Installing via `setup.py develop` fails - pip works - python

My python package footools needs html5lib via install_requires in setup.py.
setup.py develop fails
Installing via setup.py develop fails:
cd src/footools/
python setup.py develop
Processing dependencies for footools==2016.205
Searching for html5lib==0.9999999
Reading https://source.example.com/pypi/simple/html5lib/
Download error on https://source.example.com/pypi/simple/html5lib/:
[Errno 185090050] _ssl.c:354: error:0B084002:x509
certificate routines:X509_load_cert_crl_file:system lib --
Some packages may not be found!
Couldn't find index page for 'html5lib' (maybe misspelled?)
pip works
But direct download works:
bar#workdevel123:~/src/footools> pip install html5lib==0.9999999
/home/bar/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:79:
InsecurePlatformWarning: A true SSLContext object is not available.
This prevents urllib3 from configuring SSL appropriately
and may cause certain SSL connections to fail.
For more information, see
https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
InsecurePlatformWarning
Collecting html5lib==0.9999999
/home/bar/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:79:
InsecurePlatformWarning: A true SSLContext object is not available.
This prevents urllib3 from configuring SSL appropriately and
may cause certain SSL connections to fail.
For more information,
see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
InsecurePlatformWarning
Downloading https://source.example.com/pypi/packages/html5lib-0.9999999.tar.gz
Requirement already satisfied (use --upgrade to upgrade):
six in /usr/lib/python2.7/site-packages (from html5lib==0.9999999)
Installing collected packages: html5lib
Running setup.py install for html5lib
Successfully installed html5lib-0.9999999
Questions
What is the difference between these two methods?
Why are they different?
What is the correct way to install a dependency in python?
setup.py
The setup.py is not special:
import setuptools
setuptools.setup(
name='foo',
version='2016.210',
long_description=open('README.txt').read(),
packages=setuptools.find_packages(),
install_requires=[
# about twenty packages before this line
'html5lib==0.9999999'
],
include_package_data=True,
entry_points={
'console_scripts': [
'foo=foo.utils.bar:main',
],
},
)

python setup.py develop, or setuptools in general uses easy_install to satisfy dependencies which in turn uses urllib2 whereas pip uses requests. See here for easy_install vs pip.
pip is more modern and among other things has capability to uninstall packages and complies with PEP 438 -- Transitioning to release-file hosting on PyPI. You can achieve the same thing as python setup.py develop with pip install -e src/footools/, note if the project path is in the current directory use, ./footools.
The requests package bundles CA certs in the package itself, python -c 'import pip;print(pip.download.requests.certs.where())'.
setuptools uses system installed CA certs python -c 'from setuptools import ssl_support;print(ssl_support.cert_paths)'.
You have to update system installed CA certs using tools like update-ca-certificates for Ubuntu to either update CA certs automatically or download from https://curl.haxx.se/docs/caextract.html and install into one of the paths shown by setuptools or set setuptools.ssl_support.cert_paths to an empty sequence like [] and do pip install certifi.
Calling setuptools.ssl_support.find_ca_bundle() will reveal the location of CA certs.

setuptools is a collection of enhancements to the Python distutils (for Python 2.6 and up) that allow developers to more easily build and distribute Python packages, especially ones that have dependencies on other packages.
So, among other stuff, you can create packages that can be upload to Pypi, and later installed using pip (therefore distibuting your module).
That said, they actually should not be that different in the installation part. You are running the develop mode, so maybe you have to fiddle a bit with the directories or fix the authorization error.
In the Development Mode the project is deployed into a staging area (in some way similar to the process of a virtual environment)
deployment is done in such a way that changes to the project source are immediately available in the staging area(s), without needing to run a build or install step after each change.
Meaning also everything will be available for that python interpreter. It can be later unstaged.
I noticed that html5lib is being fetched from different places: /pypi/simple/in one case and /pypi/packages/ in the other.
dependency_links
A list of strings naming URLs to be searched when satisfying dependencies. These links will be used if needed to install packages specified by setup_requires or tests_require.
Back to the problem I think it is most probably the ssl issue, since in pip it handled graciously (i.e., nice warning and there is some kind of workaround), but the same does not happen with setuptools. If there is an error in the request that is not handled then Couldn't find index page for 'html5lib' could be because of that.

What is the difference between these two methods?
Nothing terribly important to you as a user, aside from their different user interfaces. They are two stops on the scenic historical train ride of Python package management. There were others along the way.
Why are they different?
Back in the day, Python didn't ship with a package management system. Third party solutions filled the void. They were designed by different people at different moments in time. If you look at other programming languages, you sometimes see similar stories; sometimes you see happier stories; sometimes more tragic.
What is the correct way to install a dependency in python?
Both of these methods are technically correct. Pip is the more modern method, and in my experience it is both more popular and handier to work with. As of Python 3.4 and up, Pip has been included in the CPython distribution and is officially 'preferred'. So you can see which way the wind is blowing.

Related

Pip wheel collects 2 versions of a package then pip install gets a conflict

We use a pipeline that first uses pip wheel to collect all the packages that are needed in the project and then it creates a docker image that calls to pip install on the collected wheels.
The issue I am encountering is that when calling pip wheel, pip is collecting 2 different versions of a package. This has started occurring once a new version of the package is available.
The project has a requirement for an internal library ecs-deployer==10.1.2 and that library has in turn a requirement in the form of: elb-listener>=3.2.1+25,<4
The relevant output of pip wheel with the verbose option says:
Collecting elb-listener>=3.2.1+25,<4
Created temporary directory: /tmp/pip-unpack-zr930807
File was already downloaded /home/user/path/dist/elb_listener-3.2.2+26-py3-none-any.whl
Added elb-listener>=3.2.1+25,<4 from https://internal-repository.com/path/elb_listener/3.2.2%2B26/elb_listener-3.2.2%2B26-py3-none-any.whl#md5=foo (from ecs-deployer==10.1.2->service==1.0.0) to build tracker '/tmp/pip-req-tracker-1tz9t5ls'
Removed elb-listener>=3.2.1+25,<4 from https://internal-repository.com/path/elb_listener/3.2.2%2B26/elb_listener-3.2.2%2B26-py3-none-any.whl#md5=blabla (from ecs-deployer==10.1.2->service==1.0.0) to build tracker '/tmp/pip-req-tracker-1tz9t5ls'
And also:
Collecting elb-listener>=3.2.1+25,<4
Created temporary directory: /tmp/pip-unpack-yfnxim_u
File was already downloaded /home/user/path/dist/elb_listener-3.2.3+27-py3-none-any.whl
Added elb-listener>=3.2.1+25,<4 from https://internal-repository.com/path/elb_listener/3.2.3%2B27/elb_listener-3.2.3%2B27-py3-none-any.whl#md5=bar (from ecs-deployer==10.1.2->service==1.0.0) to build tracker '/tmp/pip-req-tracker-1tz9t5ls'
Then when the pip install is called I get this:
ERROR: Cannot install elb-listener 3.2.2+26 (from /opt/elb_listener-3.2.2+26-py3-none-any.whl) and cad-aws-elb-listener-target-group-builder 3.2.3+27 (from /opt/elb_listener-3.2.3+27-py3-none-any.whl) because these package versions have conflicting dependencies.
The conflict is caused by:
The user requested elb-listener 3.2.2+26 (from /opt/elb_listener-3.2.2+26-py3-none-any.whl)
The user requested elb-listener 3.2.3+27 (from /opt/elb_listener-3.2.3+27-py3-none-any.whl)
We use pip 20.2.3 with the option --use-feature=2020-resolver
Is it normal that pip wheel collects several versions of the same package?
If so, can I indicate in any way to either pip wheel to only collect one of the versions or to pip install to only use the latest version?
If not, is there any way to solve this problem? I guess changing the requirement to elb-listener>=3.2.1+27,<4 would solve it, but we don't have direct access to that library and it would take a while for other team to change it.
As per #sinoroc comment, upgrading the python to 3.10 and pip version to 21.2.4 solved this particular issue.
As far as I understood, "local version identifiers" such as 3.2.1+25 are far from usual, apparently they are not meant to be used anywhere public (like PyPI), and that might be the reason for all the trouble here. I am really not sure how well they are supported by Python packaging tools and maybe they confuse the dependency resolution.
Local version identifiers SHOULD NOT be used when publishing upstream projects to a public index server, but MAY be used to identify private builds created directly from the project source. Local version identifiers SHOULD be used by downstream projects when releasing a version that is API compatible with the version of the upstream project identified by the public version identifier, but contains additional changes (such as bug fixes). As the Python Package Index is intended solely for indexing and hosting upstream projects, it MUST NOT allow the use of local version identifiers.
-- "Local version identifiers" section of _PEP 440

How does pip wheel resolves transitive dependencies?

When I run pip wheel sentry-sdk it downloads the following wheel files:
certifi-2020.6.20-py2.py3-none-any.whl
sentry_sdk-0.18.0-py2.py3-none-any.whl
urllib3-1.25.10-py2.py3-none-any.whl
Where sentry_sdk-0.18.0-py2.py3-none-any.whl is the lib I actually want to use and the other ones are transitive dependencies required by this lib to work. I understand that the file is coming from PyPI however what I do not understand is how pip wheel is choosing the version of the aforementioned transitive dependencies.
More Context
My underlying problem is that the resolved version of the urllib3 clashes with another one already added to the pex file of the project I'm working on (I'm using Bazel to generate the pex) I'm considering downgrading the version of urllib3 to match my project's existing one. Looking at the setup.py from the sentry-sdk in GitHub it says it only requires it to be greater than 1.10.0 ("urllib3>=1.10.0") so I think the downgrade would work but I wanted to be sure to avoid production crashes.
Thanks
the current version of pip (2020-10-13) does not have a dependency resolver, it picks the first constraint greedily (so if urllib3 is encountered unbounded first, it will pick the latest version -- even if a later package has a more restrictive requirement)
this is being changed in pip, you can enable the resolver as an opt-in in pip>=20.2 and it will become the default in the future (later this year)

Should setuptools be in the setup_requires entry of setup.cfg files?

The importlib_resources backport for Python < 3.7 of the importlib.resources standard library module has the following section in the setup.cfg file:
[options]
python_requires = >=2.7,!=3.0,!=3.1,!=3.2,!=3.3
setup_requires =
setuptools
wheel
install_requires =
pathlib2; python_version < '3'
typing; python_version < '3.5'
packages = find:
Why does setup_requires include setuptools? This does not seem to make sense since:
the first line of the setup.py file imports setuptools, so by the time the setup function is called and reads the setup.cfg file that instructs to install setuptools it is already too late to install setuptools:
from setuptools import setup
setup()
setuptools is already installed on any fresh Python installation (well, only tested on Windows 10 and MacOS 10.15 with Python 3.8.0):
$ python -V
Python 3.8.0
$ pip list
Package Version
---------- -------
pip 19.2.3
setuptools 41.2.0
WARNING: You are using pip version 19.2.3, however version 19.3.1 is available.
You should consider upgrading via the 'python -m pip install --upgrade pip' command.
No, setuptools should not be included in setup_requires, according to PEP 518 (bold emphasis mine):
Setuptools tried to solve this with a setup_requires argument to its
setup() function [3]. This solution has a number of issues, such as:
No tooling (besides setuptools itself) can access this information without executing the setup.py, but setup.py can't be executed without having these items installed.
While setuptools itself will install anything listed in this, they won't be installed until during the execution of the setup() function, which means that the only way to actually use anything added here is through increasingly complex machinations that delay the import and usage of these modules until later on in the execution of the setup() function.
This cannot include setuptools itself nor can it include a replacement to setuptools, which means that projects such as numpy.distutils are largely incapable of utilizing it and projects cannot take advantage of newer setuptools features until their users naturally upgrade the version of setuptools to a newer one.
The items listed in setup_requires get implicitly installed whenever you execute the setup.py but one of the common ways that the setup.py is executed is via another tool, such as pip, who is already managing dependencies. This means that a command like pip install spam might end up having both pip and setuptools downloading and installing packages and end users needing to configure both tools (and for setuptools without being in control of the invocation) to change settings like which repository it installs from. It also means that users need to be aware of the discovery rules for both tools, as one may support different package formats or determine the latest version differently.
The accepted answer is mostly correct, but where PEP 518 says.
[The setup_requires mechanism] cannot include setuptools itself...
It's technically incorrect, and as importlib_resources demonstrates, it can actually include setuptools. The problem is that including setuptools in setup_requires serves mostly as documentation. It declares that setuptools is a build requirement (required to run setup.py), but it won't be capable of satisfying that requirement if it's not already satisfied.
But, the presence of setuptools in setup_requires is technically correct and does serve the purpose of declaring the requirement and asking setuptools to verify that the requirement is in fact installed (alongside other setup-time requirements).
It is, however, just a legacy artifact and doesn't provide that much value, and as can be seen in the question and answers, it does lead to confusion. The recommended, proper, approach is to use PEP 517 and 518 declarations and builders, but that part of the ecosystem hasn't matured yet, so setuptools vestiges will remain. Try not to let them bother you.
Why does setup_requires includes setuptools? This does not seem to make sense
Does not make sense at all. On the other hand it doesn't hamper anything so why not?

How to declare build-time dependencies without breaking other packages?

I ran into a problem when installing a package which depended on python-daemon. I ultimately traced it to the latest version of the package python-daemon (2.0.3) released yesterday. Testing in a virtual environment on an Ubuntu 14.04 machine and issuing the following commands:
(venv) $ pip list
argparse (1.2.1)
pip (1.5.6)
setuptools (3.6)
wsgiref (0.1.2)
(venv) $ pip install redis
... works fine ....
(venv) $ pip install python-daemon
...
snip
...
File "/home/pwj/.virtualenvs/venv/local/lib/python2.7/site-packages/pkg_resources.py", line 2147, in load
['__name__'])
ImportError: No module named version
(venv)02:15 PM tmp$ pip list
argparse (1.2.1)
lockfile (0.10.2)
pip (1.5.6)
python-daemon (2.0.3)
setuptools (3.6)
wsgiref (0.1.2)
So the install of python-daemon seemed to work but something affected pip or setuptools because other packages (celery, flask), I try to install with pip after this gives me the same traceback:
...
snip
...
File "/home/pwj/.virtualenvs/venv/local/lib/python2.7/site-packages/pkg_resources.py", line 2147, in load
['__name__'])
ImportError: No module named version
If I uninstall python-daemon with pip things again and packages that weren't installing now install fine. Has anyone else come across this or something similar with a different project? My solution was to pip install the previous version
(venv) $ pip install python-daemon==2.0.2
... works ...
but was wondering what might be causing such an error.
(This behaviour is corrected in python-daemon version 2.0.4 and later.)
There are two sides to this:
Setuptools assumes it is the centre of everything.
Version 2.0.3 of python-daemon doesn't take that into account.
A more detailed explanation: There is some complex code using Docutils involved in the python-daemon build process, that isn't needed after install and isn't part of the library code.
It's too complex to leave in the un-importable (and therefore not-unit-testable) setup.py, so that build code is shunted to a separate testable module, version (in the file version.py), which itself uses Docutils.
But then the setup.py has a circular dependency: How to import version, when Docutils isn't yet installed? How to use Setuptools to ensure Docutils is installed, when running setup.py to completion will need version? All the feasible solutions are ugly and confusing.
The approach taken in ‘python-daemon’ 2.0.3 is to declare Docutils required for setup, and declare a Setuptools entry point for the work that needs version. That way setup.py gets to install Docutils before any of the entry points that will use version.
But now we come to the first point, that Setuptools arrogates itself as the centre of everything. By declaring an entry point, setup.py has modified every Setuptools action thereafter, and every package will fail if it can't find the entry points. And, since most of them don't have version or the specified functions in that module, they crash Setuptools.
What is essentially a bug to be fixed, reveals a poorly-understood corner case in Setuptools. So I'm voting your question up.
There doesn't seem to be a good solution to this: having modules available for setup.py but ensuring requirements are met first. Setuptools assumes it is the only build system needed to satisfy all dependencies for everything, and when that assumption fails it's very difficult to get around.
Thanks to the Python Packaging Authority folks, and the distutils-sig forum, for explaining this to me.

How to require and install a package using python 3.x distutils?

I have a program that uses dateutil from the package index. I would like to have setup.py check for for its presence and try to get it using easy_install if it is not there.
The documentation for distutils seems to indicate that this can be done using the requires keyword in setup(), but when I try, it installs on a system without dateutil without giving a warning or installing the required package.
The only thing I could find on google was this blog post about the same issue which did not have any answer either.
Am I using distutils wrong? Do I need to subclass distutils.command.install and do the checking/installing myself?
Automatic downloading of dependencies is a feature introduced by setuptools which is a third-party add-on to distutils, in particular, the install_requires argument it adds. See the setuptools documentation for more information.
Another option is to use requirements.txt file with pip rather than using easy_install as a package installer. pip has now become the recommended installer; see the Python Packaging User Guide for more information.
Update [2015-01]: The previous version of this answer referred to the distribute fork of setuptools. The distribute fork has since been merged back into a newer active setuptools project. distribute is now dead and should no longer be used. setuptools and pip are now very actively maintained and support Python 3.
The argument install_requires in setup function from distutils work for me well, only if I create sdist distributive, like: python setup.py sdist

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