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Add Tescan PFIB TIFF extractor plugin with comprehensive metadata extraction #60

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Add Tescan PFIB TIFF extractor plugin with comprehensive metadata extraction

Add Tescan PFIB TIFF extractor plugin with comprehensive metadata extraction #60

Workflow file for this run

.github/workflows/integration-tests.yml at fb47ccc
name: Integration Tests
on:
push:
branches: [main]
pull_request:
branches: [main]
workflow_dispatch:
schedule:
# Run integration tests nightly at 3 AM UTC to catch integration issues early
- cron: "0 3 * * *"
env:
REGISTRY: ghcr.io
IMAGE_PREFIX: ghcr.io/${{ github.repository_owner }}/nexuslims-test
jobs:
integration-test:
name: Integration Tests (Python ${{ matrix.python-version }})
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
python-version: ["3.11", "3.12"]
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v3
- name: Log in to Container Registry
uses: docker/login-action@v3
with:
registry: ${{ env.REGISTRY }}
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}
- name: Pull pre-built test images
run: |
docker pull ${{ env.IMAGE_PREFIX }}-nemo:latest || echo "NEMO image not found, will build locally"
docker pull ${{ env.IMAGE_PREFIX }}-cdcs:latest || echo "CDCS image not found, will build locally"
- name: Tag images for local use
continue-on-error: true
run: |
docker tag ${{ env.IMAGE_PREFIX }}-nemo:latest nexuslims-test-nemo:latest 2>/dev/null || true
docker tag ${{ env.IMAGE_PREFIX }}-cdcs:latest nexuslims-test-cdcs:latest 2>/dev/null || true
- name: Start Docker services
working-directory: tests/integration/docker
run: |
# Try to use pre-built images first, fall back to building if needed
if docker image inspect nexuslims-test-nemo:latest >/dev/null 2>&1 && \
docker image inspect nexuslims-test-cdcs:latest >/dev/null 2>&1; then
echo "Using pre-built images from registry"
docker compose -f docker-compose.ci.yml up -d
else
echo "Building images locally (pre-built images not available)"
docker compose up -d
fi
- name: Wait for services to be healthy
run: |
echo "Waiting for NEMO to be ready..."
timeout 180 bash -c 'until curl -f http://localhost:8000/ > /dev/null 2>&1; do echo -n "."; sleep 3; done'
echo "✓ NEMO is ready"
echo "Waiting for CDCS to be ready..."
timeout 240 bash -c 'until curl -f http://localhost:8080/ > /dev/null 2>&1; do echo -n "."; sleep 5; done'
echo "✓ CDCS is ready"
echo "Waiting for MailPit to be ready..."
timeout 60 bash -c 'until curl -f http://localhost:8025/ > /dev/null 2>&1; do echo -n "."; sleep 2; done'
echo "✓ MailPit is ready"
- name: Show Docker service status
if: always()
working-directory: tests/integration/docker
run: docker compose ps
- name: Install system dependencies
run: |
sudo apt-get update
sudo apt-get install -y findutils
- name: Set up uv
uses: astral-sh/setup-uv@v4
with:
enable-cache: true
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: uv sync
- name: Create test environment for module imports
run: |
# Create test directories
mkdir -p /tmp/nexuslims-test-instrument-data
mkdir -p /tmp/nexuslims-test-data
# Create empty database file (Settings validates it exists)
touch /tmp/nexuslims-test-data/nexuslims_test.db
# Create .env file with minimal config for import-time validation
cat > .env << 'EOF'
# CI Integration Test Environment
# These values allow NexusLIMS modules to be imported during test collection
# The actual test fixtures will override these with monkeypatch
# Test data paths
NX_INSTRUMENT_DATA_PATH=/tmp/nexuslims-test-instrument-data
NX_DATA_PATH=/tmp/nexuslims-test-data
NX_DB_PATH=/tmp/nexuslims-test-data/nexuslims_test.db
# CDCS configuration (will be overridden by fixtures)
NX_CDCS_URL=http://localhost:8080
NX_CDCS_USER=admin
NX_CDCS_PASS=admin
EOF
- name: Run unit tests
run: |
uv run pytest tests/ \
--ignore=tests/integration \
-v \
--mpl \
--mpl-baseline-path=tests/unit/files/figs \
--cov=nexusLIMS \
--cov-report term-missing \
--tb=short \
--maxfail=5
- name: Run integration tests
run: |
uv run pytest tests/integration/ \
-v \
-m integration \
--cov=nexusLIMS \
--cov-append \
--cov-report html:tests/coverage-combined \
--cov-report term-missing \
--cov-report=xml:coverage-combined.xml \
--tb=short \
--maxfail=5
env:
# Integration test environment variables
PYTEST_TIMEOUT: 600
- name: Upload combined test coverage
uses: actions/upload-artifact@v4
with:
name: coverage-combined-${{ matrix.python-version }}
path: |
.coverage
coverage-combined.xml
include-hidden-files: true
- name: Upload HTML coverage report
if: matrix.python-version == '3.11'
uses: actions/upload-artifact@v4
with:
name: coverage-combined-html
path: tests/coverage-combined
- name: Show Docker logs on failure
if: failure()
working-directory: tests/integration/docker
run: |
echo "=== NEMO Logs ==="
docker compose logs nemo | tail -100
echo ""
echo "=== CDCS Logs ==="
docker compose logs cdcs | tail -100
echo ""
echo "=== MongoDB Logs ==="
docker compose logs cdcs-mongo | tail -50
echo ""
echo "=== PostgreSQL Logs ==="
docker compose logs cdcs-postgres | tail -50
- name: Cleanup Docker services
if: always()
working-directory: tests/integration/docker
run: |
docker compose down -v --remove-orphans || true
upload-coverage:
name: Upload Combined Coverage to Codecov
needs: integration-test
runs-on: ubuntu-latest
if: always()
steps:
- uses: actions/checkout@v4
- name: Download all coverage artifacts
uses: actions/download-artifact@v4
with:
pattern: coverage-combined-*
path: coverage-reports
- name: Upload combined coverage to Codecov
uses: codecov/codecov-action@v5
with:
token: ${{ secrets.CODECOV_TOKEN }}
files: ./coverage-reports/**/*.xml
flags: combined
fail_ci_if_error: false