Develop Reference

How to deal with multiple, conflicting PyBoost Bindings?

In a program, I am using multiple libraries that include boost bindings to the C++ eigen library. (In my case, OMPL & Pinocchio, but I guess the problem is not related to the specific libraries)
Both of them implement a binding for the same C++ class (an STL vector of integers). My problem is, the two bindings differ from each other - in my specific case,
pinocchio.pinocchio_pywrap.StdVec_Int has a tolist() method, while ompl.util._util.vectorInt doesn't.
It seems that, whatever library is imported first, is the deciding factor for which binding is used. This is dangerous because it leads to errors that are hard to trace, especially for externals that are using the code - all of a sudden, methods fail that worked before, just because of a new import.
My preferred solution to this problem would be forcing both libraries to use their own bindings only - but I don't know if that is possible.
Alternatively - is there a way to globally define which C++ bindings to prefer in case two libraries collide?
Example for the "hard-to-explain-bug": Imagine running several unittests in one session - and the one on ompl-related methods runs first. It fails later on when the tolist() method is used on an object which is expected to be of type pinocchio.pinocchio_pywrap.StdVec_Int. You start to debug and run the failing unittest only - and it runs smoothly because ompl was not imported before...

Selecting executed method of class at runtime in python?

This question is very generic but I don't think it is opinion based. It is about software design and the example prototype is in python:
I am writing a program which goal it is to simulate some behaviour (doesn't matter). The data on which the simulation works is fixed, but the simulated behaviour I want to change at every startup time. The simulation behaviour can't be changed at runtime.
Example:
Simulation behaviour is defined like:
usedMethod = static
The program than looks something like this:
while(true)
result = static(object) # static is the method specified in the behaviour
# do something with result
The question is, how is the best way to deal with exchangeable defined functions? So another run of the simulation could look like this
while(true)
result = dynamic(object)
if dynamic is specified as usedMethod. The first thing that came in my mind was an if-else block, where I ask, which is the used method and then execute this on. This solution would not be very good, because every time I add new behaviour I have to change the if-else block and the if-else block itself would maybe cost performance, which is important, too. The simulations should be fast.
So a solution I could think of was using a function pointer (output and input of all usedMethods should be well defined and so it should not be a problem). Then I initalize the function pointer at startup, where the used method is defined.
The problem I currently have, that the used method is not a function per-se, but is a method of a class, which depends heavily on the intern members of this class, so the code is more looking like this:
balance = BalancerClass()
while(true)
result = balance.static(object)
...
balance.doSomething(input)
So my question is, what is a good solution to deal with this problem?
I thought about inheriting from the balancerClass (this would then be an abstract class, I don't know if this conecpt exists in python) and add a derived class for every used method. Then I create the correct derived object which is specified in the simulation behaviour an run-time.
In my eyes, this is a good solution, because it encapsulates the methods from the base class itself. And every used method is managed by its own class, so it can add new internal behaviour if needed.
Furthermore the doSomething method shouldn't change, so therefore it is implemented the base class, but depends on the intern changed members of the derived class.
I don't know in general if this software design is good to solve my problem or if I am missing a very basic and easy concept.
If you have a another/better solution please tell me and it would be good, if you provide the advantages/disadvantages. Also could you tell me advantages/disadvantages of my solution, which I didn't think of?

Hey I can be wrong but what you are looking for boils down to either dependency injection or strategy design pattern both of which solve the problem of executing dynamic code at runtime via a common interface without worrying about the actual implementations. There are also much simpler ways just like u desrcibed creating an abstract class(Interface) and having all the classes implement this interface.
I am giving brief examples fo which here for your reference:
Dependecy Injection(From wikipedia):
In software engineering, dependency injection is a technique whereby one object supplies the dependencies of another object. A "dependency" is an object that can be used, for example as a service. Instead of a client specifying which service it will use, something tells the client what service to use. The "injection" refers to the passing of a dependency (a service) into the object (a client) that would use it. The service is made part of the client's state.
Passing the service to the client, rather than allowing a client to build or find the service, is the fundamental requirement of the pattern.
Python does not have such a conecpt inbuilt in the language itself but there are packages out there that implements this pattern.
Here is a nice article about this in python(All credits to the original author):
Dependency Injection in Python
Strategy Pattern: This is an anti-pattern to inheritance and is an example of composition which basically means instead of inheriting from a base class we pass the required class's object to the constructor of classes we want to have the functionality in. For example:
Suppose you want to have a common add() operation but it can be implemented in different ways(add two numbers or add two strings)
Class XYZ():
def __constructor__(adder):
self.adder = adder
The only condition being all adders passed to the XYZ class should have a common Interface.
Here is a more detailed example:
Strategy Pattern in Python
Interfaces:
Interfaces are the simplest, they define a set of common attributes and methods(with or without a default implementation). Any class then can implement an interface with its own functionality or some shared common functionality. In python Interfaces are implemented via abc package.

Choose Python classes to instantiate at runtime based on either user input or on command line parameters

I am starting a new Python project that is supposed to run both sequentially and in parallel. However, because the behavior is entirely different, running in parallel would require a completely different set of classes than those used when running sequentially. But there is so much overlap between the two codes that it makes sense to have a unified code and defer the parallel/sequential behavior to a certain group of classes.
Coming from a C++ world, I would let the user set a Parallel or Serial class in the main file and use that as a template parameter to instantiate other classes at runtime. In Python there is no compilation time so I'm looking for the most Pythonic way to accomplish this. Ideally, it would be great that the code determines whether the user is running sequentially or in parallel to select the classes automatically. So if the user runs mpirun -np 4 python __main__.py the code should behave entirely different than when the user calls just python __main__.py. Somehow it makes no sense to me to have if statements to determine the type of an object at runtime, there has to be a much more elegant way to do this. In short, I would like to avoid:
if isintance(a, Parallel):
m = ParallelObject()
elif ifinstance(a, Serial):
m = SerialObject()
I've been reading about this, and it seems I can use factories (which somewhat have this conditional statement buried in the implementation). Yet, using factories for this problem is not an option because I would have to create too many factories.
In fact, it would be great if I can just "mimic" C++'s behavior here and somehow use Parallel/Serial classes to choose classes properly. Is this even possible in Python? If so, what's the most Pythonic way to do this?
Another idea would be to detect whether the user is running in parallel or sequentially and then load the appropriate module (either from a parallel or sequential folder) with the appropriate classes. For instance, I could have the user type in the main script:
from myPackage.parallel import *
or
from myPackage.serial import *
and then have the parallel or serial folders import all shared modules. This would allow me to keep all classes that differentiate parallel/serial behavior with the same names. This seems to be the best option so far, but I'm concerned about what would happen when I'm running py.test because some test files will load parallel modules and some other test files would load the serial modules. Would testing work with this setup?

You may want to check how a similar issue is solved in the stdlib: https://github.com/python/cpython/blob/master/Lib/os.py - it's not a 100% match to your own problem, nor the only possible solution FWIW, but you can safely assume this to be a rather "pythonic" solution.
wrt/ the "automagic" thing depending on execution context, if you decide to go for it, by all means make sure that 1/ both implementations can still be explicitely imported (like os.ntpath and os.posixpath) so they are truly unit-testable, and 2/ the user can still manually force the choice.
EDIT:
So if I understand it correctly, this file you points out imports modules depending on (...)
What it "depends on" is actually mostly irrelevant (in this case it's a builtin name because the target OS is known when the runtime is compiled, but this could be an environment variable, a command line argument, a value in a config file etc). The point was about both conditional import of modules with same API but different implementations while still providing direct explicit access to those modules.
So in a similar way, I could let the user type from myPackage.parallel import * and then in myPackage/init.py I could import all the required modules for the parallel calculation. Is this what you suggest?
Not exactly. I posted this as an example of conditional imports mostly, and eventually as a way to build a "bridge" module that can automagically select the appropriate implementation at runtime (on which basis it does so is up to you).
The point is that the end user should be able to either explicitely select an implementation (by explicitely importing the right submodule - serial or parallel and using it directly) OR - still explicitely - ask the system to select one or the other depending on the context.
So you'd have myPackage.serial and myPackage.parallel (just as they are now), and an additional myPackage.automagic that dynamically selects either serial or parallel. The "recommended" choice would then be to use the "automagic" module so the same code can be run either serial or parallel without the user having to care about it, but with still the ability to force using one or the other where it makes sense.
My fear is that py.test will have modules from parallel and serial while testing different files and create a mess
Why and how would this happen ? Remember that Python has no "process-global" namespace - "globals" are really "module-level" only - and that python's import is absolutely nothing like C/C++ includes.
import loads a module object (can be built directly from python source code, or from compiled C code, or even dynamically created - remember, at runtime a module is an object, instance of the module type) and binds this object (or attributes of this object) into the enclosing scope. Also, modules are garanteed (with a couple caveats, but those are to be considered as error cases) to be imported only once for a given process (and then cached) so importing the same module twice in a same process will yield the same object (IOW a module is a singleton).
All this means that given something like
# module A
def foo():
return bar(42)
def bar(x):
return x * 2
and
# module B
def foo():
return bar(33)
def bar(x):
return x / 2
It's garanteed that however you import from A and B, A.foo will ALWAYS call A.bar and NEVER call B.bar and B.foo will only ever call B.bar (unless you explicitely monkeyptach them of course but that's not the point).
Also, this means that within a module you cannot have access to the importing namespace (the module or function that's importing your module), so you cannot have a module depending on "global" names set by the importer.
To make a long story short, you really need to forget about C++ and learn how Python works, as those are wildly different languages with wildly different object models, execution models and idioms. A couple interesting reads are http://effbot.org/zone/import-confusion.htm and https://nedbatchelder.com/text/names.html
EDIT 2:
(about the 'automagic' module)
I would do that based on whether the user runs mpirun or just python. However, it seems it's not possible (see for instance this or this) in a portable way without a hack. Any ideas in that direction?
I've never ever had anything to do with mpi so I can't help with this - but if the general consensus is that there's no reliable portable way to detect this then obviously there's your answer.
This being said, simple stupid solutions are sometimes overlooked. In your case, explicitly setting an environment variable or passing a command-line switch to your main script would JustWork(tm), ie the user should for example use
SOMEFLAG=serial python main.py
vs
SOMEFLAG=parallel mpirun -np4 python main.py
or
python main.py serial
vs
mpirun -np4 python main.py parallel
(whichever works best for you needs - is the most easily portable).
This of course requires a bit more documentation and some more effort from the end-user but well...

I'm not really what you're asking here. Python classes are just (callable/instantiable) objects themselves, so you can of course select and use them conditionally. If multiple classes within multiple modules are involved, you can also make the imports conditional.
if user_says_parallel:
from myPackage.parallel import ParallelObject
ObjectClass = ParallelObject
else:
from myPackage.serial import SerialObject
ObjectClass = SerialObject
my_abstract_object = ObjectClass()
If that's very useful depends on your classes and the effort it takes to make sure they have the same API so they're compatible when replacing each other. Maybe even inheritance à la ParallelObject => SerialObject is possible, or at least a common (virtual) base class to put all the shared code. But that's just the same as in C++.

Programmaticaly detect if python code is being under test

How can python program know if it is being tested? For example:
def foo():
if foo_being_tested:
pseudorandom()
else:
random()
When in test, program should use pseudorandom sequence to be able to compare with C code version of the program and in regular execution random from numpy should be used.

You can't, not without inspecting the call stack.
Generally speaking, you should not do this at all; by altering your code when tested you are not correctly testing your code.
Instead, you'd use mocking to replace any parts your code uses (anything used by the code under test but not part of it). For your specific example, you'd mock out random(); on Python 3.3 and up you can use unittest.mock, available as mock on PyPI for other Python versions, or you can just manually swap out module_under_test.random for the duration of the test.
You could also set an environment variable in your unittests to make it explicit you are running a test, but ideally that should be avoided.

Documenting a non-existing member with Doxygen

I'm trying to document a python class using Doxygen. The class exposes a set of properties over d-bus, but these have no corresponding public getters/setters in the python class. Instead, they are implemented through a d-bus properties interface (Set/Get/GetAll/Introspect).
What I want to do is to be able to document these properties using something like this:
## #property package::Class::Name description
The whole package::Class works (the same method finds functions, so it finds the right class).
When running doxygen I get the following error:
warning: documented function ``package::Class::Name' was not declared or defined.
I can live with a warning, but unfortunately the property fails to appear in the documentation generated for the class, so it is not only a warning, but it is silenced as well.
So, my question is, how, if I can, do I make the non-existing property member appear in the generated docs?

Define the attribute inside an if 0: block:
## #class X
## #brief this is useless
class X:
if 0:
## #brief whatevs is a property that doesn't exist in spacetime
##
## It is designed to make bunny cry.
whatevs = property
This will cause it to exist in the documentation (tested with doxygen 1.8.1.2-1 on debian-squeeze). The attribute will never be made to exist at runtime, and in fact it looks like the python bytecode optimizer eliminates if statement and its body altogether.

I looked into something similar previously and couldn't find a direct way to coax Doxygen into documenting an undefined member. There are two basic kludges you can use here:
1.) generate a dummy object (or dummy members) for doxygen to inventory which don't actually exist in the live code.
2.) If the adjustments you need are fairly predictable and regular you could write an INPUT_FILTER for doxygen which takes your files and converts them before parsing. There are some issues with this method--mostly that if you plan on including the code in the documentation and the filter has to add/remove lines from the file, the line numbers it indicates will be off, and any code windows shown with the documentation will be off by that number of lines. You can also check the option to filter the displayed sources to adjust for this, but depending on who the consumer of your documentation is, it may be confusing for the copy in Doxygen not to perfectly match what's in the real source.
In our case we use a python script which Doxygen runs from the command-line with the file path as the arg. We read the file indicated and write what we want Doxygen to interpret instead to stdout. If you need the source copies displayed in doxygen to be filtered as well you can set FILTER_SOURCE_FILES to YES.