA-${{ hashFiles('.fhir/grove-fhir/Gemfile.lock', '.fhir/grove-fhir/package-lock.json', '.fhir/grove-fhir/Scripts/**', '.fhir/grove-fhir/catalog/**', '.fhir/grove-fhir/mobile/**', '.fhir/grove-fhir/sensor/**', '.fhir/grove-fhir/sensorkit/**', '.fhir/grove-fhir/healthkit/**', '.fhir/grove-fhir/questionnaire/**') }}" >> "$GITHUB_ENV"
       - name: Restore built implementation guides
         id: guide-cache
         uses: actions/cache@v6
@@ -346,7 +346,7 @@
       - name: Validate resources emitted by Grove
         env:
           FHIR_COMPONENTS: ${{ needs.detect.outputs.fhir_components }}
-          GROVE_FHIR_REF: ${{ inputs.grove_fhir_ref || 'eff5af8f58cdd99bb8988c237f2996e9e1de75ff' }}
+          GROVE_FHIR_REF: ${{ inputs.grove_fhir_ref || 'c078136f12b4713ceee19619b1bcd2ff96186ecc' }}
         run: |
           IFS=',' read -r -a COMPONENTS <<< "$FHIR_COMPONENTS"
           for component in "${COMPONENTS[@]}"; do

.periphery.yml

@@ -29,6 +29,10 @@ retain_codable_properties: true
 # Protocol requirement parameters belong to the API shape even when an implementation ignores them.
 retain_unused_protocol_func_params: true
 
+# A stored property of an Equatable or Hashable type is read by its synthesized == and hash(into:), which the
+# index does not record: a batch key, an exact decimal and an identifier set compare by every field.
+retain_equatable_properties: true
+
 # RAII tokens: the assignment holds the subscription; deallocation is the deregistration.
 retain_assign_only_property_types:
   - KVOStateDidChangeObserver

Package.swift

@@ -370,7 +370,6 @@ var targets: [Target] = [
         name: "GroveHealthKitFHIR",
         dependencies: [
             .target(name: "GroveFHIRContract"),
-            .target(name: "GroveHealthKit"),
             .product(name: "ModelsR4", package: "FHIRModels", condition: fhirModelsCondition),
             .target(name: "FHIRModelsExtensions")
         ],
@@ -382,9 +381,13 @@ var targets: [Target] = [
         name: "GroveHealthKitFHIRTests",
         dependencies: [
             .target(name: "GroveFHIRContract"),
+            .target(name: "GroveHealthKit"),
             .target(name: "GroveHealthKitFHIR")
         ],
         exclude: testTargetExcludes("GroveHealthKitFHIRTests", additional: ["UITests"]),
+        resources: [
+            .process("Resources")
+        ],
         swiftSettings: defaultSwiftSettings,
         plugins: [] + defaultPlugins
     ),
@@ -803,7 +806,8 @@ var targets: [Target] = [
         name: "GroveFHIRContract",
         dependencies: [
             .product(name: "ModelsR4", package: "FHIRModels", condition: fhirModelsCondition),
-            .product(name: "Crypto", package: "swift-crypto", condition: .when(platforms: [.linux]))
+            .product(name: "Crypto", package: "swift-crypto", condition: .when(platforms: [.linux])),
+            .target(name: "ThreadLocal")
         ],
         exclude: targetExcludes("GroveFHIRContract"),
         swiftSettings: defaultSwiftSettings,
@@ -838,6 +842,7 @@ var targets: [Target] = [
         name: "GroveFHIRTests",
         dependencies: [
             .target(name: "GroveFHIR"),
+            .target(name: "GroveFHIRContract"),
             "GroveHealthKitFHIR"
         ],
         exclude: testTargetExcludes("GroveFHIRTests", additional: ["UITests"]),
@@ -1433,7 +1438,6 @@ var targets: [Target] = [
             .target(name: "GroveQuestionnaireExtraction"),
             .target(name: "GroveFHIRContract"),
             .target(name: "GroveQuestionnaire"),
-            .product(name: "Crypto", package: "swift-crypto", condition: .when(platforms: [.linux])),
             .product(name: "ModelsR4", package: "FHIRModels", condition: fhirModelsCondition),
             .target(name: "FHIRModelsExtensions"),
             .target(name: "FHIRPathParser"),
@@ -1487,6 +1491,7 @@ var targets: [Target] = [
         dependencies: [
             .target(name: "GroveQuestionnaireExtraction"),
             .target(name: "GroveFHIRContract"),
+            .product(name: "Crypto", package: "swift-crypto", condition: .when(platforms: [.linux])),
             .product(name: "ModelsR4", package: "FHIRModels", condition: fhirModelsCondition)
         ],
         resources: [
@@ -1576,6 +1581,9 @@ var targets: [Target] = [
             .product(name: "ModelsR4", package: "FHIRModels", condition: fhirModelsCondition)
         ],
         exclude: testTargetExcludes("GroveSensorKitFHIRTests"),
+        resources: [
+            .process("Resources")
+        ],
         swiftSettings: defaultSwiftSettings,
         plugins: [] + defaultPlugins
     ),

REUSE.toml

@@ -39,8 +39,10 @@ SPDX-License-Identifier = "MIT"
 path = [
     "Sources/GroveSpeechRecognizer/Resources/**",
     "Tests/GroveChatTests/UITests/TestApp/Resources/**",
+    "Tests/GroveHealthKitFHIRTests/Resources/**",
     "Tests/GroveQuestionnaireTests/Resources/**",
     "Tests/GroveQuestionnaireExtractionTests/Resources/**",
+    "Tests/GroveSensorKitFHIRTests/Resources/**",
     "Tests/GroveQuestionnaireTests/UITests/TestApp/Resources/**"
 ]
 SPDX-FileCopyrightText = "2026 Stanford University and the project authors (see CONTRIBUTORS.md)"

Scripts/Tests/test_affected_test_matrix.py

@@ -181,7 +181,7 @@ def test_contract_generator_runs_every_conformance_lane(self):
 
     def test_a_producer_change_selects_only_its_lane(self):
         for path, component in (
-            ("Sources/GroveHealthKitFHIR/HealthKitConverter.swift", "healthkit"),
+            ("Sources/GroveHealthKitFHIR/HealthKitFHIRExporter.swift", "healthkit"),
             ("Sources/GroveQuestionnaire/Model/Questionnaire.swift", "questionnaire"),
             ("Sources/GroveSensorKitFHIR/SensorKitConverter.swift", "sensor"),
         ):
@@ -199,7 +199,7 @@ def test_explicit_all_selects_every_conformance_lane(self):
 
     def test_fhir_only_schedules_every_conformance_lane_and_no_package_jobs(self):
         result = run_selector(
-            "Sources/GroveHealthKitFHIR/HealthKitConverter.swift",
+            "Sources/GroveHealthKitFHIR/HealthKitFHIRExporter.swift",
             extra_arguments=("--fhir-only",),
         )
 

Scripts/Tests/test_build_support.py

@@ -121,6 +121,24 @@ def test_plain_command_keeps_output_streams_separate(self):
         self.assertEqual(result.stdout, b"out\n")
         self.assertEqual(result.stderr, b"err\n")
 
+    def test_stopping_a_group_that_already_exited_succeeds(self):
+        # Cancellation can arrive after a stage exited but before it was reaped; macOS then refuses
+        # to signal its group with EPERM, which must not end the script as a failure.
+        sys.path.insert(0, str(self.root))
+        self.addCleanup(sys.path.remove, str(self.root))
+        import build_support
+        process = subprocess.Popen([sys.executable, "-c", "pass"], start_new_session=True)
+        deadline = time.monotonic() + 5
+        while time.monotonic() < deadline:
+            state = subprocess.run(["ps", "-o", "stat=", "-p", str(process.pid)],
+                                   capture_output=True, text=True).stdout.strip()
+            if state.startswith("Z"):
+                break
+            time.sleep(0.01)
+        self.assertTrue(state.startswith("Z"), f"Stage did not become a zombie: {state!r}")
+        build_support._stop_processes([process])
+        self.assertEqual(process.returncode, 0)
+
     def test_cancellation_stops_command_and_its_descendant(self):
         # Exercise both the simple command and build pipeline; the child acknowledges SIGTERM
         # through a file so this assertion does not confuse a short-lived zombie with a live tool.