Rewriting a Python library function in C drops execution time from 110 microseconds to 320 nanoseconds. That’s a respectable optimization.
Category Archives: Python
High-polish use of subprocess.Popen
Python has a pretty decent facility to launch and operate a child process, subprocess.popen. However, like many “scripting systems”, it’s easy to do something that mostly works but is rough around the edges and not all that robust, and this is because sub-processes don’t all run in 100 milliseconds without errors.
First off, avoid the use of subprocess.call. It waits for the process to terminate before returning, which means that if your subprocess hangs, your Python program will hang.
Second, if you’re using Python 2.7 on POSIX, use subprocess32, which is a backport of subprocess from Python 3.
Third, stop using os.popen in favor of subprocess.Popen. It’s a little more complicated, but worth it.
Fourth, keep in mind that Popen.communicate() also blocks until the process terminates, so don’t use it either. Also, communicate() doesn’t seem to handle large amounts of output on some systems (reports of “no more than 65535 bytes of output due to Linux pipe implementation”).
Now, on to actual details. Let’s call dir on Windows and number each line in the output
from __future__ import print_function import subprocess import sys proc = subprocess.Popen(args=['dir'] + sys.argv[1:], stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, shell=True) linenum = 1 while True: line = proc.stdout.readline() if len(line) == 0: break print("%d: %s" % (linenum, line), end='') linenum += 1
We are merging stderr and stdout together in this example (stderr=subprocess.STDOUT). If we run this on C:\Windows\System32 like so
ldir.py /s C:\Windows\System32
we’ll start seeing output like this
1: Volume in drive C is OSDisk 2: Volume Serial Number is 062F-8F58 3: 4: Directory of c:\Windows\System32 5: 6: 04/23/2014 06:09 PM <DIR> . 7: 04/23/2014 06:09 PM <DIR> .. 8: 04/12/2011 12:38 AM <DIR> 0409 9: 01/14/2014 11:21 AM <DIR> 1033 10: 06/10/2009 02:16 PM 2,151 12520437.cpx 11: 06/10/2009 02:16 PM 2,233 12520850.cpx 12: 02/14/2013 09:34 PM 131,584 aaclient.dll 13: 11/20/2010 08:24 PM 3,727,872 accessibilitycpl.dll
And since this is under our control, we can pipe to more, we can control-C to stop it, and so on.
There are still complications, mostly around buffering. The default for Popen is to not buffer data, but that only affects the reader – the source process can still buffer. You can trick programs into thinking they are writing into a console, which usually means that output will be unbuffered. You can use the low-level pty module directly (on Unix) or something higher-level like pexpect
- Unix: http://pexpect.sourceforge.net/pexpect.html
- Windows: https://bitbucket.org/mherrmann_at/wexpect
Of course, not all processes write lines. You can use a more generalized approach by reading bytes from the stdout pipe. The previous program modifed to read 128 bytes at a time looks like this
while True: line = proc.stdout.read(128) if len(line) == 0: break print("<%d>: %s" % (linenum, line), end='') linenum += 1
and produces this output (with numbers changed to to stand out more)
<1>: Volume in drive C is OSDisk Volume Serial Number is 062F-8F58 Directory of c:\Windows\System32 04/23/2014 06:09 PM <DIR<2>: > . 04/23/2014 06:09 PM <DIR> .. 04/12/2011 12:38 AM <DIR> 0409 01/14/2014 11:21 AM <DIR><3>: 1033 06/10/2009 02:16 PM 2,151 12520437.cpx 06/10/2009 02:16 PM 2,233 12520850.cpx 02/14/201<4>: 3 09:34 PM 131,584 aaclient.dll 11/20/2010 08:24 PM 3,727,872 accessibilitycpl.dll
And of course this would work for programs that are reading and writing octet streams, not just text.
Reading stdout and stderr
Sometimes you want to read from stderr and stdout independently, because you need to react to output on stderr. You can’t just call read or readline, because it could block waiting for input on a handle.
On Unix systems, you can call select on the stdin and stdout handles, because select works on file-like objects, including pipes. On Windows, select only works on sockets, so you need to use some threads and a queue to have a blocking read per handle. Since this works on Unix as well, we can do it for both.
import Queue io_q = Queue.Queue(5) # somewhat arbitrary, readers block when queue is full def read_from_stream(identifier, stream): for line in stream: io_q.put((identifier, line)) if not stream.closed: stream.close() import threading threading.Thread(target=read_from_stream, name='stdout-stream', args=('STDOUT', proc.stdout)).start() threading.Thread(target=read_from_stream, name='stderr-stream', args=('STDERR', proc.stderr)).start() while True: try: item = io_q.get(False) except Queue.Empty: if proc.poll() is not None: break else: identifier, line = item print(identifier + ':', line, end='')
This works well, but has a flaw – it is basically busy-waiting, burning CPU while waiting for input to come in. We’re doing this because we don’t want to block at the reader level – consider that in a more complex situation, we might want to do processing while waiting for input to come in. There’s also a race condition here, in that we could check the queue, it could be empty, then a reader could put something in the queue while we are checking proc.poll(), and then we could miss that item.
We could do something like this, which is not clean, but works
import Queue io_q = Queue.Queue(5) def read_from_stream(identifier, stream): if not stream: print('%s does not exist' % identifier) io_q.put(('EXIT', identifier)) return for line in stream: io_q.put((identifier, line)) if not stream.closed: stream.close() print('%s is done' % identifier) io_q.put(('EXIT', identifier)) import threading active = 2 threading.Thread(target=read_from_stream, name='stdout-stream', args=('STDOUT', proc.stdout)).start() threading.Thread(target=read_from_stream, name='stderr-stream', args=('STDERR', proc.stderr)).start() while True: try: item = io_q.get(True, 1) except Queue.Empty: if proc.poll() is not None: break else: identifier, line = item if identifier == 'EXIT': active -= 1 if active == 0: break else: print(identifier + ':', line, end='') proc.wait() print(proc.returncode)
Now there’s no busy-waiting, and we exit instantly. This is also a lot of scaffolding to write for each time we use subprocess.Popen(). One answer would be to wrap this up into a helper class, or rather a set of helper classes.
stdin and stdout and stderr
There are two cases here
- Feeding a pipe that takes input and returns output.
- Running an interactive process
For the former, you could just have a file or psuedo-file feed the Popen process instead of subprocess.PIPE. For the latter, you definitely need to trick your Popen process into thinking that it’s writing to a TTY, otherwise the buffering will kill you.
Python 2.7 end-of-life extended to 2020
Guido Van Rossum evidently announced at PyCon 2014 that Python 2.7 would be supported through 2020 (the previous cut-off date was 2015).
A HackerNews thread started by intimating that this was partly in release to RedHat needing long-term support for the version of Python in RHEL 7, and that version of Python will almost certainly be Python 2.7.
I doubt that it was anything more than a very minor contributing factor.
Python for scientific computing
Delorean: Python datetime library
As of Python 2.7, the preferred command-line parsing library is argparse. The pattern is straightforward – create an ArgumentParser, add all the command-line options, then call it and extract arguments.
import argparse def commandline(): parser = argparse.ArgumentParser( description='Your command-line description', fromfile_prefix_chars='@') parser.add_argument('path', nargs='*', help='help string') parser.add_argument('--user', action='append', help='help string') parser.add_argument('--verbose', action='count', default=0, help='help string') parser.add_argument('--quiet', action='store_true', help='help string') args = parser.parser_args() print ' path = %s' % ',\n '.join(args.path) print ' user = %s' % ',\n '.join(args.user) print ' verbose= %d' % args.verbose print ' quiet = %s' % 'True' if args.quiet else 'False'
sub/one sub/three --user=sub/two --verbose --quiet --verbose
path = sub/one sub/three user = sub/two verbose = 2 quiet = True
Arguments are positional or optional. In the example above, all arguments not attached to one of the listed options is gathered up into the ‘path’ positional argument.
Learning programming through visualization
This is an awesome project
It visualizes code execution – line by line, it shows what just happened as the Python interpreter is executing your code.
http://gitstats.sourceforge.net/, source at https://github.com/hoxu/gitstats
I think this could be turned into something pretty cool with a little bit of work. As-is, it uses gnuplot to do the visualization, so that makes it a little hard to use on Windows. It would be nicer if it used matplotlib or the Python ggplot2, or the approach that IPython Notebook took.
So, speaking of “the future of visualization in Python”, here are some links.
And for fun, to emulate XKCD
Cog – interesting Python-based code generator
I like the approach, which is that you can (1) do generated code for any language and (2) edit the generated code with some freedom, because there are markers to separate generated code from non-generated code.
Cog uses Python – it runs any Python code inside the file, replacing the whole file with the output from the generation. I’ll have to try it out in conjunction with SCons.
Extending Python import
I want Python’s import to look something like this
import google.protobuf.message from ('Python Google Protocol Buffers', '2.5.0', 'c9818b6c4f44a10a96d8409044da41a540b40272')
The extra information is hints – hints to the import system to make sure that it found the correct google package, hints to a search/download system on where to look for it if it’s not already present locally. This would basically replace pip. I don’t want to need to install packages. I don’t mind installing packages, you can prebake a system, but it should be an option for efficiency’s sake, not something that everyone must do.
Go has taken a big step in this direction, but it’s a little inflexible. It will download a package from a remote repository, but you have to specify the path, and it’s to a specific repository. This has long-term implications, all your code will need updating if the repository moves. Also, this is not very distributed, and you can’t package things up easily for bundle distribution. Every first-time run of a Go program is going to hit the remote repositories – packages are cached in your local program, but not even system-wide.
What I want is very loose coupling. If I have modules preinstalled on my system and they are the right modules, they get used. If not, my import casts a net to find it, and this search process can be enhanced as desired. For example, a company might want to keep a local cache server of packages so that most searches can be satisfied locally, only going out to other networks for unknown packages. Or an organization might push a giant set of likely-defined modules to every system.
I also want as much flexibility as possible. I like the Google search approach – no schema that has to absolutely be followed, it’s all hints, hints to a search engine. But the hints are specific enough that you’ll find exactly what you are looking for.
Also, I want something that automatically handles architecture differences, platform differences, compiler/interpreter differences, and so on. If I run my code in Python 2.7, I want it to use a Python 2.7-compatible library (e.g. perhaps already precompiled for my exact version of Python), but if I run it in Python 3.3, I might expect a different Python 3.3-savvy library to be used. Or if I’m running on a Windows 7 64-bit machine, then I want any native code to be specific to my architecture and operating system.
surrogate is a library used to create stubs for non-existing modules in sys.modules. Its aim is for unit testing, but it’s an example of manipulating sys.modules.
PEP 302 — New Import Hooks is the original specification for import hooks, kept around because the current system uses it for documentation on how to make custom importers.
The current system is described in The import system and importlib in the Python 3 documentation; also see sys.meta_path and related in the sys module reference. I don’t yet know how much of this is in Python 2.7. However, this still doesn’t let me get extra hint information to my custom importer.
The sum of all knowledge of Python packaging is contained herein: Python Packaging User Guide. OK, maybe not quite, but this is from the Python Packaging Authority, a group working on packaging and installing distributions in Python.
Bento is another interesting Python package system.
Some related module-system PEPs
- PEP 328 — Imports: Multi-Line and Absolute/Relative
- PEP 338 — Executing modules as scripts
- PEP 366 — Main module explicit relative imports
- PEP 273 — Import Modules from Zip Archives
- New import hooks + Import from Zip files
- PEP 376 — Database of Installed Python Distributions
- PEP 426 — Metadata for Python Software Packages 2.0