We Keep Coding

Cythonize installs .so files to wrong location

I'd like to ask a question about how to configure setup.py with Cython, setuptools extensions etc. I'm trying cythonize a submodule with Cython.Distutils's build_ext. But the issue isn't Cython.Distutils's Extentsion module, (if it exists) because it isn't loaded. Only build_ext. So I create a setuptools.extension Extension in a list, and then cythonize the list of Extension objects. There's only one Extension in the list, an its as follows.
Extension("distance", ["kmerdb/distance.pyx"], include_dirs=[np.get_include()])
I've tried different methods of installation, from python setup.py install to pip install -e . to generating the wheel file and installing the wheel. I couldn't find anything that worked...
Okay, so I know very little about the process and that's probably why I am getting hung up but I've searched the whole site, no luck. So here goes.
I'm running the following shell script to install my package locally, and it works fine. The problem is the installation doesn't move the .so and the .py file into the kmerdb module I'm trying to export. Any suggestions? Thanks
>python setup.py sdist bdist_wheel
>/bin/auditwheel repair --plat manylinux2014_x86_64 dist/kmerdb-*linux_x86_64.whl
>mv wheelhouse/* dist
>rm dist/*linux_x86_64.whl
>pip install dist/kmerdb-*-manylinux2014_x86_64.whl
>ls ~/.pyenv/versions/kdb/lib/python3.10/site-packages/kmerdb-0.6.5-py3.10-linux-x86_64.egg/
distance.cpython-310-x86_64-linux-gnu.so distance.py kmerdb ...
Again, the files distance.cpython-310-x86_64-linux-gno.so is not moved into the kmerdb module, my Python packages, which I'm trying to install locally and configure for .whl upload to PyPI.
Python 3.10.1 (main, Jan 1 2022, 21:28:19) [GCC 11.1.0] on linux
Cython==0.29.26
setup.py
Extension("distance", ["kmerdb/distance.pyx"], include_dirs=[np.get_include()], define_macros=[("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION")],),
setup(
name=NAME,
version=VERSION,
description=DESCRIPTION,
long_description=long_description,
long_description_content_type='text/markdown',
author=AUTHOR,
author_email=EMAIL,
python_requires=REQUIRES_PYTHON,
url=URL,
download_url=CURRENT_RELEASE,
keywords = ["k-mer", "kmer", "k-merdb", "kmerdb", "kdb"],
classifiers=[
"Development Status :: 1 - Planning",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.6",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Topic :: Scientific/Engineering",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Software Development :: Libraries :: Python Modules",
],
packages=find_packages(exclude=["tests", "*.tests", "*.tests.*", "tests.*"]),
package_dir={'kmerdb': 'kmerdb'},
package_data={'kmerdb': ['CITATION']},
# If your package is a single module, use this instead of 'packages':
#py_modules=['kmerdb'],
#scripts=['bin/kmerdb', 'bin/kmerdb_report.R'],
entry_points={
'console_scripts': ['kmerdb=kmerdb:cli'],
},
install_requires=REQUIRED,#['Cython==0.29.21', 'numpy==1.18.1'],
extras_require=EXTRAS,
include_package_data=True,
license='GPLv3+',
test_suite='test',
# tests_require=['mamba', 'expect'],
ext_modules=cythonize(extensions),
library_dirs=["."],
zip_safe=False,
)

I'm going to self answer here. The issue stemmed from an improperly specified Extension.
Extension("kmerdb.distance", ["kmerdb/distance.pyx"], include_dirs=[np.get_include()])
All I had to do was include the module name for the fully specified submodule hierarchy. Fixed it!

Use different version of python package in the same environment

I need to have different versions of elasticseach-dsl installed in the same virtualenv. I would like to be able to import them using some sort of alias:
import elasticsearch_dsl1
import elasticsearch_dsl2
import elasticsearch_dsl5
I was thinking to create packages called elasricsearch_dsl* and in their setup.py add install requirements for the proper version of elasticsearch_dsl but when I install the packages it results in a conflict because all my packages require different versions of the same library.
I have no clue on how to proceed and if this is possible.
Thanks a lot to everyone

Short answer:
It is not possible.

I was able to find a solution to my problem.
I downloaded the source code of the elasticsearch-dsl libraries of different versions
Then changed the import statements to use elasticsearch1, elasticsearch2 etc.libraries instead of elasticsearch v1.x and v2.x
# example `elasticsearch-dsl` v5.4.0
from elasticsearch import Elasticsearch # --> from elasticsearch5 import Elasticsearch
Modified the setup.py to change the dependencies from elasticsearch to elasticsearch1, elasticsearch2 and so on for each version of the elasticsearch-dsl
I've been very lucky because of the existence of elasticsearch1, elasticsearch2... otherwise I would have to repeat the same procedure for them. And more lucky for the compatibility of dependencies of the various versions of the library.
I'm not proud of this hack but it worked.
setup.py
An example of a setup.py file for elasticsearch-dls==7.3.0, then elasticsearch-dsl7
from os.path import join, dirname
from setuptools import setup, find_packages
VERSION = (7, 3, 0)
__version__ = VERSION
__versionstr__ = ".".join(map(str, VERSION))
f = open(join(dirname(__file__), "README"))
long_description = f.read().strip()
f.close()
install_requires = [
"six",
"python-dateutil",
"elasticsearch7", # before "elasticsearch>=7.0.0,<8.0.0" <---
# ipaddress is included in stdlib since python 3.3
'ipaddress; python_version<"3.3"',
]
tests_require = [
"mock",
"pytest>=3.0.0",
"pytest-cov",
"pytest-mock<3.0.0",
"pytz",
"coverage<5.0.0",
]
setup(
name="elasticsearch-dsl7", # <---
description="Python client for Elasticsearch",
license="Apache-2.0",
url="https://github.com/elasticsearch/elasticsearch-dsl-py",
long_description=long_description,
version=__versionstr__,
author="Honza Král",
author_email="honza.kral#gmail.com",
maintainer="Seth Michael Larson",
maintainer_email="seth.larson#elastic.co",
packages=find_packages(where=".", exclude=("test_elasticsearch_dsl*",)),
python_requires=">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*",
classifiers=[
"Development Status :: 4 - Beta",
"License :: OSI Approved :: Apache Software License",
"Intended Audience :: Developers",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Programming Language :: Python :: 2",
"Programming Language :: Python :: 2.7",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.4",
"Programming Language :: Python :: 3.5",
"Programming Language :: Python :: 3.6",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: Implementation :: CPython",
"Programming Language :: Python :: Implementation :: PyPy",
],
install_requires=install_requires,
test_suite="test_elasticsearch_dsl.run_tests.run_all",
tests_require=tests_require,
extras_require={"develop": tests_require + ["sphinx", "sphinx_rtd_theme"]},
)

How do I install a python package to /usr/local/bin?

I am trying to install a python package on my ubuntu.I am trying to install it through a setup script which i had written.The setup.py script looks like this:
from setuptools import setup
try:
from setuptools import setup
except ImportError:
from distutils.core import setup
setup(
name = 'pyduino',
description = 'PyDuino project aims to make python interactive with hardware particularly arduino.',
url = '###',
keywords = 'python arduino',
author = '###',
author_email = '###',
version = '0.0.0',
license = 'GNU',
packages = ['pyduino'],
install_requires = ['pyserial'],
classifiers = [
# How mature is this project? Common values are
# 3 - Alpha
# 4 - Beta
# 5 - Production/Stable
'Development Status :: 3 - Alpha',
'Intended Audience :: Developers',
'Topic :: Software Development :: Build Tools',
'Programming Language :: Python :: 2',
'Programming Language :: Python :: 2.6',
'Programming Language :: Python :: 2.7',
'Programming Language :: Python :: 3',
'Programming Language :: Python :: 3.3',
'Programming Language :: Python :: 3.4',
'Programming Language :: Python :: 3.5',
],
scripts=['pyduino/pyduino.py'],
)
Package installs in /usr/local/bin directory.But when I am importing the modules outside the /usr/local/bin,import error occurs.I tried changing path to /usr/local/bin and it works perfectly and import error doesn't occur.How can I install the package so that I can import the modules in any directory? Thanks in advance...

Try install your packages with pip using this
pip install --install-option="--prefix=$PREFIX_PATH" package_name
as described here Install a Python package into a different directory using pip?
and i'll suggest to read what are 1. pip 2. virtualenv
Good luck :)
EDIT: i found the package is installed with pip like:
pip install --install-option="--prefix=/usr/local/bin" pyduino_mk

Currently, you're using a scripts tag to install your python code. This will put your code in /usr/local/bin, which is not in PYTHONPATH.
According to the documentation, you use scripts when you want to install executable scripts (stuff you want to call from command line). Otherwise, you need to use packages.
My approach would be like this:
install the pyduino/pyduino.py in the library with something like packages=['pyduino']
create a wrapper (shell or python) capable of calling your installed script and install that via scripts=[...]
Using the packages tag for your module will install it in /usr/local/lib/python..., which is in PYTHONPATH. This will allow you to import your script with something like import pyduino.pyduino.*.
For the wrapper script part:
A best practice is to isolate the code to be executed if the script is triggered from command line in something like:
def main():
# insert your code here
pass
if __name__ == '__main__':
main()
Assuming there is a def main() as above
create a directory scripts in your tree (at the same level with setup.py)
create a file scripts/pyduino
in scripts/pyduino:
#!/usr/bin/env python
from pydiuno.pyduino import main
if __name__ == '__main__':
main()
add a `scripts = ['scripts/pyduino'] to your setup.py code

Bundle library to application using pybuilder

I'm new to python and writing an application which I want to package for debian. Therefore, I'd like to (and I have to) use pybuilder. My goal is to create a .deb package (currently using stdeb), which makes sure, that all required libraries are installed, too.
My application uses a third party library, that is only available via pip(3) install (no debian package).
My build.py looks like:
[...]
use_plugin("python.core")
use_plugin("python.unittest")
use_plugin("python.install_dependencies")
use_plugin("python.distutils")
use_plugin("copy_resources")
use_plugin("source_distribution")
use_plugin("python.flake8")
use_plugin("python.coverage")
use_plugin("python.stdeb")
#init
def initialize(project):
project.build_depends_on('coverage')
project.build_depends_on('flake8')
project.build_depends_on('jsonmerge')
project.build_depends_on('mock')
project.build_depends_on('setuptools')
project.build_depends_on('stdeb')
project.build_depends_on('unittest-xml-reporting')
project.build_depends_on('xmlrunner')
project.depends_on('<pip-only-library>')
project.set_property('coverage_threshold_warn', 50)
project.set_property('flake8_break_build', False)
project.set_property('flake8_ignore', 'E501,E402,E731')
project.set_property('flake8_include_test_sources', True)
project.set_property('flake8_verbose_output', True)
project.set_property('verbose', True)
project.set_property("copy_resources_target", "$dir_dist")
project.set_property("coverage_break_build", False)
project.set_property("coverage_reset_modules", True)
project.set_property("dir_dist_scripts", 'scripts')
project.set_property("distutils_classifiers", [
'Programming Language :: Python :: 3',
'Programming Language :: Python :: 3.3',
'Programming Language :: Python :: 3.4',
'Development Status :: 4',
'Environment :: Console',
'Intended Audience :: Systems Administration',
'License :: OSI Approved :: BSD License'])
project.set_property('distutils_commands', ['bdist'])
project.set_property('distutils_commands', ['sdist'])
Generation of debian package works in general. Calling pyb successfully creates a python3-mypackage_1.0-1_all.deb package.
The generated setup.py looks like:
# `target/dist/mypackage-1.0/setup.py`
[...]
if __name__ == '__main__':
setup(
[...]
packages = [],
[...]
entry_points = {},
data_files = [],
package_data = {},
install_requires = ['pip-only-library'],
dependency_links = [],
zip_safe=True,
cmdclass={'install': install},
)
Testing package installation using sudo dpkg -i python3-mypackage_1.0-1_all.deb fails as dpkg refers to a dependent package python3-<pip-only-library>, which is not available.
During build time, the library is present on the local machine.
So, now comes the newbie question: How to change build.py to make sure, that the created debian package provides my application and makes sure, that library requirements are met.
Maybe, is it possible to bundle the pip-only library (i.e. taken from /usr/local/lib/python3.4/dist-packages during build-time) to my application and ship them within an 'application with all dependencies'-package? Or is there an alternative approach?
I've already seen this answer but it doesn't help.

No distributions at all found, even though I recently published the package

Hello fellow programmers,
So lately I've been working on a project at my work that we want to open source. It's the package called django-push-notifications-manager (yes, what a unusual long name I know).
So I already did the registration and the uploading of the package, but for some kind of reason pip install django-push-notifications-manager will not work and will give the error:
Downloading/unpacking django-push-notifications-manager
Could not find any downloads that satisfy the requirement django-push-notifications-manager
Cleaning up...
No distributions at all found for django-push-notifications-manager
Storing debug log for failure in /Users/pauloostenrijk/.pip/pip.log
So I haven't been able to fix it by removing and replacing the package, deleting it, making a new version. None of them worked.
I think you guys would like to know what my setup.py was, so hereby:
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import sys
import push_notifications
def get_packages(package):
"""
Return root package and all sub-packages.
"""
return [dirpath
for dirpath, dirnames, filenames in os.walk(package)
if os.path.exists(os.path.join(dirpath, '__init__.py'))]
try:
from setuptools import setup
except ImportError:
from distutils.core import setup
version = push_notifications.__version__
if sys.argv[-1] == 'publish':
os.system('python setup.py sdist upload')
print("You probably want to also tag the version now:")
print(" git tag -a %s -m 'version %s'" % (version, version))
print(" git push --tags")
sys.exit()
readme = open('README.rst').read()
setup(
name='django-push-notifications-manager',
version=version,
description="""A plug and play package to handle push devices and push notifications for services such as ZeroPush and Urban Airship""",
long_description=readme,
author='Paul Oostenrijk',
author_email='paul#glemma.nl',
url='https://github.com/glemmaPaul/django-push-notifications-manager',
packages=get_packages('push_notifications'),
include_package_data=True,
install_requires=[
'django>=1.5.1',
'requests>=2.5.1'
],
license="BSD",
zip_safe=False,
keywords='django-push-notifications-manager',
classifiers=[
'Development Status :: 2 - Pre-Alpha',
'Framework :: Django',
'Intended Audience :: Developers',
'License :: OSI Approved :: BSD License',
'Natural Language :: English',
'Programming Language :: Python :: 2',
'Programming Language :: Python :: 2.6',
'Programming Language :: Python :: 2.7',
'Programming Language :: Python :: 3',
'Programming Language :: Python :: 3.3',
],
)
Hope any of you guys could help me out! Thanks in advance :)

So after spending a long time of trying and figuring out I finally found the problem.
Don't look strange to me, but apparently PyPi has problems with the name django-push-notifications-manager, I think there can be 2 causes:
The length of the name
That having 2 dashes in the name is the maximum
I hope nobody will ever get this problem, it was head cracking!
Thanks for your time!