[codex] Harden build entrypoints and consolidate electrochem helpers

+labkit/AGENTS.md

@@ -34,7 +34,11 @@
 
 ## Validation Routing
 
-- Always run `scripts/run_matlab_tests.sh --suite project` for package boundary or public surface changes.
-- DTA changes: also run `scripts/run_matlab_tests.sh --suite labkit/dta`; add `--suite apps/electrochem` when app-facing behavior may be affected.
-- Biosignal changes: also run `scripts/run_matlab_tests.sh --suite labkit/biosignal`; add `--suite apps/wearable` when app-facing behavior may be affected.
-- UI changes: also run `scripts/run_matlab_tests.sh --suite labkit/ui`; add `--suite apps --gui` for layout, launch, callback, or app shell changes.
+- Always run `buildtool testProject` for package boundary or public surface changes.
+- DTA changes: also run `buildtool testLabkitDta`; add
+  `buildtool testAppsElectrochem` when app-facing behavior may be affected.
+- Biosignal changes: also run `buildtool testLabkitBiosignal`; add
+  `buildtool testAppsWearableGui` when app-facing behavior may be affected.
+- UI changes: also run `buildtool testLabkitUi`; add
+  `buildtool testLabkitUiGui testAppsGui` for layout, launch, callback, or app
+  shell changes.

.github/workflows/matlab-tests.yml

@@ -15,6 +15,30 @@ env:
   MATLAB_RELEASE: R2025a
 
 jobs:
+  shell-wrapper:
+    name: Shell Wrapper Checks
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v6
+
+      - name: Check Bash wrapper syntax
+        run: bash -n scripts/run_matlab_tests.sh
+
+      - name: Check Bash wrapper help
+        run: bash scripts/run_matlab_tests.sh --help
+
+      - name: Check Bash wrapper build task smoke
+        run: MATLAB_CMD=true bash scripts/run_matlab_tests.sh testProject
+
+      - name: Check removed selector flags are rejected
+        run: |
+          if bash scripts/run_matlab_tests.sh --suite; then
+            echo "Expected --suite to be rejected"
+            exit 1
+          fi
+
   quality:
     name: Quality Guardrails
     runs-on: ubuntu-latest
@@ -31,7 +55,7 @@ jobs:
           release: ${{ env.MATLAB_RELEASE }}
 
       - name: Prepare artifact directories
-        run: mkdir -p artifacts/logs artifacts/test-results/html
+        run: mkdir -p artifacts/logs
 
       - name: Run quality guardrails
         uses: matlab-actions/run-build@v3
@@ -47,9 +71,8 @@ jobs:
           if-no-files-found: warn
           retention-days: 14
           path: |
-            artifacts/test-results/junit.xml
-            artifacts/test-results/html/**
-            artifacts/logs/matlab.log
+            artifacts/test-results/**
+            artifacts/logs/**
 
   unit:
     name: Unit And Coverage
@@ -67,7 +90,7 @@ jobs:
           release: ${{ env.MATLAB_RELEASE }}
 
       - name: Prepare artifact directories
-        run: mkdir -p artifacts/logs artifacts/test-results/html artifacts/coverage/html
+        run: mkdir -p artifacts/logs
 
       - name: Run unit tests and coverage
         uses: matlab-actions/run-build@v3
@@ -83,11 +106,9 @@ jobs:
           if-no-files-found: warn
           retention-days: 14
           path: |
-            artifacts/test-results/junit.xml
-            artifacts/test-results/html/**
-            artifacts/coverage/cobertura.xml
-            artifacts/coverage/html/**
-            artifacts/logs/matlab.log
+            artifacts/test-results/**
+            artifacts/coverage/**
+            artifacts/logs/**
 
   integration:
     name: Integration Tests
@@ -105,7 +126,7 @@ jobs:
           release: ${{ env.MATLAB_RELEASE }}
 
       - name: Prepare artifact directories
-        run: mkdir -p artifacts/logs artifacts/test-results/html
+        run: mkdir -p artifacts/logs
 
       - name: Run integration tests
         uses: matlab-actions/run-build@v3
@@ -121,9 +142,8 @@ jobs:
           if-no-files-found: warn
           retention-days: 14
           path: |
-            artifacts/test-results/junit.xml
-            artifacts/test-results/html/**
-            artifacts/logs/matlab.log
+            artifacts/test-results/**
+            artifacts/logs/**
 
   gui-structural:
     name: GUI Structural Tests
@@ -142,7 +162,7 @@ jobs:
           release: ${{ env.MATLAB_RELEASE }}
 
       - name: Prepare artifact directories
-        run: mkdir -p artifacts/logs artifacts/test-results/html artifacts/gui/trace artifacts/gui/snapshots
+        run: mkdir -p artifacts/logs
 
       - name: Run GUI structural tests
         uses: matlab-actions/run-build@v3
@@ -158,11 +178,9 @@ jobs:
           if-no-files-found: warn
           retention-days: 14
           path: |
-            artifacts/test-results/junit.xml
-            artifacts/test-results/html/**
-            artifacts/gui/trace/**
-            artifacts/gui/snapshots/**
-            artifacts/logs/matlab.log
+            artifacts/test-results/**
+            artifacts/gui/**
+            artifacts/logs/**
 
   gui-gesture:
     name: GUI Gesture Tests
@@ -182,7 +200,7 @@ jobs:
           release: ${{ env.MATLAB_RELEASE }}
 
       - name: Prepare artifact directories
-        run: mkdir -p artifacts/logs artifacts/test-results/html artifacts/gui/trace artifacts/gui/snapshots
+        run: mkdir -p artifacts/logs
 
       - name: Run GUI gesture tests
         uses: matlab-actions/run-build@v3
@@ -198,8 +216,6 @@ jobs:
           if-no-files-found: warn
           retention-days: 14
           path: |
-            artifacts/test-results/junit.xml
-            artifacts/test-results/html/**
-            artifacts/gui/trace/**
-            artifacts/gui/snapshots/**
-            artifacts/logs/matlab.log
+            artifacts/test-results/**
+            artifacts/gui/**
+            artifacts/logs/**

apps/AGENTS.md

@@ -38,8 +38,12 @@ Apps are first-class deliverables. Do not treat them as examples for a hidden pl
 
 ## Validation Routing
 
-- Electrochem app change: `scripts/run_matlab_tests.sh --suite apps/electrochem`; add `--gui` for layout, launch, or callback wiring.
-- DIC app change: `scripts/run_matlab_tests.sh --suite apps/dic --gui`.
-- Image measurement app change: `scripts/run_matlab_tests.sh --suite apps/image_measurement --gui`.
-- Wearable app change: `scripts/run_matlab_tests.sh --suite apps/wearable --gui`; add `--suite labkit/biosignal` when the biosignal facade contract may be affected.
-- App entrypoint or boundary changes also run `scripts/run_matlab_tests.sh --suite project`.
+- Electrochem app change: `buildtool testAppsElectrochem`; use
+  `buildtool testAppsElectrochemGui` for layout, launch, or callback wiring.
+- DIC app change: `buildtool testAppsDicGui`.
+- Image measurement app change: `buildtool testAppsImageMeasurement`; use
+  `buildtool testAppsImageMeasurementGui` for layout, launch, or callback wiring.
+- Wearable app change: `buildtool testAppsWearableGui`; add
+  `buildtool testLabkitBiosignal` when the biosignal facade contract may be
+  affected.
+- App entrypoint or boundary changes also run `buildtool testProject`.

apps/electrochem/electrochemWorkflow.m

@@ -2,8 +2,8 @@
 %ELECTROCHEMWORKFLOW Dispatch app-owned electrochem workflow helpers.
 % Expected caller: electrochem app tests and migration-time workflow checks.
 % Inputs are an app key, a workflow command, and command-specific arguments.
-% Outputs match the selected app-owned helper. File side effects are limited to
-% CSV export commands.
+% Outputs match the selected app-owned helper. Side effects are limited to CSV
+% export commands and app-owned plot drawing commands on caller axes.
 
     switch string(appKey)
         case "chronoOverlay"

apps/electrochem/private/chronoOverlayWorkflow.m

@@ -1,12 +1,14 @@
 % App-owned chrono overlay workflow helper dispatch. Expected caller:
 % labkit_ChronoOverlay_app callbacks and workflow tests.
 % Inputs are a command string plus the original helper arguments; outputs match
-% the selected helper. This helper has no file side effects.
+% the selected helper. Side effects are limited to drawing app-owned overlay
+% plots on caller axes.
 function varargout = chronoOverlayWorkflow(command, varargin)
 %CHRONOOVERLAYWORKFLOW Dispatch app-owned chrono overlay helpers.
 % Expected caller: labkit_ChronoOverlay_app callbacks and temporary compatibility
 % workflow tests. Inputs are a command string plus the original helper arguments.
-% Outputs match the selected helper. This helper has no file side effects.
+% Outputs match the selected helper. Side effects are limited to drawing
+% app-owned overlay plots on caller axes.
 
     switch string(command)
         case "alignByPulseGap"

apps/electrochem/private/cicWorkflow.m

@@ -1,12 +1,13 @@
 % App-owned CIC workflow helper dispatch. Expected caller: labkit_CIC_app
-% callbacks and workflow tests. Inputs are a command
-% string plus the original helper arguments; outputs match the selected helper.
-% Side effects are limited to writeResultsCSV file writes.
+% callbacks and workflow tests. Inputs are a command string plus the original
+% helper arguments; outputs match the selected helper. Side effects are limited
+% to CSV export writes and drawing app-owned plot annotations on caller axes.
 function varargout = cicWorkflow(command, varargin)
 %CICWORKFLOW Dispatch app-owned CIC analysis/export helpers.
 % Expected caller: labkit_CIC_app callbacks and workflow tests.
 % Inputs are a command string plus the original helper arguments. Outputs match
-% the selected helper. Side effects are limited to writeResultsCSV file writes.
+% the selected helper. Side effects are limited to CSV export writes and drawing
+% app-owned plot annotations on caller axes.
 
     switch string(command)
         case "computeCIC"
@@ -17,6 +18,20 @@
             varargout{1} = buildResultsTable(varargin{:});
         case "writeResultsCSV"
             [varargout{1:nargout}] = writeResultsCSV(varargin{:});
+        case "formatChargeDensity"
+            varargout{1} = formatChargeDensity(varargin{:});
+        case "formatMaybeNum"
+            varargout{1} = formatMaybeNum(varargin{:});
+        case "interp1Safe"
+            varargout{1} = interp1Safe(varargin{:});
+        case "shadeWindow"
+            shadeWindow(varargin{:});
+        case "addBaselineYLines"
+            addBaselineYLines(varargin{:});
+        case "addPaperStyleVTAnnotations"
+            addPaperStyleVTAnnotations(varargin{:});
+        case "addPaperStyleITAnnotations"
+            addPaperStyleITAnnotations(varargin{:});
         otherwise
             error('labkit:CIC:UnknownWorkflowCommand', ...
                 'Unknown CIC workflow helper command: %s.', command);