StreamFlow/.github/workflows/build-java.yml at main · arunviswanathan91/StreamFlow · GitHub

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name: build-java

# CI for the JavaFX desktop app (app/) + headless compute engine (engine/).
#
# The app is now Python-first: the Java bridge spawns the Python (FlowKit) engine
# by default, with the legacy R engine kept as a fallback until it is retired. This
# job therefore stands up BOTH engines so the test suite exercises the real data
# path on each:
#   * Python  — a venv at engine/py-env with FlowKit installed. PyEngineTest and the
#               command tests auto-detect this exact path and run against it.
#   * R       — R 4.4 + jsonlite so the JavaFX<->R ProtocolConformanceTest runs for
#               real (it auto-skips if R is missing).
#
# Tests that need large FCS fixtures (test-assests/, gitignored) self-skip in CI via
# JUnit assumptions — that is expected. The heavy Bioconductor/CytoExploreR stack is
# NOT installed here; module integration tests get their own gated job later.
#
# This job does NOT produce the packaged StreamFLOW.exe — jpackage packaging
# (app/package.ps1) is a separate release pipeline and is still being aligned with
# the Python engine.

on:
  push:
    paths:
      - 'app/**'
      - 'engine/**'
      - '.github/workflows/build-java.yml'
  pull_request:
    paths:
      - 'app/**'
      - 'engine/**'
  workflow_dispatch:

env:
  # Run all JavaScript actions on Node 24 — Node 20 is deprecated on the runners.
  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true

jobs:
  build:
    runs-on: windows-latest
    timeout-minutes: 30
    steps:
      - uses: actions/checkout@v4

      - name: Set up JDK 25 (Microsoft, LTS)
        uses: actions/setup-java@v4
        with:
          distribution: 'microsoft'
          java-version: '25'
          cache: maven

      - name: Set up Python 3.11
        uses: actions/setup-python@v5
        with:
          python-version: '3.11'
          # No pip cache — packages are installed inline below, not from a
          # requirements.txt, so setup-python's pip-cache detection would fail.

      - name: Create engine venv + install FlowKit
        shell: pwsh
        run: |
          # PyEngineTest / command tests expect the venv at engine\py-env (the same
          # path run-dev.ps1 uses), so create it there exactly.
          python -m venv engine\py-env
          engine\py-env\Scripts\python.exe -m pip install --upgrade pip
          # flowkit pulls flowio, flowutils, numpy, scipy, pandas; matplotlib is used
          # by the render/stats commands; scikit-learn/umap-learn/openTSNE power the
          # Dim. Reduction, Clustering and Classifier modules.
          engine\py-env\Scripts\python.exe -m pip install flowkit matplotlib scikit-learn umap-learn openTSNE phenograph flowsom
          engine\py-env\Scripts\python.exe -c "import flowkit; print('FlowKit', flowkit.__version__)"

      - name: Set up R 4.4 (legacy engine fallback)
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: '4.4'

      - name: Install jsonlite
        run: Rscript -e "install.packages('jsonlite', repos='https://cloud.r-project.org')"
        shell: cmd

      - name: Build and test (Python + R engine bridges)
        working-directory: app
        shell: cmd
        run: >
          mvn -B clean test
          "-Dstreamflow.rscript=%RSCRIPT_PATH%"
        env:
          # r-lib/actions exposes R on PATH; resolve Rscript explicitly for the bridge.
          # The Python tests self-configure via the engine\py-env path created above.
          RSCRIPT_PATH: Rscript

      - name: Upload test reports
        if: always()
        uses: actions/upload-artifact@v4
        with:
          name: surefire-reports
          path: app/target/surefire-reports/