def test_tutorial_notebook():
from IPython.nbformat.current import read
from runipy.notebook_runner import NotebookRunner
rootdir = os.path.join(aospy.__path__[0], 'examples')
with open(os.path.join(rootdir, 'tutorial.ipynb')) as nb:
notebook = read(nb, 'json')
r = NotebookRunner(notebook)
r.run_notebook()
r.shutdown_kernel()
class IPyNbFile(pytest.File):
def collect(self):
with self.fspath.open() as f:
self.notebook_folder = self.fspath.dirname
self.nb = reads(f.read(), 'json')
self.runner = NotebookRunner(self.nb)
cell_num = 0
for cell in self.runner.iter_code_cells():
yield IPyNbCell(self.name, self, cell_num, cell)
cell_num += 1
def setup(self):
self.fixture_cell = None
def teardown(self):
self.runner.shutdown_kernel()
def run(self):
# Now convert the lecture notes, problem sets, and practice problems to
# HTML notebooks.
from runipy.notebook_runner import NotebookRunner
from IPython.nbformat.current import read, write
start_dir = os.path.abspath('.')
for notebook in glob.glob('?.???/*.ipynb'):
print("Running {0}...".format(notebook))
os.chdir(os.path.dirname(notebook))
with open(os.path.basename(notebook)) as f:
r = NotebookRunner(read(f, 'json'), pylab=False)
r.run_notebook(skip_exceptions=True)
with open(os.path.basename(notebook), 'w') as f:
write(r.nb, f, 'json')
os.chdir(start_dir)
r.shutdown_kernel()
def run(self):
# Now convert the lecture notes, problem sets, and practice problems to
# HTML notebooks.
from runipy.notebook_runner import NotebookRunner
from IPython.nbformat.current import read, write
start_dir = os.path.abspath('.')
for notebook in glob.glob('?.???/*.ipynb'):
print("Running {0}...".format(notebook))
os.chdir(os.path.dirname(notebook))
with open(os.path.basename(notebook)) as f:
r = NotebookRunner(read(f, 'json'), pylab=False)
r.run_notebook(skip_exceptions=True)
with open(os.path.basename(notebook), 'w') as f:
write(r.nb, f, 'json')
os.chdir(start_dir)
r.shutdown_kernel()
class IPyNbFile(pytest.File):
def collect(self):
with self.fspath.open() as f: payload = f.read()
self.nb = nbformat.reads(payload, 3)
# kernel needs to start from the same dir the ipynb is in
notebook_dir = self.fspath.dirname
cwd = os.getcwd()
if cwd != notebook_dir: os.chdir(notebook_dir)
self.runner = NotebookRunner(self.nb)
os.chdir(cwd)
cell_num = 1
for cell in self.runner.iter_code_cells():
yield IPyNbCell.from_parent(self, name=self.name, cell_num=cell_num, cell=cell)
cell_num += 1
def setup(self):
self.fixture_cell = None
def teardown(self):
self.runner.shutdown_kernel()
class IPyNbFile(pytest.File):
def collect(self):
with self.fspath.open() as f:
payload = f.read()
self.notebook_folder = self.fspath.dirname
try:
# Ipython 3
self.nb = reads(payload, 3)
except (TypeError, NBFormatError):
# Ipython 2
self.nb = reads(payload, 'json')
self.runner = NotebookRunner(self.nb)
cell_num = 1
for cell in self.runner.iter_code_cells():
yield IPyNbCell(self.name, self, cell_num, cell)
cell_num += 1
def setup(self):
self.fixture_cell = None
def teardown(self):
self.runner.shutdown_kernel()
class IPyNbFile(pytest.File):
def collect(self):
with self.fspath.open() as f:
payload = f.read()
self.notebook_folder = self.fspath.dirname
try:
# Ipython 3
self.nb = reads(payload, 3)
except (TypeError, NBFormatError):
# Ipython 2
self.nb = reads(payload, 'json')
self.runner = NotebookRunner(self.nb)
cell_num = 1
for cell in self.runner.iter_code_cells():
yield IPyNbCell(self.name, self, cell_num, cell)
cell_num += 1
def setup(self):
self.fixture_cell = None
def teardown(self):
self.runner.shutdown_kernel()
def parse(root):
"""returns list of the NB in root
"""
dirs = sorted([dn for dn in os.listdir(root) if '00' < dn < '99'])
r = []
for sub_dir in dirs:
f = sorted([
os.path.join(root, sub_dir, fn)
for fn in os.listdir(os.path.join(root, sub_dir))
if ('00' < fn < '99' or fn.startswith('content'))
and fn.endswith('.ipynb')
])
r.extend(f)
return r
nb_filenames = ["Index.ipynb", "Index-labs1-6.ipynb"]
nb_filenames.extend(parse('./LABS'))
nb_filenames.extend(parse('.'))
for nb_filename in nb_filenames:
print('*' * 80)
print(nb_filename)
print('*' * 80)
notebook = read(open(nb_filename), 'json')
r = NotebookRunner(notebook)
r.run_notebook()
r.shutdown_kernel()
def main():
log_format = '%(asctime)s %(levelname)s: %(message)s'
log_datefmt = '%m/%d/%Y %I:%M:%S %p'
parser = argparse.ArgumentParser()
parser.add_argument('--version',
'-v',
action='version',
version=runipy.__version__,
help='print version information')
parser.add_argument('input_file',
nargs='?',
help='.ipynb file to run (or stdin)')
parser.add_argument('output_file',
nargs='?',
help='.ipynb file to save cell output to')
parser.add_argument('--quiet',
'-q',
action='store_true',
help='don\'t print anything unless things go wrong')
parser.add_argument('--overwrite',
'-o',
action='store_true',
help='write notebook output back to original notebook')
parser.add_argument('--html',
nargs='?',
default=False,
help='output an HTML snapshot of the notebook')
parser.add_argument('--template',
nargs='?',
default=False,
help='template to use for HTML output')
parser.add_argument('--pylab',
action='store_true',
help='start notebook with pylab enabled')
parser.add_argument('--matplotlib',
action='store_true',
help='start notebook with matplotlib inlined')
parser.add_argument('--skip-exceptions',
'-s',
action='store_true',
help='if an exception occurs in a cell,' +
' continue running the subsequent cells')
parser.add_argument(
'--stdout',
action='store_true',
help='print notebook to stdout (or use - as output_file')
parser.add_argument(
'--stdin',
action='store_true',
help='read notebook from stdin (or use - as input_file)')
parser.add_argument(
'--no-chdir',
action='store_true',
help="do not change directory to notebook's at kernel startup")
parser.add_argument('--profile-dir',
help="set the profile location directly")
args = parser.parse_args()
if args.overwrite:
if args.output_file is not None:
print(
'Error: output_filename must not be provided if '
'--overwrite (-o) given',
file=stderr)
exit(1)
else:
args.output_file = args.input_file
if not args.quiet:
logging.basicConfig(level=logging.INFO,
format=log_format,
datefmt=log_datefmt)
working_dir = None
payload_source = ""
payload = ""
if args.input_file == '-' or args.stdin: # force stdin
payload_source = stdin.name
payload = stdin.read()
elif not args.input_file and stdin.isatty(): # no force, empty stdin
parser.print_help()
exit()
elif not args.input_file: # no file -> default stdin
payload_source = stdin.name
payload = stdin.read()
else: # must have specified normal input_file
with open(args.input_file) as input_file:
payload_source = input_file.name
payload = input_file.read()
working_dir = os.path.dirname(args.input_file)
if args.no_chdir:
working_dir = None
if args.profile_dir:
profile_dir = os.path.expanduser(args.profile_dir)
else:
profile_dir = None
logging.info('Reading notebook %s', payload_source)
try:
# Ipython 3
nb = reads(payload, 3)
except (TypeError, NBFormatError):
# Ipython 2
nb = reads(payload, 'json')
nb_runner = NotebookRunner(nb, args.pylab, args.matplotlib, profile_dir,
working_dir)
exit_status = 0
try:
nb_runner.run_notebook(skip_exceptions=args.skip_exceptions)
except NotebookError:
exit_status = 1
if args.output_file and args.output_file != '-':
logging.info('Saving to %s', args.output_file)
with open(args.output_file, 'w') as output_filehandle:
try:
# Ipython 3
write(nb_runner.nb, output_filehandle, 3)
except (TypeError, NBFormatError):
# Ipython 2
write(nb_runner.nb, output_filehandle, 'json')
if args.stdout or args.output_file == '-':
try:
# Ipython 3
write(nb_runner.nb, stdout, 3)
except (TypeError, NBFormatError):
# Ipython 2
write(nb_runner.nb, stdout, 'json')
print()
if args.html is not False:
if args.html is None:
# if --html is given but no filename is provided,
# come up with a sane output name based on the
# input filename
if args.input_file.endswith('.ipynb'):
args.html = args.input_file[:-6] + '.html'
else:
args.html = args.input_file + '.html'
if args.template is False:
exporter = HTMLExporter()
else:
exporter = HTMLExporter(config=Config({
'HTMLExporter': {
'template_file': args.template,
'template_path': ['.', '/']
}
}))
logging.info('Saving HTML snapshot to %s' % args.html)
output, resources = exporter.from_notebook_node(
convert(nb_runner.nb, current_nbformat))
codecs.open(args.html, 'w', encoding='utf-8').write(output)
nb_runner.shutdown_kernel()
if exit_status != 0:
logging.warning('Exiting with nonzero exit status')
exit(exit_status)
def main():
log_format = '%(asctime)s %(levelname)s: %(message)s'
log_datefmt = '%m/%d/%Y %I:%M:%S %p'
parser = argparse.ArgumentParser()
parser.add_argument('--version', '-v', action='version', version=runipy.__version__,
help='print version information')
parser.add_argument('input_file', nargs='?',
help='.ipynb file to run (or stdin)')
parser.add_argument('output_file', nargs='?',
help='.ipynb file to save cell output to')
parser.add_argument('--quiet', '-q', action='store_true',
help='don\'t print anything unless things go wrong')
parser.add_argument('--overwrite', '-o', action='store_true',
help='write notebook output back to original notebook')
parser.add_argument('--html', nargs='?', default=False,
help='output an HTML snapshot of the notebook')
parser.add_argument('--template', nargs='?', default=False,
help='template to use for HTML output')
parser.add_argument('--pylab', action='store_true',
help='start notebook with pylab enabled')
parser.add_argument('--matplotlib', action='store_true',
help='start notebook with matplotlib inlined')
parser.add_argument('--skip-exceptions', '-s', action='store_true',
help='if an exception occurs in a cell, continue running the subsequent cells')
parser.add_argument('--stdout', action='store_true',
help='print notebook to stdout (or use - as output_file')
parser.add_argument('--stdin', action='store_true',
help='read notebook from stdin (or use - as input_file)')
parser.add_argument('--no-chdir', action='store_true',
help="do not change directory to notebook's at kernel startup")
parser.add_argument('--profile-dir',
help="set the profile location directly")
args = parser.parse_args()
if args.overwrite:
if args.output_file is not None:
print('Error: output_filename must not be provided if '
'--overwrite (-o) given', file=stderr)
exit(1)
else:
args.output_file = args.input_file
if not args.quiet:
logging.basicConfig(level=logging.INFO, format=log_format, datefmt=log_datefmt)
working_dir = None
if args.input_file == '-' or args.stdin: # force stdin
payload = stdin
elif not args.input_file and stdin.isatty(): # no force, empty stdin
parser.print_help()
exit()
elif not args.input_file: # no file -> default stdin
payload = stdin
else: # must have specified normal input_file
payload = open(args.input_file)
working_dir = os.path.dirname(args.input_file)
if args.no_chdir:
working_dir = None
if args.profile_dir:
profile_dir = os.path.expanduser(args.profile_dir)
else:
profile_dir = None
logging.info('Reading notebook %s', payload.name)
nb = read(payload, 'json')
nb_runner = NotebookRunner(nb, args.pylab, args.matplotlib, profile_dir, working_dir)
exit_status = 0
try:
nb_runner.run_notebook(skip_exceptions=args.skip_exceptions)
except NotebookError:
exit_status = 1
if args.output_file and args.output_file != '-':
logging.info('Saving to %s', args.output_file)
write(nb_runner.nb, open(args.output_file, 'w'), 'json')
if args.stdout or args.output_file == '-':
write(nb_runner.nb, stdout, 'json')
print()
if args.html is not False:
if args.html is None:
# if --html is given but no filename is provided,
# come up with a sane output name based on the
# input filename
if args.input_file.endswith('.ipynb'):
args.html = args.input_file[:-6] + '.html'
else:
args.html = args.input_file + '.html'
if args.template is False:
exporter = HTMLExporter()
else:
exporter = HTMLExporter(
config=Config({'HTMLExporter':{'template_file':args.template, 'template_path': ['.', '/']}}))
logging.info('Saving HTML snapshot to %s' % args.html)
output, resources = exporter.from_notebook_node(nb_runner.nb)
codecs.open(args.html, 'w', encoding='utf-8').write(output)
nb_runner.shutdown_kernel()
if exit_status != 0:
logging.warning('Exiting with nonzero exit status')
exit(exit_status)
def run_notebook(parser, args):
"""Run notebook. Input parameters are in args. To run this inside script,
put args to some object, i.e.
>>> class Args(object): pass
>>> args = Args()
>>> args.output_file = ...
>>> exit_status = run_notebook(args)
"""
if args.overwrite:
if args.output_file is not None:
print('Error: output_filename must not be provided if '
'--overwrite (-o) given', file=stderr)
exit(1)
else:
args.output_file = args.input_file
if not args.quiet:
logging.basicConfig(level=logging.INFO, format=log_format, datefmt=log_datefmt)
if args.debug:
logging.basicConfig(level=logging.DEBUG, format=log_format, datefmt=log_datefmt)
working_dir = None
if args.profile_dir:
profile_dir = os.path.expanduser(args.profile_dir)
else:
profile_dir = None
if args.input_file == '-' or args.stdin: # force stdin
payload = stdin
elif not args.input_file and stdin.isatty(): # no force, empty stdin
parser.print_help()
exit()
elif not args.input_file: # no file -> default stdin
payload = stdin
else: # must have specified normal input_file
payload = open(args.input_file)
working_dir = os.path.dirname(args.input_file)
if args.no_chdir:
working_dir = None
logging.info('Reading notebook %s', payload.name)
nb = read(payload, 'json')
nb_runner = NotebookRunner(nb, args.pylab, args.matplotlib, profile_dir, working_dir, kernel=args.kernel, port=args.port)
exit_status = 0
try:
nb_runner.run_notebook(skip_exceptions=args.skip_exceptions)
except NotebookError:
exit_status = 1
if args.output_file and args.output_file != '-':
logging.info('Saving to %s', args.output_file)
write(nb_runner.nb, open(args.output_file, 'w'), 'json')
if args.stdout or args.output_file == '-':
write(nb_runner.nb, stdout, 'json')
print()
if args.html is not False:
export_to_html(nb_runner, args)
if args.rst is not False:
export_to_rst(nb_runner, args)
nb_runner.shutdown_kernel()
return exit_status
from runipy.notebook_runner import NotebookRunner
from IPython.nbformat.current import read
import os
def parse(root):
"""returns list of the NB in root
"""
dirs = sorted([dn for dn in os.listdir(root) if '00'<dn<'99'])
r = []
for sub_dir in dirs:
f = sorted([os.path.join(root,sub_dir,fn) for fn in os.listdir(os.path.join(root,sub_dir)) if ('00'<fn<'99' or fn.startswith('content')) and fn.endswith('.ipynb')])
r.extend(f)
return r
nb_filenames = ["Index.ipynb","Index-labs1-6.ipynb"]
nb_filenames.extend(parse('./LABS'))
nb_filenames.extend(parse('.'))
for nb_filename in nb_filenames:
print('*'*80)
print(nb_filename)
print('*'*80)
notebook = read(open(nb_filename), 'json')
r = NotebookRunner(notebook)
r.run_notebook()
r.shutdown_kernel()
def main():
log_format = "%(asctime)s %(levelname)s: %(message)s"
log_datefmt = "%m/%d/%Y %I:%M:%S %p"
parser = argparse.ArgumentParser()
parser.add_argument(
"--version", "-v", action="version", version=runipy.__version__, help="print version information"
)
parser.add_argument("input_file", nargs="?", help=".ipynb file to run (or stdin)")
parser.add_argument("output_file", nargs="?", help=".ipynb file to save cell output to")
parser.add_argument("--quiet", "-q", action="store_true", help="don't print anything unless things go wrong")
parser.add_argument(
"--overwrite", "-o", action="store_true", help="write notebook output back to original notebook"
)
format_grp = parser.add_mutually_exclusive_group()
format_grp.add_argument("--html", nargs="?", default=False, help="output an HTML snapshot of the notebook")
format_grp.add_argument("--pdf", nargs="?", default=False, help="output a PDF snapshot of the notebook")
parser.add_argument("--template", nargs="?", default=False, help="template to use for HTML output")
parser.add_argument("--pylab", action="store_true", help="start notebook with pylab enabled")
parser.add_argument("--matplotlib", action="store_true", help="start notebook with matplotlib inlined")
parser.add_argument(
"--skip-exceptions",
"-s",
action="store_true",
help="if an exception occurs in a cell," + " continue running the subsequent cells",
)
parser.add_argument("--stdout", action="store_true", help="print notebook to stdout (or use - as output_file")
parser.add_argument("--stdin", action="store_true", help="read notebook from stdin (or use - as input_file)")
parser.add_argument(
"--no-chdir", action="store_true", help="do not change directory to notebook's at kernel startup"
)
parser.add_argument("--profile-dir", help="set the profile location directly")
args = parser.parse_args()
if args.overwrite:
if args.output_file is not None:
print("Error: output_filename must not be provided if " "--overwrite (-o) given", file=stderr)
exit(1)
else:
args.output_file = args.input_file
if not args.quiet:
logging.basicConfig(level=logging.INFO, format=log_format, datefmt=log_datefmt)
working_dir = None
payload_source = ""
payload = ""
if args.input_file == "-" or args.stdin: # force stdin
payload_source = stdin.name
payload = stdin.read()
elif not args.input_file and stdin.isatty(): # no force, empty stdin
parser.print_help()
exit()
elif not args.input_file: # no file -> default stdin
payload_source = stdin.name
payload = stdin.read()
else: # must have specified normal input_file
with open(args.input_file) as input_file:
payload_source = input_file.name
payload = input_file.read()
working_dir = os.path.dirname(args.input_file)
if args.no_chdir:
working_dir = None
if args.profile_dir:
profile_dir = os.path.expanduser(args.profile_dir)
else:
profile_dir = None
logging.info("Reading notebook %s", payload_source)
try:
# Ipython 3
nb = reads(payload, 3)
except (TypeError, NBFormatError):
# Ipython 2
nb = reads(payload, "json")
nb_runner = NotebookRunner(nb, args.pylab, args.matplotlib, profile_dir, working_dir)
exit_status = 0
try:
nb_runner.run_notebook(skip_exceptions=args.skip_exceptions)
except NotebookError:
exit_status = 1
if args.output_file and args.output_file != "-":
logging.info("Saving to %s", args.output_file)
with open(args.output_file, "w") as output_filehandle:
try:
# Ipython 3
write(nb_runner.nb, output_filehandle, 3)
except (TypeError, NBFormatError):
# Ipython 2
write(nb_runner.nb, output_filehandle, "json")
if args.stdout or args.output_file == "-":
try:
# Ipython 3
write(nb_runner.nb, stdout, 3)
except (TypeError, NBFormatError):
# Ipython 2
write(nb_runner.nb, stdout, "json")
print()
if args.html is not False:
if args.html is None:
# if --html is given but no filename is provided,
# come up with a sane output name based on the
# input filename
if args.input_file.endswith(".ipynb"):
args.html = args.input_file[:-6] + ".html"
else:
args.html = args.input_file + ".html"
if args.template is False:
exporter = HTMLExporter()
else:
exporter = HTMLExporter(
config=Config({"HTMLExporter": {"template_file": args.template, "template_path": [".", "/"]}})
)
logging.info("Saving HTML snapshot to %s" % args.html)
output, resources = exporter.from_notebook_node(convert(nb_runner.nb, current_nbformat))
codecs.open(args.html, "w", encoding="utf-8").write(output)
elif args.pdf is not False:
if args.pdf is None:
# if --html is given but no filename is provided,
# come up with a sane output name based on the
# input filename
if args.input_file.endswith(".ipynb"):
args.pdf = args.input_file[:-6] + ".pdf"
else:
args.pdf = args.input_file + ".pdf"
if args.template is False:
exporter = PDFExporter()
else:
exporter = PDFExporter(
config=Config({"PDFExporter": {"template_file": args.template, "template_path": [".", "/"]}})
)
logging.info("Saving PDF snapshot to %s" % args.pdf)
output, resources = exporter.from_notebook_node(convert(nb_runner.nb, current_nbformat))
writer = FilesWriter()
writer.build_directory = os.path.dirname(args.pdf)
writer.write(output, resources, os.path.splitext(os.path.basename(args.pdf))[0])
nb_runner.shutdown_kernel()
if exit_status != 0:
logging.warning("Exiting with nonzero exit status")
exit(exit_status)
