Assume the folder structure is
src
-__init__.py
-A
-__init__.py
-lib.py
-B
-__init__.py
-script.py
I am in script.py trying to import a function p() from A.lib. The file script.py contains
import os
print(os.listdir())
from A.lib import fkt
if __name__ == "__main__":
fkt()
I am calling os to show that my current working directory is in src/ so the module A should be in reach. The return from the print statements is
['A', '.vscode', 'B', '__init__.py']
Is there a "correct" way to do this? I figure importing the path via sys isn't "correct" so I'd like to avoid doing this.
Note: I have tried almost every version of from src.A.lib, from .A.lib, or from A.lib and all of these return either that src is not a package or that there is no module A.
OS: I am running on ubuntu 18.04 LTS with python 3.6.9 using vscode with "cwd" set to "${workspaceFolder}".
Related
I want to pass library location while running unittest command. As I have to import library for using. Suppose the library name is some_lib . Same library will be executed on Linux as well as Windows.
Using python version 3.7.11
Used command : python3 -m unittest test_file.py lib_location
Details of test file.
import sys
sys.path.append(sys.argv[1]) # Hard code of path works fine.
import some_lib
import unittest
class TestCasesForSerializePy(unittest.TestCase):
#classmethod
def setUpClass(self):
self.archive_handler = some_lib.open('./test.archive')
def test_existing_archive(self):
self.assertTrue(self.archive_handler.isOpen())
if __name__ == '__main__':
# unittest.main(argv = [sys.argv[0]])
# sys.argv.pop()
unittest.main()
Error: ModuleNotFoundError: No module named 'C:/REC_158/build/lib'
Tried different approach as available on google.
Approach 1:
sys.argv.pop()
unittest.main()
Approach 2:
del sys.argv[1:]
unittest.main()
Approach 3:
unittest.main(argv=[sys.argv[0]]
Is it possible to add bash script as an entrypoint (console script) to Python package via poetry? It looks like it only accepts python files (see code here).
I want entry.sh to be an entry script
#!/usr/bin/env bash
set -e
echo "Running entrypoint"
via setup.py
entry_points={
"console_scripts": [
"entry=entry.sh",
],
},
On the other hand setuptools seems to be supporting shell scripts (see code here).
Is it possible to include shell script into a package and add it to the entrypoints after installing when working with Poetry?
UPD. setuptools does not support that as well (it generates code below)
def importlib_load_entry_point(spec, group, name):
dist_name, _, _ = spec.partition('==')
matches = (
entry_point
for entry_point in distribution(dist_name).entry_points
if entry_point.group == group and entry_point.name == name
)
return next(matches).load()
globals().setdefault('load_entry_point', importlib_load_entry_point)
Is it design decision? It looks to me that packaging should provide such a feature to deliver complex applications as a single bundle.
So I ended up using this workaround: have my script in place and add it to the bundle via package_data and call it from within Python code which I made as an entrypoint.
import subprocess
def _run(bash_script):
return subprocess.call(bash_script, shell=True)
def entrypoint():
return _run("./scripts/my_entrypoint.sh")
def another_entrypoint_if_needed():
return _run("./scripts/some_other_script.sh")
and pyproject.toml
[tool.poetry.scripts]
entrypoint = 'bash_runner:entrypoint'
another = 'bash_runner:another_entrypoint_if_needed'
Same works for console_scripts in setup.py file.
What I am trying to achieve.
Run a python script saved On pythonanywhere host from google sheets on a button press.
Check the answer by Dustin Michels
Task of Each File?
app.py: contains code of REST API made using Flask.
runMe.py: contains code for that get values from(google sheet cell A1:A2). And sum both values send sum back to A3.
main.py: contains code for a GET request with an argument as name(runMe.py).filename may change if the user wants to run another file.
I Made an API by using Flask.it works online and offline perfectly but still, if you want to recommend anything related to the app.py.Code Review App.py
from flask import Flask, jsonify
from flask_restful import Api, Resource
import os
app = Flask(__name__)
api = Api(app)
class callApi(Resource):
def get(self, file_name):
my_dir = os.path.dirname(__file__)
file_path = os.path.join(my_dir, file_name)
file = open(file_path)
getvalues = {}
exec(file.read(), getvalues)
return jsonify({'data': getvalues['total']})
api.add_resource(callApi, "/callApi/<string:file_name>")
if __name__ == '__main__':
app.run()
Here is the Code of runMe2.py
import gspread
from oauth2client.service_account import ServiceAccountCredentials
# use creds to create a client to interact with the Google Drive API
scopes =['https://www.googleapis.com/auth/spreadsheets',"https://www.googleapis.com/auth/drive.file","https://www.googleapis.com/auth/drive"]
creds = ServiceAccountCredentials.from_json_keyfile_name('service_account.json', scopes)
client = gspread.authorize(creds)
# Find a workbook by name and open the first sheet
# Make sure you use the right name here.
sheet = client.open("Demosheet").sheet1
# Extract and print all of the values
list_of_hashes = sheet.get_all_records()
print(list_of_hashes)
below is the main.py code
import requests
BASE = 'https://username.pythonanywhere.com/callApi/test.py'
response = requests.get(BASE)
print(response.json())
main.py output
{'data': 54}
Test.py code
a = 20
b = 34
total = a+b
print(total)
PROBLEM IS
if I request runMe2.py at that time I am got this error.
check runMe2.py code above
app.py is hosted on https://www.pythonanywhere.com/
ModuleNotFoundError: No module named 'gspread'
However, I installed gspread on pythonanywhere why using the command. but it's not working.
You either haven't installed the gspread package on your current python environment or it is installed somewhere (e.g. in a diff. virtual env) and your script cant find it.
Try installing the package inside the environment your running your script in using pip3:
pip3 install gspread
You can try something like this on Windows
pip install gspread
or on Mac
pip3 install gspread
If you're running on Docker, or building with a requirements.txt you can try adding this line you your requirements.txt file
gspread==3.7.0
Any other instructions for this package can be found here => https://github.com/burnash/gspread
Download gspread here
Download the tar file: gspread-3.7.0.tar.gz from the above link
Extract file and convert folder in zip then upload it back on server
Open bash console and use command as
$ unzip gspread-3.7.0
$ cd gspread-3.7.0
$ python3.7 setup.py install --user
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.
I am trying to import some of my personal modules into my IPython Clusters. I am using Anacondas on Windows Vista 64 bit
from IPython.parallel import Client
rc = Client()
dview = rc[:]
with dview.sync_imports():
import lib.rf
It is giving me this error:
No module named 'lib.rf'
I can import the module in the rest of my IPython notebook, as I have this .bat file to start ipython notebook:
cd C:\Users\Jon\workspace\bf
set PYTHONPATH=%PYTHONPATH%;C:\Users\Jon\workspace\bf
C:\Anaconda\envs\p33\scripts\ipython notebook
I am using this similar code to start my ip clusters:
cd C:\Users\Jon\workspace\bf
set PYTHONPATH=%PYTHONPATH%;C:\Users\Jon\workspace\bf
C:\Anaconda\envs\p33\Scripts\ipcluster start --n=7
Why is this not working?
More info:
If I print out sys.path, I get a list that contains C:\Users\Jon\workspace\bf
If I print out the paths of my clusters, I get the same list:
%px sys.path
['',
'',
'',
'C:\\Anaconda\\envs\\p33\\lib\\site-packages\\distribute-0.6.28-py3.3.egg',
'C:\\Anaconda\\envs\\p33\\lib\\site-packages\\pykalman-0.9.5-py3.3.egg',
'C:\\Anaconda\\envs\\p33\\lib\\site-packages\\patsy-0.2.1-py3.3.egg',
'C:\\Anaconda\\envs\\p33\\lib\\site-packages\\joblib-0.8.3_r1-py3.3.egg',
'C:\\Users\\Jon\\workspace\\bf',
'C:\\Users\\Jon\\workspace\\bf\\my_numba',
'C:\\Anaconda\\envs\\p33\\python33.zip',
'C:\\Anaconda\\envs\\p33\\DLLs',
'C:\\Anaconda\\envs\\p33\\lib',
'C:\\Anaconda\\envs\\p33',
'C:\\Anaconda\\envs\\p33\\lib\\site-packages',
'C:\\Anaconda\\envs\\p33\\lib\\site-packages\\Sphinx-1.2.3-py3.3.egg',
'C:\\Anaconda\\envs\\p33\\lib\\site-packages\\win32',
'C:\\Anaconda\\envs\\p33\\lib\\site-packages\\win32\\lib',
'C:\\Anaconda\\envs\\p33\\lib\\site-packages\\Pythonwin',
'C:\\Anaconda\\envs\\p33\\lib\\site-packages\\runipy-0.1.1-py3.3.egg',
'C:\\Anaconda\\envs\\p33\\lib\\site-packages\\setuptools-7.0-py3.3.egg',
'C:\\Anaconda\\envs\\p33\\lib\\site-packages\\IPython\\extensions']
In [45]:
Further analysis:
%px lib.__path__
Out[0:11]: _NamespacePath(['C:\\Anaconda\\envs\\p33\\lib\\site-packages\\win32\\lib'])
lib.__path__
Out[57]: ['.\\lib']
Looks like the ipcluster and notebook are looking at lib in different places. I have tried renaming lib to mylib. It has not helped.
It seems that with dview.sync_imports() is being run someplace other than your IPython Notebook environment and is therefore relying a different PYTHONPATH. It is definitely not being run on one of the cluster engines and so wouldn't expect it to leverage your cluster settings of PYTHONPATH.
I'm thinking you'll need to have that directory in your PYTHONPATH (not your PATH) for the calling python environment because that is the location from which you are importing the modules.
The impact of the bit you have about setting the PYTHONPATH in the DOS shell from which you invoke ipclusters isn't clear to me. I can see that one might expect this to let the engines know about your directory, but I'm wondering if that PYTHONPATH gets initilized to the environment from which you call IPython.parallel.Client.