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#! /usr/bin/env python
"""Execute a .ipynb file, write out a processed .rst and clean .ipynb.
Some functions in this script were copied from the nbstripout tool:
Copyright (c) 2015 Min RK, Florian Rathgeber, Michael McNeil Forbes
2019 Casper da Costa-Luis
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
import os
import sys
import nbformat
from nbconvert import RSTExporter
from nbconvert.preprocessors import (
ExecutePreprocessor,
TagRemovePreprocessor,
ExtractOutputPreprocessor
)
from traitlets.config import Config
class MetadataError(Exception):
pass
def pop_recursive(d, key, default=None):
"""dict.pop(key) where `key` is a `.`-delimited list of nested keys.
>>> d = {'a': {'b': 1, 'c': 2}}
>>> pop_recursive(d, 'a.c')
2
>>> d
{'a': {'b': 1}}
"""
nested = key.split('.')
current = d
for k in nested[:-1]:
if hasattr(current, 'get'):
current = current.get(k, {})
else:
return default
if not hasattr(current, 'pop'):
return default
return current.pop(nested[-1], default)
def strip_output(nb):
"""
Strip the outputs, execution count/prompt number and miscellaneous
metadata from a notebook object, unless specified to keep either the
outputs or counts.
"""
keys = {'metadata': [], 'cell': {'metadata': ["execution"]}}
nb.metadata.pop('signature', None)
nb.metadata.pop('widgets', None)
for field in keys['metadata']:
pop_recursive(nb.metadata, field)
if 'NB_KERNEL' in os.environ:
nb.metadata['kernelspec']['name'] = os.environ['NB_KERNEL']
nb.metadata['kernelspec']['display_name'] = os.environ['NB_KERNEL']
for cell in nb.cells:
if 'outputs' in cell:
cell['outputs'] = []
if 'prompt_number' in cell:
cell['prompt_number'] = None
if 'execution_count' in cell:
cell['execution_count'] = None
# Always remove this metadata
for output_style in ['collapsed', 'scrolled']:
if output_style in cell.metadata:
cell.metadata[output_style] = False
if 'metadata' in cell:
for field in ['collapsed', 'scrolled', 'ExecuteTime']:
cell.metadata.pop(field, None)
for (extra, fields) in keys['cell'].items():
if extra in cell:
for field in fields:
pop_recursive(getattr(cell, extra), field)
return nb
if __name__ == "__main__":
# Get the desired ipynb file path and parse into components
_, fpath, outdir = sys.argv
basedir, fname = os.path.split(fpath)
fstem = fname[:-6]
# Read the notebook
with open(fpath) as f:
nb = nbformat.read(f, as_version=4)
# Run the notebook
kernel = os.environ.get("NB_KERNEL", None)
if kernel is None:
kernel = nb["metadata"]["kernelspec"]["name"]
ep = ExecutePreprocessor(
timeout=600,
kernel_name=kernel,
extra_arguments=["--InlineBackend.rc=figure.dpi=88"]
)
ep.preprocess(nb, {"metadata": {"path": basedir}})
# Remove plain text execution result outputs
for cell in nb.get("cells", {}):
if "show-output" in cell["metadata"].get("tags", []):
continue
fields = cell.get("outputs", [])
for field in fields:
if field["output_type"] == "execute_result":
data_keys = field["data"].keys()
for key in list(data_keys):
if key == "text/plain":
field["data"].pop(key)
if not field["data"]:
fields.remove(field)
# Convert to .rst formats
exp = RSTExporter()
c = Config()
c.TagRemovePreprocessor.remove_cell_tags = {"hide"}
c.TagRemovePreprocessor.remove_input_tags = {"hide-input"}
c.TagRemovePreprocessor.remove_all_outputs_tags = {"hide-output"}
c.ExtractOutputPreprocessor.output_filename_template = \
f"{fstem}_files/{fstem}_" + "{cell_index}_{index}{extension}"
exp.register_preprocessor(TagRemovePreprocessor(config=c), True)
exp.register_preprocessor(ExtractOutputPreprocessor(config=c), True)
body, resources = exp.from_notebook_node(nb)
# Clean the output on the notebook and save a .ipynb back to disk
nb = strip_output(nb)
with open(fpath, "wt") as f:
nbformat.write(nb, f)
# Write the .rst file
rst_path = os.path.join(outdir, f"{fstem}.rst")
with open(rst_path, "w") as f:
f.write(body)
# Write the individual image outputs
imdir = os.path.join(outdir, f"{fstem}_files")
if not os.path.exists(imdir):
os.mkdir(imdir)
for imname, imdata in resources["outputs"].items():
if imname.startswith(fstem):
impath = os.path.join(outdir, f"{imname}")
with open(impath, "wb") as f:
f.write(imdata)
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