Cannot install pandas 0.24.2 from source with Python 2.7 into an environment without NumPy #27435

didip · 2019-07-17T18:09:20Z

Code Sample, a copy-pastable example if possible

RuntimeError: Python version >= 3.5 required.

Problem description

Under this docs: https://pandas.pydata.org/pandas-docs/stable/whatsnew/v0.24.0.html

0.24.x is supposed to be backward compatible to Python 2.

The 0.24.x series of releases will be the last to support Python 2. Future feature releases will support Python 3 only. See Plan for dropping Python 2.7 for more details

Expected Output

0.24.2 should still work on Python 2.

The text was updated successfully, but these errors were encountered:

jreback · 2019-07-17T18:38:03Z

are you sure you actually tried to install 0.24.x? and not the 0.25rc1

didip · 2019-07-17T18:51:47Z

Looks like it is trying to download numpy that is really new.

Our specified version for numpy is numpy==1.16.2

      File "/tmp/pip-install-E4jz9w/pandas/setup.py", line 746, in <module>
        **setuptools_kwargs)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/__init__.py", line 144, in setup
        _install_setup_requires(attrs)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/__init__.py", line 139, in _install_setup_requires
        dist.fetch_build_eggs(dist.setup_requires)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/dist.py", line 724, in fetch_build_eggs
        replace_conflicting=True,
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/pkg_resources/__init__.py", line 782, in resolve
        replace_conflicting=replace_conflicting
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1065, in best_match
        return self.obtain(req, installer)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1077, in obtain
        return installer(requirement)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/dist.py", line 791, in fetch_build_egg
        return cmd.easy_install(req)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 679, in easy_install
        return self.install_item(spec, dist.location, tmpdir, deps)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 705, in install_item
        dists = self.install_eggs(spec, download, tmpdir)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 890, in install_eggs
        return self.build_and_install(setup_script, setup_base)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1158, in build_and_install
        self.run_setup(setup_script, setup_base, args)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1144, in run_setup
        run_setup(setup_script, args)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/sandbox.py", line 253, in run_setup
        raise
      File "/code/.cicd/runtime/python/.python/lib/python2.7/contextlib.py", line 35, in __exit__
        self.gen.throw(type, value, traceback)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
        yield
      File "/code/.cicd/runtime/python/.python/lib/python2.7/contextlib.py", line 35, in __exit__
        self.gen.throw(type, value, traceback)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/sandbox.py", line 166, in save_modules
        saved_exc.resume()
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/sandbox.py", line 141, in resume
        six.reraise(type, exc, self._tb)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/sandbox.py", line 154, in save_modules
        yield saved
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
        yield
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/sandbox.py", line 250, in run_setup
        _execfile(setup_script, ns)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/sandbox.py", line 45, in _execfile
        exec(code, globals, locals)
      File "/tmp/easy_install-dglvOb/numpy-1.17.0rc2/setup.py", line 31, in <module>
    
    RuntimeError: Python version >= 3.5 required.

jreback · 2019-07-17T19:02:02Z

right so numpy 1.17 is also python 3 only. guess would be that you have a too old pip, or are doing some odd type of installation.

didip · 2019-07-17T20:34:47Z

Inside setup.py, should this block of logic check for Python version first and set max version of numpy for Python 2?

min_numpy_ver = "1.13.3"
setuptools_kwargs = {
    "install_requires": [
        "python-dateutil >= 2.6.1",
        "pytz >= 2017.2",
        "numpy >= {numpy_ver}".format(numpy_ver=min_numpy_ver),
    ],
    "setup_requires": ["numpy >= {numpy_ver}".format(numpy_ver=min_numpy_ver)],
    "zip_safe": False,
}

TomAugspurger · 2019-07-17T20:51:31Z

Can you show the command you're running? You shouldn't be executing setup.py, pip would be doing it for you if needed.

didip · 2019-07-17T21:00:34Z

Fairly standard procedure: pip install -r requirements.txt.

...
numpy==1.16.2
pandas==0.24.2
...

During pip install, when it's collecting pandas...

Collecting pandas==0.24.2...

pandas ended up downloading much newer numpy: numpy-1.17.0rc2 instead of what I specified in requirements.txt: numpy==1.16.2. numpy==1.16.2 is downloaded correctly.

TomAugspurger · 2019-07-17T21:03:13Z

What platform? Are you passing --pre or --no-binary anywhere? I'm confused why you aren't getting a wheel for NumPy and pandas.

TomAugspurger · 2019-07-17T21:03:27Z

You might also post the full output.

didip · 2019-07-17T21:06:18Z

Collecting pandas==0.24.2 (from redacted==0.0.0)
  Downloading https://pypi.redacted.com/packages/b2/4c/b6f966ac91c5670ba4ef0b0b5613b5379e3c7abdfad4e7b89a87d73bae13/pandas-0.24.2.tar.gz (11.8MB)
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-E4jz9w/pandas/setup.py", line 746, in <module>
        **setuptools_kwargs)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/__init__.py", line 144, in setup
        _install_setup_requires(attrs)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/__init__.py", line 139, in _install_setup_requires
        dist.fetch_build_eggs(dist.setup_requires)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/dist.py", line 724, in fetch_build_eggs
        replace_conflicting=True,
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/pkg_resources/__init__.py", line 782, in resolve
        replace_conflicting=replace_conflicting
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1065, in best_match
        return self.obtain(req, installer)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1077, in obtain
        return installer(requirement)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/dist.py", line 791, in fetch_build_egg
        return cmd.easy_install(req)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 679, in easy_install
        return self.install_item(spec, dist.location, tmpdir, deps)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 705, in install_item
        dists = self.install_eggs(spec, download, tmpdir)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 890, in install_eggs
        return self.build_and_install(setup_script, setup_base)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1158, in build_and_install
        self.run_setup(setup_script, setup_base, args)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1144, in run_setup
        run_setup(setup_script, args)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/sandbox.py", line 253, in run_setup
        raise
      File "/code/.cicd/runtime/python/.python/lib/python2.7/contextlib.py", line 35, in __exit__
        self.gen.throw(type, value, traceback)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
        yield
      File "/code/.cicd/runtime/python/.python/lib/python2.7/contextlib.py", line 35, in __exit__
        self.gen.throw(type, value, traceback)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/sandbox.py", line 166, in save_modules
        saved_exc.resume()
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/sandbox.py", line 141, in resume
        six.reraise(type, exc, self._tb)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/sandbox.py", line 154, in save_modules
        yield saved
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
        yield
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/sandbox.py", line 250, in run_setup
        _execfile(setup_script, ns)
      File "/code/.cicd/runtime/python/.python/lib/python2.7/site-packages/setuptools/sandbox.py", line 45, in _execfile
        exec(code, globals, locals)
      File "/tmp/easy_install-dglvOb/numpy-1.17.0rc2/setup.py", line 31, in <module>
    
    RuntimeError: Python version >= 3.5 required.

requirements.txt

blinker==1.4
Flask==0.10.1
Flask-KVSession==0.4
Flask-Statsd-Ext==0.0.3
gevent==1.1.1
greenlet==0.4.9
gunicorn==19.4.5
itsdangerous==0.24
Jinja2==2.8
MarkupSafe==0.23
mysql-connector-python-rf==2.0.4
numpy==1.16.2
pandas==0.24.2
psycopg2==2.7.1
pyjwt==1.6.4
pylru==1.0.9
python-dateutil==2.5.0
python-ldap==2.3.13
pytest==3.3.0
pytest-cov==2.5.1
pytz==2016.3
raven==6.6.0
redis==2.10.5
requests==2.10.0
simplekv==0.7.1.dev1
six==1.10.0
SQLAlchemy==1.3.3
Werkzeug==0.11.9
Unidecode==0.4.21

setup.py

from setuptools import setup, find_packages


import os

here = os.path.abspath(os.path.dirname(__file__))
README = open(os.path.join(here, 'README.md')).read()

exclude_dirs = ['venv', 'scripts']

with open('requirements.txt') as f:
    install_requires = f.read().splitlines()


setup(name='redacted',
    long_description=README,
    packages=find_packages(exclude=exclude_dirs),
    include_package_data=True,
    scripts=[],

    install_requires=install_requires,
    dependency_links=[],
    tests_require=[],
    zip_safe=False
)

And we call python setup.py test to build our app, installing dependencies, etc.

Note that I am redacting a lot of business logic related stuff, but the flow looks like that.

TomAugspurger · 2019-07-17T21:14:13Z

So pip install -r requirements.txt works?

didip · 2019-07-17T21:24:58Z

pip install -r requirements.txt failed because pandas tried to download numpy-1.17.0rc2

didip · 2019-07-17T21:44:39Z

Should the setup.py be updated like this? Essentially check Python 2 version?

import sys

min_numpy_ver = "1.13.3"
max_numpy_ver = ""

if (sys.version_info < (3, 0)):
    max_numpy_ver = "1.16.4"

numpy_install_rule = "numpy >= {numpy_ver}".format(numpy_ver=min_numpy_ver)
if max_numpy_ver:
    numpy_install_rule += ", <= {numpy_ver}".format(numpy_ver=max_numpy_ver)

setuptools_kwargs = {
    "install_requires": [
        "python-dateutil >= 2.6.1",
        "pytz >= 2017.2",
        numpy_install_rule,
    ],
    "setup_requires": [numpy_install_rule],
    "zip_safe": False,
}

didip · 2019-07-18T18:15:08Z

The above snippet works on our internal fork of pandas. All of our Py 2 apps have correct dependencies now.
What do you guys think of updating the setup.py?

jreback · 2019-07-18T19:59:29Z

there are no more updates planned to the 0.24.x branch

closing this issue as won't fix.

didip · 2019-07-19T01:20:54Z

Why not publish 0.24.3? There is no other changes beside setup.py. This way people who are unfortunately stuck on Python 2 won't have broken deployment.

TomAugspurger · 2019-07-19T01:29:39Z

This seems more like an issue with your build process than with pandas.

…

On Thu, Jul 18, 2019 at 8:21 PM Didip Kerabat ***@***.***> wrote: Why not publish 0.24.3? There is no other changes beside setup.py. This way people who are unfortunately stuck on Python 2 won't have broken deployment. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#27435?email_source=notifications&email_token=AAKAOIVFU4FPN7BPZK7BVYDQAEJH7A5CNFSM4IETDH4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2KI57I#issuecomment-513052413>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAKAOIWG2L5M3IHDS4DGP3TQAEJH7ANCNFSM4IETDH4A> .

maxsond · 2019-08-01T16:19:57Z

I ran into this as well and figured out how to work around it without code modifications thanks to the comments here. I was originally building a Docker image from alpine:3.7, and in that container pip downloaded archive files for Numpy and Pandas rather than wheels. But when I switched my container image to python:2.7-stretch instead, then pip downloaded wheels for the versions it was supposed to and everything installed fine (I haven't tried python:2.7-alpine, though).

So although if it was up to me I'd probably apply the proposed setup.py change just for ease of use, the actual source of the problem is external to pandas. If I was going to chase this further I'd probably start with pip's source and see how it would handle running in the alpine:3.7 image to figure out why it would select archive files in that situation.

TomAugspurger · 2019-08-01T17:05:44Z

Just to summarize the workaround: if you're seeing this issue with Python 2.7, you need to ensure that you have NumPy installed in the environment pip install pandas is run.

jorisvandenbossche · 2019-09-10T10:16:51Z

Note that this is very easy to run into, simply doing

pip install pandas==0.24.2 --no-binary :all:

in a clean env with python 2.7 and latest pip gives the error (I am using --no-binary to mimic a platform that has no wheels).

Does anybody know what is actually the underlying reason, or if this has been reported to pip / setuptools?

jorisvandenbossche · 2019-09-10T10:39:39Z

OK, there is pypa/pip#6667.

So if I understand correctly, this is (within the limitations of setuptools handling of setup_requires) not an issue due to pip or how people are using it (installing should work without first needing to install the dependencies), but something we can fix on our end.

I think we should consider doing a 0.24.3 release for this.

TomAugspurger · 2019-09-10T19:40:49Z

What's the fix? Adding a pyproject.toml to 0.24.3?

jorisvandenbossche · 2019-09-11T07:00:43Z

Adding a "< 1.17" to numpy in setup_requires (and probably as well to install_requires, and probably only if you're running python 2).

That's the basically the only change they did in the "pandas27" (Tuxprogrammer#1, only need to look at changes in setup.py)

jorisvandenbossche · 2019-09-11T07:01:58Z

The proper fix is to add a pyproject.toml, but let's try to do that again on master first and not in a bug-fix release. But as long as we don't use pyproject.toml, that means we don't get the proper build isolation of pip and we need to work with legacy setuptools / setup_requires.

TomAugspurger · 2019-09-11T11:37:58Z

Adding a "< 1.17" to numpy in setup_requires (and probably as well to install_requires, and probably only if you're running python 2).

It would have to be Py2 only right? Else you can't install 0.24.2 with Python 3 and NumPy 1.17.

Is anyone actually going to do the release though? I suppose we can cut corners and not build conda packages. Not sure if we can skip building docs. But we have to build both an sdist & wheels, even though the issue is just with the sdist.

didip · 2019-09-11T18:10:23Z

@TomAugspurger I have a patch to setup.py above for both Py 2 and 3.

import sys

min_numpy_ver = "1.13.3"
max_numpy_ver = ""

if (sys.version_info < (3, 0)):
    max_numpy_ver = "1.17"

numpy_install_rule = "numpy >= {numpy_ver}".format(numpy_ver=min_numpy_ver)
if max_numpy_ver:
    numpy_install_rule += ", < {numpy_ver}".format(numpy_ver=max_numpy_ver)

setuptools_kwargs = {
    "install_requires": [
        "python-dateutil >= 2.6.1",
        "pytz >= 2017.2",
        numpy_install_rule,
    ],
    "setup_requires": [numpy_install_rule],
    "zip_safe": False,
}

jorisvandenbossche · 2019-09-11T18:15:26Z

@didip would you like to do a PR for this?

TomAugspurger · 2019-09-11T18:48:49Z

This came up in the dev call today. We're interested in fixing this, but I'm not sure if any maintainer is willing to spend too much time on it. That said, we are happy to 1. Accept a PR on the 0.24.x branch adding a max NumPy version for Python 2.7 (and a release note in 0.24.3 indicating this) 2. Make a tag and GitHub release with an sdist for 0.24.3 with just that change from 0.24.2 3. Upload binaries and an sdist to PyPI So, from anyone interested in fixing this, we're looking for a PR against 0.24.x, and someone interested in going through pieces of the release https://github.com/pandas-dev/pandas-release. Mainly 1. Building docs for 0.24.3 (we'll take care of uploading them) 2. Opening a PR on GitHub.com/macpython/pandas-wheels building wheels for 0.24.3

…

On Wed, Sep 11, 2019 at 1:15 PM Joris Van den Bossche < ***@***.***> wrote: @didip <https://github.com/didip> would you like to do a PR for this? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#27435?email_source=notifications&email_token=AAKAOIWXRC3XR2CPQEC3CGDQJEYUNA5CNFSM4IETDH4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD6PM6GA#issuecomment-530501400>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAKAOIW7KMSXOHLEUMHA3KDQJEYUNANCNFSM4IETDH4A> .

didip · 2019-09-11T23:15:57Z

@jorisvandenbossche yes I can send a PR.

jorisvandenbossche · 2019-09-13T10:15:34Z

@didip that would be very welcome!

WillAyd · 2019-10-22T01:24:43Z

At this point we don't have any further plans for a 24.x release, so unfortunately I don't think this is something we will address (if anyone disagrees feel free to reopen)

jorisvandenbossche · 2019-10-22T06:25:28Z

For people reading this: there is an open PR fixing this, but that needs some further updates to get CI passing.
If people are still interested in seeing this fixed, you can contribute to that PR: #28511

hudasami · 2020-04-03T14:57:32Z

This is how it worked for me for a similar problem:
Python Version : 2.7.12
First download .whl of compatible NumPy : https://pypi.org/project/numpy/1.12.1/#files
Install using pip install "above file"
Then download .whl of compatible pandas : https://pypi.org/project/pandas/0.20.1/#files
Install using pip install "above file"

Workaround for pandas-dev#27435

jreback closed this as completed Jul 18, 2019

jreback added the Build Library building on various platforms label Jul 18, 2019

Tuxprogrammer mentioned this issue Sep 7, 2019

Pandas27 Release v0.24.3 Tuxprogrammer/pandas#1

Open

jorisvandenbossche reopened this Sep 10, 2019

TomAugspurger mentioned this issue Sep 11, 2019

BLD: Add pyproject.toml #28374

Merged

jorisvandenbossche added this to the 0.24.3 milestone Sep 11, 2019

datapythonista mentioned this issue Sep 11, 2019

Release manager needed for pandas 0.24.3 python-sprints/pandas-mentoring#166

Open

didip mentioned this issue Sep 18, 2019

Pick and choose numpy version based on Python 2 or 3. #28511

Closed

5 tasks

TomAugspurger changed the title ~~Version 0.24.2 is suddenly Python 3 only. I was under the impression that 0.24.x supports both Python 2 and 3.~~ Cannot pandas 0.24.2 from source with Python 2.7 into an environment without NumPy Oct 15, 2019

TomAugspurger changed the title ~~Cannot pandas 0.24.2 from source with Python 2.7 into an environment without NumPy~~ Cannot install pandas 0.24.2 from source with Python 2.7 into an environment without NumPy Oct 15, 2019

WillAyd closed this as completed Oct 22, 2019

StefanRijnhart added a commit to EssentNovaTeam/pandas that referenced this issue Apr 30, 2020

[RFR] Pin numpy to 1.15.4

fe058c2

Workaround for pandas-dev#27435

StefanRijnhart added a commit to EssentNovaTeam/pandas that referenced this issue Apr 30, 2020

[RFR] Pin numpy to 1.15.4

5fdcd62

Workaround for pandas-dev#27435

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Cannot install pandas 0.24.2 from source with Python 2.7 into an environment without NumPy #27435

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Cannot install pandas 0.24.2 from source with Python 2.7 into an environment without NumPy #27435

Cannot install pandas 0.24.2 from source with Python 2.7 into an environment without NumPy #27435

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didip commented Jul 17, 2019

Code Sample, a copy-pastable example if possible

Problem description

Expected Output

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didip commented Jul 17, 2019 •

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didip commented Jul 17, 2019 •

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didip commented Jul 17, 2019 •

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didip commented Jul 18, 2019 •

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TomAugspurger commented Jul 19, 2019 via email •

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didip commented Sep 11, 2019 •

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