def put(self, function=''):
script_exporter = ScriptExporter()
path = urllib.parse.unquote(function)
out, resources = script_exporter.from_notebook_node(
nbformat.read(path, as_version=4))
data = {'name': function, 'script': out, 'raw': path}
if function:
self.logger.info('add functions {path}: {data}'.format(path=path,
data=data))
self.db.add_function(**data)
func = self.db.query_function(function)
func = func.front()
func.logger = self.logger
schedule = func.get_schedule()
if schedule and isinstance(schedule, dict):
data = {'method': 'SCHEDULE', 'query': {}, 'body': {}}
add_job(function, schedule, func, data)
self.logger.info(
'add function to schedule, current scheduled: {count}'.
format(count=len(default_scheduler.jobs)))
else:
self.logger.info('schedule not found or not valid, '
'current scheduled: {count}'.format(
count=len(default_scheduler.jobs)))
remove_job(function)
self.logger.info('handle add function {data}'.format(data=data))
self.finish({'code': 'success'})
else:
self.finish({'code': 'fail', 'message': 'function name not found'})
def run(notebook, executable=None, rules=None):
nb = nbformat.read(notebook, 4)
extra_metadata = extract_extrametadata(nb)
ret = ''
passed = True
rules = rules or {}
extra_metadata.update(rules)
if 'lines_per_cell' in extra_metadata:
lines_per_cell = extra_metadata.get('lines_per_cell', -1)
lintret, lintfail = lint_lines_per_cell(lines_per_cell, extra_metadata)
ret += lintret
passed = passed and lintfail
if 'cells_per_notebook' in extra_metadata:
cells_per_notebook = extra_metadata.get('cells_per_notebook', -1)
lintret, lintfail = lint_cells_per_notebook(cells_per_notebook,
extra_metadata)
ret += lintret + '\n'
passed = passed and lintfail
if 'function_definitions' in extra_metadata:
function_definitions = extra_metadata.get('function_definitions', -1)
lintret, lintfail = lint_function_definitions(function_definitions,
extra_metadata)
ret += lintret + '\n'
passed = passed and lintfail
if 'class_definitions' in extra_metadata:
class_definitions = extra_metadata.get('class_definitions', -1)
lintret, lintfail = lint_class_definitions(class_definitions,
extra_metadata)
ret += lintret + '\n'
passed = passed and lintfail
if 'cell_coverage' in extra_metadata:
cell_coverage = extra_metadata.get('cell_coverage', 0)
lintret, lintfail = lint_cell_coverage(cell_coverage, extra_metadata)
ret += lintret + '\n'
passed = passed and lintfail
if executable:
exp = ScriptExporter()
(body, resources) = exp.from_notebook_node(nb)
tf = NamedTemporaryFile(mode='w', suffix='.py', delete=False)
tf.write(body)
executable.append(tf.name)
ret2 = subprocess.run(executable,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
ret += '\n' + ret2.stdout.decode('ascii') + '\n' + ret2.stderr.decode(
'asii')
os.remove(tf.name)
return ret, passed
def param_rest_provider(files, endpoint):
"""
Returns a Param based REST API given the scripts or notebooks
containing the tranquilized functions.
Arguments
---------
files: list(str)
A list of paths being served
endpoint: str
The endpoint to serve the REST API on
Returns
-------
A Tornado routing pattern containing the route and handler
"""
for filename in files:
extension = filename.split('.')[-1]
if extension == 'py':
try:
run_path(filename)
except Exception:
param.main.warning(
"Could not run app script on REST server startup.")
elif extension == 'ipynb':
try:
import nbconvert # noqa
except ImportError:
raise ImportError(
"Please install nbconvert to serve Jupyter Notebooks.")
from nbconvert import ScriptExporter
exporter = ScriptExporter()
source, _ = exporter.from_filename(filename)
source_dir = os.path.dirname(filename)
with tempfile.NamedTemporaryFile(mode='w',
dir=source_dir,
delete=True) as tmp:
tmp.write(source)
tmp.flush()
try:
run_path(tmp.name,
init_globals={'get_ipython': MagicMock()})
except Exception:
param.main.warning(
"Could not run app notebook on REST server startup.")
else:
raise ValueError(
'{} is not a script (.py) or notebook (.ipynb)'.format(
filename))
if endpoint and not endpoint.endswith('/'):
endpoint += '/'
return [((r"^/%s.*" % endpoint if endpoint else r"^.*"), ParamHandler,
dict(root=endpoint))]
def parse(self):
from nbconvert import ScriptExporter
exporter = ScriptExporter()
source, _ = exporter.from_filename(self.fn)
self.nodes = ast.parse(source, self.fn)
with tempfile.NamedTemporaryFile(mode='w',
dir=dirname(self.fn),
delete=True) as tmp:
tmp.write(source)
tmp.flush()
self.module = run_path(tmp.name,
init_globals={'get_ipython': MagicMock()})
def get_imported_modules(glob_path: str) -> Set[str]:
nb_paths = glob.glob(glob_path, recursive=True)
if len(nb_paths) == 0:
raise Exception(
f"No notebooks found with glob {glob_path}, cwd {os.getcwd()}")
se: Any = ScriptExporter()
all_imported_modules = set()
for path in nb_paths:
try:
[script, _] = se.from_filename(path)
except Exception as ex:
capture_exception(ex)
click.echo(f"Import checker cannot read {path}")
continue
lines = script.split("\n")
for line in lines:
from_match = from_regexp.match(line)
if from_match:
all_imported_modules.add(from_match.group(1))
continue
import_match = import_regexp.match(line)
if import_match:
all_imported_modules.add(import_match.group(1))
continue
return all_imported_modules
def gen_tutorials(repo_dir: str) -> None:
"""Generate HTML tutorials for captum Docusaurus site from Jupyter notebooks.
Also create ipynb and py versions of tutorial in Docusaurus site for
download.
"""
with open(os.path.join(repo_dir, "website", "tutorials.json"),
"r") as infile:
tutorial_config = json.loads(infile.read())
tutorial_ids = {x["id"] for v in tutorial_config.values() for x in v}
for tid in tutorial_ids:
print("Generating {} tutorial".format(tid))
# convert notebook to HTML
ipynb_in_path = os.path.join(repo_dir, "tutorials",
"{}.ipynb".format(tid))
with open(ipynb_in_path, "r") as infile:
nb_str = infile.read()
nb = nbformat.reads(nb_str, nbformat.NO_CONVERT)
# displayname is absent from notebook metadata
nb["metadata"]["kernelspec"]["display_name"] = "python3"
exporter = HTMLExporter()
html, meta = exporter.from_notebook_node(nb)
# pull out html div for notebook
soup = BeautifulSoup(html, "html.parser")
nb_meat = soup.find("div", {"id": "notebook-container"})
del nb_meat.attrs["id"]
nb_meat.attrs["class"] = ["notebook"]
html_out = JS_SCRIPTS + str(nb_meat)
# generate html file
html_out_path = os.path.join(repo_dir, "website", "_tutorials",
"{}.html".format(tid))
with open(html_out_path, "w") as html_outfile:
html_outfile.write(html_out)
# generate JS file
script = TEMPLATE.format(tid)
js_out_path = os.path.join(repo_dir, "website", "pages", "tutorials",
"{}.js".format(tid))
with open(js_out_path, "w") as js_outfile:
js_outfile.write(script)
# output tutorial in both ipynb & py form
ipynb_out_path = os.path.join(repo_dir, "website", "static", "files",
"{}.ipynb".format(tid))
with open(ipynb_out_path, "w") as ipynb_outfile:
ipynb_outfile.write(nb_str)
exporter = ScriptExporter()
script, meta = exporter.from_notebook_node(nb)
py_out_path = os.path.join(repo_dir, "website", "static", "files",
"{}.py".format(tid))
with open(py_out_path, "w") as py_outfile:
py_outfile.write(script)
def gen_tutorials(repo_dir: str,
exec_tutorials: bool,
kernel_name: Optional[str] = None) -> None:
"""Generate HTML tutorials for Docusaurus Ax site from Jupyter notebooks.
Also create ipynb and py versions of tutorial in Docusaurus site for
download.
"""
with open(os.path.join(repo_dir, "website", "tutorials.json"),
"r") as infile:
tutorial_config = json.loads(infile.read())
# flatten config dict
tutorial_configs = [
config for category in tutorial_config.values() for config in category
]
# prepare paths for converted tutorials & files
os.makedirs(os.path.join(repo_dir, "website", "_tutorials"), exist_ok=True)
os.makedirs(os.path.join(repo_dir, "website", "static", "files"),
exist_ok=True)
for config in tutorial_configs:
tid = config["id"]
t_dir = config.get("dir")
exec_on_build = config.get("exec_on_build", True)
print("Generating {} tutorial".format(tid))
if t_dir is not None:
tutorial_dir = os.path.join(repo_dir, "tutorials", t_dir)
html_dir = os.path.join(repo_dir, "website", "_tutorials", t_dir)
js_dir = os.path.join(repo_dir, "website", "pages", "tutorials",
t_dir)
py_dir = os.path.join(repo_dir, "website", "static", "files",
t_dir)
for d in [tutorial_dir, html_dir, js_dir, py_dir]:
os.makedirs(d, exist_ok=True)
tutorial_path = os.path.join(tutorial_dir, "{}.ipynb".format(tid))
html_path = os.path.join(html_dir, "{}.html".format(tid))
js_path = os.path.join(js_dir, "{}.js".format(tid))
ipynb_path = os.path.join(py_dir, "{}.ipynb".format(tid))
py_path = os.path.join(py_dir, "{}.py".format(tid))
tar_path = os.path.join(py_dir, "{}.tar.gz".format(tid))
else:
tutorial_dir = os.path.join(repo_dir, "tutorials")
tutorial_path = os.path.join(repo_dir, "tutorials",
"{}.ipynb".format(tid))
html_path = os.path.join(repo_dir, "website", "_tutorials",
"{}.html".format(tid))
js_path = os.path.join(repo_dir, "website", "pages", "tutorials",
"{}.js".format(tid))
ipynb_path = os.path.join(repo_dir, "website", "static", "files",
"{}.ipynb".format(tid))
py_path = os.path.join(repo_dir, "website", "static", "files",
"{}.py".format(tid))
# load notebook
with open(tutorial_path, "r") as infile:
nb_str = infile.read()
nb = nbformat.reads(nb_str, nbformat.NO_CONVERT)
# track total exec time (non-None if exec_on_build=True)
total_time = None
if exec_tutorials and exec_on_build:
print("Executing tutorial {}".format(tid))
kwargs = {
"kernel_name": kernel_name
} if kernel_name is not None else {}
ep = ExecutePreprocessor(timeout=600, **kwargs)
start_time = time.time()
# try / catch failures for now; should remove once tutorials
# more stable
try:
# execute notebook, using `tutorial_dir` as working directory
ep.preprocess(nb, {"metadata": {"path": tutorial_dir}})
total_time = time.time() - start_time
print(
"Done executing tutorial {}. Took {:.2f} seconds.".format(
tid, total_time))
except Exception as exc:
print("Couldn't execute tutorial {}!".format(tid))
print(exc)
total_time = None
# convert notebook to HTML
exporter = HTMLExporter()
html, meta = exporter.from_notebook_node(nb)
# pull out html div for notebook
soup = BeautifulSoup(html, "html.parser")
nb_meat = soup.find("div", {"id": "notebook-container"})
del nb_meat.attrs["id"]
nb_meat.attrs["class"] = ["notebook"]
# when output html, iframe it (useful for Ax reports)
for html_div in nb_meat.findAll("div", {"class": "output_html"}):
if html_div.html is not None:
iframe = soup.new_tag("iframe")
iframe.attrs["src"] = "data:text/html;charset=utf-8," + str(
html_div.html)
# replace `#` in CSS
iframe.attrs["src"] = iframe.attrs["src"].replace("#", "%23")
html_div.contents = [iframe]
html_out = MOCK_JS_REQUIRES + str(nb_meat)
# generate HTML file
with open(html_path, "w") as html_outfile:
html_outfile.write(html_out)
# generate JS file
t_dir_js = t_dir if t_dir else ""
script = TEMPLATE.format(
t_dir=t_dir_js,
tid=tid,
total_time=total_time if total_time is not None else "null",
)
with open(js_path, "w") as js_outfile:
js_outfile.write(script)
# output tutorial in both ipynb & py form
nbformat.write(nb, ipynb_path)
exporter = ScriptExporter()
script, meta = exporter.from_notebook_node(nb)
with open(py_path, "w") as py_outfile:
py_outfile.write(script)
# create .tar archive (if necessary)
if t_dir is not None:
with tarfile.open(tar_path, "w:gz") as tar:
tar.add(tutorial_dir, arcname=os.path.basename(tutorial_dir))
def run(notebook, executable=None, rules=None, noqa_regex=None):
nb = nbformat.read(notebook, 4)
extra_metadata = extract_extrametadata(nb, noqa_regex=noqa_regex)
ret = []
passed = True
rules = rules or {}
extra_metadata.update(rules)
# TODO: consider warning if referring to non-existent rules
rules_to_remove = extra_metadata['noqa'] & extra_metadata.keys()
for rule in rules_to_remove:
del extra_metadata[rule]
# TODO: lintfail is more like lintpassed?
if 'lines_per_cell' in extra_metadata:
lintret, lintfail = lint_lines_per_cell(
extra_metadata['cell_lines'],
max_lines_per_cell=extra_metadata['lines_per_cell'])
ret.extend(lintret)
passed = passed and lintfail
if 'cells_per_notebook' in extra_metadata:
lintret, lintfail = lint_cells_per_notebook(
extra_metadata['cell_count'],
max_cells_per_notebook=extra_metadata['cells_per_notebook'])
ret.extend(lintret)
passed = passed and lintfail
if 'function_definitions' in extra_metadata:
lintret, lintfail = lint_function_definitions(
extra_metadata['functions'],
max_function_definitions=extra_metadata['function_definitions'])
ret.extend(lintret)
passed = passed and lintfail
if 'class_definitions' in extra_metadata:
lintret, lintfail = lint_class_definitions(
extra_metadata['classes'],
max_class_definitions=extra_metadata['class_definitions'])
ret.extend(lintret)
passed = passed and lintfail
if 'kernelspec_requirements' in extra_metadata:
lintret, lintfail = lint_kernelspec(
kernelspec=extra_metadata['kernelspec'],
kernelspec_requirements=extra_metadata['kernelspec_requirements'])
ret.extend(lintret)
passed = passed and lintfail
if 'magics_whitelist' in extra_metadata or 'magics_blacklist' in extra_metadata:
lintret, lintfail = lint_magics(
magics=extra_metadata['magics'],
whitelist=extra_metadata.get('magics_whitelist', None),
blacklist=extra_metadata.get('magics_blacklist', None))
ret.extend(lintret)
passed = passed and lintfail
if executable:
exp = ScriptExporter()
(body, resources) = exp.from_notebook_node(nb)
tf = NamedTemporaryFile(mode='w',
suffix='.py',
delete=False,
encoding='utf8')
tf_name = tf.name
try:
tf.write(body)
tf.close()
executable.append(tf_name)
ret2 = _run_and_capture_utf8(executable)
msg = ret2.stdout + '\t' + ret2.stderr
ret.append(
LintMessage(-1, 'Checking lint:\n' + msg.strip(),
LintType.LINTER, False if msg.strip() else True))
finally:
os.remove(tf_name)
return ret, passed
def gen_tutorials(repo_dir: str) -> None:
"""Generate HTML tutorials for Docusaurus Ax site from Jupyter notebooks.
Also create ipynb and py versions of tutorial in Docusaurus site for
download.
"""
with open(os.path.join(repo_dir, "website", "tutorials.json"),
"r") as infile:
tutorial_config = json.loads(infile.read())
tutorial_ids = [x["id"] for v in tutorial_config.values() for x in v]
tutorial_dirs = [x.get("dir") for v in tutorial_config.values() for x in v]
for tid, t_dir in zip(tutorial_ids, tutorial_dirs):
print("Generating {} tutorial".format(tid))
if t_dir is not None:
tutorial_dir = os.path.join(repo_dir, "tutorials", t_dir)
html_dir = os.path.join(repo_dir, "website", "_tutorials", t_dir)
js_dir = os.path.join(repo_dir, "website", "pages", "tutorials",
t_dir)
py_dir = os.path.join(repo_dir, "website", "static", "files",
t_dir)
for d in [tutorial_dir, html_dir, js_dir, py_dir]:
os.makedirs(d, exist_ok=True)
tutorial_path = os.path.join(tutorial_dir, "{}.ipynb".format(tid))
html_path = os.path.join(html_dir, "{}.html".format(tid))
js_path = os.path.join(js_dir, "{}.js".format(tid))
ipynb_path = os.path.join(py_dir, "{}.ipynb".format(tid))
py_path = os.path.join(py_dir, "{}.py".format(tid))
tar_path = os.path.join(py_dir, "{}.tar.gz".format(tid))
else:
tutorial_path = os.path.join(repo_dir, "tutorials",
"{}.ipynb".format(tid))
html_path = os.path.join(repo_dir, "website", "_tutorials",
"{}.html".format(tid))
js_path = os.path.join(repo_dir, "website", "pages", "tutorials",
"{}.js".format(tid))
ipynb_path = os.path.join(repo_dir, "website", "static", "files",
"{}.ipynb".format(tid))
py_path = os.path.join(repo_dir, "website", "static", "files",
"{}.py".format(tid))
# convert notebook to HTML
with open(tutorial_path, "r") as infile:
nb_str = infile.read()
nb = nbformat.reads(nb_str, nbformat.NO_CONVERT)
exporter = HTMLExporter()
html, meta = exporter.from_notebook_node(nb)
# pull out html div for notebook
soup = BeautifulSoup(html, "html.parser")
nb_meat = soup.find("div", {"id": "notebook-container"})
del nb_meat.attrs["id"]
nb_meat.attrs["class"] = ["notebook"]
# when output html, iframe it (useful for Ax reports)
for html_div in nb_meat.findAll("div", {"class": "output_html"}):
if html_div.html is not None:
iframe = soup.new_tag("iframe")
iframe.attrs["src"] = "data:text/html;charset=utf-8," + str(
html_div.html)
# replace `#` in CSS
iframe.attrs["src"] = iframe.attrs["src"].replace("#", "%23")
html_div.contents = [iframe]
html_out = "".join([JS_SCRIPT_TAGS.format(src)
for src in SRCS]) + str(nb_meat)
# generate HTML file
with open(html_path, "w") as html_outfile:
html_outfile.write(html_out)
# generate JS file
t_dir_js = t_dir if t_dir else ""
script = TEMPLATE.format(t_dir=t_dir_js, tid=tid)
with open(js_path, "w") as js_outfile:
js_outfile.write(script)
# output tutorial in both ipynb & py form
with open(ipynb_path, "w") as ipynb_outfile:
ipynb_outfile.write(nb_str)
exporter = ScriptExporter()
script, meta = exporter.from_notebook_node(nb)
with open(py_path, "w") as py_outfile:
py_outfile.write(script)
# create .tar archive (if necessary)
if t_dir is not None:
with tarfile.open(tar_path, "w:gz") as tar:
tar.add(tutorial_dir, arcname=os.path.basename(tutorial_dir))
def export(self, exporter=ScriptExporter()):
(body, resources) = exporter.from_notebook_node(self.notebook)
return dict(
body=body,
resources=resources
)
def gen_tutorials(repo_dir: str) -> None:
"""Generate HTML tutorials for PyTorch3D Docusaurus site from Jupyter notebooks.
Also create ipynb and py versions of tutorial in Docusaurus site for
download.
"""
with open(
os.path.join(repo_dir, 'website', 'tutorials.json'), 'r'
) as infile:
tutorial_config = json.loads(infile.read())
tutorial_ids = {x['id'] for v in tutorial_config.values() for x in v}
for tid in tutorial_ids:
print('Generating {} tutorial'.format(tid))
# convert notebook to HTML
ipynb_in_path = os.path.join(
repo_dir, 'docs', 'tutorials', '{}.ipynb'.format(tid)
)
with open(ipynb_in_path, 'r') as infile:
nb_str = infile.read()
nb = nbformat.reads(nb_str, nbformat.NO_CONVERT)
# displayname is absent from notebook metadata
nb['metadata']['kernelspec']['display_name'] = 'python3'
exporter = HTMLExporter()
html, meta = exporter.from_notebook_node(nb)
# pull out html div for notebook
soup = BeautifulSoup(html, 'html.parser')
nb_meat = soup.find('div', {'id': 'notebook-container'})
del nb_meat.attrs['id']
nb_meat.attrs['class'] = ['notebook']
html_out = JS_SCRIPTS + str(nb_meat)
# generate html file
html_out_path = os.path.join(
repo_dir, 'website', '_tutorials', '{}.html'.format(tid)
)
with open(html_out_path, 'w') as html_outfile:
html_outfile.write(html_out)
# generate JS file
script = TEMPLATE.format(tid)
js_out_path = os.path.join(
repo_dir, 'website', 'pages', 'tutorials', '{}.js'.format(tid)
)
with open(js_out_path, 'w') as js_outfile:
js_outfile.write(script)
# output tutorial in both ipynb & py form
ipynb_out_path = os.path.join(
repo_dir, 'website', 'static', 'files', '{}.ipynb'.format(tid)
)
with open(ipynb_out_path, 'w') as ipynb_outfile:
ipynb_outfile.write(nb_str)
exporter = ScriptExporter()
script, meta = exporter.from_notebook_node(nb)
py_out_path = os.path.join(
repo_dir, 'website', 'static', 'files', '{}.py'.format(tid)
)
with open(py_out_path, 'w') as py_outfile:
py_outfile.write(script)
