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run-tests.py
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run-tests.py
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#!/usr/bin/env python
#
# Runs all unit tests included in PyBaMM.
#
# The code in this file is adapted from Pints
# (see https://github.com/pints-team/pints)
#
import re
import os
import pybamm
import sys
import argparse
import unittest
import subprocess
def run_code_tests(executable=False, folder: str = "unit", interpreter="python"):
"""
Runs tests, exits if they don't finish.
Parameters
----------
executable : bool (default False)
If True, tests are run in subprocesses using the executable 'python'.
Must be True for travis tests (otherwise tests always 'pass')
folder : str
Which folder to run the tests from (unit, integration or both ('all'))
"""
if folder == "all":
tests = "tests/"
else:
tests = "tests/" + folder
if folder == "unit":
pybamm.settings.debug_mode = True
if interpreter == "python":
# Make sure to refer to the interpreter for the
# currently activated virtual environment
interpreter = sys.executable
if executable is False:
suite = unittest.defaultTestLoader.discover(tests, pattern="test*.py")
result = unittest.TextTestRunner(verbosity=2).run(suite)
ret = int(not result.wasSuccessful())
else:
print("Running {} tests with executable '{}'".format(folder, interpreter))
cmd = [interpreter, "-m", "unittest", "discover", "-v", tests]
p = subprocess.Popen(cmd)
try:
ret = p.wait()
except KeyboardInterrupt:
try:
p.terminate()
except OSError:
pass
p.wait()
print("")
sys.exit(1)
if ret != 0:
sys.exit(ret)
def run_doc_tests():
"""
Checks if the documentation can be built, runs any doctests (currently not
used).
"""
print("Checking if docs can be built.")
p = subprocess.Popen(
["sphinx-build", "-b", "doctest", "docs", "docs/build/html", "-W"]
)
try:
ret = p.wait()
except KeyboardInterrupt:
try:
p.terminate()
except OSError:
pass
p.wait()
print("")
sys.exit(1)
if ret != 0:
print("FAILED")
sys.exit(ret)
def run_notebook_and_scripts(executable="python"):
"""
Runs Jupyter notebook tests. Exits if they fail.
"""
# Scan and run
print("Testing notebooks and scripts with executable `" + str(executable) + "`")
if not scan_for_nb_and_scripts("examples", True, executable):
print("\nErrors encountered in notebooks")
sys.exit(1)
print("\nOK")
def scan_for_nb_and_scripts(root, recursive=True, executable="python"):
"""
Scans for, and tests, all notebooks and scripts in a directory.
"""
ok = True
debug = False
# Scan path
for filename in os.listdir(root):
path = os.path.join(root, filename)
# Recurse into subdirectories
if recursive and os.path.isdir(path):
# Ignore hidden directories
if filename[:1] == ".":
continue
ok &= scan_for_nb_and_scripts(path, recursive, executable)
# Test notebooks
if os.path.splitext(path)[1] == ".ipynb":
if debug:
print(path)
else:
ok &= test_notebook(path, executable)
# Test scripts
elif os.path.splitext(path)[1] == ".py":
if debug:
print(path)
else:
ok &= test_script(path, executable)
# Return True if every notebook is ok
return ok
def test_notebook(path, executable="python"):
"""
Tests a single notebook, exists if it doesn't finish.
"""
import nbconvert
import pybamm
b = pybamm.Timer()
print("Test " + path + " ... ", end="")
sys.stdout.flush()
# Make sure the notebook has a "%pip install pybamm -q" command, for using Google
# Colab
with open(path, "r") as f:
if "%pip install pybamm -q" not in f.read():
# print error and exit
print("\n" + "-" * 70)
print("ERROR")
print("-" * 70)
print("Installation command '%pip install pybamm -q' not found in notebook")
print("-" * 70)
return False
# Make sure the notebook has "pybamm.print_citations()" to print the relevant papers
with open(path, "r") as f:
if "pybamm.print_citations()" not in f.read():
# print error and exit
print("\n" + "-" * 70)
print("ERROR")
print("-" * 70)
print(
"Print citations command 'pybamm.print_citations()' not found in "
"notebook"
)
print("-" * 70)
return False
# Load notebook, convert to Python
e = nbconvert.exporters.PythonExporter()
code, __ = e.from_filename(path)
# Remove coding statement, if present
code = "\n".join([x for x in code.splitlines() if x[:9] != "# coding"])
# Tell matplotlib not to produce any figures
env = dict(os.environ)
env["MPLBACKEND"] = "Template"
# If notebook makes use of magic commands then
# the script must be run using ipython
# https://github.com/jupyter/nbconvert/issues/503#issuecomment-269527834
executable = (
"ipython"
if (("run_cell_magic(" in code) or ("run_line_magic(" in code))
else executable
)
# Run in subprocess
cmd = [executable] + ["-c", code]
try:
p = subprocess.Popen(
cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, env=env
)
stdout, stderr = p.communicate()
# TODO: Use p.communicate(timeout=3600) if Python3 only
if p.returncode != 0:
# Show failing code, output and errors before returning
print("ERROR")
print("-- script " + "-" * (79 - 10))
for i, line in enumerate(code.splitlines()):
j = str(1 + i)
print(j + " " * (5 - len(j)) + line)
print("-- stdout " + "-" * (79 - 10))
print(str(stdout, "utf-8"))
print("-- stderr " + "-" * (79 - 10))
print(str(stderr, "utf-8"))
print("-" * 79)
return False
except KeyboardInterrupt:
p.terminate()
print("ABORTED")
sys.exit(1)
# Sucessfully run
print("ok ({})".format(b.time()))
return True
def test_script(path, executable="python"):
"""
Tests a single notebook, exists if it doesn't finish.
"""
import pybamm
b = pybamm.Timer()
print("Test " + path + " ... ", end="")
sys.stdout.flush()
# Tell matplotlib not to produce any figures
env = dict(os.environ)
env["MPLBACKEND"] = "Template"
# Run in subprocess
cmd = [executable] + [path]
try:
p = subprocess.Popen(
cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, env=env
)
stdout, stderr = p.communicate()
# TODO: Use p.communicate(timeout=3600) if Python3 only
if p.returncode != 0:
# Show failing code, output and errors before returning
print("ERROR")
print("-- stdout " + "-" * (79 - 10))
print(str(stdout, "utf-8"))
print("-- stderr " + "-" * (79 - 10))
print(str(stderr, "utf-8"))
print("-" * 79)
return False
except KeyboardInterrupt:
p.terminate()
print("ABORTED")
sys.exit(1)
# Sucessfully run
print("ok ({})".format(b.time()))
return True
def export_notebook(ipath, opath):
"""
Exports the notebook at `ipath` to a Python file at `opath`.
"""
import nbconvert
from traitlets.config import Config
# Create nbconvert configuration to ignore text cells
c = Config()
c.TemplateExporter.exclude_markdown = True
# Load notebook, convert to Python
e = nbconvert.exporters.PythonExporter(config=c)
code, __ = e.from_filename(ipath)
# Remove "In [1]:" comments
r = re.compile(r"(\s*)# In\[([^]]*)\]:(\s)*")
code = r.sub("\n\n", code)
# Store as executable script file
with open(opath, "w") as f:
f.write("#!/usr/bin/env python")
f.write(code)
os.chmod(opath, 0o775)
if __name__ == "__main__":
# Set up argument parsing
parser = argparse.ArgumentParser(
description="Run unit tests for PyBaMM.",
epilog="To run individual unit tests, use e.g. '$ tests/unit/test_timer.py'",
)
# Unit tests
parser.add_argument(
"--integration",
action="store_true",
help="Run integration tests using the python interpreter.",
)
parser.add_argument(
"--unit",
action="store_true",
help="Run unit tests using the `python` interpreter.",
)
parser.add_argument(
"--all",
action="store_true",
help="Run all tests (unit and integration) using the `python` interpreter.",
)
parser.add_argument(
"--nosub",
action="store_true",
help="Run unit tests without starting a subprocess.",
)
# Notebook tests
parser.add_argument(
"--examples",
action="store_true",
help="Test all Jupyter notebooks and scripts in `examples`.",
)
parser.add_argument(
"-debook",
nargs=2,
metavar=("in", "out"),
help="Export a Jupyter notebook to a Python file for manual testing.",
)
# Flake8 (deprecated)
parser.add_argument(
"--flake8",
action="store_true",
help="Run flake8 to check for style issues (deprecated, use pre-commit)",
)
# Doctests
parser.add_argument(
"--doctest",
action="store_true",
help="Run any doctests, check if docs can be built",
)
# Combined test sets
parser.add_argument(
"--quick",
action="store_true",
help="Run quick checks (code tests, docs)",
)
# Non-standard Python interpreter name for subprocesses
parser.add_argument(
"--interpreter",
nargs="?",
default="python",
metavar="python",
help="Give the name of the Python interpreter if it is not 'python'",
)
# Parse!
args = parser.parse_args()
# Run tests
has_run = False
# Unit vs integration
interpreter = args.interpreter
# Unit tests
if args.integration:
has_run = True
run_code_tests(True, "integration", interpreter)
if args.unit:
has_run = True
run_code_tests(True, "unit", interpreter)
if args.all:
has_run = True
run_code_tests(True, "all", interpreter)
if args.nosub:
has_run = True
run_code_tests(folder="unit", interpreter=interpreter)
# Flake8
if args.flake8:
raise NotImplementedError("flake8 is no longer used. Use pre-commit instead.")
# Doctests
if args.doctest:
has_run = True
run_doc_tests()
# Notebook tests
elif args.examples:
has_run = True
run_notebook_and_scripts(interpreter)
if args.debook:
has_run = True
export_notebook(*args.debook)
# Combined test sets
if args.quick:
has_run = True
run_code_tests("all", interpreter=interpreter)
run_doc_tests()
# Help
if not has_run:
parser.print_help()