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Commit 7e7036ca authored by Ronald Jäpel's avatar Ronald Jäpel
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Add ipynb test

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tests/print_random_number.py 0 → 100644
+ 3
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View file @ 7e7036ca
print(203)
with open("output/data.txt", "w") as handle:
handle.write(203)
tests/test_jupyter.ipynb 0 → 100644
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View file @ 7e7036ca
%% Cell type:code id:a5c6949c-da6a-40ab-aec7-de4534582ab2 tags:
``` python
import nbformat as nbf
import sys
import os
from pathlib import Path
import nbformat
import time
from nbconvert.preprocessors import ExecutePreprocessor
from nbconvert.nbconvertapp import NbConvertApp
from ipylab import JupyterFrontEnd
```
%% Cell type:code id:e4dd4791-5e5b-4fa7-89f1-8a9e574c300e tags:
``` python
print(1)
```
%% Output
1
%% Cell type:code id:e983e571-58f5-4310-8584-064fe4ac3570 tags:
``` python
print(2)
```
%% Output
2
%% Cell type:code id:b28fb6d3-faa9-4788-86a1-4ec0d1026aa8 tags:
``` python
def check_execution_order(notebook_path,
check_all_executed=False,
check_all_except_last_executed=True,
check_top_to_bottom=False,
check_in_order=True,
exclude_last_cell=False):
ntbk = nbf.read(notebook_path, nbf.NO_CONVERT)
# extract all code cells (disregard markdown, raw and others), then extract the execution order
output_cells = [cell for cell in ntbk.cells if cell["cell_type"] == "code"]
# remove empty cells
non_empty_cells = [cell for cell in output_cells if cell["source"] != ""]
execution_counts = [cell["execution_count"] for cell in non_empty_cells]
def _all_none(item_list):
return all([i is None for i in item_list])
# return early if no cells were executed
if _all_none(execution_counts):
return True
pass_check = [True]
def _check_all_executed(execution_counts: list) -> bool:
"""Check all cells were executed.
Parameters
----------
execution_counts : list
execution_counts
Returns
-------
bool
"""
return not None in execution_counts
def _check_in_order(execution_counts: list) -> bool:
"""Check that execution counts that aren't None go from 1 to N.
Parameters
----------
execution_counts : list
execution counts
Returns
-------
bool
"""
print(execution_counts)
execution_counts = [x for x in execution_counts if x is not None]
count_range = len(execution_counts)
if exclude_last_cell:
count_range = count_range - 1
is_in_order = all([execution_counts[i] < execution_counts[i + 1] for i in range(count_range - 1)])
return is_in_order
if check_in_order:
pass_check.append(_check_in_order(execution_counts))
if check_all_executed:
pass_check.append(_check_all_executed(execution_counts))
if check_all_except_last_executed:
pass_check.append(_check_all_executed(execution_counts[:-1]))
if check_top_to_bottom:
pass_check.append(
_check_all_executed(execution_counts) and _check_in_order(execution_counts)
)
return all(pass_check)
def save_ipynb():
app = JupyterFrontEnd()
print("Saving", end="")
# note: docmanager:save doesn't lock the python thread until saving is completed.
# Sometimes, new changes aren't completely saved before checks are performed.
# Waiting for 0.1 seconds seems to prevent that.
app.commands.execute('docmanager:save')
time.sleep(0.1)
print("")
def reload_notebook():
app = JupyterFrontEnd()
app.commands.execute('docmanager:reload')
def wait_for_user(message):
proceed = input(message + " Y/n")
if proceed.lower() == "y" or proceed == "":
return True
else:
return False
def clear_and_rerun_notebook(notebook_filename, force_rerun=False, timeout=600):
if "nbconvert_call" in sys.argv:
print("Finished rerun")
return
save_ipynb()
time.sleep(1)
is_in_order = check_execution_order(notebook_filename)
if is_in_order and not force_rerun:
print("Notebook was already executed in order.")
return
else:
rerun_confirmed_bool = wait_for_user("Notebook was not in order, rerun notebook now?")
if not rerun_confirmed_bool and not force_rerun:
print("Aborting.")
return
print("Rerunning.")
with open(notebook_filename) as f:
nb = nbformat.read(f, as_version=4)
ep = ExecutePreprocessor(timeout=timeout, kernel_name='python3', extra_arguments=["nbconvert_call"])
ep.preprocess(nb, )
with open(notebook_filename, 'w', encoding='utf-8') as f:
nbformat.write(nb, f)
reload_notebook()
def convert_ipynb(filepath, formats=None):
if formats is None:
formats = ["html", "python"]
app = NbConvertApp()
app.initialize()
output_root_directory = os.path.join(r"C:\Users\ronal\PycharmProjects\git_lfs_test_2", "results",
os.path.basename(filepath.replace('.', '_')))
for format in formats:
app.export_format = format
app.notebooks = [filepath]
app.output_base = os.path.join(output_root_directory, os.path.basename(filepath.replace('.ipynb', '')))
if not os.path.exists(output_root_directory):
os.makedirs(output_root_directory)
app.start()
def export_all_figures():
import junix
for file in os.listdir(git_repo.working_dir):
if file.endswith("ipynb"):
file_without_extension = Path(file).stem
images = junix.export_images(filepath=os.path.join(git_repo.working_dir, file),
output_dir=os.path.join(git_repo.working_dir, "results",
file.replace(".", "_")),
prefix=file_without_extension)
convert_ipynb(filepath=os.path.join(git_repo.working_dir, file), formats=["html"])
```
%% Cell type:code id:99404052-11f1-499b-a23f-4a90ed917300 tags:
``` python
clear_and_rerun_notebook("test_jupyter.ipynb")
```
%% Output
Saving
[13, 14, 15, 24, None, 25, 26]
Notebook was not in order, rerun notebook now? Y/n n
Aborting.
%% Cell type:code id:fec9df11-5622-49d8-8e08-c6e8bbe73dfd tags:
``` python
save_ipynb()
time.sleep(1)
check_execution_order("test_jupyter.ipynb")
```
%% Output
Saving
[13, 14, 15, 24, 27, None, 26]
False
%% Cell type:code id:81841f17-c8d7-4a1e-b13d-d3f5a19adfd4 tags:
``` python
clear_and_rerun_notebook("test_jupyter.ipynb")
```
%% Output
Saving
[13, 14, 15, 24, 27, 28, None]
Notebook was already executed in order.
token instructions.png 0 → 100644
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− 0
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token instructions.png

57.5 KiB

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