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Commit be9e1d33 authored by Jens Henrik Goebbert's avatar Jens Henrik Goebbert
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001-Jupyter/001-Tutorials/SanityCheck-Tutorials.ipynb
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%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
## Sanity Check ## Sanity Check
This notebook checks if the available general tutorials run without errors. This notebook checks if the available general tutorials run without errors.
This particulary tests the installed python packages and their interoperability for standard features and examples. Running these checks can take **a lot of time** and there for will not finish in the max. cpu-time we provide for a process on a login node. Hence the jupyter kernel for this notebook will eventually be killed by the system. These Sanity Checks are primarily usefull for system administrators. This particulary tests the installed python packages and their interoperability for standard features and examples. Running these checks can take **a lot of time** and there for will not finish in the max. cpu-time we provide for a process on a login node. Hence the jupyter kernel for this notebook will eventually be killed by the system. These Sanity Checks are primarily usefull for system administrators.
If you want to run them anyway - ensure your Jupyter is running as a **batch job** with far more compute time available. If you want to run them anyway - ensure your Jupyter is running as a **batch job** with far more compute time available.
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
### Grab Tutorials from Git-Repo ### Grab Tutorials from Git-Repo
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
from git import Repo from git import Repo
#repo = Repo.clone_from("https://gitlab.version.fz-juelich.de/jupyter4jsc/j4j_notebooks.git", './j4j_notebooks') #repo = Repo.clone_from("https://gitlab.version.fz-juelich.de/jupyter4jsc/j4j_notebooks.git", './j4j_notebooks')
#repo.git.checkout('integration') #repo.git.checkout('integration')
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
### Define Funktions for later Sanity Check ### Define Funktions for later Sanity Check
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
from typing import Any, Tuple, Dict, Mapping from typing import Any, Tuple, Dict, Mapping
from collections import defaultdict from collections import defaultdict
from nbformat import NotebookNode from nbformat import NotebookNode
def count_source(source: str) -> Tuple[int, int, int]: def count_source(source: str) -> Tuple[int, int, int]:
"""Count number of non-blank lines, words, and non-whitespace characters. """Count number of non-blank lines, words, and non-whitespace characters.
:param source: string to count :param source: string to count
:return: number of non-blank lines, words, and non-whitespace characters :return: number of non-blank lines, words, and non-whitespace characters
""" """
lines = [line for line in source.split('\n') if line and not line.isspace()] lines = [line for line in source.split('\n') if line and not line.isspace()]
words = source.split() words = source.split()
chars = ''.join(words) chars = ''.join(words)
return len(lines), len(words), len(chars) return len(lines), len(words), len(chars)
REQUIRED_NB_FIELDS = {"metadata", "nbformat_minor", "nbformat", "cells"} REQUIRED_NB_FIELDS = {"metadata", "nbformat_minor", "nbformat", "cells"}
REQUIRED_NB_METADATA_FIELDS = {"kernelspec", "language_info"} REQUIRED_NB_METADATA_FIELDS = {"kernelspec", "language_info"}
CELL_TYPES = ('markdown', 'code', 'raw', ) CELL_TYPES = ('markdown', 'code', 'raw', )
REQUIRED_CELL_FIELDS = { REQUIRED_CELL_FIELDS = {
'markdown': {"cell_type", "metadata", "source"}, 'markdown': {"cell_type", "metadata", "source"},
'code': {"cell_type", "metadata", "source", "execution_count", "outputs"}, 'code': {"cell_type", "metadata", "source", "execution_count", "outputs"},
'raw': {"cell_type", "metadata", "source"} 'raw': {"cell_type", "metadata", "source"}
} }
OPTIONAL_CELL_FIELDS = { OPTIONAL_CELL_FIELDS = {
'markdown': {"attachments"}, 'markdown': {"attachments"},
'code': set(), 'code': set(),
'raw': {"attachments"} 'raw': {"attachments"}
} }
OPTIONAL_OUTPUT_TYPES = { OPTIONAL_OUTPUT_TYPES = {
'execute_result': {'data', 'metadata' ,'execution_count'}, 'execute_result': {'data', 'metadata' ,'execution_count'},
'stream': {'name', 'text'}, 'stream': {'name', 'text'},
'display_data': {'data', 'metadata', }, 'display_data': {'data', 'metadata', },
'error': {'ename', 'evalue', 'traceback'}, 'error': {'ename', 'evalue', 'traceback'},
} }
CELL_STATISTICS = ( CELL_STATISTICS = (
'cell_types', #: cell type counts 'cell_types', #: cell type counts
'sources', #: cell sources counts 'sources', #: cell sources counts
'cell_metadata', #: cell metadata counts, including separate ``tags`` 'cell_metadata', #: cell metadata counts, including separate ``tags``
'cell_attachments', #: cell attachment MIME type counts, and total 'cell_attachments', #: cell attachment MIME type counts, and total
'code_execution', #: code cell execution count statistics 'code_execution', #: code cell execution count statistics
'code_outputs', #: code cell counts per output_type, subcounts per ``stream`` and ``error``, and total 'code_outputs', #: code cell counts per output_type, subcounts per ``stream`` and ``error``, and total
'cell_extra', #: counts for extra (unknown) fields in cells 'cell_extra', #: counts for extra (unknown) fields in cells
) )
# dictionary keys for source statistics # dictionary keys for source statistics
EMPTY_SOURCES = 'total empty sources' EMPTY_SOURCES = 'total empty sources'
SOURCE_LINES = 'total source lines' SOURCE_LINES = 'total source lines'
SOURCE_WORDS = 'total source words' SOURCE_WORDS = 'total source words'
SOURCE_CHARS = 'total source chars' SOURCE_CHARS = 'total source chars'
EMPTY_SOURCES_MD = 'markdown empty sources' EMPTY_SOURCES_MD = 'markdown empty sources'
SOURCE_LINES_MD = 'markdown source lines' SOURCE_LINES_MD = 'markdown source lines'
SOURCE_WORDS_MD = 'markdown source words' SOURCE_WORDS_MD = 'markdown source words'
SOURCE_CHARS_MD = 'markdown source chars' SOURCE_CHARS_MD = 'markdown source chars'
EMPTY_SOURCES_CODE = 'code empty sources' EMPTY_SOURCES_CODE = 'code empty sources'
SOURCE_LINES_CODE = 'code source lines' SOURCE_LINES_CODE = 'code source lines'
SOURCE_WORDS_CODE = 'code source words' SOURCE_WORDS_CODE = 'code source words'
SOURCE_CHARS_CODE = 'code source chars' SOURCE_CHARS_CODE = 'code source chars'
EMPTY_SOURCES_RAW = 'raw empty sources' EMPTY_SOURCES_RAW = 'raw empty sources'
SOURCE_LINES_RAW = 'raw source lines' SOURCE_LINES_RAW = 'raw source lines'
SOURCE_WORDS_RAW = 'raw source words' SOURCE_WORDS_RAW = 'raw source words'
SOURCE_CHARS_RAW = 'raw source chars' SOURCE_CHARS_RAW = 'raw source chars'
def nb_cell_stats(nb: NotebookNode) -> Dict[str, Dict[str, int]]: def nb_cell_stats(nb: NotebookNode) -> Dict[str, Dict[str, int]]:
"""Count occurrences of various elements in notebook cells. """Count occurrences of various elements in notebook cells.
:param nb: notebook to inspect :param nb: notebook to inspect
:return: dictionary of dictionaries with counts per section; :return: dictionary of dictionaries with counts per section;
each section has its own key; see CELL_STATISTICS each section has its own key; see CELL_STATISTICS
""" """
# process the notebook cells # process the notebook cells
result = {key: defaultdict(int) for key in CELL_STATISTICS} result = {key: defaultdict(int) for key in CELL_STATISTICS}
# traverse all cells and gather statistics # traverse all cells and gather statistics
for index, cell in enumerate(nb.cells): # index can be used for debug output for index, cell in enumerate(nb.cells): # index can be used for debug output
result['cell_types']['total cell count'] += 1 # count all cells result['cell_types']['total cell count'] += 1 # count all cells
ct = cell.cell_type ct = cell.cell_type
result['cell_types'][ct] += 1 # count each cell type result['cell_types'][ct] += 1 # count each cell type
# compute source statistics # compute source statistics
lines, words, chars = count_source(cell.source) # cell.source should always be present lines, words, chars = count_source(cell.source) # cell.source should always be present
empty_cell = chars == 0 empty_cell = chars == 0
if empty_cell: if empty_cell:
result['sources'][EMPTY_SOURCES] += 1 result['sources'][EMPTY_SOURCES] += 1
if ct == 'markdown': if ct == 'markdown':
result['sources'][EMPTY_SOURCES_MD] += 1 result['sources'][EMPTY_SOURCES_MD] += 1
elif ct == 'code': elif ct == 'code':
result['sources'][EMPTY_SOURCES_CODE] += 1 result['sources'][EMPTY_SOURCES_CODE] += 1
elif ct == 'raw': elif ct == 'raw':
result['sources'][EMPTY_SOURCES_RAW] += 1 result['sources'][EMPTY_SOURCES_RAW] += 1
if chars: if chars:
result['sources'][SOURCE_LINES] += lines result['sources'][SOURCE_LINES] += lines
result['sources'][SOURCE_WORDS] += words result['sources'][SOURCE_WORDS] += words
result['sources'][SOURCE_CHARS] += chars result['sources'][SOURCE_CHARS] += chars
if ct == 'markdown': if ct == 'markdown':
result['sources'][SOURCE_LINES_MD] += lines result['sources'][SOURCE_LINES_MD] += lines
result['sources'][SOURCE_WORDS_MD] += words result['sources'][SOURCE_WORDS_MD] += words
result['sources'][SOURCE_CHARS_MD] += chars result['sources'][SOURCE_CHARS_MD] += chars
elif ct == 'code': elif ct == 'code':
result['sources'][SOURCE_LINES_CODE] += lines result['sources'][SOURCE_LINES_CODE] += lines
result['sources'][SOURCE_WORDS_CODE] += words result['sources'][SOURCE_WORDS_CODE] += words
result['sources'][SOURCE_CHARS_CODE] += chars result['sources'][SOURCE_CHARS_CODE] += chars
elif ct == 'raw': elif ct == 'raw':
result['sources'][SOURCE_LINES_RAW] += lines result['sources'][SOURCE_LINES_RAW] += lines
result['sources'][SOURCE_WORDS_RAW] += words result['sources'][SOURCE_WORDS_RAW] += words
result['sources'][SOURCE_CHARS_RAW] += chars result['sources'][SOURCE_CHARS_RAW] += chars
# count each metadata key # count each metadata key
for attr in cell.metadata: # cell.metadata should always be present for attr in cell.metadata: # cell.metadata should always be present
result['cell_metadata'][attr] += 1 result['cell_metadata'][attr] += 1
# count each tag in tags metadata # count each tag in tags metadata
if 'tags' in cell.metadata: if 'tags' in cell.metadata:
for tag in cell.metadata.tags: for tag in cell.metadata.tags:
result['cell_metadata']['tag ' + tag] += 1 result['cell_metadata']['tag ' + tag] += 1
# count each attachment mime type # count each attachment mime type
if 'attachments' in cell: if 'attachments' in cell:
result['cell_attachments']['total count of cells with attachments'] += 1 result['cell_attachments']['total count of cells with attachments'] += 1
for attachment in cell.attachments.values(): for attachment in cell.attachments.values():
for key in attachment: for key in attachment:
result['cell_attachments']['total attachments count'] += 1 result['cell_attachments']['total attachments count'] += 1
result['cell_attachments'][key] += 1 result['cell_attachments'][key] += 1
# count non-standard fields in cells # count non-standard fields in cells
for field in cell: for field in cell:
if field not in REQUIRED_CELL_FIELDS[ct].union(OPTIONAL_CELL_FIELDS[ct]): if field not in REQUIRED_CELL_FIELDS[ct].union(OPTIONAL_CELL_FIELDS[ct]):
result['cell_extra'][field] += 1 result['cell_extra'][field] += 1
return result return result
from colorama import Fore, Back, Style from colorama import Fore, Back, Style
DEFAULT_WIDTH = 10 DEFAULT_WIDTH = 10
def print_dict(d: Dict[str, Any], header: str=None, width: int=DEFAULT_WIDTH) -> None: def print_dict(d: Dict[str, Any], header: str=None, width: int=DEFAULT_WIDTH) -> None:
"""Print dictionary d with section header. """Print dictionary d with section header.
:param d: dictionary to print :param d: dictionary to print
:param header: header of the table :param header: header of the table
:param width: width of the left column :param width: width of the left column
""" """
if d: if d:
if header: if header:
print('{}:'.format(header)) print('{}:'.format(header))
for key in sorted(d): for key in sorted(d):
if key == 'raw': if key == 'raw':
style = Fore.RED style = Fore.RED
else: else:
style = '' style = ''
left = str(d[key]) left = str(d[key])
print(style + ' {:>{}} {}'.format(left, width, key) + Style.RESET_ALL) print(style + ' {:>{}} {}'.format(left, width, key) + Style.RESET_ALL)
from pathlib import Path from pathlib import Path
from nbformat import NotebookNode from nbformat import NotebookNode
from typing import List, Union from typing import List, Union
import nbformat import nbformat
import sys import sys
def read_nb(nb_path: Path) -> Union[None, NotebookNode]: def read_nb(nb_path: Path) -> Union[None, NotebookNode]:
"""Read notebook from given path, and return it. """Read notebook from given path, and return it.
Uses ``args.debug``: in debug mode, a read error results in an exception, else it returns ``None``. Uses ``args.debug``: in debug mode, a read error results in an exception, else it returns ``None``.
:param nb_path: path to read from :param nb_path: path to read from
:param args: to check debug mode :param args: to check debug mode
:return: notebook read from ``nb_path`` or None if reading failed`` :return: notebook read from ``nb_path`` or None if reading failed``
""" """
try: try:
nb = nbformat.read(nb_path.open(encoding='utf-8'), as_version=4) nb = nbformat.read(nb_path.open(encoding='utf-8'), as_version=4)
except Exception as e: except Exception as e:
ename = type(e).__name__ ename = type(e).__name__
print('Reading of "{}" failed ({}):\n {}'.format(nb_path.name, ename, e), file=sys.stderr) print('Reading of "{}" failed ({}):\n {}'.format(nb_path.name, ename, e), file=sys.stderr)
return None return None
return nb return nb
``` ```
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
### Run the Sanity Check ### Run the Sanity Check
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
import os import os
import papermill as pm import papermill as pm
from papermill.exceptions import PapermillExecutionError from papermill.exceptions import PapermillExecutionError
failed_notebooks = list() failed_notebooks = list()
dirbase="/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/" dirbase="/p/project/cjsc/goebbert1/j4j_notebooks/001-Jupyter/001-Tutorials/"
for dirpath, dirs, files in os.walk(dirbase): for dirpath, dirs, files in os.walk(dirbase):
dirs.sort() dirs.sort()
if os.path.basename(dirpath).startswith('.'): if os.path.basename(dirpath).startswith('.'):
continue continue
for filename in sorted(files): for filename in sorted(files):
if filename.endswith('.ipynb') and not filename.startswith('papermill_'): if filename.endswith('.ipynb') and not filename.startswith('papermill_'):
print(os.path.join(dirpath,filename)) print(os.path.join(dirpath,filename))
if filename == "SanityCheck-Tutorials.ipynb": if filename == "SanityCheck-Tutorials.ipynb":
continue continue
try: try:
os.chdir(dirpath) os.chdir(dirpath)
nb_path = os.path.join(dirpath, filename) nb_path = os.path.join(dirpath, filename)
# get notebook statistics # get notebook statistics
nb = read_nb(Path(nb_path)) nb = read_nb(Path(nb_path))
cell_stats = nb_cell_stats(nb) cell_stats = nb_cell_stats(nb)
print_dict(cell_stats['cell_types'], "Cell types") print_dict(cell_stats['cell_types'], "Cell types")
#print_dict(cell_stats['sources'], "Cell sources") #print_dict(cell_stats['sources'], "Cell sources")
#print_dict(cell_stats['cell_metadata'], "Cell metadata fields") #print_dict(cell_stats['cell_metadata'], "Cell metadata fields")
#print_dict(cell_stats['cell_attachments'], "Cell attachments") #print_dict(cell_stats['cell_attachments'], "Cell attachments")
# execute notebook # execute notebook
nb = pm.execute_notebook( try:
nb_path, nb = pm.execute_notebook(
os.path.join(dirpath, 'papermill_' + filename), nb_path,
#kernel_name="Python3" os.path.join(dirpath, 'papermill_' + filename),
#kernel_name="Python3"
) )
except:
print("FAILED !!!!")
os.chdir(dirbase) os.chdir(dirbase)
except PapermillExecutionError as e: except PapermillExecutionError as e:
failed_notebooks.append([os.path.join(dirpath, filename), e.evalue]) failed_notebooks.append([os.path.join(dirpath, filename), e.evalue])
print(e.evalue) print(e.evalue)
``` ```
%% Output
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
<ipython-input-2-4fe21cbd60c3> in <module>
1 import os
----> 2 import papermill as pm
3 from papermill.exceptions import PapermillExecutionError
4
5 failed_notebooks = list()
ModuleNotFoundError: No module named 'papermill'
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
# Check Results # Check Results
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
failed_notebooks failed_notebooks
``` ```
%% Output
[['/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/001-Basic-Tutorials/002-Interactive-Widgets/Example - Beat Frequencies.ipynb',
'too many values to unpack (expected 2)'],
['/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/002-IPython-Cookbook/chapter05_hpc/08_cuda.ipynb',
'Error at driver init: \n[100] Call to cuInit results in CUDA_ERROR_NO_DEVICE:'],
['/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/002-IPython-Cookbook/chapter05_hpc/09_ipyparallel.ipynb',
"Can't build targets without any engines"],
['/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/002-IPython-Cookbook/chapter07_stats/06_kde.ipynb',
"No module named 'cartopy'"],
['/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/002-IPython-Cookbook/chapter09_numoptim/03_curvefitting.ipynb',
'Optimal parameters not found: Number of calls to function has reached maxfev = 1000.'],
['/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/002-IPython-Cookbook/chapter11_image/05_faces.ipynb',
"No module named 'cv2'"],
['/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/002-IPython-Cookbook/chapter14_graphgeo/02_airports.ipynb',
"No module named 'cartopy'"],
['/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/002-IPython-Cookbook/chapter14_graphgeo/06_gis.ipynb',
"No module named 'cartopy'"],
['/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/002-IPython-Cookbook/chapter14_graphgeo/07_gps.ipynb',
'read_shp requires OGR: http://www.gdal.org/'],
['/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/003-IPython-in-Depth/examples/IPython Kernel/Animations Using clear_output.ipynb',
"Connection file '~/.ipython/profile_default/security/ipcontroller-client.json' not found.\nYou have attempted to connect to an IPython Cluster but no Controller could be found.\nPlease double-check your configuration and ensure that a cluster is running."],
['/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/003-IPython-in-Depth/examples/Parallel Computing/Data Publication API.ipynb',
"Connection file '~/.ipython/profile_default/security/ipcontroller-client.json' not found.\nYou have attempted to connect to an IPython Cluster but no Controller could be found.\nPlease double-check your configuration and ensure that a cluster is running."],
['/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/003-IPython-in-Depth/examples/Parallel Computing/Monitoring an MPI Simulation - 1.ipynb',
'You have attempted to connect to an IPython Cluster but no Controller could be found.\nPlease double-check your configuration and ensure that a cluster is running.'],
['/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/003-IPython-in-Depth/examples/Parallel Computing/Monitoring an MPI Simulation - 2.ipynb',
'You have attempted to connect to an IPython Cluster but no Controller could be found.\nPlease double-check your configuration and ensure that a cluster is running.'],
['/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/003-IPython-in-Depth/examples/Parallel Computing/Monte Carlo Options.ipynb',
"Connection file '~/.ipython/profile_default/security/ipcontroller-client.json' not found.\nYou have attempted to connect to an IPython Cluster but no Controller could be found.\nPlease double-check your configuration and ensure that a cluster is running."],
['/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/003-IPython-in-Depth/examples/Parallel Computing/Parallel Decorator and map.ipynb',
"Connection file '~/.ipython/profile_default/security/ipcontroller-client.json' not found.\nYou have attempted to connect to an IPython Cluster but no Controller could be found.\nPlease double-check your configuration and ensure that a cluster is running."],
['/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/003-IPython-in-Depth/examples/Parallel Computing/Parallel Magics.ipynb',
"Connection file '~/.ipython/profile_default/security/ipcontroller-client.json' not found.\nYou have attempted to connect to an IPython Cluster but no Controller could be found.\nPlease double-check your configuration and ensure that a cluster is running."],
['/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/003-IPython-in-Depth/examples/Parallel Computing/Using Dill.ipynb',
"Connection file '~/.ipython/profile_default/security/ipcontroller-client.json' not found.\nYou have attempted to connect to an IPython Cluster but no Controller could be found.\nPlease double-check your configuration and ensure that a cluster is running."],
['/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/003-IPython-in-Depth/examples/Parallel Computing/Using MPI with IPython Parallel.ipynb',
"Connection file '~/.ipython/profile_default/security/ipcontroller-client.json' not found.\nYou have attempted to connect to an IPython Cluster but no Controller could be found.\nPlease double-check your configuration and ensure that a cluster is running."],
['/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/003-IPython-in-Depth/examples/Parallel Computing/rmt/rmt.ipynb',
"Connection file '~/.ipython/profile_default/security/ipcontroller-client.json' not found.\nYou have attempted to connect to an IPython Cluster but no Controller could be found.\nPlease double-check your configuration and ensure that a cluster is running."],
['/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/003-IPython-in-Depth/exercises/Notebook/Notebook Exercises.ipynb',
'HTTP Error 404: Not Found'],
['/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/004-Scientific-Python-Lectures/Lecture-6B-HPC.ipynb',
"Can't build targets without any engines"]]
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
# Clean Up # Clean Up
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
import os import os
import papermill as pm import papermill as pm
from papermill.exceptions import PapermillExecutionError from papermill.exceptions import PapermillExecutionError
failed_notebooks = list() failed_notebooks = list()
dirbase="/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/" dirbase="/p/project/cjsc/goebbert1/j4j_notebooks/001-Jupyter/001-Tutorials/"
for dirpath, dirs, files in os.walk(dirbase): for dirpath, dirs, files in os.walk(dirbase):
if os.path.basename(dirpath).startswith('.'): if os.path.basename(dirpath).startswith('.'):
continue continue
for filename in files: for filename in files:
if filename.endswith('.ipynb') and filename.startswith('papermill_'): if filename.endswith('.ipynb') and filename.startswith('papermill_'):
nb_path = os.path.join(dirpath,filename) nb_path = os.path.join(dirpath,filename)
print(nb_path) print(nb_path)
os.remove(nb_path) os.remove(nb_path)
``` ```
%% Output
/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/papermill_SanityCheck-Tutorials.ipynb
/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/001-Basic-Tutorials/001-IPython-Kernel/papermill_Beyond Plain Python.ipynb
/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/001-Basic-Tutorials/001-IPython-Kernel/papermill_Cell Magics.ipynb
/p/home/jusers/goebbert1/jureca/j4j_notebooks_2/001-Tutorials/001-Basic-Tutorials/001-IPython-Kernel/papermill_Working With External Code.ipynb
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%% Cell type:code id: tags:
``` python
```
......
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