When making changes to larger modules, this is my current (inefficient) process:
Make needed change to code
Run program to test (using pdb - python3 -m pdb path/to/script.py
Program will throw an error
Fix error/create an exception
Run again
New error appears
Rinse an repeat
The data processing module I'm working on has many steps, and rerunning every time I make a code change to make sure there are no errors takes a long time and it's frustating. It's also obviously an inefficient way to develop a program, but I don't know what alternative
What advice do you have so that I don't have to run, and wait for, my whole data processing pipeline to find what the next error will be? Is there any way to make changes on the code and continue executing before the last error appeared?
You could do unit testing for every module and for every steps. Basically it's "create fake data to pass to every step and check if the result after the step is what you want", obviously automated.
Check the internet to learn about testing in general and testing in Python.
In the PyCharm debugger we can pause a process. I have a program to debug that takes a lot of time before we arrive to the part I'm debugging.
The program can be modeled like that: GOOD_CODE -> CODE_TO_DEBUG.
I'm wondering if there is a way to..
run GOOD_CODE
save the process
edit the code in CODE_TO_DEBUG
restore the process and with the edited CODE_TO_DEBUG
Is serialization the good way to do it or is there some tool to do that?
I'm working on OSX with PyCharm.
Thank you for your kind answers.
The classic method is to write a program that reproduces the conditions that lead into the buggy code, without taking a bunch of time -- say, read in the data from a file instead of generating it -- and then paste in the code you're trying to fix. If you get it fixed in the test wrapper, and it still doesn't work in the original program, you then "only" have to find the interaction with the rest of the program that's faulty (global variables, bad parameters passes, etc.)
I have a problem that I seriously spent months on now!
Essentially I am running code that requires to read from and save to HD5 files. I am using h5py for this.
It's very hard to debug because the problem (whatever it is) only occurs in like 5% of the cases (each run takes several hours) and when it gets there it crashes python completely so debugging with python itself is impossible. Using simple logs it's also impossible to pinpoint to the exact crashing situation - it appears to be very random, crashing at different points within the code, or with a lag.
I tried using OllyDbg to figure out whats happening and can safely conclude that it consistently crashes at the following location: http://i.imgur.com/c4X5W.png
It seems to be shortly after calling the python native PyObject_ClearWeakRefs, with an access violation error message. The weird thing is that the file is successfully written to. What would cause the access violation error? Or is that python internal (e.g. the stack?) and not file (i.e. my code) related?
Has anyone an idea whats happening here? If not, is there a smarter way of finding out what exactly is happening? maybe some hidden python logs or something I don't know about?
Thank you
PyObject_ClearWeakRefs is in the python interpreter itself. But if it only happens in a small number of runs, it could be hardware related. Things you could try:
Run your program on a different machine. if it doesn't crash there, it is probably a hardware issue.
Reinstall python, in case the installed version has somehow become corrupted.
Run a memory test program.
Thanks for all the answers. I ran two versions this time, one with a new python install and my same program, another one on my original computer/install, but replacing all HDF5 read/write procedures with numpy read/write procedures.
The program continued to crash on my second computer at odd times, but on my primary computer I had zero crashes with the changed code. I think it is thus safe to conclude that the problems were HDF5 or more specifically h5py related. It appears that more people encountered issues with h5py in that respect. Given that any error in my application translates to potentially large financial losses I decided to dump HDF5 completely in favor of other stable solutions.
Use a try catch statement. This can be put into the program in order to stop the program from crashing when erroneous data is entered
I am working on a project using python 2.7.2, sqlalchemy 0.7, unittest, eclipse 3.7.2 and pydev 2.4. I am setting breakpoints in python files (unit test files), but they are completely ignored (before, at some point, they worked). By now i have upgraded all related software (see above), started new projects, played around with settings, hypnotized my screen, but nothing works.
The only idea i got from some post is that it has something to de with changing some .py file names to lower case.
Does anyone have any ideas?
added: I even installed the aptana version of eclipse and copied the .py files to it => same result; breakpoints are still ignored.
still no progress: I have changed some code that might be seen as unusual and replaced it with a more straightforward solution.
some more info: it probably has something to do with module unittest:
breakpoints in my files defining test suites work,
breakpoints in the standard unittest files themselves work
breakpoints in my tests methods in classes derived from unittest.TestCase do not work
breakpoints in my code being tested in the test cases do not work
at some point before i could define working breakpoints in test methods or the code being tested
some things i changed after that are: started using test suites, changed some filenames to lowercase, ...
this problem also occurs if my code works without exceptions or test failures.
what I already tried is:
remove .pyc files
define new project and copy only .py files to it
rebooted several times in between
upgraded to eclipse 3.7.2
installed latest pydev on eclipse 3.7.2
switch to aptana (and back)
removed code that 'manually' added classes to my module
fiddled with some configurations
what I can still do is:
start new project with my code, start removing/changing code until breakpoints work and sort of black box figure out if this has something to do with some part of my code
Does anyone have any idea what might cause these problems or how they might be solved?
Is there any other place i could look for a solution?
Do pydev developers look into the questions on stackoverflow?
Is there an older version of pydev that i might try?
I have been working with pydev/eclipse for a long time and it works well for me, but without debugging i'd forced to switch IDE.
In answer to Fabio's questions below:
The python version is 2.7.2,
The sys.gettrace gives None (but I have no idea what in my code could influence that)
This is the output of the debugger after changing the suggested parameters:
pydev debugger:
starting
('Executing file ', 'D:\\.eclipse\\org.eclipse.platform_3.7.0_248562372\\plugins\\org.python.pydev.debug_2.4.0.2012020116\\pysrc\\runfiles.py')
('arguments:', "['D:\\\\.eclipse\\\\org.eclipse.platform_3.7.0_248562372\\\\plugins\\\\org.python.pydev.debug_2.4.0.2012020116\\\\pysrc\\\\runfiles.py', 'D:\\\\Documents\\\\Code\\\\Eclipse\\\\workspace\\\\sqladata\\\\src\\\\unit_test.py', '--port', '49856', '--verbosity', '0']")
('Connecting to ', '127.0.0.1', ':', '49857')
('Connected.',)
('received command ', '501\t1\t1.1')
sending cmd: CMD_VERSION 501 1 1.1
sending cmd: CMD_THREAD_CREATE 103 2 <xml><thread name="pydevd.reader" id="-1"/></xml>
sending cmd: CMD_THREAD_CREATE 103 4 <xml><thread name="pydevd.writer" id="-1"/></xml>
('received command ', '111\t3\tD:\\Documents\\Code\\Eclipse\\workspace\\sqladata\\src\\testData.py\t85\t**FUNC**testAdjacency\tNone')
Added breakpoint:d:\documents\code\eclipse\workspace\sqladata\src\testdata.py - line:85 - func_name:testAdjacency
('received command ', '122\t5\t;;')
Exceptions to hook : []
('received command ', '124\t7\t')
('received command ', '101\t9\t')
Finding files... done.
Importing test modules ... testAtomic (testTypes.TypeTest) ... ok
testCyclic (testTypes.TypeTest) ...
The rest is output of the unit test.
Continuing from Fabio's answer part 2:
I have added the code at the start of the program and the debugger stops working at the last line of following the method in sqlalchemy\orm\attributes.py (it is a descriptor, but how or whther it interferes with the debugging is beyond my current knowledge):
class InstrumentedAttribute(QueryableAttribute):
"""Class bound instrumented attribute which adds descriptor methods."""
def __set__(self, instance, value):
self.impl.set(instance_state(instance),
instance_dict(instance), value, None)
def __delete__(self, instance):
self.impl.delete(instance_state(instance), instance_dict(instance))
def __get__(self, instance, owner):
if instance is None:
return self
dict_ = instance_dict(instance)
if self._supports_population and self.key in dict_:
return dict_[self.key]
else:
return self.impl.get(instance_state(instance),dict_) #<= last line of debugging
From there the debugger steps into the __getattr__ method of one of my own classes, derived from a declarative_base() class of sqlalchemy.
Probably solved (though not understood):
The problem seemed to be that the __getattr__ mentioned above, created something similar to infinite recursion, however the program/unittest/sqlalchemy recovered without reporting any error. I do not understand the sqlalchemy code sufficiently to understand why the __getattr__ method was called.
I changed the __getattr__ method to call super for the attribute name for which the recursion occurred (most likely not my final solution) and the breakpoint problem seems gone.
If i can formulate the problem in a consise manner, i will probably try to get some more info on the google sqlalchemy newsgroup, or at least check my solution for robustness.
Thank you Fabio for your support, the trace_func() function pinpointed the problem for me.
Seems really strange... I need some more info to better diagnose the issue:
Open \plugins\org.python.pydev.debug\pysrc\pydevd_constants.py and change
DEBUG_TRACE_LEVEL = 3
DEBUG_TRACE_BREAKPOINTS = 3
run your use-case with the problem and add the output to your question...
Also, it could be that for some reason the debugging facility is reset in some library you use or in your code, so, do the following: in the same place that you'd put the breakpoint do:
import sys
print 'current trace function', sys.gettrace()
(note: when running in the debugger, it'd be expected that the trace function is something as: <bound method PyDB.trace_dispatch of <__main__.PyDB instance at 0x01D44878>> )
Also, please post which Python version you're using.
Answer part 2:
The fact that sys.gettrace() returns None is probably the real issue... I know some external libraries which mess with it (i.e.:DecoratorTools -- read: http://pydev.blogspot.com/2007/06/why-cant-pydev-debugger-work-with.html) and have even seen Python bugs and compiled extensions break it...
Still, the most common reason it breaks is probably because Python will silently disable the tracing (and thus the debugger) when a recursion throws a stack overflow error (i.e.: RuntimeError: maximum recursion depth exceeded).
You can probably put a breakpoint in the very beginning of your program and step in the debugger until it stops working.
Or maybe simpler is the following: Add the code below to the very beginning of your program and see how far it goes with the printing... The last thing printed is the code just before it broke (so, you could put a breakpoint at the last line printed knowing it should be the last line where it'd work) -- note that if it's a large program, printing may take a long time -- it may even be faster printing to a file instead of a console (such as cmd, bash or eclipse) and later opening that file (just redirect the print from the example to a file).
import sys
def trace_func(frame, event, arg):
print 'Context: ', frame.f_code.co_name, '\tFile:', frame.f_code.co_filename, '\tLine:', frame.f_lineno, '\tEvent:', event
return trace_func
sys.settrace(trace_func)
If you still can't figure it out, please post more information on the obtained results...
Note: a workaround until you don't find the actual place is using:
import pydevd;pydevd.settrace()
on the place where you'd put the breakpoint -- that way you'd have a breakpoint in code which should definitely work, as it'll force setting the tracing facility at that point (it's very similar to the remote debugging: http://pydev.org/manual_adv_remote_debugger.html except that as the debugger was already previously connected, you don't really have to start the remote debugger, just do the settrace to emulate a breakpoint)
Coming late into the conversation, but just in case it helps. I just run into a similar problem and I found that the debugger is very particular w.r.t. what lines it considers "executable" and available to break on.
If you are using line continuations, or multi-line expressions (e.g. inside a list), put the breakpoint in the last line of the statement.
I hope it helps.
Try removing the corresponding .pyc file (compiled) and then running.
Also I have sometimes realized I was running more than one instance of a program.. which confused pydev.
I've definitely seen this before too. Quite a few times.
Ran into a similar situation running a django app in Eclipse/pydev. what was happening was that the code that was running was the one installed in my virtualenv, not my source code. I removed my project from my virtual env site-packages, restarted the django up in the eclipse/pydev debugger and everything was fine.
I had similar-sounding symptoms. It turned out that my module import sequence was rexec'ing my entry-point python module because a binary (non-Python) library had to be dynamically loaded, i.e., the LD_LIBRARY_PATH was dynamically reset. I don't know why this causes the debugger to ignore subsequent breakpoints. Perhaps the rexec call is not specifying debug=true; it should specify debug=true/false based on the calling context state?
Try setting a breakpoint at your first import statement being cognizant of whether you are then s(tep)'ing into or n(ext)'ing over the imports. When I would "next" over the 3rdparty import that required the dynamic lib loading, the debug interpreter would just continue past all breakpoints.
I have a python script to allocate a huge memory space and eventually ended up overflow. Is there anyway nosetests can peacefully handle this?
Unfortunately the only way to survive such a thing would be to have your test fixture run that particular test in a subcommand using subprocess.Popen(), and capture its output and error code so that you can see the nonzero error code and “out of memory” traceback that result. Note that sys.executable is the full path to the current Python executable, if that helps you build a Popen() command line to run Python on the little test script that runs out of memory.
Once a process it out of memory, there is typically no way to recover, because nearly anything it might try to do — format a string to print out, for example — takes even more memory which is, by definition, now exhausted. :)