def variant(time, source, past, durl, max_distance, notebook_path):
"""Generate and run a variant of an analysis notebook based on a specific
substitution-detection model."""
# Create the model defined on the command line.
time, source, past, durl = map(lambda s: s.split('.')[1],
[time, source, past, durl])
model = Model(time=Time[time], source=Source[source], past=Past[past],
durl=Durl[durl], max_distance=max_distance)
notebook_folder, notebook_file = split(notebook_path)
variant_path = settings.NOTEBOOK.format(model=model,
notebook=notebook_file)
_, variant_file = split(variant_path)
# Read the source notebook and generate the appropriate variant.
if not exists(notebook_path):
raise Exception("Couldn't find notebook '{}'".format(notebook_path))
logger.debug("Reading notebook '{}'".format(notebook_file))
with open(notebook_path) as f:
notebook = nbformat.read(f, as_version=4)
logger.info("Creating notebook '{}'".format(variant_file))
model_str = '{}'.format(model)
for cell in notebook.cells:
cell['source'] = re.sub(r'Model\(.*?\)', model_str, cell['source'])
# Execute the notebook and extract its figures.
logger.info("Executing and extracting figures from notebook '{}'"
.format(variant_file))
config = Config()
config.Exporter.preprocessors = [
'nbconvert.preprocessors.ExecutePreprocessor',
'nbconvert.preprocessors.ExtractOutputPreprocessor'
]
config.ExecutePreprocessor.timeout = 12 * 3600
exporter = Exporter(config=config)
variant, resources = exporter.from_notebook_node(notebook, {
'metadata': {'path': notebook_folder},
'unique_key': 'figure'
})
# Save the resulting notebook and figures.
logger.debug("Saving notebook '{}'".format(variant_file))
with open(variant_path, 'wt') as f:
nbformat.write(variant, f)
logger.debug("Saving figures from notebook '{}'".format(variant_file))
figures_dir = settings.FIGURE_VARIANTS.format(
notebook=notebook_file, model=model)
mkdirp(figures_dir)
for figure_file, figure_data in resources['outputs'].items():
with open(join(figures_dir, figure_file), 'wb') as f:
f.write(figure_data)
