File size: 2,521 Bytes
fefb9a6 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 | #!/usr/bin/env python3
"""Regenerate every figure and table in the paper from the committed data.
Runs each analysis notebook headless (no display, no widgets). Every notebook reads the in-repo
data/<name>/ files and writes its figures to <notebook>/figures/ and its tables to
<notebook>/documents/. The notebooks are stored without outputs, so this script is how the figures
and tables are produced. No environment variables and no network are needed.
Usage:
python reproduce.py # run all notebooks
python reproduce.py fig3 s10 # run only notebooks whose path contains one of these strings
"""
import argparse
import glob
import os
import sys
import time
HERE = os.path.dirname(os.path.abspath(__file__))
def main():
ap = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter)
ap.add_argument("filters", nargs="*", help="only run notebooks whose path contains one of these")
ap.add_argument("--timeout", type=int, default=900, help="per-cell timeout in seconds (default 900)")
args = ap.parse_args()
try:
import nbformat
from nbconvert.preprocessors import ExecutePreprocessor
except ImportError:
sys.exit("reproduce.py needs the analysis dependencies: pip install -r requirements.txt")
notebooks = sorted(glob.glob(os.path.join(HERE, "analysis", "*", "*.ipynb")))
if args.filters:
notebooks = [p for p in notebooks if any(f in p for f in args.filters)]
if not notebooks:
sys.exit("no matching notebooks")
print("running {} notebooks headless".format(len(notebooks)))
n_ok = n_fail = 0
for path in notebooks:
rel = os.path.relpath(path, HERE)
start = time.time()
notebook = nbformat.read(path, as_version=4)
# run each notebook from its own directory so its in-repo data and figures/ paths resolve
executor = ExecutePreprocessor(timeout=args.timeout)
try:
executor.preprocess(notebook, {"metadata": {"path": os.path.dirname(path)}})
print(" OK ({:5.0f}s) {}".format(time.time() - start, rel))
n_ok += 1
except Exception as error:
print(" FAIL ({:5.0f}s) {}: {}: {}".format(
time.time() - start, rel, type(error).__name__, str(error)[:120]))
n_fail += 1
print("\n{} ok, {} failed".format(n_ok, n_fail))
sys.exit(1 if n_fail else 0)
if __name__ == "__main__":
main()
|