testing.yml

# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: Testing

on:
  push:
    branches:
      - master
      - development
  pull_request:
    branches:
      - master
      - development

# Cancel any in-progress or queued Testing run on the same source
# branch when a new push arrives. Collapses duplicate push + PR runs
# from the same commit into a single active run, so rapid iteration
# does not stack up stale jobs.
#
# The group key uses github.head_ref (populated on PRs with the
# source branch) falling back to github.ref_name (populated on pushes
# with the branch short name), so a push to development and a PR
# with development as the source end up in the same group. The
# pull_request.head.repo.full_name fallback namespaces the group by
# fork identity, so two different forks with the same branch name
# do not collide.
#
# testing-cron.yml intentionally does not use concurrency because
# each scheduled cron trigger is an independent run.
concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.head.repo.full_name || github.repository }}-${{ github.head_ref || github.ref_name }}
  cancel-in-progress: true

jobs:
  build:
    runs-on: ${{ matrix.os }}
    timeout-minutes: 60

    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, windows-latest]
        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
        # macOS is pinned to a single Python version because Apple Silicon
        # runners were intermittently not finishing the non-torch test suite
        # within the job timeout on 3.10-3.13 even though 3.9 passes
        # reliably. Ubuntu and Windows cover the full Python matrix, so the
        # single macOS cell is a smoke-test canary for Apple Silicon rather
        # than full per-version coverage.
        # TODO: re-enable 3.10-3.13 on macOS once the Apple Silicon slowness
        # is understood (profile via pytest --durations=20 first).
        include:
          - os: macos-latest
            python-version: "3.9"

    steps:
    - uses: actions/checkout@v4
    - name: Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Install libomp for macOS
      if: startsWith(matrix.os, 'macos')
      run: brew install libomp

    - name: Install dependencies (non-macOS, full deps including torch)
      if: ${{ !startsWith(matrix.os, 'macos') }}
      run: |
        python -m pip install --upgrade pip
        pip install -r docs/requirements.txt
        pip install pytest
        pip install coverage
        pip install coveralls

    # macOS CI deliberately skips torch and torch_geometric because of
    # the upstream PyTorch NNPACK slowdown on Apple Silicon
    # (https://github.com/pytorch/pytorch/issues/107534). Conv-heavy
    # torch tests run ~36x slower on Apple Silicon and exhaust any
    # reasonable job timeout. Torch-dependent tests are auto-skipped
    # by pyod/test/conftest.py when torch is absent.
    # TODO: remove this macOS-specific step and the conftest shim once
    # upstream PyTorch fixes NNPACK on ARM and a fixed wheel is released.
    - name: Install dependencies (macOS, skip torch and torch_geometric)
      if: startsWith(matrix.os, 'macos')
      run: |
        python -m pip install --upgrade pip
        grep -vE '^(torch|torch_geometric)$' docs/requirements.txt > /tmp/mac-reqs.txt
        pip install -r /tmp/mac-reqs.txt
        pip install pytest
        pip install coverage
        pip install coveralls

    - name: Test with pytest
      run: |
        coverage run --source=pyod -m pytest

    - name: Coverage report
      shell: bash
      continue-on-error: true
      env:
        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        COVERALLS_SERVICE_NAME: github-actions
      run: |
        if ! coveralls --service=github; then
          echo "Coveralls upload failed; retrying once in 15s for best effort."
          sleep 15
          coveralls --service=github || true
        fi

  packaging-smoke-test:
    name: packaging smoke test (sdist + wheel from a clean build)
    runs-on: ubuntu-latest
    timeout-minutes: 15
    steps:
      - uses: actions/checkout@v4

      - name: Set up Python 3.11
        uses: actions/setup-python@v5
        with:
          python-version: '3.11'

      - name: Install build tooling
        run: python -m pip install --upgrade pip build twine

      - name: Build sdist and wheel
        run: python -m build

      - name: Inspect sdist contents
        run: |
          set -euo pipefail
          sdist=$(ls dist/*.tar.gz | head -1)
          echo "Inspecting $sdist"
          tar tzf "$sdist" > /tmp/sdist-listing.txt
          knowledge_count=$(grep -c 'pyod/utils/knowledge/.*\.json' /tmp/sdist-listing.txt || true)
          analysis_count=$(grep -c 'pyod/utils/model_analysis_jsons/.*\.json' /tmp/sdist-listing.txt || true)
          echo "knowledge JSONs in sdist: $knowledge_count"
          echo "model_analysis JSONs in sdist: $analysis_count"
          test "$knowledge_count" -ge 4 || { echo "ERROR: expected >=4 knowledge JSONs in sdist"; exit 1; }
          test "$analysis_count" -ge 10 || { echo "ERROR: expected >=10 model_analysis JSONs in sdist"; exit 1; }

      - name: Inspect wheel contents
        run: |
          set -euo pipefail
          wheel=$(ls dist/*.whl | head -1)
          echo "Inspecting $wheel"
          python -m zipfile -l "$wheel" > /tmp/wheel-listing.txt
          knowledge_count=$(grep -c 'pyod/utils/knowledge/.*\.json' /tmp/wheel-listing.txt || true)
          analysis_count=$(grep -c 'pyod/utils/model_analysis_jsons/.*\.json' /tmp/wheel-listing.txt || true)
          skill_count=$(grep -c 'pyod/skills/od_expert/SKILL\.md' /tmp/wheel-listing.txt || true)
          test_count=$(grep -c 'pyod/test/' /tmp/wheel-listing.txt || true)
          docs_count=$(grep -cE '^docs/' /tmp/wheel-listing.txt || true)
          echo "knowledge JSONs in wheel: $knowledge_count"
          echo "model_analysis JSONs in wheel: $analysis_count"
          echo "od_expert SKILL.md in wheel: $skill_count"
          echo "test files in wheel: $test_count"
          echo "docs files in wheel: $docs_count"
          test "$knowledge_count" -ge 4 || { echo "ERROR: expected >=4 knowledge JSONs in wheel"; exit 1; }
          test "$analysis_count" -ge 10 || { echo "ERROR: expected >=10 model_analysis JSONs in wheel"; exit 1; }
          test "$skill_count" -eq 1 || { echo "ERROR: expected exactly 1 od_expert SKILL.md in wheel"; exit 1; }
          test "$test_count" -eq 0 || { echo "ERROR: wheel contains $test_count pyod/test files; should be 0"; exit 1; }
          test "$docs_count" -eq 0 || { echo "ERROR: wheel contains $docs_count docs/ files; should be 0"; exit 1; }

      - name: Validate metadata with twine
        run: twine check dist/*

      - name: Fresh-venv install from sdist and import smoke test
        run: |
          set -euo pipefail
          python -m venv /tmp/pyod-smoke
          /tmp/pyod-smoke/bin/python -m pip install --upgrade pip
          /tmp/pyod-smoke/bin/python -m pip install dist/*.tar.gz
          /tmp/pyod-smoke/bin/python - <<'PY'
          import pyod
          from pyod.models.iforest import IForest
          from pyod.utils.ad_engine import ADEngine

          print("pyod version:", pyod.__version__)
          assert pyod.__version__.startswith("3."), f"unexpected version {pyod.__version__}"

          engine = ADEngine()
          detectors = engine.list_detectors()
          assert len(detectors) > 0, "ADEngine knowledge base loaded 0 detectors"
          print("ADEngine detectors loaded:", len(detectors))

          import numpy as np
          rng = np.random.default_rng(42)
          X = rng.standard_normal((50, 5))
          clf = IForest(contamination=0.1, random_state=42)
          clf.fit(X)
          print("IForest fit OK; decision_scores_ shape:", clf.decision_scores_.shape)
          PY

      - name: Verify unified pyod CLI end-to-end
        run: |
          set -euo pipefail
          /tmp/pyod-smoke/bin/pyod --help
          /tmp/pyod-smoke/bin/pyod info
          /tmp/pyod-smoke/bin/pyod install skill --help
          /tmp/pyod-smoke/bin/pyod install skill --list
          rm -rf /tmp/pyod-cli-skill-test
          /tmp/pyod-smoke/bin/pyod install skill --target /tmp/pyod-cli-skill-test
          test -f /tmp/pyod-cli-skill-test/od-expert/SKILL.md \
            || { echo "ERROR: pyod install skill did not create SKILL.md"; exit 1; }
          # v3.2.0: verify references/ subdir was copied alongside SKILL.md
          test -d /tmp/pyod-cli-skill-test/od-expert/references \
            || { echo "ERROR: references/ subdir not installed"; exit 1; }
          test -f /tmp/pyod-cli-skill-test/od-expert/references/workflow.md \
            || { echo "ERROR: references/workflow.md not installed"; exit 1; }
          test -f /tmp/pyod-cli-skill-test/od-expert/references/pitfalls.md \
            || { echo "ERROR: references/pitfalls.md not installed"; exit 1; }
          test -f /tmp/pyod-cli-skill-test/od-expert/references/tabular.md \
            || { echo "ERROR: references/tabular.md not installed"; exit 1; }
          test -f /tmp/pyod-cli-skill-test/od-expert/references/time_series.md \
            || { echo "ERROR: references/time_series.md not installed"; exit 1; }
          test -f /tmp/pyod-cli-skill-test/od-expert/references/graph.md \
            || { echo "ERROR: references/graph.md not installed"; exit 1; }
          test -f /tmp/pyod-cli-skill-test/od-expert/references/text_image.md \
            || { echo "ERROR: references/text_image.md not installed"; exit 1; }
          # v3.2.0: __pycache__ and __init__.py must NOT be installed
          test ! -e /tmp/pyod-cli-skill-test/od-expert/__pycache__ \
            || { echo "ERROR: __pycache__ leaked into install"; exit 1; }
          test ! -e /tmp/pyod-cli-skill-test/od-expert/__init__.py \
            || { echo "ERROR: __init__.py leaked into install"; exit 1; }
          # Regression guard: `import pyod.mcp_server` in a smoke venv
          # that deliberately does NOT have pyod[mcp] must not sys.exit.
          /tmp/pyod-smoke/bin/python -c "import importlib.util; assert importlib.util.find_spec('mcp') is None, 'smoke venv unexpectedly has mcp'"
          /tmp/pyod-smoke/bin/python -c "import pyod.mcp_server"
          # Canonical-name assertion: underscore input → hyphen output
          rm -rf /tmp/pyod-cli-underscore-test
          /tmp/pyod-smoke/bin/pyod install skill --skill od_expert \
            --target /tmp/pyod-cli-underscore-test \
            | tee /tmp/pyod-cli-underscore.log
          grep -q "Installed od-expert skill" /tmp/pyod-cli-underscore.log \
            || { echo "ERROR: canonical name not used in output"; exit 1; }
          test -f /tmp/pyod-cli-underscore-test/od-expert/SKILL.md
          echo "unified pyod CLI works end-to-end"