unix-build-v2.yml

# Variables:
#   CACHE_VERSION: unique cache identifier
#   CURRENT_WEEK: weekly changing cache identifier
#   PYTHON_VERSION: string in the form of "3.x"
#   TODAY_ISO: today's date in ISO format, eg. "20200531"

steps:

# Obtain a shallow clone of the DXTBX repository.
# DXTBX will not be able to report proper version numbers
- checkout: self
  path: ./dxtbx-checkout
  fetchDepth: 1
  displayName: Checkout $(Build.SourceBranch)

# Download other source repositories
- bash: |
    set -e
    mkdir -p modules
    ln -nsf ../dxtbx-checkout modules/dxtbx
    python3 modules/dxtbx/.azure-pipelines/bootstrap.py update
  displayName: Repository checkout (initial)
  workingDirectory: $(Pipeline.Workspace)

# Download additional source repositories required by cctbx-base (but not dxtbx)
- bash: |
    set -e
    git clone https://github.com/dials/annlib.git modules/annlib
    git clone https://github.com/dials/annlib_adaptbx.git modules/annlib_adaptbx
    git clone https://github.com/dials/ccp4io.git modules/ccp4io
    git clone https://github.com/dials/ccp4io_adaptbx.git modules/ccp4io_adaptbx
    git clone https://github.com/dials/gui_resources.git modules/gui_resources
    git clone https://github.com/dials/tntbx.git modules/tntbx
  displayName: Repository checkout (additional)
  workingDirectory: $(Pipeline.Workspace)

# Create a new conda environment using the bootstrap script
- script: |
    python3 modules/dxtbx/.azure-pipelines/bootstrap.py base --python $(PYTHON_VERSION)

    # Immediately recover disk space used by miniconda installation
    du -sh miniconda
    rm -r miniconda
  displayName: Create python $(PYTHON_VERSION) environment
  workingDirectory: $(Pipeline.Workspace)

# Install cctbx and testing packages in the conda environment
- bash: |
    set -e
    . conda_base/bin/activate
    conda install -y cctbx-base dials-data pytest-azurepipelines pytest-cov pytest-timeout
    echo
    echo Environment:
    ls -la
    echo
    echo Modules:
    ls -la modules
  displayName: Install further dependencies
  workingDirectory: $(Pipeline.Workspace)

# Build dxtbx
- bash: |
    set -e
    . conda_base/bin/activate
    mkdir build
    cd build
    libtbx.configure dxtbx cbflib_adaptbx
    make
  displayName: Build dxtbx
  workingDirectory: $(Pipeline.Workspace)

# Finally, run the full regression test suite
- bash: |
    set -e
    . conda_base/bin/activate
    . build/setpaths.sh
    cd modules/dxtbx
    export PYTHONDEVMODE=1
    pytest -v -ra -n auto --basetemp="$(Pipeline.Workspace)/tests" --durations=10 \
        --cov=$(pwd) --cov-report=html --cov-report=xml --cov-branch \
        --timeout=5400 --regression || echo "##vso[task.complete result=Failed;]Some tests failed"
  displayName: Run tests
  workingDirectory: $(Pipeline.Workspace)

- script: |
    bash <(curl -s https://codecov.io/bash) -n "Python $(PYTHON_VERSION) $(Agent.OS)"
  displayName: 'Publish coverage stats'
  continueOnError: True
  timeoutInMinutes: 3
  workingDirectory: $(Pipeline.Workspace)/modules/dxtbx