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e76b79a | 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 65 | # Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import os
import subprocess
import pytest
from pathlib import Path
notebook_dir = Path(__file__).parents[1] / "examples"
notebook_fns = notebook_dir.glob("*.ipynb")
def convert_notebook_to_py(nb_fn: Path, py_fn: Path) -> None:
"""
From https://stackoverflow.com/questions/17077494/how-do-i-convert-a-ipython-notebook-into-a-python-file-via-commandline
"""
import nbformat
from nbconvert import PythonExporter
with open(nb_fn) as fh:
nb = nbformat.reads(fh.read(), nbformat.NO_CONVERT)
exporter = PythonExporter()
source, meta = exporter.from_notebook_node(nb)
# Skip the magic, which gets converted to `get_ipython()`
source.replace("get_ipython", "# get_ipython")
with open(py_fn, "w+") as fh:
fh.writelines(source)
def run_multiple(cmds):
for cmd in cmds.strip().split("\n"):
print(cmd)
subprocess.run(cmd.strip(), shell=True, check=True)
def do_setup(nb_name):
""" Do any setup work; see intro of the notebook """
if nb_name == "sup_variant_prediction":
cmds = """
curl -O https://dl.fbaipublicfiles.com/fair-esm/examples/P62593_reprs.tar.gz
tar -xzf P62593_reprs.tar.gz
curl -O https://dl.fbaipublicfiles.com/fair-esm/examples/P62593.fasta
"""
run_multiple(cmds)
else:
print(f"No setup work for {nb_name}")
@pytest.mark.parametrize("nb_fn", list(notebook_fns))
def test_run_notebook(nb_fn: Path, tmp_path: Path):
""" Simply make sure the notebooks run from a-z """
py_fn = tmp_path / (nb_fn.stem + ".py")
print(py_fn)
convert_notebook_to_py(nb_fn, py_fn)
os.chdir(notebook_dir)
do_setup(nb_fn.stem)
_globals = {}
exec(py_fn.read_text(), _globals)
# No asserts, just running is enough for now
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