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run_all.py
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run_all.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Script used to convert all notebooks into restructured text
"""
#import nbformat
import argparse
import nbconvert, nbformat
from pyaerocom import const
from nbconvert.preprocessors import ExecutePreprocessor
import fnmatch
import shutil
import os
lustre_avail = const.has_access_lustre
user_server_avail = const.has_access_users_database
# Dictionary that specifies which notebooks (keys) are executed only if
# a certain condition (value, True / False) is met
SOURCE_DIR = 'notebooks'
OUT_DIR = "../pyaerocom/docs/"
RUN_PREFIX = ['tut', 'add']
RUN_IF = {'add01_intro_time_handling.ipynb': lustre_avail,
'add02_read_ebas_nasa_ames.ipynb': lustre_avail,
'add03_ebas_database_browser.ipynb': lustre_avail,
'add04_stationdata_merging.ipynb': lustre_avail,
'tut001_setup_userserver.ipynb': user_server_avail,
'tut00_get_started.ipynb': lustre_avail,
'tut01_intro_regions.ipynb': lustre_avail,
'tut02_intro_class_ReadGridded.ipynb': lustre_avail,
'tut03_intro_class_ReadGriddedMulti.ipynb': lustre_avail,
'tut04_intro_class_GriddedData.ipynb': lustre_avail,
'tut05_intro_ungridded_reading.ipynb': lustre_avail,
'tut06_intro_colocation.ipynb': lustre_avail}
def init_single_notebook_resources(notebook_filename):
"""Step 1: Initialize resources
Note
----
This method was copied and adapted from the nbconvert app main class
NbConvertApp in order to instantiate all output in subdirectories
This initializes the resources dictionary for a single notebook.
Returns
-------
dict
resources dictionary for a single notebook that MUST include the following keys:
- unique_key: the notebook name
- output_files_dir: a directory where output files (not
including the notebook itself) should be saved
"""
basename = os.path.basename(notebook_filename)
notebook_name = basename[:basename.rfind('.')]
# first initialize the resources we want to use
resources = {}
resources['unique_key'] = notebook_name
resources['output_files_dir'] = notebook_name
return resources
def execute_and_save_notebook(file):
try:
print("Executing notebook: {}".format(file))
with open(file) as f:
nb = nbformat.read(f, as_version=4)
ep = ExecutePreprocessor(kernel_name="python3")
ep.timeout = 600
ep.preprocess(nb, {'metadata': {'path': '.'}})
with open(file, 'wt') as f:
nbformat.write(nb, f)
print("Success!")
return True
except Exception as e:
print("Failed: {}".format(repr(e)))
return False
if __name__=="__main__":
parser = argparse.ArgumentParser()
parser.add_argument('--noexec', action="store_true",
default=False,
help=("Don't execute notebooks"))
parser.add_argument('--noconv', default=False, action='store_true',
help=("No conversion to rst"))
parser.add_argument('--outdir', default=OUT_DIR, type=str,
help="Output directory for converted notebooks")
parser.add_argument('--clearold', action='store_true',
default=False,
help=("Delete all existing converted notebooks "
"in output direcory (i.e. all files and folders "
"with trailing number)"))
args = parser.parse_args()
outdir = args.outdir
if not os.path.exists(outdir):
raise IOError("Specified output directory {} does not exist".format(outdir))
files = []
skipped = []
patterns = []
for prefix in RUN_PREFIX:
pattern = "{}[0-9]*.ipynb".format(prefix)
patterns.append(pattern)
for f in sorted(fnmatch.filter(os.listdir(SOURCE_DIR), pattern)):
if not f in RUN_IF:
files.append(f)
else:
if RUN_IF[f]:
files.append(f)
else:
skipped.append(f)
success, failed = [], []
conv_success, conv_fail = [], []
if files:
if args.clearold:
### DELETE OLD NOTEBOOKS (if applicable)
for pattern in patterns:
matches = fnmatch.filter(os.listdir(outdir), pattern)
old = [os.path.join(outdir, x) for x in matches]
for item in old:
try:
os.remove(item)
except:
shutil.rmtree(item)
print("Deleted: {}".format(item))
### RUN ALL NOTEBOOKS
EXEC = not args.noexec
if EXEC:
for f in files:
fp = os.path.join(SOURCE_DIR, f)
if execute_and_save_notebook(fp):
success.append(f)
else:
failed.append(f)
if not args.noconv:
converter = nbconvert.RSTExporter()
writer = nbconvert.writers.FilesWriter()
writer.build_directory = outdir
for f in files:
fp = os.path.join(SOURCE_DIR, f)
try:
resources = init_single_notebook_resources(fp)
(body, resources) = converter.from_file(fp,
resources=resources)
writer.write(body, resources, os.path.splitext(f)[0])
conv_success.append(f)
except Exception as e:
conv_fail.append(f)
print("Failed to convert {} (Error: {})".format(f, repr(e)))
print('\n\n')
print('\n--------------\nSKIPPED NOTEBOOK\n--------------\n')
for f in skipped:
print(f)
print()
print('\n--------------\nEXECUTION SUCCESSFUL\n--------------\n')
for f in success:
print(f)
print()
print('\n--------------\nEXECUTION FAILED\n--------------\n')
for f in failed:
print(f)
print()
if not args.noconv:
print('\n--------------\nCONVERSION RST SUCCESSFUL\n--------------\n')
for f in conv_success:
print(f)
print()
print('--------------\nCONVERSION RST FAILED\n--------------\n')
for f in conv_fail:
print(f)
print()