run-examples

#!/usr/bin/env bash

# Runs all Python examples in `examples/` directory

# Dependencies:
# sudo apt-get install parallel
# pip3 install biopython matplotlib numpy pandas pygments scipy

set -euo pipefail
trap 'echo 🟦 Cancelled; exit 0' INT

SKIP_SLOW=0

case "${1:-}" in
"--skip-slow")
  shift
  SKIP_SLOW=1
  ;;
esac

export SKIP_SLOW


function run_example() {
  set -euo pipefail

  example=$(basename -- "${1}")

  # List of examples that are slow to run. We skip them in CI.
  slow_examples=( \
    "benefits_of_sex.py" \
    "genealogies_with_selection.py" \
    "measuring_fixation_probabilities.py" \
    "multi_sample_adaptive.py" \
    "mutation_selection_balance_highd.py" \
    "neutral_LD_highd.py" \
    "speed_highd.py" \
    "speed_lowd.py" \
  )

  printf '%s\n' '--------------------------------------------------------'
  printf '\n⬜ BEGIN   "%s"\n' "${example}"

  if [ "${SKIP_SLOW}" == "1" ] && [[ " ${slow_examples[*]} " =~ ${example} ]]; then
    echo "Skipping slow example '${example}' due to '--skip-slow' argument"
    return 0
  fi

  pushd "examples/" >/dev/null
  if (python3 "${example}" 2>&1 1>/dev/null | pygmentize -l pytb -O style=material); then
    printf '🟩 SUCCESS "%s"\n\n\n' "${example}"
    return 0
  else
    printf '\n🟥 FAILURE "%s"\n\n\n' "${example}"
    return 1
  fi
  popd >/dev/null

}

export -f run_example


JOBS=$(nproc 2>/dev/null || sysctl -n hw.ncpu 2>/dev/null || getconf _NPROCESSORS_ONLN 2>/dev/null)

find "examples/" -maxdepth 1 -type f -iname '*.py' | sort | parallel -j "${JOBS}" run_example