def execute_notebook(nb, src, cell_separator):
"""
Run the notebook in a python3 kernel. The ESPResSo visualizers are
disabled to prevent the kernel from crashing and to allow running
the notebook in a CI environment.
"""
import nbconvert.preprocessors
notebook_dirname = os.path.dirname(notebook_filepath)
# disable OpenGL/Mayavi GUI
src_no_gui = iw.mock_es_visualization(src)
# update notebook with new code
set_code_cells(nb, src_no_gui.split(cell_separator))
# execute notebook
ep = nbconvert.preprocessors.ExecutePreprocessor(timeout=20 * 60,
kernel_name='python3')
ep.preprocess(nb, {'metadata': {'path': notebook_dirname}})
# restore notebook with code before the GUI removal step
set_code_cells(nb, src.split(cell_separator))
def test_mock_es_visualization(self):
statement = "import espressomd.visualization"
expected = """
try:
import espressomd.visualization
if hasattr(espressomd.visualization.mayaviLive, 'deferred_ImportError') or \\
hasattr(espressomd.visualization.openGLLive, 'deferred_ImportError'):
raise ImportError()
except ImportError:
from unittest.mock import MagicMock
import espressomd
espressomd.visualization = MagicMock()
"""
self.assertEqual(iw.mock_es_visualization(statement), expected[1:])
statement = "import espressomd.visualization as test"
expected = """
try:
import espressomd.visualization as test
if hasattr(test.mayaviLive, 'deferred_ImportError') or \\
hasattr(test.openGLLive, 'deferred_ImportError'):
raise ImportError()
except ImportError:
from unittest.mock import MagicMock
import espressomd
test = MagicMock()
"""
self.assertEqual(iw.mock_es_visualization(statement), expected[1:])
statement = "from espressomd import visualization"
expected = """
try:
from espressomd import visualization
if hasattr(visualization.mayaviLive, 'deferred_ImportError') or \\
hasattr(visualization.openGLLive, 'deferred_ImportError'):
raise ImportError()
except ImportError:
from unittest.mock import MagicMock
import espressomd
visualization = MagicMock()
"""
self.assertEqual(iw.mock_es_visualization(statement), expected[1:])
statement = "from espressomd import visualization as test"
expected = """
try:
from espressomd import visualization as test
if hasattr(test.mayaviLive, 'deferred_ImportError') or \\
hasattr(test.openGLLive, 'deferred_ImportError'):
raise ImportError()
except ImportError:
from unittest.mock import MagicMock
import espressomd
test = MagicMock()
"""
self.assertEqual(iw.mock_es_visualization(statement), expected[1:])
statement = "from espressomd import visualization_mayavi"
expected = """
try:
from espressomd import visualization_mayavi
except ImportError:
from unittest.mock import MagicMock
import espressomd
visualization_mayavi = MagicMock()
"""
self.assertEqual(iw.mock_es_visualization(statement), expected[1:])
statement = "from espressomd import visualization_mayavi as test"
expected = """
try:
from espressomd import visualization_mayavi as test
except ImportError:
from unittest.mock import MagicMock
import espressomd
test = MagicMock()
"""
self.assertEqual(iw.mock_es_visualization(statement), expected[1:])
statement = "from espressomd.visualization_mayavi import mayaviLive"
expected = """
try:
from espressomd.visualization_mayavi import mayaviLive
except ImportError:
from unittest.mock import MagicMock
import espressomd
mayaviLive = MagicMock()
"""
self.assertEqual(iw.mock_es_visualization(statement), expected[1:])
statement = "from espressomd.visualization_mayavi import mayaviLive as test"
expected = """
try:
from espressomd.visualization_mayavi import mayaviLive as test
except ImportError:
from unittest.mock import MagicMock
import espressomd
test = MagicMock()
"""
self.assertEqual(iw.mock_es_visualization(statement), expected[1:])
statement = "from espressomd.visualization_mayavi import a as b, c"
expected = """
try:
from espressomd.visualization_mayavi import a as b
except ImportError:
from unittest.mock import MagicMock
import espressomd
b = MagicMock()
try:
from espressomd.visualization_mayavi import c
except ImportError:
from unittest.mock import MagicMock
import espressomd
c = MagicMock()
"""
self.assertEqual(iw.mock_es_visualization(statement), expected[1:])
statement = "from espressomd.visualization import openGLLive"
expected = """
try:
from espressomd.visualization import openGLLive
if hasattr(openGLLive, 'deferred_ImportError'):
raise openGLLive.deferred_ImportError
except ImportError:
from unittest.mock import MagicMock
import espressomd
openGLLive = MagicMock()
"""
self.assertEqual(iw.mock_es_visualization(statement), expected[1:])
statement = "from espressomd.visualization import openGLLive as test"
expected = """
try:
from espressomd.visualization import openGLLive as test
if hasattr(test, 'deferred_ImportError'):
raise test.deferred_ImportError
except ImportError:
from unittest.mock import MagicMock
import espressomd
test = MagicMock()
"""
self.assertEqual(iw.mock_es_visualization(statement), expected[1:])
# test exceptions
statements_without_namespace = [
"from espressomd.visualization import *",
"from espressomd.visualization_opengl import *",
"from espressomd.visualization_mayavi import *"
]
for s in statements_without_namespace:
self.assertRaises(AssertionError, iw.mock_es_visualization, s)
lineno_end = mapping[visitor.matplotlib_first]
split_code = '\n'.join(lines[lineno_end:]).lstrip('\n')
if split_code:
new_cell = nbformat.v4.new_code_cell(source=split_code)
nb['cells'].insert(i + 1, new_cell)
lines = lines[:lineno_end]
nb['cells'][i]['source'] = '\n'.join(lines).rstrip('\n')
break
# substitute global variables and disable OpenGL/Mayavi GUI
cell_separator = '\n##{}\n'.format(uuid.uuid4().hex)
src = cell_separator.join(get_code_cells(nb))
parameters = dict(x.split('=', 1) for x in new_values)
src = iw.substitute_variable_values(src, strings_as_is=True,
keep_original=False, **parameters)
src_no_gui = iw.mock_es_visualization(src)
# update notebook with new code
set_code_cells(nb, src_no_gui.split(cell_separator))
# execute notebook
ep = ExecutePreprocessor(timeout=20 * 60, kernel_name='python3')
ep.preprocess(nb, {'metadata': {'path': notebook_dirname}})
# restore notebook with code before the GUI removal step
set_code_cells(nb, src.split(cell_separator))
# write edited notebook
with open(notebook_filepath_edited, 'w', encoding='utf-8') as f:
nbformat.write(nb, f)
def test_mock_es_visualization(self):
statement = "import espressomd.visualization"
expected = f"""
try:
{statement}
except ImportError:
import unittest.mock
import espressomd
espressomd.visualization = unittest.mock.MagicMock()
"""
self.assertEqual(iw.mock_es_visualization(statement), expected[1:])
statement = "import espressomd.visualization as test"
expected = f"""
try:
{statement}
except ImportError:
import unittest.mock
import espressomd
test = unittest.mock.MagicMock()
"""
self.assertEqual(iw.mock_es_visualization(statement), expected[1:])
statement = "import espressomd.visualization, espressomd.visualization as test"
expected = """
try:
import espressomd.visualization
except ImportError:
import unittest.mock
import espressomd
espressomd.visualization = unittest.mock.MagicMock()
try:
import espressomd.visualization as test
except ImportError:
import unittest.mock
import espressomd
test = unittest.mock.MagicMock()
"""
self.assertEqual(iw.mock_es_visualization(statement), expected[1:])
statement = "from espressomd import visualization"
expected = f"""
try:
{statement}
except ImportError:
import unittest.mock
import espressomd
visualization = unittest.mock.MagicMock()
"""
self.assertEqual(iw.mock_es_visualization(statement), expected[1:])
statement = "from espressomd import visualization as test"
expected = f"""
try:
{statement}
except ImportError:
import unittest.mock
import espressomd
test = unittest.mock.MagicMock()
"""
self.assertEqual(iw.mock_es_visualization(statement), expected[1:])
statement = "from espressomd.visualization import openGLLive"
expected = f"""
try:
{statement}
except ImportError:
import unittest.mock
import espressomd
openGLLive = unittest.mock.MagicMock()
"""
self.assertEqual(iw.mock_es_visualization(statement), expected[1:])
statement = "from espressomd.visualization import openGLLive as test"
expected = f"""
try:
{statement}
except ImportError:
import unittest.mock
import espressomd
test = unittest.mock.MagicMock()
"""
self.assertEqual(iw.mock_es_visualization(statement), expected[1:])
statement = "from espressomd.visualization import a as b, openGLLive"
expected = """
try:
from espressomd.visualization import a as b
except ImportError:
import unittest.mock
import espressomd
b = unittest.mock.MagicMock()
try:
from espressomd.visualization import openGLLive
except ImportError:
import unittest.mock
import espressomd
openGLLive = unittest.mock.MagicMock()
"""
self.assertEqual(iw.mock_es_visualization(statement), expected[1:])
# test exceptions
self.assertRaises(ValueError, iw.mock_es_visualization,
"from espressomd.visualization import *")