Unit C: contrast-enhanced T1 detection + non-contrast anchor preferen… #233
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| name: Validate Scripts | |
| on: | |
| push: | |
| branches: ['**'] | |
| pull_request: | |
| branches: [main] | |
| jobs: | |
| syntax-check: | |
| name: Bash Syntax Check | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Check bash syntax with bash -n | |
| run: | | |
| echo "Checking syntax of all .sh files..." | |
| failed=0 | |
| count=0 | |
| while IFS= read -r file; do | |
| if ! bash -n "$file" 2>/tmp/syntax_err; then | |
| echo "FAIL: $file" | |
| cat /tmp/syntax_err | |
| failed=$((failed + 1)) | |
| fi | |
| count=$((count + 1)) | |
| done < <(find . -name '*.sh' -not -path './.git/*' | sort) | |
| echo "" | |
| echo "Checked $count files, $failed failed" | |
| [ "$failed" -eq 0 ] | |
| shellcheck: | |
| name: ShellCheck (advisory) | |
| runs-on: ubuntu-latest | |
| continue-on-error: true | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install shellcheck | |
| run: sudo apt-get update && sudo apt-get install -y shellcheck | |
| - name: Run shellcheck --severity=error | |
| run: | | |
| echo "Running shellcheck (error-level only)..." | |
| failed=0 | |
| count=0 | |
| while IFS= read -r file; do | |
| if ! shellcheck --severity=error "$file" 2>/dev/null; then | |
| failed=$((failed + 1)) | |
| fi | |
| count=$((count + 1)) | |
| done < <(find . -name '*.sh' -not -path './.git/*' | sort) | |
| echo "" | |
| echo "Checked $count files, $failed had errors" | |
| [ "$failed" -eq 0 ] | |
| unit-tests: | |
| name: Unit Tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Run unit test suites | |
| run: | | |
| failed=0 | |
| for suite in tests/test_environment_unit.sh tests/test_pipeline_control_unit.sh tests/test_import_unit.sh; do | |
| echo "" | |
| echo "========================================" | |
| echo "Running: $suite" | |
| echo "========================================" | |
| if bash "$suite"; then | |
| echo "PASS: $suite" | |
| else | |
| echo "FAIL: $suite (exit code: $?)" | |
| failed=$((failed + 1)) | |
| fi | |
| done | |
| echo "" | |
| echo "========================================" | |
| if [ "$failed" -gt 0 ]; then | |
| echo "$failed test suite(s) failed" | |
| exit 1 | |
| else | |
| echo "All test suites passed" | |
| fi | |
| pipeline-smoke-test: | |
| name: Pipeline Smoke Test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Verify pipeline.sh --help works | |
| run: | | |
| # Provide a dummy FSL config so the early `source $FSLDIR/etc/fslconf/fsl.sh` | |
| # in pipeline.sh succeeds under `set -e` (no real FSL install in CI). | |
| export FSLDIR=/tmp/fake_fsl | |
| mkdir -p "$FSLDIR/etc/fslconf" | |
| printf '# dummy FSL config for CI smoke test\n' > "$FSLDIR/etc/fslconf/fsl.sh" | |
| output=$(bash src/pipeline.sh --help 2>&1) | |
| echo "$output" | |
| echo "" | |
| echo "--- Validating help output ---" | |
| echo "$output" | grep -q "Usage:" || { echo "FAIL: missing Usage line"; exit 1; } | |
| echo "$output" | grep -q "Pipeline Stages:" || { echo "FAIL: missing Pipeline Stages"; exit 1; } | |
| echo "PASS: --help output looks correct" | |
| - name: Verify pipeline loads all modules and fails gracefully on missing tools | |
| run: | | |
| # Set required vars to dummy values so module sourcing doesn't crash | |
| # on unbound variables. The pipeline should still fail at the | |
| # dependency check stage — that's exactly what we want to verify. | |
| export FSLDIR=/tmp/fake_fsl | |
| export ANTS_PATH=/tmp/fake_ants | |
| # Provide a dummy FSL config so the early `source $FSLDIR/etc/fslconf/fsl.sh` | |
| # in pipeline.sh succeeds under `set -e` (no real FSL install in CI). | |
| mkdir -p "$FSLDIR/etc/fslconf" | |
| printf '# dummy FSL config for CI smoke test\n' > "$FSLDIR/etc/fslconf/fsl.sh" | |
| echo "Running pipeline.sh with no input data..." | |
| output=$(bash src/pipeline.sh 2>&1 || true) | |
| echo "$output" | |
| echo "" | |
| echo "--- Validating module loading ---" | |
| check() { | |
| if echo "$output" | grep -q "$1"; then | |
| echo "PASS: found '$1'" | |
| else | |
| echo "FAIL: missing '$1'" | |
| return 1 | |
| fi | |
| } | |
| failed=0 | |
| # Confirm key modules loaded successfully | |
| check "Environment module loaded" || failed=$((failed + 1)) | |
| check "Import module loaded" || failed=$((failed + 1)) | |
| check "Registration module loaded" || failed=$((failed + 1)) | |
| check "Segmentation module loaded" || failed=$((failed + 1)) | |
| check "Analysis module loaded" || failed=$((failed + 1)) | |
| check "Visualization module loaded" || failed=$((failed + 1)) | |
| # Confirm pipeline got past module loading to actual execution | |
| check "Arguments parsed:" || failed=$((failed + 1)) | |
| check "Comprehensive Pipeline Dependency Check" || failed=$((failed + 1)) | |
| # Confirm the dependency check section ran (outcome varies by environment) | |
| check "Dependency Check Summary" || failed=$((failed + 1)) | |
| echo "" | |
| if [ "$failed" -gt 0 ]; then | |
| echo "$failed checks failed — pipeline may not be loading correctly" | |
| exit 1 | |
| else | |
| echo "All checks passed — pipeline loads and fails gracefully" | |
| fi |