I'm having trouble with relative imports, but I can't seem to figure out what's wrong in this case. It seems like a straightforward relative import from another module in the same package, so I'm at a loss for how to debug this.
My project is set up like so:
.
├── ckmeans
│ ├── __init__.py
│ ├── _ckmeans.pxd
│ ├── _ckmeans_wrapper.pyx
│ ├── _ckmeans.py
│ ├── _evaluation.py
│ └── _utils.py
└── setup.py
At the top of __init__.py:
from ._ckmeans import ckmeans # _ckmeans.py
And at the top of _ckmeans.py:
from . import _ckmeans_wrapper # _ckmeans_wrapper.pyx
And at the top of _ckmeans_wrapper.pyx:
cimport _ckmeans # _ckmeans.pxd
I run pip install --ignore-installed --upgrade -e ., and everything seems to go smoothly. Then when I try to run my test suite, or import ckmeans in the interpreter, I get the error:
ImportError: cannot import name '_ckmeans_wrapper'
When I comment out the import statement from __init__.py and then import ckmeans in the interpreter, it does indeed seem to be missing the _ckmeans_wrapper module. I suspect that something is failing silently in the Cython build, but I don't have any idea how to debug.
Here's the setup.py:
import numpy as np
from Cython.Build import cythonize
from setuptools import setup, Extension
extension = Extension(
name='_ckmeans_wrapper',
sources=['ckmeans/_ckmeans_wrapper.pyx'],
language="c++",
include_dirs=[np.get_include()]
)
setup(
name='ckmeans',
version='1.0.0',
packages=['ckmeans'],
ext_modules = cythonize(extension),
install_requires=['numpy', 'Cython']
)
The name argument to Extension was incorrect. It should be name='ckmeans._ckmeans_wrapper'.
Related
I have the following layout:
└── folder_1
└── __init__.py
└── level_1.py
└── folder_2
└── __init__.py
└── level_2.py
└── test
└── __init__.py
└── test_in.py
└── test_out.py
└── setup.py
And in my setup.py I specify packages=["folder_1", "test"]
In the test_out.py file I can import from level_1.py and level_2.py with no problem, but for some reason in the test_in.py file I can only import from level_1.py. If I try to import from level_2.py I get the error
ModuleNotFoundError: No module named 'folder_1.folder_2'
I also get errors if I try to do the import in the init.py from folder_1.
I'm running this on a jupyter lab and can't find a way to make this work. Is there a way to fix this without using the PYTHONPATH or things like that?
EDIT:
Just found out that if I add folder_1.folder_2 to the content of packages in setup.py it works, however I'm not sure if this is the correct way to fix this?
I have a Python project that uses the MicroKernel pattern where I want each of the modules to be completely independent. I import each of the modules into the kernel and that works fine. However, when I am in a module I want the root of the module to be the module dir. This is the part that is not working.
Project structure;
.
├── requirements.txt
├── ...
├── kernel
│ ├── config.py
│ ├── main.py
│ ├── src
│ │ ├── __init__.py
│ │ ├── ...
│ └── test
│ ├── __init__.py
│ ├── ...
├── modules
│ └── img_select
│ ├── __init__.py
│ ├── config.py
│ ├── main.py
│ └── test
│ ├── __init__.py
│ └── test_main.py
If I import from main import somefunction in modules/img_select/test/test_main.py I get the following error:
ImportError: cannot import name 'somefunction' from 'main' (./kernel/main.py)
So it clearly does not see the modules/img_select as the root of the module, which leads to the following question:
How can I set the root for imports in a module?
Some additional info, I did add the paths with sys.path in the config files;
kernel/config.py;
import os
import sys
ROOT_DIR = os.path.dirname(os.path.abspath(__file__))
MODULES_DIR = os.path.join(ROOT_DIR, '../modules')
sys.path.insert(0, os.path.abspath(MODULES_DIR))
modules/img_select/config.py;
import os
import sys
ROOT_DIR = os.path.dirname(os.path.abspath(__file__))
sys.path.insert(0, os.path.abspath(ROOT_DIR))
And my python version is 3.7.3
I do realise that there are a lot of excellent resources out there, but I have tried most approaches and can't seem to get it to work.
I'm not sure what main you are trying to import from. I think python is confused from the pathing as well. How does test_main.py choose which main to run? Typically when you have a package (directory with __init__.py) you import from the package and not individual modules.
# test_main.py
# If img_select is in the path and has __init__.py
from img_select.main import somefunction
If img_select does not have __init__.py and you have img_select in the path then you can import from main.
# test_main.py
# If img_select is in the path without __init__.py
from main import somefunction
In your case I do not know how you are trying to indicate which main.py to import from. How are you importing and calling the proper config.py?
You might be able to get away with changing the current directory with os.chdir. I think your main problem is that img_select is a package with __init__.py. Python doesn't like to use from main import ... when main is in a package. Python is expecting from img_select.main import ....
Working Directory
If you are in the directory modules/img_select/test/ and call python test_main.py then this directory is known as your working directory. Your working directory is wherever you call python. If you are in the top level directory (where requirements.txt lives) and call python modules/img_select/test/test_main.py then the top level directory is the working directory. Python uses this working directory as path.
If kernel has an __init__.py then python will find kernel from the top level directory. If kernel is not a package then you need add the kernel directory to the path in order for python to see kernel/main.py. One way is to modify sys.path or PYTHONPATH like you suggested. However, if your working directory is modules/img_select/test/ then you have to go up several directories to find the correct path.
# test_main.py
import sys
TEST_DIR = os.path.dirname(__file__) # modules/img_select/test/
IMG_DIR = os.path.dirname(TEST_DIR)
MOD_DIR = os.path.dirname(IMG_DIR)
KERNEL_DIR = os.path.join(os.path.dirname(MOD_DIR), 'kernel')
sys.path.append(KERNEL_DIR)
from main import somefunction
If your top level directory (where requirements.txt lives) is your working directory then you still need to add kernel to the path.
# modules/img_select/test/test_main.py
import sys
sys.path.append('kernel')
As you can see this can change depending on your working directory, and you would have to modify every running file manually. You can get around this with abspath like you are doing. However, every file needs the path modified. I do not recommend manually changing the path.
Libraries
Python pathing can be a pain. I suggest making a library.
You just make a setup.py file to install the kernel or other packages as a library. The setup.py file should be at the same level as requirements.txt
# setup.py
"""
setup.py - Setup file to distribute the library
See Also:
* https://github.com/pypa/sampleproject
* https://packaging.python.org/en/latest/distributing.html
* https://pythonhosted.org/an_example_pypi_project/setuptools.html
"""
from setuptools import setup, Extension, find_packages
setup(name='kernel',
version='0.0.1',
# Specify packages (directories with __init__.py) to install.
# You could use find_packages(exclude=['modules']) as well
packages=['kernel'], # kernel needs to have __init__.py
include_package_data=True,
)
The kernel directory needs an __init__.py. Install the library as editable if you are still working on it. Call pip install -e . in the top level directory that has the setup.py file.
After you install the library python will have copied or linked the kernel directory into its site-packages path. Now your test_main.py file just needs to import kernel correctly
# test_main.py
from kernel.main import somefunction
somefunction()
Customizing init.py
Since kernel now has an __init__.py you can control the functions available from importing kernel
# __init__.py
# The "." indicates a relative import
from .main import somefunction
from .config import ...
try:
from .src.mymodule import myfunc
except (ImportError, Exception):
def myfunc(*args, **kwargs):
raise EnvironmentError('Function not available. Missing dependency "X".')
After changing the __init__.py you can import from kernel instead of kernel.main
# test_main.py
from kernel import somefunction
somefunction()
If you delete the NumPy (any library) from the site manager and save that folder in another location then use:
import sys
sys.path.append("/home/shubhangi/numpy") # path of numpy dir (which is removed from site manager and paste into another directory)
from numpy import __init__ as np
import numpy as np
arr = np.array([1, 2, 3, 4, 5])
print(arr)
print(type(arr))
I am new to building packages so bear with me. I am having a problem importing the subpackages of my latest python project.
My directory structure is the following:
├── package
│ ├── __init__.py
│ ├── subpackage_a
│ │ ├── __init__.py
│ │ └── functions_a.py
│ └── subpackage_b
│ ├── __init__.py
│ └── functions_b.py
└── setup.py
The files look as follows
setup.py
:
from setuptools import setup
setup(name='test_package',
version='0.3',
description='',
author='me',
packages=['package']
)
package/__init__.py: empty.
subpackage_a/__init__.py: from .functions_a import *
subpackage_b/__init__.py: from .functions_b import *
functions_a.py
contains
def hello_world_a():
print('hello its a')
and functions_b.py contains
def hello_world_b():
print('hello its b')
Now I open a virtualenv go to the setup.py's directory and I pip install .. I was expecting to access the functions contained in the subpackages a and b. But when I try to import the functions I get a module not found error.
from package.subpackage_a import hello_world_a
ModuleNotFoundError: No module named 'package.subpackage_a'
and the same thing holds for subpackage_b. But if I import package this is recognised. I have a feeling that this approach used to work, as I have some old packages written this way which don't work any longer.
Perhaps I have to change my init.py files ? What am I doing wrong ?
setuptools.setup doesn't know that subpackage_a and subpackage_b exist. You only specified the top-level package. So it won't include these subpackages in the installation. Instead you should also specify them:
setup(
...,
packages=['package', 'subpackage_a', 'subpackage_b']
)
This process can be automatized via find_packages():
from setuptools import find_packages
setup(
...,
packages=find_packages()
)
VSCode Version: 1.41.1
OS Version:Ubuntu 18.04
Steps to Reproduce:
# tree:
.
├── demo1
│ ├── __init__.py
│ └── test.py
├── __init__.py
├── auto.py
# auto.py
def func():
print("1")
# test.py
from auto import func
func()
Use examples to solve problems that arise in a project
Run the test.py file, and I get "ModuleNotFoundError: No module named 'func'"
I used 'CTRL '+ left mouse button in test.py to jump to func
The same code can be run in pycharm
If you run test.py directly then you need to add the parent folder to PYTHONPATH. Try:
import sys
sys.path.append("..\<parent_folder>")
from auto import func
Otherwise, if you merely want to import test.py in another .py file, you can use relative import of python
from . import auto #another dot '.' to go up two packages
auto.func()
Reference
Add this in test.py, before import:
import sys
sys.path.insert(0, "/path/to/project/root/directory")
For me it's not a good file organization. A better practice might be as below:
Let your project file tree be like:
.
├── __init__.py
├── lib
│ ├── auto.py
│ └── __init__.py
└── test.py
And write test.py like:
from lib.auto import func
func()
Simple one-line solution
from ... import auto
and call the function by using auto.func().
I have 4 files: main.py, helper.py, clf.pkl, and tests.py.
Main.py has core classes. It needs to import helper.py for some methods and clf.pkl for data.
What is the minimal structure I can have for a Python library with 4 files?
I would use a package to hold your files, along with a pyproject.toml to describe your project, like this:
.
├── pyproject.toml
├── MANIFEST.in
├── your_package_name
│ ├── __main__.py
│ ├── helper.py
│ └── __init__.py
└── tests
└── tests.py
In your __init__.py file write at least:
"""A short description of your project"""
__version__ = "0.0.1"
(Change description and version accordingly).
To create your pyproject.toml you can use flit init:
pip install flit
flit init
Name your entry point __main__.py in the package so you can run it using:
python -m your_package_name
(Yes it's still a good idea to use an if __name__ == "__main__": in it, so you can import your main from your tests if needed).
You can import helper.py from __main__.py using:
from your_package_name import helper
or:
from . import helper
(I prefer the first one but I don't know if there a concensus.)
For your clf.pkl to be included in your package you'll need to create a MANIFEST.in with:
include your_package_name/clf.pkl
Your pkl will be available at:
os.path.join(os.path.dirname(os.path.abspath(__file__)), "clf.pkl")
To test it use flit install -s and to publish it on PyPI flit publish.