directions for setup and a script
This commit is contained in:
Jonathan Taylor
170
setup_notebook_env.py
Executable file
170
setup_notebook_env.py
Executable file
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#!/usr/bin/env python
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import argparse
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import subprocess
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import sys
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import tempfile
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from pathlib import Path
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def run_command(command, cwd):
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"""Runs a command and prints its output."""
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print(f"Running command: {' '.join(command)} in {cwd}")
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process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, cwd=cwd, text=True)
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for line in iter(process.stdout.readline, ''):
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print(line, end='')
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process.wait()
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if process.returncode != 0:
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raise subprocess.CalledProcessError(process.returncode, command)
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def setup_env(outdir,
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commit,
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python_version,
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nbfiles,
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uv_executable,
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timeout,
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kernel,
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nb_allow_errors):
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"""
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Sets up a student environment for ISLP_labs.
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Parameters
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----------
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outdir : Path
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Output directory.
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commit : str
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Commit hash or tag to checkout.
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python_version : str
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Python version to use for the virtual environment.
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nbfiles : list
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List of notebook files to run.
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uv_executable : str
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The `uv` executable.
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timeout : int
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Timeout for running notebooks.
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kernel : str
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Kernel to use for running notebooks.
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nb_allow_errors : bool
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Allow errors when running notebooks.
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"""
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repo_url = 'https://github.com/intro-stat-learning/ISLP_labs.git'
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if outdir is None:
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with tempfile.TemporaryDirectory() as tmpdir:
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setup_env(Path(tmpdir),
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commit,
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python_version,
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nbfiles,
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uv_executable,
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timeout,
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nb_allow_errors)
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return
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if outdir.exists():
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if any(outdir.iterdir()): # Check if directory is not empty (including hidden files)
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raise FileExistsError(f"Output directory '{outdir}' already exists and is not empty. Please specify an empty directory or a non-existent path.")
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else:
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outdir.mkdir(parents=True)
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try:
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print(f"Initializing repository in {outdir}...")
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run_command(['git', 'init'], cwd=str(outdir))
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run_command(['git', 'remote', 'add', 'origin', repo_url], cwd=str(outdir))
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print(f"Fetching commit {commit}...")
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run_command(['git', 'fetch', 'origin', commit, '--depth=1'], cwd=str(outdir))
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print(f"Checking out commit {commit}...")
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run_command(['git', 'checkout', 'FETCH_HEAD'], cwd=str(outdir))
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print(f"Setting up Python {python_version} with {uv_executable}...")
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run_command([uv_executable, 'python', 'install', python_version], cwd=str(outdir))
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print("Creating virtual environment...")
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run_command([uv_executable, 'venv', '--python', python_version, '--seed'], cwd=str(outdir))
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print("Installing requirements...")
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venv_dir = Path('.venv')
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uv_bin = venv_dir / 'Scripts' if sys.platform == 'win32' else venv_dir / 'bin'
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run_command([str(uv_bin / 'pip'), 'install', '-r', 'requirements.txt', 'jupyterlab'], cwd=str(outdir))
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if nbfiles:
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if nb_allow_errors:
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for nbfile in nbfiles:
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notebook_path = outdir / nbfile
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if not notebook_path.exists():
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print(f"Error: Notebook '{nbfile}' not found in the repository.", file=sys.stderr)
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continue
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print(f"Running notebook {notebook_path} with jupyter nbconvert...")
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nbconvert_command = [str(uv_bin / 'jupyter'),
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'nbconvert',
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'--to',
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'notebook',
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'--execute',
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'--inplace',
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f'--ExecutePreprocessor.timeout={timeout}',
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str(nbfile)]
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if kernel:
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nbconvert_command.extend(['--kernel', kernel])
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nbconvert_command.append('--allow-errors')
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run_command(nbconvert_command, cwd=str(outdir))
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else:
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run_command([str(uv_bin / 'pip'), 'install', 'pytest', 'nbmake'], cwd=str(outdir))
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for nbfile in nbfiles:
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notebook_path = outdir / nbfile
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if not notebook_path.exists():
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print(f"Error: Notebook '{nbfile}' not found in the repository.", file=sys.stderr)
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continue
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print(f"Running notebook {notebook_path} with pytest nbmake...")
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pytest_command = [str(uv_bin / 'pytest'),
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'--nbmake',
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f'--nbmake-timeout={timeout}',
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'-vv',
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str(nbfile)]
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if kernel:
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pytest_command.append(f'--nbmake-kernel={kernel}')
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# nbmake does not have --allow-errors in the same way as nbconvert
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# If errors are not allowed, nbmake will fail on first error naturally
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run_command(pytest_command, cwd=str(outdir))
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print("Setup completed successfully.")
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print(f"Environment is in: {outdir}")
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if sys.platform == 'win32':
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print(f"Activate it with: .\\{outdir.name}\\.venv\\Scripts\\activate")
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else:
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print(f"Activate it with: source {outdir.name}/.venv/bin/activate")
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except subprocess.CalledProcessError as e:
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print(f"An error occurred: {e}", file=sys.stderr)
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sys.exit(1)
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def main():
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parser = argparse.ArgumentParser(description='Setup a student environment for ISLP_labs.')
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parser.add_argument('--outdir', type=Path, default=None, help='The output directory to checkout the labs (default: a temporary directory)')
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parser.add_argument('--commit', default='main', help='The git commit, tag, or branch to checkout (default: main)')
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parser.add_argument('--python-version', default='3.11', help='Python version to use (default: 3.11)')
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parser.add_argument('--uv-executable', default='uv', help='The `uv` executable to use (default: "uv")')
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parser.add_argument('--timeout', type=int, default=3600, help='Timeout for running notebooks (default: 3600)')
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parser.add_argument('--kernel', default=None, help='Kernel to use for running notebooks')
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parser.add_argument('--allow-errors', action='store_true', help='Allow errors when running notebooks')
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parser.add_argument('nbfiles', nargs='*', help='Optional list of notebooks to run.')
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args = parser.parse_args()
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setup_env(args.outdir,
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args.commit,
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args.python_version,
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args.nbfiles,
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args.uv_executable,
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args.timeout,
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args.kernel,
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args.allow_errors)
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if __name__ == '__main__':
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main()
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