test_wheels.sh

#!/usr/bin/env bash
# A simple set of tests checking if a wheel is working correctly
set -xe

# See CMake's CMAKE_HOST_SYSTEM_PROCESSOR documentation
# On the systems where we are building wheel we can rely
# on uname -m. Note that this is just wheel testing script.
ARCH_DIR="$(uname -m)"

if [ ! -f pyproject.toml ]; then
    echo "Error: Please launch $0 from the root dir"
    exit 1
fi

if [ "$#" -lt 2 ]; then
    echo "Usage: $(basename "$0") python_exe python_wheel [use_virtual_env]"
    exit 1
fi

# cli parameters
python_exe=$1   # python to be used for testing
python_wheel=$2 # python wheel to be tested
use_venv=$3     # if $3 is not "false" then use virtual environment

has_coreneuron=false   # true if coreneuron support is available

# python version being used
python_ver=$("$python_exe" -c "import sys; print('%d%d' % tuple(sys.version_info)[:2])")


run_mpi_test () {
  mpi_launcher=${1}
  mpi_name=${2}
  mpi_module=${3}

  echo "======= Testing $mpi_name ========"
  if [ -n "$mpi_module" ]; then
     echo "Loading module $mpi_module"
     module load $mpi_module
  fi

  # hoc and python based test
  $mpi_launcher -n 2 $python_exe src/parallel/test0.py -mpi --expected-hosts 2
  $mpi_launcher -n 2 nrniv src/parallel/test0.hoc -mpi --expected-hosts 2

  # TODO: run coreneuron binary shipped inside wheel. This can not be executed in platform
  #       independent manner because we need to pre-load libmpi library beforehand e.g. using
  #       LD_PRELOAD mechanism. For now, execute without --mpi argument
  if [[ "$has_coreneuron" == "true" ]] && [[ $mpi_name == *"MPICH"* || $mpi_name == *"Intel MPI"* ]]; then
      site_package_dir=`$python_exe -c 'import os, neuron; print(os.path.dirname(neuron.__file__))'`
      corenrn_mpi_lib=`ls $site_package_dir/.data/lib/libcorenrnmpi_mpich*`

      HOC_LIBRARY_PATH=${PWD}/test/ringtest nrniv test/ringtest/ring.hoc
      mv out.dat out.nrn.dat
      $mpi_launcher -n 1 nrniv-core --datpath . --mpi-lib=$corenrn_mpi_lib
      diff -w out.dat out.nrn.dat
      rm -rf *.dat
  fi

  # build new special
  rm -rf $ARCH_DIR
  nrnivmodl tmp_mod

  # run python test via nrniv and special (except on azure pipelines)
  if [[ "$SKIP_EMBEDED_PYTHON_TEST" != "true" ]]; then
    $mpi_launcher -n 2 ./$ARCH_DIR/special -python src/parallel/test0.py -mpi --expected-hosts 2
    $mpi_launcher -n 2 nrniv -python src/parallel/test0.py -mpi --expected-hosts 2
  fi

  # coreneuron execution via neuron
  if [[ "$has_coreneuron" == "true" ]]; then
    rm -rf $ARCH_DIR
    TEMP_DIR="${TMPDIR:-/tmp}/test/coreneuron/mod files/"
    if [ ! -d "${TEMP_DIR}" ]; then
        mkdir -p "${TEMP_DIR}"
    fi
    cp "test/coreneuron/mod files/"* "${TEMP_DIR}/"
    # also copy one MOD file containing sparse solver
    cp share/examples/nrniv/nmodl/capmp.mod "${TEMP_DIR}"
    nrnivmodl -coreneuron "${TEMP_DIR}"

    $mpi_launcher -n 1 $python_exe test/coreneuron/test_direct.py

    # using -python doesn't work on Azure CI
    if [[ "$SKIP_EMBEDED_PYTHON_TEST" != "true" ]]; then
      $mpi_launcher -n 2 nrniv -python -mpi test/coreneuron/test_direct.py
      NVCOMPILER_ACC_TIME=1 CORENRN_ENABLE_GPU=0 $mpi_launcher -n 2 ./$ARCH_DIR/special -python -mpi test/coreneuron/test_direct.py
    fi
  fi

  if [ -n "$mpi_module" ]; then
     echo "Unloading module $mpi_module"
     module unload $mpi_module
  fi
  echo -e "----------------------\n\n"
}


run_serial_test () {
    # Test 1: run base tests for within python
    $python_exe -c "import neuron; neuron.test(); neuron.test_rxd()"

    # Test 2: execute nrniv
    nrniv -c "print \"hello\""

    # Test 3: run coreneuron binary shipped inside wheel
    if [[ "$has_coreneuron" == "true" ]]; then
        $python_exe -c "from neuron.tests import test_nmodl; test_nmodl.test_nmodl()"
        HOC_LIBRARY_PATH=${PWD}/test/ringtest nrniv test/ringtest/ring.hoc
        mv out.dat out.nrn.dat
        nrniv-core --datpath .
        diff -w out.dat out.nrn.dat
        rm -rf *.dat
    fi

    # Test 4: execute nrnivmodl
    rm -rf $ARCH_DIR
    nrnivmodl tmp_mod

    # Test 5: execute special hoc interpreter
    ./$ARCH_DIR/special -c "print \"hello\""

    # Test 6: run basic tests via python while loading shared library
    $python_exe -c "import neuron; neuron.test(); neuron.test_rxd(); quit()"

    # Test 7: run basic test to use compiled mod file
    $python_exe -c "import neuron; from neuron import h; s = h.Section(); s.insert('cacum'); quit()"

    # Test 8: run basic tests via special : azure pipelines get stuck with their
    # own python from hosted cache (most likely security settings).
    if [[ "$SKIP_EMBEDED_PYTHON_TEST" != "true" ]]; then
      ./$ARCH_DIR/special -python -c "import neuron; neuron.test(); neuron.test_rxd(); quit()"
      nrniv -python -c "import neuron; neuron.test(); neuron.test_rxd(); quit()"
    else
      $python_exe -c "import neuron; neuron.test(); neuron.test_rxd(); quit()"
    fi

    # Test 9: coreneuron execution via neuron
    if [[ "$has_coreneuron" == "true" ]]; then
      rm -rf $ARCH_DIR

      # first test vanialla coreneuron support, without nrnivmodl
      $python_exe test/coreneuron/test_psolve.py

      nrnivmodl -coreneuron "test/coreneuron/mod files/"

      # coreneuron+gpu can be used via python but special only
      $python_exe test/coreneuron/test_direct.py

      # using -python doesn't work on Azure CI
      if [[ "$SKIP_EMBEDED_PYTHON_TEST" != "true" ]]; then
        ./$ARCH_DIR/special -python test/coreneuron/test_direct.py
        nrniv -python test/coreneuron/test_direct.py
      fi

      rm -rf $ARCH_DIR
    fi


    # Test 10: run demo
    neurondemo -c 'demo(4)' -c 'run()' -c 'quit()'

    # Test 11: modlunit available (and can find nrnunits.lib)
    modlunit tmp_mod/cacum.mod
}


run_parallel_test() {
    # this is for MacOS system
    if [[ "$OSTYPE" == "darwin"* ]]; then
      # assume both MPIs are installed via brew.
      BREW_PREFIX=$(brew --prefix)

      brew unlink openmpi
      brew link mpich
      export DYLD_LIBRARY_PATH=${BREW_PREFIX}/opt/mpich/lib:$DYLD_LIBRARY_PATH
      run_mpi_test "${BREW_PREFIX}/opt/mpich/bin/mpirun" "MPICH" ""

      brew unlink mpich
      brew link openmpi
      export DYLD_LIBRARY_PATH=${BREW_PREFIX}/opt/open-mpi/lib:$DYLD_LIBRARY_PATH
      run_mpi_test "${BREW_PREFIX}/opt/open-mpi/bin/mpirun" "OpenMPI" ""

    # CI Linux or Azure Linux or circleCI build (all on Debian/Ubuntu)
    elif [[ "$CI_OS_NAME" == "linux" || "$AGENT_OS" == "Linux" || "$CIRCLECI" == "true" ]]; then
      # make debugging easier
      sudo update-alternatives --get-selections | grep mpi
      sudo update-alternatives --list mpi-${ARCH_DIR}-linux-gnu
      # choose mpich
      sudo update-alternatives --set mpi-${ARCH_DIR}-linux-gnu /usr/include/${ARCH_DIR}-linux-gnu/mpich
      run_mpi_test "mpirun.mpich" "MPICH" ""
      # choose openmpi
      sudo update-alternatives --set mpi-${ARCH_DIR}-linux-gnu /usr/lib/${ARCH_DIR}-linux-gnu/openmpi/include
      run_mpi_test "mpirun.openmpi --oversubscribe" "OpenMPI" ""

    # linux desktop or docker container used for wheel
    else
      export PATH=/opt/mpich/bin:$PATH
      export LD_LIBRARY_PATH=/opt/mpich/lib:$LD_LIBRARY_PATH
      run_mpi_test "mpirun" "MPICH" ""

      export PATH=/opt/openmpi/bin:$PATH
      export LD_LIBRARY_PATH=/opt/openmpi/lib:$LD_LIBRARY_PATH
      run_mpi_test "mpirun" "OpenMPI" ""
    fi
}


test_wheel () {
    # sample mod file for nrnivmodl check
    mkdir -p tmp_mod
    # delete tmp_mod and arch dir on EXIT or SIGINT
    trap "rm -fr tmp_mod ${ARCH_DIR}" EXIT SIGINT
    cp share/examples/nrniv/nmodl/cacum.mod tmp_mod/

    # check gcc and python versions
    gcc --version && python --version

    echo "Using `which $python_exe` : `$python_exe --version`"
    echo "=========== SERIAL TESTS ==========="
    run_serial_test

    echo "=========== MPI TESTS ============"
    run_parallel_test
}


test_wheel_basic_python () {
    echo "=========== BASIC PYTHON TESTS ==========="
    $python_exe -c "import neuron; neuron.test(); neuron.test_rxd()"
}


echo "== Testing $python_wheel using $python_exe ($python_ver) =="


# creat python virtual environment and use `python` as binary name
# because it will be correct one from venv.
if [[ "$use_venv" != "false" ]]; then
  echo " == Creating virtual environment == "
  venv_name="nrn_test_venv_${python_ver}"
  $python_exe -m venv $venv_name
  . $venv_name/bin/activate
  python_exe="$(command -v python)"
  # delete venv on EXIT or SIGINT
  trap "rm -fr ${venv_name}" EXIT SIGINT
else
  echo " == Using global install == "
fi


$python_exe -m pip install -r ci/uv_requirements.txt

# install test requirements
$python_exe -m uv pip install -r packaging/python/test_requirements.txt
$python_exe -m uv pip install --force-reinstall $python_wheel
$python_exe -m uv pip show neuron || $python_exe -m uv pip show neuron-nightly

# neuron.__version__ is nrnversion(5)/GIT_DESCRIBE; empty breaks ModelDB workdir naming
$python_exe -c "import neuron; v = neuron.__version__; assert v and str(v).strip(), repr(v)"

# check the existence of coreneuron support
compile_options="$(nrniv -nobanner -nogui -c 'nrnversion(6)')"
if echo $compile_options | grep "NRN_ENABLE_CORENEURON=ON" > /dev/null ; then
  has_coreneuron=true
fi

# run tests with latest NumPy
echo " == Running tests with latest NumPy == "
test_wheel

# run basic python tests with oldest supported NumPy
echo " == Running basic python tests with oldest supported NumPy == "
$python_exe -m uv pip install -r packaging/python/oldest_numpy_requirements.txt
test_wheel_basic_python