azure-pipelines.yml

trigger:
  # start a new build for every push
  batch: False
  branches:
    include:
      - develop
  paths:
    include:
      - '*'

pr:
  branches:
    include:
    - '*'  # must quote since "*" is a YAML reserved character; we want a string


jobs:
- job: Precommit_Lint
  displayName: 'Pre-commit checks'
  pool:
    vmImage: 'ubuntu-latest'
  variables:
    PRE_COMMIT_HOME: '$(Pipeline.Workspace)/.pre-commit-cache'
  steps:
  - task: UsePythonVersion@0
    inputs:
      versionSpec: '3.11'
      addToPath: true
      architecture: 'x64'
  - task: Cache@2
    inputs:
      key: 'pre-commit | "$(Agent.OS)" | .pre-commit-config.yaml'
      path: '$(PRE_COMMIT_HOME)'
      restoreKeys: |
        pre-commit | "$(Agent.OS)"
  - script: python -m pip install --upgrade pip pre-commit
    displayName: 'Install pre-commit'
  - script: PRE_COMMIT_HOME=$(PRE_COMMIT_HOME) pre-commit run --all-files
    displayName: 'Run pre-commit hooks'

- job: Ruff_Lint
  displayName: 'Ruff lint checks'
  pool:
    vmImage: 'ubuntu-latest'
  steps:
  - task: UsePythonVersion@0
    inputs:
      versionSpec: '3.11'
      addToPath: true
      architecture: 'x64'
  - script: python -m pip install --upgrade pip ruff
    displayName: 'Install ruff'
  - script: ruff check package testsuite
    displayName: 'Run ruff checks'

- job: Smoke_Tests
  displayName: 'Smoke tests'
  pool:
    vmImage: 'ubuntu-latest'
  steps:
  - task: UsePythonVersion@0
    inputs:
      versionSpec: '3.11'
      addToPath: true
      architecture: 'x64'
  - script: python -m pip install --upgrade pip setuptools wheel
    displayName: 'Install tools'
  - script: >-
      python -m pip install --only-binary=scipy,h5py
      cython
      h5py>=2.10
      matplotlib
      numpy
      packaging
      pytest
      tqdm
      threadpoolctl
      filelock
    displayName: 'Install smoke dependencies'
  - script: >-
      python -m pip install
      ./package
      ./testsuite
    displayName: 'Install package and testsuite'
  - script: >-
      pytest testsuite/MDAnalysisTests/test_api.py
      --disable-pytest-warnings
      -q
    displayName: 'Run smoke tests'

- job: Azure_Tests
  dependsOn:
    - Precommit_Lint
    - Ruff_Lint
    - Smoke_Tests
  condition: and(succeeded(), ne(variables['Build.SourceBranch'], 'refs/heads/develop'))  # skip for PR merges
  variables:
    MPLBACKEND: agg
  strategy:
    matrix:
        Win-Python311-64bit-full:
          PYTHON_VERSION: '3.11'
          PYTHON_ARCH: 'x64'
          BUILD_TYPE: 'normal'
          imageName: 'windows-latest'
        Win-Python313-64bit-full:
          PYTHON_VERSION: '3.13'
          PYTHON_ARCH: 'x64'
          BUILD_TYPE: 'normal'
          imageName: 'windows-latest'
        Win-Python313-64bit-full-wheel:
          PYTHON_VERSION: '3.13'
          PYTHON_ARCH: 'x64'
          BUILD_TYPE: 'wheel'
          NUMPY_MIN: '2.1.0'
          imageName: 'windows-latest'
        Win-Python311-64bit-full-wheel:
          PYTHON_VERSION: '3.11'
          PYTHON_ARCH: 'x64'
          BUILD_TYPE: 'wheel'
          NUMPY_MIN: '1.26.0'
          imageName: 'windows-latest'
        Linux-Python313-64bit-full-wheel:
          PYTHON_VERSION: '3.13'
          PYTHON_ARCH: 'x64'
          BUILD_TYPE: 'wheel'
          NUMPY_MIN: '2.1.0'
          imageName: 'ubuntu-latest'
        Linux-Python311-64bit-full-wheel:
          PYTHON_VERSION: '3.11'
          PYTHON_ARCH: 'x64'
          BUILD_TYPE: 'wheel'
          NUMPY_MIN: '1.26.0'
          imageName: 'ubuntu-latest'
  pool:
    vmImage: $(imageName)
  steps:
  - task: UsePythonVersion@0
    inputs:
      versionSpec: $(PYTHON_VERSION)
      addToPath: true
      architecture: $(PYTHON_ARCH)
  # a PEP518 compliant wheel build shoud be
  # able to build MDAnalysis in an isolated
  # environment *before* any deps are installed
  # "manually"
  - powershell: |
      cd package
      python -m pip -v install .
      cd ..
    displayName: 'Build MDAnalysis (wheel)'
    condition: and(succeeded(), eq(variables['BUILD_TYPE'], 'wheel'))
  - script: python -m pip install --upgrade pip setuptools wheel
    displayName: 'Install tools'
  - script: >-
      python -m pip install --only-binary=scipy,h5py
      cython
      hypothesis
      h5py>=2.10
      matplotlib
      numpy
      packaging
      pytest
      pytest-cov
      pytest-timeout
      pytest-xdist
      scikit-learn
      tqdm
      threadpoolctl
      filelock
    displayName: 'Install dependencies'
  # for wheel install testing, we pin to an
  # older NumPy, the oldest version we support and that
  # supports the Python version in use
  # to check the ABI compatibility of our wheels
  - script: >-
      python -m pip install numpy==$(NUMPY_MIN)
    displayName: 'pin to older NumPy (wheel test)'
    condition: and(succeeded(), ne(variables['NUMPY_MIN'], ''))
  - script: >-
      python -m pip install -vvv
      biopython
      chemfiles>=0.10
      duecredit
      joblib
      GridDataFormats
      mmtf-python
      networkx
      parmed
      rdkit>=2024.03.4
      tidynamics>=1.0.0
      imdclient>=0.2.2
      pytng>=0.3.4

    # remove from azure to avoid test hanging #4707
    # "gsd>3.0.0"
    displayName: 'Install additional dependencies for 64-bit tests'
    condition: and(succeeded(), eq(variables['PYTHON_ARCH'], 'x64'))
  - script: >-
      pip list
    displayName: 'List of installed dependencies'
  - powershell: |
      python -m pip install ./package
      python -m pip install ./testsuite
    displayName: 'Build MDAnalysis'
    condition: and(succeeded(), eq(variables['BUILD_TYPE'], 'normal'))
  - powershell: pip list
    displayName: 'Check installed packages'
  - powershell: |
      cd testsuite
      pytest MDAnalysisTests --disable-pytest-warnings -n logical --timeout=200 -rsx --cov=MDAnalysis
    displayName: 'Run MDAnalysis Test Suite'
  - script: |
      curl -s https://codecov.io/bash | bash
    condition: succeeded()
    displayName: 'Codecov Coverage Data Upload'