Best way to have a python script copy itself?

Question

I am using python for scientific applications. I run simulations with various parameters, my script outputs the data to an appropriate directory for that parameter set. Later I use that data. However sometimes I edit my script; in order to be able to reproduce my results if needed I would like to have a copy of whatever version of the script was used to generate the data live right in the directory with the data. So basically I would like to have my python script copy itself to the data directory. What's the best way to do this?

Thanks!

Answer 1

I stumbled across this question as I wanted to do the same thing. Although I agree with the comments that git/VCS with revision and everything would be the cleanest solution, sometimes you just want something quick and dirty that does the job. So if anyone is still interested:

With __file__ you can access the running scripts filename (with path), and as already suggested you can use a high-level file manipulation lib like shutil to copy it to some place. In one line:

shutil.copy(__file__, 'experiment_folder_path/copied_script_name.py') 

With the corresponding imports and some bells and whistles:

import shutil
import os     # optional: for extracting basename / creating new filepath
import time   # optional: for appending time string to copied script

# generate filename with timestring
copied_script_name = time.strftime("%Y-%m-%d_%H%M") + '_' + os.path.basename(__file__)

# copy script
shutil.copy(__file__, 'my_experiment_folder_path' + os.sep + copied_script_name) 

Answer 2

Copying the script can be done with shutil.copy().

But you should consider keeping your script under revision control. That enables you to retain a revision history.

E.g. I keep my scripts under revision control with git. In Python files I tend to keep a version string like this;

__version__ = '$Revision: a42ef58 $'[11:-2]

This version string is updated with the git short hash tag every time the file in question is changed. (this is done by running a script called update-modified-keywords.py from git's post-commit hook.)

If you have a version string like this, you can embed that in the output, so you always know which version has produced the output.

Edit:

The update-modified-keywords script is shown below;

#!/usr/bin/env python2
# -*- coding: utf-8 -*-
#
# Author: R.F. Smith <[email protected]>
# $Date: 2013-11-24 22:20:54 +0100 $
# $Revision: 3d4f750 $
#
# To the extent possible under law, Roland Smith has waived all copyright and
# related or neighboring rights to update-modified-keywords.py. This work is
# published from the Netherlands.
# See http://creativecommons.org/publicdomain/zero/1.0/

"""Remove and check out those files that that contain keywords and have
changed since in the last commit in the current working directory."""

from __future__ import print_function, division
import os
import mmap
import sys
import subprocess


def checkfor(args):
    """Make sure that a program necessary for using this script is
    available.

    Arguments:
    args -- string or list of strings of commands. A single string may
            not contain spaces.
    """
    if isinstance(args, str):
        if ' ' in args:
            raise ValueError('No spaces in single command allowed.')
        args = [args]
    try:
        with open(os.devnull, 'w') as bb:
            subprocess.check_call(args, stdout=bb, stderr=bb)
    except subprocess.CalledProcessError:
        print("Required program '{}' not found! exiting.".format(args[0]))
        sys.exit(1)


def modifiedfiles():
    """Find files that have been modified in the last commit.

    :returns: A list of filenames.
    """
    fnl = []
    try:
        args = ['git', 'diff-tree', 'HEAD~1', 'HEAD', '--name-only', '-r',
                '--diff-filter=ACMRT']
        with open(os.devnull, 'w') as bb:
            fnl = subprocess.check_output(args, stderr=bb).splitlines()
            # Deal with unmodified repositories
            if len(fnl) == 1 and fnl[0] is 'clean':
                return []
    except subprocess.CalledProcessError as e:
        if e.returncode == 128:  # new repository
            args = ['git', 'ls-files']
            with open(os.devnull, 'w') as bb:
                fnl = subprocess.check_output(args, stderr=bb).splitlines()
    # Only return regular files.
    fnl = [i for i in fnl if os.path.isfile(i)]
    return fnl


def keywordfiles(fns):
    """Filter those files that have keywords in them

    :fns: A list of filenames
    :returns: A list for filenames for files that contain keywords.
    """
    # These lines are encoded otherwise they would be mangled if this file
    # is checked in my git repo!
    datekw = 'JERhdGU='.decode('base64')
    revkw = 'JFJldmlzaW9u'.decode('base64')
    rv = []
    for fn in fns:
        with open(fn, 'rb') as f:
            try:
                mm = mmap.mmap(f.fileno(), 0, access=mmap.ACCESS_READ)
                if mm.find(datekw) > -1 or mm.find(revkw) > -1:
                    rv.append(fn)
                mm.close()
            except ValueError:
                pass
    return rv


def main(args):
    """Main program.

    :args: command line arguments
    """
    # Check if git is available.
    checkfor(['git', '--version'])
    # Check if .git exists
    if not os.access('.git', os.F_OK):
        print('No .git directory found!')
        sys.exit(1)
    print('{}: Updating modified files.'.format(args[0]))
    # Get modified files
    files = modifiedfiles()
    if not files:
        print('{}: Nothing to do.'.format(args[0]))
        sys.exit(0)
    files.sort()
    # Find files that have keywords in them
    kwfn = keywordfiles(files)
    for fn in kwfn:
        os.remove(fn)
    args = ['git', 'checkout', '-f'] + kwfn
    subprocess.call(args)


if __name__ == '__main__':
    main(sys.argv)

If you don't want keyword expansion to clutter up your git history, you can use the smudge and clean filters. I have the following set in my ~/.gitconfig;

[filter "kw"]
    clean = kwclean
    smudge = kwset

Both kwclean and kwset are Python scripts.

#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Author: R.F. Smith <[email protected]>
# $Date: 2013-11-24 22:20:54 +0100 $
#
# To the extent possible under law, Roland Smith has waived all copyright and
# related or neighboring rights to kwset.py. This work is published from
# the Netherlands. See http://creativecommons.org/publicdomain/zero/1.0/

"""Fill the Date and Revision keywords from the latest git commit and tag and
   subtitutes them in the standard input."""

import os
import sys
import subprocess
import re


def gitdate():
    """Get the date from the latest commit in ISO8601 format.
    """
    args = ['git', 'log',  '-1', '--date=iso']
    dline = [l for l in subprocess.check_output(args).splitlines()
             if l.startswith('Date')]
    try:
        dat = dline[0][5:].strip()
        return ''.join(['$', 'Date: ', dat, ' $'])
    except IndexError:
        raise ValueError('Date not found in git output')


def gitrev():
    """Get the latest tag and use it as the revision number. This presumes the
    habit of using numerical tags. Use the short hash if no tag available.
    """
    args = ['git', 'describe',  '--tags', '--always']
    try:
        with open(os.devnull, 'w') as bb:
            r = subprocess.check_output(args, stderr=bb)[:-1]
    except subprocess.CalledProcessError:
        return ''.join(['$', 'Revision', '$'])
    return ''.join(['$', 'Revision: ', r, ' $'])


def main():
    """Main program.
    """
    dre = re.compile(''.join([r'\$', r'Date:?\$']))
    rre = re.compile(''.join([r'\$', r'Revision:?\$']))
    currp = os.getcwd()
    if not os.path.exists(currp+'/.git'):
        print >> sys.stderr, 'This directory is not controlled by git!'
        sys.exit(1)
    date = gitdate()
    rev = gitrev()
    for line in sys.stdin:
        line = dre.sub(date, line)
        print rre.sub(rev, line),


if __name__ == '__main__':
    main()

and

#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Author: R.F. Smith <[email protected]>
# $Date: 2013-11-24 22:20:54 +0100 $
#
# To the extent possible under law, Roland Smith has waived all copyright and
# related or neighboring rights to kwclean.py. This work is published from the
# Netherlands. See http://creativecommons.org/publicdomain/zero/1.0/

"""Remove the Date and Revision keyword contents from the standard input."""

import sys
import re

## This is the main program ##
if __name__ == '__main__':
    dre = re.compile(''.join([r'\$', r'Date.*\$']))
    drep = ''.join(['$', 'Date', '$'])
    rre = re.compile(''.join([r'\$', r'Revision.*\$']))
    rrep = ''.join(['$', 'Revision', '$'])
    for line in sys.stdin:
        line = dre.sub(drep, line)
        print rre.sub(rrep, line),

Both of these scripts are installed (without an extension at the end of the filename, as usual for executables) in a directory that is in my $PATH, and have their executable bit set.

In the .gitattributes file of my repository I choose for which files I want keyword expansion. So for e.g. Python files;

*.py filter=kw