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# execute the notebook according to the current execution order (sorted by execution_count)
# the order in the .ipynb file stays the same
# [re-execute] lines mean that cell is executed twice
# the outputs should be updated (after execution)
import nbformat
import os
import sys
import tempfile
import subprocess
from nbformat import NotebookNode
def set_notebook_path(path_in):
notebook_dir = os.path.dirname(os.path.abspath(path_in))
if notebook_dir not in sys.path:
sys.path.insert(0, notebook_dir)
def reexecute_cells(path_in):
# Load notebook
with open(path_in, encoding="utf-8") as f:
nb = nbformat.read(f, as_version=4)
# Identify execution order from execution_count (ignore None)
code_cells = [
(i, cell) for i, cell in enumerate(nb.cells)
if cell.cell_type == "code" and (cell.execution_count is not None)
]
sorted_cells = sorted(code_cells, key=lambda x: x[1].execution_count)
# For each cell: if [re-execute], duplicate once right after
i = 0
while i < len(sorted_cells):
_, cell = sorted_cells[i]
first_line = cell.source.strip().splitlines()[0] if cell.source.strip() else ""
if ("[re-execute]" in first_line) or ("[reexecute]" in first_line):
# Append a duplicate of this cell to be executed again
dup = NotebookNode(nbformat.from_dict(cell))
# Find this cell's execution order position
sorted_cells.insert(i + 1, (None, dup))
i += 1
i += 1
nb.cells = [cell for (_, cell) in sorted_cells]
return nb
def execute_notebook_via_nbconvert(nb: NotebookNode, output_path: str):
notebook_dir = os.path.dirname(os.path.abspath(output_path))
os.makedirs(notebook_dir, exist_ok=True)
# Save to a temp file in the same folder as notebook
with tempfile.NamedTemporaryFile(delete=False, suffix=".ipynb", dir=notebook_dir, mode='w', encoding='utf-8') as tmp:
nbformat.write(nb, tmp)
tmp_filename = os.path.basename(tmp.name)
# Change working directory to notebook's folder
cwd = os.getcwd()
os.chdir(notebook_dir)
try:
# Run nbconvert in the notebook's own directory
subprocess.run([
"jupyter", "nbconvert",
"--to", "notebook",
"--execute",
"--inplace",
tmp_filename
], check=True)
# Load and write final output
executed_nb = nbformat.read(open(tmp_filename, encoding="utf-8"), as_version=4)
with open(output_path, "w", encoding="utf-8") as f:
nbformat.write(executed_nb, f)
finally:
os.chdir(cwd)
os.remove(os.path.join(notebook_dir, tmp_filename))
def main():
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("input", help="Input notebook path")
parser.add_argument("-o", "--output", help="Output notebook path (optional)")
args = parser.parse_args()
path_in = args.input
path_out = args.output or path_in.replace(".ipynb", "_executed.ipynb")
set_notebook_path(path_in)
modified_nb = reexecute_cells(path_in)
execute_notebook_via_nbconvert(modified_nb, path_out)
print(f"Notebook executed and saved to: {path_out}")
if __name__ == "__main__":
main()
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