def __init__(self, config=None, reorder=False, reset_index=False, add_header=False,
no_index=False, remove_magic=False,
**kwargs):
self.reorder = reorder
self.reset_index = reset_index
self.add_header = add_header
self.no_index = no_index
self.remove_magic = remove_magic
self.output_extension = '.sos'
self.output_mimetype = 'text/x-sos'
Exporter.__init__(self, config, **kwargs)
def __init__(self, config=None, reorder=False, reset_index=False, add_header=False,
no_index=False, remove_magic=False,
**kwargs):
self.reorder = reorder
self.reset_index = reset_index
self.add_header = add_header
self.no_index = no_index
self.remove_magic = remove_magic
self.output_extension = '.sos'
self.output_mimetype = 'text/x-sos'
Exporter.__init__(self, config, **kwargs)
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)
def notebook_tester(fname, kernelspec='python'):
raw_nb = Exporter().from_filename(fname)
raw_nb[0].metadata.setdefault('kernelspec', {})['name'] = kernelspec
preproc = ExecutePreprocessor(timeout=-1)
try:
exec_nb = preproc.preprocess(*raw_nb)
except Exception as e:
return '[Failed]\n{}'.format(e)
out_nb = HTMLExporter().from_notebook_node(*exec_nb)
fout = fname.replace('.ipynb', '.html')
with io.open(fout, 'w') as f:
f.write(out_nb[0])
return '[Passed]'
def run_notebook(filename):
export = Exporter()
execute = ExecutePreprocessor()
execute.timeout = 600
export.register_preprocessor(execute, True)
export.from_filename(filename)
def run_notebook(filename):
export = Exporter()
execute = ExecutePreprocessor()
execute.timeout = 600
export.register_preprocessor(execute, True)
export.from_filename(filename)
def notebook_tester(fname, kernelspec='python'):
raw_nb = Exporter().from_filename(fname)
raw_nb[0].metadata.setdefault('kernelspec', {})['name'] = kernelspec
preproc = ExecutePreprocessor(timeout=-1)
preproc.preprocess(*raw_nb)
def load_notebook(fname):
notebook, resources = Exporter().from_filename(fname)
return notebook, resources
def __init__(self, config=None, **kwargs):
self.output_extension = '.sos'
self.output_mimetype = 'text/x-sos'
Exporter.__init__(self, config, **kwargs)