test_examples.py

#!/usr/bin/env python

# ======================================================================
# MODULE DOCSTRING
# ======================================================================

"""
Test that the examples in the repo run without errors.
"""

# ======================================================================
# GLOBAL IMPORTS
# ======================================================================

import sys

import pathlib
import pytest
import subprocess
from perses.tests.utils import enter_temp_directory

ROOT_DIR_PATH = pathlib.Path(__file__).joinpath("../../../").resolve()
SLOW_EXAMPLES_KEYWORDS = ("barnase-barstar", "kinase-neq-switching")
NOT_EXAMPLES_KEYWORDS = ("analyze-benchmark", "moonshot-mainseries")


def run_script_file(file_path, cmd_args=None):
    """Run through the shell a python script."""
    with enter_temp_directory():
        # Make sure we grab the python executable in our env
        cmd = [f"{sys.executable}", file_path]
        print(cmd)
        # Extend cmd list with given cmd_args
        if cmd_args:
            cmd.extend(cmd_args)
        try:
            subprocess.run(cmd, capture_output=True, check=True, shell=True)
        except subprocess.CalledProcessError as error:
            raise Exception(f"Example {file_path} failed. STDERR: {error.stderr.decode()}")


def find_example_scripts():
    """Find all Python scripts, excluding Jupyter notebooks, in the examples folder.
    Returns
    -------
    example_file_paths : List[str]
        List of full paths to python scripts to execute.
    """
    examples_dir_path = ROOT_DIR_PATH.joinpath("examples")

    example_file_paths = []
    for example_file_path in examples_dir_path.glob("*/*.py"):
        # TODO: find a better way to mark slow examples
        example_posix_path = example_file_path.as_posix()
        # mark slow examples
        if any(example in example_posix_path for example in SLOW_EXAMPLES_KEYWORDS):
            example_posix_path = pytest.param(example_posix_path, marks=pytest.mark.slow)
        # mark non-examples
        elif any(example in example_posix_path for example in NOT_EXAMPLES_KEYWORDS):
            example_posix_path = pytest.param(example_posix_path, marks=pytest.mark.skip("not an example"))
        example_file_paths.append(example_posix_path)

    return example_file_paths


# ======================================================================
# TESTS
# ======================================================================
@pytest.mark.parametrize("example_file_path", find_example_scripts())
def test_examples(example_file_path):
    """Test that the example run without errors."""
    run_script_file(example_file_path)