I'm trying to debug a python codebase that uses tox for unit tests. One of the failing tests is proving difficult due to figure out, and I'd like to use pudb to step through the code.
At first thought, one would think to just pip install pudb then in the unit test code add in import pudb and pudb.settrace(). But that results in a ModuleNotFoundError:
> import pudb
>E ModuleNotFoundError: No module named 'pudb'
>tests/mytest.py:130: ModuleNotFoundError
> ERROR: InvocationError for command '/Users/me/myproject/.tox/py3/bin/pytest tests' (exited with code 1)
Noticing the .tox project folder leads one to realize there's a site-packages folder within tox, which makes sense since the point of tox is to manage testing under different virtualenv scenarios. This also means there's a tox.ini configuration file, with a deps section that may look like this:
[tox]
envlist = lint, py3
[testenv]
deps =
pytest
commands = pytest tests
adding pudb to the deps list should solve the ModuleNotFoundError, but leads to another error:
self = <_pytest.capture.DontReadFromInput object at 0x103bd2b00>
def fileno(self):
> raise UnsupportedOperation("redirected stdin is pseudofile, "
"has no fileno()")
E io.UnsupportedOperation: redirected stdin is pseudofile, has no fileno()
.tox/py3/lib/python3.6/site-packages/_pytest/capture.py:583: UnsupportedOperation
So, I'm stuck at this point. Is it not possible to use pudb instead of pdb within Tox?
There's a package called pytest-pudb which overrides the pudb entry points within an automated test environment like tox to successfully jump into the debugger.
To use it, just make your tox.ini file have both the pudb and pytest-pudb entries in its testenv dependencies, similar to this:
[tox]
envlist = lint, py3
[testenv]
deps =
pytest
pudb
pytest-pudb
commands = pytest tests
Using the original PDB (not PUDB) could work too. At least it works on Django and Nose testers. Without changing tox.ini, simply add a pdb breakpoint wherever you need, with:
import pdb; pdb.set_trace()
Then, when it get to that breakpoint, you can use the regular PDB commands:
w - print stacktrace
s - step into
n - step over
c - continue
p - print an argument value
a - print arguments of current function
Related
I have the following tox.ini file:
[tox]
envlist = py310, flake8
isolated_build = True
[testenv]
skip_install = True
deps = -rtest_requirements.txt
passenv = *
commands =
pytest {posargs} --teamcity
[testenv:flake8]
deps = flake8
skip_install = True
commands = flake8 tests/
On teamcity, I run my python test through tox from within a script build step where I call the following shell script
#! /bin/sh
python -m tox .
Now, there is one red test that I want to mute. When I mute it, however, teamcity makes my build red even though it marked my test as muted, like so:
The problem is well-known, since 11 years, as reported here.
How can I modify my command in my tox.ini file to make my build green again? I don't want to mark my python test with the skip tag. I don't want to change the tox command from
commands =
pytest {posargs} --teamcity
to
commands =
- pytest {posargs} --teamcity
because that will just ignore any error that might happen during the pytest run (like "Internal error happened while executing tests", or "No tests were collected" for example).
Ideally, I would like to call
commands =
pytest {posargs} --teamcity || [ $? = 1 ]
but apparently tox does not understand the symbol ||.
What can I do?
You can call a custom shell script in your commands section, and there you can do whatever you want, including using ||.
e.g.
commands = my_custom_script.sh
With PyTest, you can limit the scope of test collection by passing directories/files/nodeids as command line arguments, e.g., pytest tests, pytest tests/my_tests.py and pytest tests/my_tests.py::test_1. Is it possible to override this behavior from within a plugin, i.e., to set them to something else programmatically?
So far I've attempted setting file_or_dir to my own list within config.option and config.known_args_namespace from the pytest_configure hook, but this appears to have no effect on anything.
You are probably looking for config.args:
# conftest.py
def pytest_configure(config):
config.args = ['foo', 'bar/baz.py::test_spam']
Running pytest now will be essentially the same as running pytest foo bar/baz.py::test_spam. However, putting stuff in pytest.ini would be IMO a better solution:
# pytest.ini
[pytest]
addopts = foo bar/baz.py::test_spam
I want to execute a Python script from Matlab (on a Windows 7 machine). The libraries necessary are installed in an Anaconda virtual environment. When running the script from command line, it runs flawlessly.
When calling the script from Matlab as follows:
[status, commandOut] = system('C:/Users/user/AppData/Local/Continuum/anaconda3/envs/tf/python.exe test.py');
or with shell commands, I get an Import Error:
commandOut =
'Traceback (most recent call last):
File "C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\lib\site-packages\numpy\core\__init__.py", line 16, in <module>
from . import multiarray
ImportError: DLL load failed: The specified path is invalid.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "test.py", line 2, in <module>
import numpy as np
File "C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\lib\site-packages\numpy\__init__.py", line 142, in <module>
from . import add_newdocs
File "C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\lib\site-packages\numpy\add_newdocs.py", line 13, in <module>
from numpy.lib import add_newdoc
File "C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\lib\site-packages\numpy\lib\__init__.py", line 8, in <module>
from .type_check import *
File "C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\lib\site-packages\numpy\lib\type_check.py", line 11, in <module>
import numpy.core.numeric as _nx
File "C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\lib\site-packages\numpy\core\__init__.py", line 26, in <module>
raise ImportError(msg)
ImportError:
Importing the multiarray numpy extension module failed. Most
likely you are trying to import a failed build of numpy.
If you're working with a numpy git repo, try `git clean -xdf` (removes all
files not under version control). Otherwise reinstall numpy.
Original error was: DLL load failed: The specified path is invalid.
I already changed the default Matlab Python version to the Anaconda env, but no change:
version: '3.5'
executable: 'C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\python.exe'
library: 'C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf\python35.dll'
home: 'C:\Users\user\AppData\Local\Continuum\anaconda3\envs\tf'
isloaded: 1
Just running my test script without importing numpy works. Reloading numpy (py.importlib.import_module('numpy');) didn't work but threw the same error as before.
Does anyone have an idea how to fix this?
So after corresponding with Matlab support I found out that Matlab depends on the path environment (paths which are deliberately not set when using a virtual environment) and therefore numpy fails to find the necessary paths when called from within Matlab (even if the call contains the path to the virtual environment).
The solution is either to call Matlab from within the virtual environment (via command line) or add the missing paths manually in the path environment.
Maybe this information can help someone else.
First Method
You can change the python interpreter with:
pyversion("/home/nibalysc/Programs/anaconda3/bin/python");
And check it with:
pyversion();
You could also do this in a
startup.m
file in your project folder and every time you start MATLAB from this folder the python interpreter will be changed automatically.
Now you can try to use:
py.importlib.import_module('numpy');
Read up the documentation on how to use the integrated python in MATLAB:
Call user defined custom module
Call modified python module
Alternative Method
Alternative method would be to create a
matlab_shell.sh
file with following content, this is basically the appended code from .bashrc when anaconda is installed and asks you if the installer should modify the .bashrc file:
#!/bin/bash
__conda_setup="$(CONDA_REPORT_ERRORS=false '$HOME/path/to/anaconda3/bin/conda' shell.bash hook 2> /dev/null)"
if [ $? -eq 0 ]; then
\eval "$__conda_setup"
else
if [ -f "$HOME/path/to/anaconda3/etc/profile.d/conda.sh" ]; then
CONDA_CHANGEPS1=false conda activate base
else
\export PATH="$HOME/path/to/anaconda3/bin:$PATH"
fi
fi
unset __conda_setup
# <<< conda init <<<
# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('$HOME/path/to/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "$HOME/path/to/anaconda3/etc/profile.d/conda.sh" ]; then
. "$HOME/path/to/anaconda3/etc/profile.d/conda.sh"
else
export PATH="$HOME/path/to/anaconda3/bin:$PATH"
fi
fi
unset __conda_setup
# <<< conda initialize <<<
conda activate base
eval $2
Then you need to set the MATLAB_SHELL environment variable either before running MATLAB or in MATLAB itself. The best thing in my opinion would be to do it also in the startup.m file like that:
setenv("MATLAB_SHELL", "/path/to/matlab_shell.sh");
Afterwards you can use the system(...) function to run conda python with all your modules installed like that...
String notation:
system("python -c ""python code goes here"");
Char notation:
system('python -c "python code goes here"');
Hope this helps!
Firstly, if you execute your Python script like a regular system command ([status, commandOut] = system('...python.exe test.py'))
the pyversion (and pyenv, since R2019b) got no effect at all. It only matters if you utilize the py. integration, as in the code below (and, in most cases, this is a way better approach).
Currently (I use R2019b update 5) there's a number of pitfalls, that might cause issues similar to yours. I'd recommend to start from the following:
Create a new clean conda environment:
conda create -n test_py36 python=3.6 numpy
Create the following dummy demo1.py:
def dummy_py_method(x):
return x+1
Create the following run_py_code.m:
function run_py_code()
% explicit module import sometimes show more detailed error messages
py.importlib.import_module('numpy');
% to reloads if there would be any changes:
pymodule = py.importlib.import_module('demo1');
py.importlib.reload(pymodule);
% passing data back and forth
x = rand([3 3]);
x_np = py.numpy.array(x);
y_np=pymodule.dummy_py_method(x_np);
y = double(y_np);
disp(y-x);
Create the following before_first_run.m:
setenv('PYTHONUNBUFFERED','1');
setenv('path',['C:\Users\username\Anaconda3\envs\test_py36\Library\bin;'...
getenv('path')]);
pe=pyenv('Version','C:\users\username\Anaconda3\envs\test_py36\pythonw.exe',...
'ExecutionMode','InProcess'...
);
% add "demo1.py" to path
py_file_path = 'W:\tests\Matlab\python_demos\call_pycode\pycode';
if count(py.sys.path,py_file_path) == 0
insert(py.sys.path,int32(0),py_file_path);
end
Run the before_first_run.m first and run the run_py_code.m next.
Notes:
As already mentioned in this answer, one key point is to add the folder, containing the necessary dll files to the %PATH%, before starting python. This could be achieved with setenv from withing Matlab. Usually, the Library\bin is what should be added.
It might be a good idea to try clean officially-supported CPython distribution (e.g. CPython 3.6.8 ). Only install numpy (python -m pip install numpy). To my experience, the setenv is not necessary in this case.
For me, OutOfProcess mode proved to be buggy. Thus, I'd recommend to explicitly setting InProcess mode (for versions before R2019b, the OutOfProcess option is not present, as well as pyenv).
Do not concatenate the two .m files above into one - the py.importlib statements seem to be pre-executed and thus conflict with pyenv.
TLDR: How can I get better output from pytest?
I'm using Django with regular python3 unittests.
I've just switched to pytest-django for running tests.
pytest throws an error for almost all my tests (149 in total).
Pages and pages with this error.
self = <RegexURLResolver 'project.urls' (None:None) ^/>
#property
def reverse_dict(self):
language_code = get_language()
if language_code not in self._reverse_dict:
self._populate()
> return self._reverse_dict[language_code]
E KeyError: 'en-us'
Which wasn't the problem. It led me down to a wrong path.
I had a syntax error in one of my views.py files.
./manage.py test resulted in:
snip
File "/home/roland/project/views.py", line 20
code = zip(list1, list2])
SyntaxError: invalid syntax
Notice the last: ] which was the problem.
So: How can I get more useful output on problems when using pytest?
Btw:
After finding this and scrolling back into the pytest output there was mention of the syntax error. It was just buried in the output.
You can use the --maxfail=1 option so it will stop immediately on first failure.
Also, make sure your pytest.ini is setup properly so that pytest knows it should be using django-pyest.
[pytest]
DJANGO_SETTINGS_MODULE='myapp.settings'
For my workflow, I usually do the following:
run pytest --maxfail=1 myfile.py &> pytest-output.txt
tail, grep, or search he text file for errors.
Fix and iterate
There are a lot of other configuration options that will help you to get more meaningful input from pytest.
I created a test module by following all the conventions, but when I run the test, I get the following message:
collecting 0 items
Here's my directory hierarchy:
integration_tests (Directory)-> tests (Directory)-> test_integration_use_cases.py (python file)
And this is the content of the file:
import pytest
from some_tests.integration_tests.backbone.SomeIntegrationTestBase import SomeIntegrationTestBase
class TestSomeIntegration(SomeIntegrationTestBase):
#pytest.mark.p1
def test_some_integration_use_cases(self):
print("**** Executing integration tests ****")
result = self.execute_test(4)
assert (True == result)
when I run the following command:
pytest test_integration_use_cases.py
I see the following result without any errors:
collecting 0 items
FYI: I am running this on a development machine (Like vagrant)
so I had the same problem as you have even after following all the recommended conventions. My application structure was as follows;
Application
-- API
app.py
-- docs
-- venv
-- tests
-- unit_test
test_factory
...
...
I, however, resolved the issue by moving the tests directory under the API package so that my application structure looked as below;
Application
-- API
app.py
-- tests
-- unit_test
test_factory
...
-- docs
-- venv
...
Although pytest is supposed to auto-discover the tests, it seems to do that if they are placed in the application root. Check out the pytest for flask
I also found this resource helpful.