A while ago I made pycallgraph which generates a visualisation from your Python code. Edit: I've updated the example to work with 3.3, the latest release as of this writing.

After a pip install pycallgraph and installing GraphViz you can run it from the command line:

pycallgraph graphviz -- ./mypythonscript.py

Or, you can profile particular parts of your code:

from pycallgraph import PyCallGraph
from pycallgraph.output import GraphvizOutput

with PyCallGraph(output=GraphvizOutput()):
    code_to_profile()

Either of these will generate a pycallgraph.png file similar to the image below:

It's worth pointing out that using the profiler only works (by default) on the main thread, and you won't get any information from other threads if you use them. This can be a bit of a gotcha as it is completely unmentioned in the profiler documentation.

If you also want to profile threads, you'll want to look at the threading.setprofile() function in the docs.

You could also create your own threading.Thread subclass to do it:

class ProfiledThread(threading.Thread):
    # Overrides threading.Thread.run()
    def run(self):
        profiler = cProfile.Profile()
        try:
            return profiler.runcall(threading.Thread.run, self)
        finally:
            profiler.dump_stats('myprofile-%d.profile' % (self.ident,))

and use that ProfiledThread class instead of the standard one. It might give you more flexibility, but I'm not sure it's worth it, especially if you are using third-party code which wouldn't use your class.

The python wiki is a great page for profiling resources:

as is the python docs:

as shown by Chris Lawlor cProfile is a great tool and can easily be used to print to the screen:

python -m cProfile -s time mine.py <args>

or to file:

python -m cProfile -o output.file mine.py <args>

PS> If you are using Ubuntu, make sure to install python-profile

apt-get install python-profiler 

If you output to file you can get nice visualizations using the following tools

PyCallGraph : a tool to create call graph images
install:

 pip install pycallgraph

run:

 pycallgraph mine.py args

view:

 gimp pycallgraph.png

You can use whatever you like to view the png file, I used gimp
Unfortunately I often get

dot: graph is too large for cairo-renderer bitmaps. Scaling by 0.257079 to fit

which makes my images unusably small. So I generally create svg files:

pycallgraph -f svg -o pycallgraph.svg mine.py <args>

PS> make sure to install graphviz (which provides the dot program):

pip install graphviz

Alternative Graphing using gprof2dot via @maxy / @quodlibetor :

pip install gprof2dot
python -m cProfile -o profile.pstats mine.py
gprof2dot -f pstats profile.pstats | dot -Tsvg -o mine.svg

@Maxy's comment on this answer helped me out enough that I think it deserves its own answer: I already had cProfile-generated .pstats files and I didn't want to re-run things with pycallgraph, so I used gprof2dot, and got pretty svgs:

$ sudo apt-get install graphviz
$ git clone 
$ ln -s "$PWD"/gprof2dot/gprof2dot.py ~/bin
$ cd $PROJECT_DIR
$ gprof2dot.py -f pstats profile.pstats | dot -Tsvg -o callgraph.svg

and BLAM!

It uses dot (the same thing that pycallgraph uses) so output looks similar. I get the impression that gprof2dot loses less information though:

Simplest and quickest way to find where all the time is going.

1. pip install snakeviz

2. python -m cProfile -o temp.dat <PROGRAM>.py

3. snakeviz temp.dat

Draws a pie chart in a browser. Biggest piece is the problem function. Very simple.

I ran into a handy tool called SnakeViz when researching this topic. SnakeViz is a web-based profiling visualization tool. It is very easy to install and use. The usual way I use it is to generate a stat file with %prun and then do analysis in SnakeViz.

The main viz technique used is Sunburst chart as shown below, in which the hierarchy of function calls is arranged as layers of arcs and time info encoded in their angular widths.

The best thing is you can interact with the chart. For example, to zoom in one can click on an arc, and the arc and its descendants will be enlarged as a new sunburst to display more details.

cProfile is great for profiling, while kcachegrind is great for visualizing the results. The pyprof2calltree in between handles the file conversion.

python -m cProfile -o script.profile script.py
pyprof2calltree -i script.profile -o script.calltree
kcachegrind script.calltree

Required system packages:

• kcachegrind (Linux), qcachegrind (MacOs)

Setup on Ubuntu:

apt-get install kcachegrind 
pip install pyprof2calltree

The result:

I recently created tuna for visualizing Python runtime and import profiles; this may be helpful here.

Install with

pip install tuna

Create a runtime profile

python3 -m cProfile -o program.prof yourfile.py

or an import profile (Python 3.7+ required)

python3 -X importprofile yourfile.py 2> import.log

Then just run tuna on the file

tuna program.prof

Also worth mentioning is the GUI cProfile dump viewer RunSnakeRun. It allows you to sort and select, thereby zooming in on the relevant parts of the program. The sizes of the rectangles in the picture is proportional to the time taken. If you mouse over a rectangle it highlights that call in the table and everywhere on the map. When you double-click on a rectangle it zooms in on that portion. It will show you who calls that portion and what that portion calls.

The descriptive information is very helpful. It shows you the code for that bit which can be helpful when you are dealing with built-in library calls. It tells you what file and what line to find the code.

Also want to point at that the OP said 'profiling' but it appears he meant 'timing'. Keep in mind programs will run slower when profiled.

A nice profiling module is the line_profiler (called using the script kernprof.py). It can be downloaded here.

My understanding is that cProfile only gives information about total time spent in each function. So individual lines of code are not timed. This is an issue in scientific computing since often one single line can take a lot of time. Also, as I remember, cProfile didn't catch the time I was spending in say numpy.dot.

pprofile

line_profiler (already presented here) also inspired pprofile, which is described as:

Line-granularity, thread-aware deterministic and statistic pure-python profiler

It provides line-granularity as line_profiler, is pure Python, can be used as a standalone command or a module, and can even generate callgrind-format files that can be easily analyzed with [k|q]cachegrind.

vprof

There is also vprof, a Python package described as:

[...] providing rich and interactive visualizations for various Python program characteristics such as running time and memory usage.

The terminal-only (and simplest) solution, in case all those fancy UI's fail to install or to run:
ignore cProfile completely and replace it with pyinstrument, that will collect and display the tree of calls right after execution.

Install:

$ pip install pyinstrument

Profile and display result:

$ python -m pyinstrument ./prog.py

Works with python2 and 3.

[EDIT] The documentation of the API, for profiling only a part of the code, can be found here.

There's a lot of great answers but they either use command line or some external program for profiling and/or sorting the results.

I really missed some way I could use in my IDE (eclipse-PyDev) without touching the command line or installing anything. So here it is.

Profiling without command line

def count():
    from math import sqrt
    for x in range(10**5):
        sqrt(x)

if __name__ == '__main__':
    import cProfile, pstats
    cProfile.run("count()", "{}.profile".format(__file__))
    s = pstats.Stats("{}.profile".format(__file__))
    s.strip_dirs()
    s.sort_stats("time").print_stats(10)

See docs or other answers for more info.

Following Joe Shaw's answer about multi-threaded code not to work as expected, I figured that the runcall method in cProfile is merely doing self.enable() and self.disable() calls around the profiled function call, so you can simply do that yourself and have whatever code you want in-between with minimal interference with existing code.

With a statistical profiler like austin, no instrumentation is required, meaning that you can get profiling data out of a Python application simply with

austin python3 my_script.py

The raw output isn't very useful, but you can pipe that to flamegraph.pl to get a flame graph representation of that data that gives you a breakdown of where the time (measured in microseconds of real time) is being spent.

austin python3 my_script.py | flamegraph.pl > my_script_profile.svg

Alternatively, you can also use the web application Speedscope.app for quick visualisation of the collected samples. If you have pprof installed, you can also get austin-python (with e.g. pipx install austin-python) and use the austin2pprof to covert to the pprof format.

However, if you have VS Code installed you could use the Austin extension for a more interactive experience, with source code heat maps, top functions and collected call stacks

In Virtaal's source there's a very useful class and decorator that can make profiling (even for specific methods/functions) very easy. The output can then be viewed very comfortably in KCacheGrind.

If you want to make a cumulative profiler, meaning to run the function several times in a row and watch the sum of the results.

you can use this cumulative_profiler decorator:

it's python >= 3.6 specific, but you can remove nonlocal for it work on older versions.

import cProfile, pstats

class _ProfileFunc:
    def __init__(self, func, sort_stats_by):
        self.func =  func
        self.profile_runs = []
        self.sort_stats_by = sort_stats_by

    def __call__(self, *args, **kwargs):
        pr = cProfile.Profile()
        pr.enable()  # this is the profiling section
        retval = self.func(*args, **kwargs)
        pr.disable()

        self.profile_runs.append(pr)
        ps = pstats.Stats(*self.profile_runs).sort_stats(self.sort_stats_by)
        return retval, ps

def cumulative_profiler(amount_of_times, sort_stats_by='time'):
    def real_decorator(function):
        def wrapper(*args, **kwargs):
            nonlocal function, amount_of_times, sort_stats_by  # for python 2.x remove this row

            profiled_func = _ProfileFunc(function, sort_stats_by)
            for i in range(amount_of_times):
                retval, ps = profiled_func(*args, **kwargs)
            ps.print_stats()
            return retval  # returns the results of the function
        return wrapper

    if callable(amount_of_times):  # incase you don't want to specify the amount of times
        func = amount_of_times  # amount_of_times is the function in here
        amount_of_times = 5  # the default amount
        return real_decorator(func)
    return real_decorator

Example

profiling the function baz

import time

@cumulative_profiler
def baz():
    time.sleep(1)
    time.sleep(2)
    return 1

baz()

baz ran 5 times and printed this:

         20 function calls in 15.003 seconds

   Ordered by: internal time

   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
       10   15.003    1.500   15.003    1.500 {built-in method time.sleep}
        5    0.000    0.000   15.003    3.001 <ipython-input-9-c89afe010372>:3(baz)
        5    0.000    0.000    0.000    0.000 {method 'disable' of '_lsprof.Profiler' objects}

specifying the amount of times

@cumulative_profiler(3)
def baz():
    ...

Recently I created a plugin for PyCharm with which you can easily analyse and visualise the results of line_profiler in the PyCharm editor.

line_profiler has been mentioned in other answers as well and is a great tool to analyse exactly how much time is spent by the python interpreter in certain lines.

The PyCharm plugin I've created can be found here:

It needs a helper package in your python environment called line-profiler-pycharm which can be installed with pip or by the plugin itself.

After installing the plugin in PyCharm:

1. Decorate any function you want to profile with the line_profiler_pycharm.profile decorator
2. Run with the 'Profile Lines' runner

Screenshot of results:

cProfile is great for quick profiling but most of the time it was ending for me with the errors. Function runctx solves this problem by initializing correctly the environment and variables, hope it can be useful for someone:

import cProfile
cProfile.runctx('foo()', None, locals())

For getting quick profile stats on an IPython notebook. One can embed line_profiler and memory_profiler straight into their notebooks.

Another useful package is Pympler. It is a powerful profiling package that's capable to track classes,objects,functions,memory leaks etc. Examples below, Docs attached.

Get it!

!pip install line_profiler
!pip install memory_profiler
!pip install pympler