We have a flake8 build stage in our circle-ci workflow, and more often than not this step fails due to timeout:
Too long with no output (exceeded 10m0s): context deadline exceeded
At the same time, this same stage runs quite ok locally on our macbooks:
% time make lint
poetry run black .
All done! ✨ 🍰 ✨
226 files left unchanged.
isort -y
Skipped 2 files
PYTHONPATH=/path/to/project poetry run flake8 --show-source
0
make lint 44.00s user 4.90s system 102% cpu 47.810 total
We tried to debug the issue by adding the -vv flag to flake8 thinking we would get some plugin name that takes too long, but we don't even have the timestamps in the log:
flake8.processor ForkPoolWorker-31 1004 WARNING Plugin requested optional parameter "visitor" but this is not an available parameter.
flake8.processor ForkPoolWorker-8 1080 WARNING Plugin requested optional parameter "visitor" but this is not an available parameter.
flake8.bugbear ForkPoolWorker-26 1082 INFO Optional warning B950 not present in selected warnings: ['E', 'F', 'W', 'C90']. Not firing it at all.
Are there any known reasons why flake8 would freeze on CircleCI? How can one debug the issue?
When using a virtual-environment such as venv you should ignore the folder in the [flake8]-config (that's what happened to me). Assuming you are creating a virtualenv with virtualenv .venv it would look like this:
[flake8]
exclude = .venv
The same was for my coverage which was fixed by adding an omit to that config (solution found here):
# pyproject.toml file content
[tool.coverage.run]
omit = [
"tests/*",
".venv/*",
]
For now, the solution we seem to have found was to limit the number of cores running flake8:
.flake8
[flake8]
...
jobs = 6
Not sure it is the correct solution, but there you go. I will accept a better solution if there is one.
I've also experienced a timeout in circle-ci only, but it was due to the specific way dependencies are installed on the pipeline, creating a .venv folder which was not excluded in flake8 configuration.
The -v option helped me to notice the huge amount of files flkae8 was analyzing.
Pytest test discovery is failing. The UI states:
Test discovery error, please check the configuration settings for the tests
The output window states:
Test Discovery failed:
Error: Traceback (most recent call last):
File "C:\Users\mikep\.vscode\extensions\ms-python.python-2019.4.11987\pythonFiles\testing_tools\run_adapter.py", line 16, in <module>
main(tool, cmd, subargs, toolargs)
File "C:\Users\mikep\.vscode\extensions\ms-python.python-2019.4.11987\pythonFiles\testing_tools\adapter\__main__.py", line 90, in main
parents, result = run(toolargs, **subargs)
File "C:\Users\mikep\.vscode\extensions\ms-python.python-2019.4.11987\pythonFiles\testing_tools\adapter\pytest.py", line 43, in discover
raise Exception('pytest discovery failed (exit code {})'.format(ec))
Exception: pytest discovery failed (exit code 3)
Here are my settings:
{
"python.pythonPath": ".venv\\Scripts\\python.exe",
"python.testing.pyTestArgs": [
"tests"
],
"python.testing.unittestEnabled": false,
"python.testing.nosetestsEnabled": false,
"python.testing.pyTestEnabled": true
}
I can run pytest from the command line successfully FWIW.
I spent ages trying to decipher this unhelpful error after creating a test that had import errors. Verify that your test suite can actually be executed before doing any deeper troubleshooting.
pytest --collect-only is your friend.
This is not a complete answer as I do not know why this is happening and may not relate to your problem, depending how you have your tests structured.
I resolved this issue by putting an __init__.py file in my tests folder
E.G.:
├───.vscode
│ settings.json
│
├───app
│ myapp.py
│
└───tests
test_myapp.py
__init__.py
this was working a few days ago without this but the python extension was recently updated. I am not sure if this is the intended behavior or a side effect of how discoveries are now being made
https://github.com/Microsoft/vscode-python/blob/master/CHANGELOG.md
Use Python code for discovery of tests when using pytest. (#4795)
I just thought I would add my answer here as this might well affect someone who uses a .env file for their project's environment settings since it is such a common configuration for 12 factor apps.
My example assumes that you're using pipenv for your virtual environment management and that you have a .env file at the project's root directory.
My vscode workspace settings json file looks like below. The crucial line for me here was "python.envFile": "${workspaceFolder}/.env",
{
"python.pythonPath": ".venv/bin/python",
"python.linting.enabled": true,
"python.linting.pylintEnabled": true,
"python.linting.pycodestyleEnabled": false,
"python.linting.flake8Enabled": false,
"python.linting.pylintPath": ".venv/bin/pylint",
"python.linting.pylintArgs": [
"--load-plugins=pylint_django",
],
"python.formatting.provider": "black",
"python.formatting.blackArgs": [
"--line-length",
"100"
],
"python.testing.unittestEnabled": false,
"python.testing.nosetestsEnabled": false,
"python.testing.pytestEnabled": true,
"python.testing.pytestPath": ".venv/bin/pytest",
"python.envFile": "${workspaceFolder}/.env",
"python.testing.pytestArgs": [
"--no-cov"
],
}
I hope this saves someone the time I spent figuring this out.
In my case the problem with vscode being unable to discover tests was the coverage module being enabled in the setup.cfg (alternatively this could be a pytest.ini), i.e.
addopts= --cov <path> -ra
which caused the test discovery to fail due to low coverage. The solution was to remove that line from the config file.
Also, as suggested in the documentation:
You can also configure testing manually by setting one and only one of the following settings to true: python.testing.unittestEnabled, python.testing.pytestEnabled, and python.testing.nosetestsEnabled.
In settings.json you can also disable coverage using --no-cov flag:
"python.testing.pytestArgs": ["--no-cov"],
EDIT:
Slightly related - in case of more complex projects it might be also necessary to change the rootdir parameter (inside your settings.json) when running tests with pytest (in case of ModuleNotFoundError):
"python.testing.pytestArgs": [
"--rootdir","${workspaceFolder}/<path-to-directory-with-tests>"
],
Seems like a bug in the latest version of VS Code Python extension. I had the same issue, then I downgraded the Python extension to 2019.3.6558 and then it works again. So we should go to our VS Code extensions list, select the Python extension and "Install another version..." from the setting of that extension.
I hope this works for you too.
I resolved the issue by upgrading pytest to the latest version: 4.4.1 with "pip install --upgrade pytest". I was apparently running an old version 3.4.2
Before begin the tests discovery, check that python.testing.cwd points correctly to your tests dir and your python.testing.pytestEnabled is set to true.
Once those requirements are set correctly, run tests discovery and its output (see OUTPUT window). You should see something like this:
python $HOME/.vscode/extensions/ms-python.python-$VERSION/pythonFiles/testing_tools/run_adapter.py discover pytest -- --rootdir $ROOT_DIR_OF_YOUR_PROJECT -s --cache-clear
Test Discovery failed:
Error: ============================= test session starts ==============================
<SETTINGS RELATED TO YOUR MACHINE, PYTHON VERSION, PYTEST VERSION,...>
collected N items / M errors
...
It's important to highlight here the last line: collected N items / M errors. The following lines will contain info about the tests discovered by pytest. So your tests are discoverable but there are errors related to their correct execution.
The following lines will contain the errors which in most of the cases will be related to an incorrect import.
Check that all your dependencies have been downloaded previously. If you are working with specific versions of dependencies (on therequirements.txt file you have something like your_package == X.Y.Z) be sure that it's the right version that you need to.
If you are having trouble with pytest I was struggling with the discovery test part.
Reading some open issue (other) in vscode I found a workaround using the test-adapter extension
market_place_link
The extention works like a charm. (and solve my discovery problem)
In my case, it was the vscode python extension problem.
I switched the test platform from pytest and switched to it back again, and the tests got discovered.
It seems that when testing is universally enabled for all python projects and it fails to discover tests at the beginning, it fails forever!
Test files need to be named test_*.py or *_test.py for pytest collection to work.
Then run pytest --collect-only at the command line to make sure all of the tests are found. Then magically, the flask icon in VSCode suddenly shows the test files and their tests.
As a noob, I was putting my unit tests inside the module files, since I was following the pattern of unittest, and then running pytest *.py. That doesn't work with pytest, and I didn't find a command line argument override the naming convention.
I searched in the settings for "python" and found this:
Switching to pytest automatically detect my tests:
This error is so frustrating..
In my case the error fixed by modifying the python.pythonPath parameter in settings.json (found inside .vscode folder under project root directory), to the path which I obtained using which python in terminal (e.g. /usr/local/var/pyenv/shims/python)
I use pyenv with python3.9, and my error said previously:
Error: Process returned an error: /Users/"user-name"/.pyenv/shims/python:
line 21: /usr/local/Cellar/pyenv/1.2.23/libexec/pyenv: No such file or
directory
at ChildProcess.
(/Users/"user-name"/.vscode/extensions/littlefoxteam.vscode-python-test-adapter-0.6.8/out/src/processRunner.js:35:36)
at Object.onceWrapper (events.js:422:26) at ChildProcess.emit
(events.js:315:20) at maybeClose (internal/child_process.js:1021:16)
at Process.ChildProcess._handle.onexit
(internal/child_process.js:286:5)
In my case, I had to make sure that I was using the right interpreter where the libraries where installed (I used a virtual environment) but the interpreter was pointing to the globally installed python. After changing the interpreter to that of the virtual environment, it worked.
Looking at https://docs.pytest.org/en/latest/usage.html#possible-exit-codes it seems pytest itself is falling over do to some internal error.
I had this same issue and tracked it down to my pytest.ini file. Removing most of the addopts from that file fixed the issue.
I had this problem and struggle with it for hours. I think that there is a special resolution for every other platform configuration. My platform is:
VSCode: 1.55.0 (Ubuntu)
Pytest: 6.2.3
MS Python extension (ms-python.python 2021.3.680753044)
Python Test Explorer for Visual Studio Code (littlefoxteam.vscode-python-test-adapter - 0.6.7)
The worst thing has that the tool itself does not have a standard output (at least that I know of or could find easily on the internet).
In the end, the problem was
--no-cov
parameters that was not recognized by the VSCode testing explorer tool (that I copied from some page on the internet) and the error was showed by the extension littlefoxteam.vscode-python-test-adapter and it may help you to find where things are broken.
In my case, same problem appeared each time when flake8 linter reported errors. Even one error was enough to fail VS Code test discovery.
So the fix is either disable the linter or fix linter errors.
I use setup described here.
2021-12-22
Please find below the settings I used to get pytest working in VsCode after much frustration. I found many helpful pieces of advice here and elsewhere on the internet, but none were complete enough to spare me a bit of cursing. I hope the following will help someone out. This setup allows me to run testing visually from the test explorer extension and also from the integrated terminal. I am using a src format in my workspace and Conda for environment management. The settings related to the terminal setup keep me from having to manually enable my Conda environment or set the python path. Possibly people who have been using VSCODE for more than two days could add something nice to make this better and/or more complete.
##### Vscode info:
Version: 1.63.2 (Universal)
Commit: 899d46d82c4c95423fb7e10e68eba52050e30ba3
Date: 2021-12-15T09:37:28.172Z (1 wk ago)
Electron: 13.5.2
Chromium: 91.0.4472.164
Node.js: 14.16.0
V8: 9.1.269.39-electron.0
OS: Darwin x64 20.6.0
##### Testing Extension:
Python Test Explorer for Visual Studio Code
extension installed, v. 0.7.0
##### Pytest version
pytest 6.2.5
##### Directory Structure:
workspace
.env
./src
__init__.py
code1.py
code2.py
./tests
__init__.py
test_code1.py
test_code2.py
##### .env file (in root, but see the "python.envFile" setting in settings.json)
PYTHONPATH=src
#####. settings.json
{
"workbench.colorTheme": "Visual Studio Dark",
"editor.fontFamily": " monospace, Menlo, Monaco, Courier New",
"python.testing.unittestEnabled": false,
"python.testing.cwd": ".",
"terminal.integrated.inheritEnv": true,
"python.envFile": "${workspaceFolder}/.env",
"python.defaultInterpreterPath":
"~/anaconda3/envs/mycurrentenv/bin/python",
"pythonTestExplorer.testFramework": "pytest",
"python.testing.pytestEnabled": true,
"python.testing.pytestArgs": [
"tests"
],
"python.terminal.activateEnvironment": true,
"python.terminal.activateEnvInCurrentTerminal": true,
"terminal.integrated.env.osx": {
"PYTHONPATH": "${workspaceFolder}/src:${env:PYTHONPATH}"
}
}
Here is generic way to get Django tests to run with full vscode support
Configure python tests
Choose unittest
Root Directory
test*.py
Then each test case will need to look like the following:
from django.test import TestCase
class views(TestCase):
#classmethod
def setUpClass(cls):
import django
django.setup()
def test_something(self,):
from user.model import something
...
Any functions you want to import have to be imported inside the test case (like shown). The setUpClass runs before the test class is setup and will setup your django project. Once it's setup you can import functions inside the test methods. If you try to import models/views at the top of your script, it will raise an exception since django isn't setup. If you have any other preinitialization that needs to run for your django project to work, run it inside setUpClass. Pytest might work the same way, I haven't tested it.
There are several causes for this.
The simple answer is, it is not perfect. Furthermore, Python is not native to VS Code; Python extensions may not be playing nice either.
I have observed some mitigating measures, though.
NB VS Code didn't "design" test discovery; that is the job of the testing framework. Make sure you have a basic grasp on how it works.
Troubleshooting
For every "battery" of tests, VS Code will gladly tell you what went wrong, right in the Test view panel. To see this, expand the bar with the name of the project, and hover your mouse over the line that is revealed. Look at the traceback.
In the image above, the error is "No module named src". This is more interesting than it sounds. If I import a file from another file, that import path may not be visible to the test discovery mechanism. It may be running from a different "cwd". The best you can do is try to figure out the topmost path of your project, and either add or remove path qualifiers. Until it works.
Main causes
From time to time, VS Code will lose info on the project test configuration. Use command window (Ctrl + Shift + P) to either:
(re)scan tests
(re)configure test spec for the project <-- important!
restart Python Language Server
Python is supposed to remove the need for the empty __init__.py; it seems VS Code loves those. They should be in each folder that leads to a test folder. Not every folder, but the top-down path.
Depending on what you select as the "root test folder" in the test configuration, it might have different meaning based on what VS Code thinks is the root of your project. That probably goes for any specific folder too.
import. VS Code doesn't like syntax errors. It is possible some syntax errors will not get highlighted in the code.
This (unfortunately) goes for all the imports in your file. But you shouldn't test invalid code anyway, right?
Minor buggy behaviors
Running some other visible test might help refresh the discovery process.
VS Code should automatically (by setting) refresh tests on each Save operation. But it doesn't hurt to refresh it manually.
TLDR
Look at the error items in the test panel
Re-configure project test discovery parameters from time to time
Make sure you don't have syntax errors (visible or not)
Create empty __init__.pys in each folder of your project that leads to the test folder
Clean up your import logic
P.S. The Test view has been extensively worked on and improved much over the course of 1 year. Expect changes in behavior.
I was trying to clone a git repo with access key, but when I am trying to run it, It throws an exception saying git executable not found.
But i have installed git and the in_it.py shows correct path "C:\Program Files\Git\bin" Also I have installed gitpython to use the library in python
here's my code...
import git
git.Git("D:/madhav/myrep/").clone("#github.com:myrepo/scripts")
========= and it throws the following exception =================
Traceback (most recent call last): File
"C:\Users\1096506\Desktop\gitclone.py", line 1, in <module>
from git import Repo File "C:\Users\1096506\AppData\Local\Programs\Python\Python36-32\lib\site-packages\git\__init__.py",
line 84, in <module>
refresh() File "C:\Users\1096506\AppData\Local\Programs\Python\Python36-32\lib\site-packages\git\__init__.py",
line 73, in refresh
if not Git.refresh(path=path): File "C:\Users\1096506\AppData\Local\Programs\Python\Python36-32\lib\site-packages\git\cmd.py",
line 293, in refresh
raise ImportError(err) ImportError: Bad git executable. The git executable must be specified in one of the following ways:
- be included in your $PATH
- be set via $GIT_PYTHON_GIT_EXECUTABLE
- explicitly set via git.refresh()
All git commands will error until this is rectified.
This initial warning can be silenced or aggravated in the future by setting the
$GIT_PYTHON_REFRESH environment variable. Use one of the following values:
- quiet|q|silence|s|none|n|0: for no warning or exception
- warn|w|warning|1: for a printed warning
- error|e|raise|r|2: for a raised exception
Example:
export GIT_PYTHON_REFRESH=quiet
I had the same issue. What I did is:
I went to: System Properties -> Environment Variables
On System Variables Section I clicked Path, Edit and Move Up.
Environment Variables
Edit and Moved Up two places from the bottom
Error occurs because git is not in the path. So its not able to import git module.
Couple of ways to resolve it.
As suggested above adding the git binary path to environment variable path.
If git is not being used directly in the module and its only a dependent module import thats throwing this exception before importing git we could add
os.environ["GIT_PYTHON_REFRESH"] = "quiet"
and import git after this line, this would suppress the error caused due to git import
Had the same problem got it to work thanks to Muthukumaran. Just make Muthukumaran answer more clear.
Follow these steps:
import os
os.environ["GIT_PYTHON_REFRESH"] = "quiet"
import git
See if you have installed Git in the OS.
If not install git first this will solve your error.
Centos
sudo yum -y install git
Ubuntu/Debian
sudo apt-get install git
Mac Os
sudo brew install git
This solved my problem.
Make sure you're not in an inaccessible directory on *nix, such as when you've just been root and then done a su username
you may still be in root's home folder and that will trigger this error (assuming you have the correct environment variables set, and have sourced the .profile or .bashrc etc with source ~/.bashrc )
which git
/usr/bin/git
I was getting this error even after setting the environment:
in ~/.bashrc
# for bench
PATH=$PATH:/usr/bin/git
export PATH
GIT_PYTHON_GIT_EXECUTABLE=/usr/bin/git
export GIT_PYTHON_GIT_EXECUTABLE
cd
and it's working
$ bench --version
WARN: Command not being executed in bench directory
5.3.0
I came across similar problem recently and installing git followed by restarting Windows Powershell CommandLine solved the problem. May it helps.
For those who are using a Lambda layer with it. It worked adding as the comment above says just adding GIT_PYTHON_REFRESH=quiet as an environment variable.
Execute GIT_PYTHON_REFRESH=quiet in your terminal and then try to run the code.
Im using pylint 1.6.4 and git-pylint-commit-hook 2.1.1 to lint my files on pre-commit. I also use alembic to generate my migrations, they are stored in <project-root>/migrations/versions.
The problem is that the generated migrations are not valid and pylint generates a warning for them. I can ignore migrations with --ignore=migrations. (Pylint ignores them by default anyway because migrations isn't a python module, it's simply a directory). But git-pylint-commit-hook calls pylint with list of changed files to validate. And pylint doesn't check if the file should be ignored if you give it a list of filenames, not modules.
This causes the pre-commit hook to fail when there is a new migration to be commited.
Running pylint on migrations/versions/d1f0e08ea6d2_skill_table.py (file 2/13).. 8.6/10.00 FAILED
************* Module d1f0e08ea6d2_skill_table.py
C: 5, 0: Trailing whitespace (trailing-whitespace)
C: 1, 0: Invalid module name "d1f0e08ea6d2_skill_table" (invalid-name)
C: 16, 0: Import "from alembic import op" should be placed at the top of the module (wrong-import-position)
C: 17, 0: Import "import sqlalchemy as sa" should be placed at the top of the module (wrong-import-position)
C: 20, 0: Missing function docstring (missing-docstring)
C:171, 0: Missing function docstring (missing-docstring)
I tried to add #pylint: skip-file to beginning of each migration file. This skips the file but generates and error that the file was skipped:
Running pylint on migrations/versions/d1f0e08ea6d2_skill_table.py (file 2/13).. 0/10.00 FAILED
************* Module d1f0e08ea6d2_skill_table.py
I: 1, 0: Ignoring entire file (file-ignored)
So I tried to ignore error file-ignored in .pylintrc like this:
[messages control]
disable=unused-argument
It works and the error is no longer reported but pre-commit hook fails because it doesn't find any statements:
Running pylint on migrations/versions/d1f0e08ea6d2_skill_table.py (file 2/13).. 0/10.00 FAILED
Report
======
0 statements analysed.
Notice that in both cases pylint evaluates the files as 0.0/10.0 so setting lower threshold for failure isn't the solution.
The question is, how do I make git-pylint-commit-hook and pylint to ignore my migrations?
This is an old question but I have just ran into this issue myself. I found the answer while searching this thread.
To solve this problem, just add an exclude directive with a regex that matches your folder.
If you want to exclude the migrations folder, by example, just add:
exclude: ^tests/
To your Pylint settings. Mine looks like this:
- repo: local
hooks:
- id: system
name: PyLint
entry: poetry run pylint
language: system
exclude: ^alembic/
files: \.py$
I am using someone else's code, available on GitHub. To run their code I created a virtualenv and installed all the dependencies listed - both python libraries and clones of other repositories. When I proceed to run the included tests, I get an ImportError:
Namespace(all=False, regr=False, sci=False, unit=True)
[localhost] local: py.test -x -v engine/test
==================================================================================== test session starts =====================================================================================
platform linux2 -- Python 2.7.6, pytest-2.8.2, py-1.4.31, pluggy-0.3.1 -- /home/compomics/local/METASPACE/SM_distributed/SM_engine/bin/python
cachedir: engine/test/.cache
rootdir: /home/compomics/local/METASPACE/SM_distributed/engine/test, inifile:
collecting 6 items / 1 errors
=========================================================================================== ERRORS ===========================================================================================
_______________________________________________________________________ ERROR collecting test_formula_img_validator.py _______________________________________________________________________
engine/test/test_formula_img_validator.py:7: in <module>
from engine.formula_img_validator import filter_sf_images,get_compute_img_measures, ImgMeasures
engine/formula_img_validator.py:7: in <module>
from pyIMS.image_measures import measure_of_chaos, isotope_image_correlation, isotope_pattern_match
E ImportError: cannot import name measure_of_chaos
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: stopping after 1 failures !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
================================================================================== 1 error in 0.99 seconds ===================================================================================
Fatal error: local() encountered an error (return code 2) while executing 'py.test -x -v engine/test'
However, if I open the python interpreter and try to do the exact same imports, it does it just fine without any error. Similar questions suggested:
adding an empty __init__.py to the test directory
making sure pytest is installed in the virtualenv
I did both these things, and the error persists.
I added to the beginning of the test script:
import os
print(os.environ["PYTHONPATH"].split(os.pathsep))
print(os.listdir("."))
and confirmed that the folder from where I'm trying to import is indeed in the resulting list.
Not sure how to proceed. Would appreciate any help I can get :)
In file formula_img_validator.py change
from pyIMS.image_measures import measure_of_chaos,isotope_image_correlation, isotope_pattern_match
to
from engine.pyIMS.image_measures import measure_of_chaos, isotope_image_correlation, isotope_pattern_match
That'll solve the problem. For complete solution go to GitHub for new updated code.
there was a conflict with other library
EDIT - this was my own stupidity for not remembering I had cloned a previous version of the dependent repos, which was also on my path, and that did not include the function this code was trying to load. Sorry for not having deleted the question when I noticed, I couldn't for the life of me find the delete button :)