can no longer pip install numpy & scipy from source at the same time

[1fish2]

Environment

• pip version: 19.2.3
• Python version: 2.7.16
• OS: macOS 10.14.6
• pyenv 1.2.13
• setuptools 41.2.0
• wheel 0.33.6

Description

Installing numpy and scipy from source at the same time like this:

pip install numpy==1.14.6 scipy==1.0.1 --no-binary numpy,scipy --force-reinstall

worked fine recently, with these same versions of numpy and scipy, but now it produces a strange error [full error text below]:

RuntimeError: Python version >= 3.5 required.
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

Expected behavior
Successful installation of numpy and scipy.

How to Reproduce

1. Install pyenv, pyenv-virtualenv, and pyenv-virtualenvwrapper via brew.

2. Install python 2.7.16 via pyenv.

3. Install OpenBLAS 0.3.5 from source into /usr/local/opt/openblas/. Maybe that works now via brew. I don't know if openblas is needed to reproduce this problem.

4. Create ~/.numpy-site.cfg containing text that points to the openblas installation, e.g.:

   [openblas]
   libraries = openblas
   library_dirs = /usr/local/opt/openblas/lib
   include_dirs = /usr/local/opt/openblas/include
   

5. Run these commands in a new directory:

   pyenv local 2.7.16
   pyenv virtualenv issue
   pyenv local issue
   python -V   # --> Python 2.7.16
   pip install --upgrade pip setuptools virtualenv virtualenvwrapper virtualenv-clone wheel
   pip list
   
       Package           Version
       ----------------- -------
       pbr               5.4.2
       pip               19.2.3
       setuptools        41.2.0
       six               1.12.0
       stevedore         1.30.1
       virtualenv        16.7.4
       virtualenv-clone  0.5.3
       virtualenvwrapper 4.8.4
       wheel             0.33.6
   
   pip install numpy==1.14.6 scipy==1.0.1 --no-binary numpy,scipy --force-reinstall
   

6. This produces the error output, below, in about 8 seconds. That is, it fails during the preparation stage before installing anything.

7. Workaround: Install numpy then scipy:

   pip install numpy==1.14.6 --no-binary numpy --force-reinstall
   pip install scipy==1.0.1 --no-binary scipy --force-reinstall
   

8. Note: We've long needed to install numpy before the rest of requirements.txt to avoid an installation dependency error. That error message states that it can't find numpy.

The present case produces a surprising error saying that it needs Python 3.5+. I don't know why installing numpy first avoids that scipy installation error. It succeeds if I install numpy then install all requirements.txt including scipy.

Output

DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Collecting numpy==1.14.6
  Using cached https://files.pythonhosted.org/packages/86/c2/84dc6f58171bca90326f71e098438b87aa0c0d4a21bceda9caba2af6554e/numpy-1.14.6.zip
Collecting scipy==1.0.1
  Using cached https://files.pythonhosted.org/packages/bd/f4/3882758754dc083fea6ea66a6e8ceef55e7df173d06a12a074612958800f/scipy-1.0.1.tar.gz
    ERROR: Command errored out with exit status 1:
     command: /usr/local/var/pyenv/versions/2.7.16/envs/issue/bin/python2.7 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/_b/q30qg_l50b5gvqd8y4_wb9h00000gn/T/pip-install-MCTUmd/scipy/setup.py'"'"'; __file__='"'"'/private/var/folders/_b/q30qg_l50b5gvqd8y4_wb9h00000gn/T/pip-install-MCTUmd/scipy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base pip-egg-info
         cwd: /private/var/folders/_b/q30qg_l50b5gvqd8y4_wb9h00000gn/T/pip-install-MCTUmd/scipy/
    Complete output (53 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/private/var/folders/_b/q30qg_l50b5gvqd8y4_wb9h00000gn/T/pip-install-MCTUmd/scipy/setup.py", line 418, in <module>
        setup_package()
      File "/private/var/folders/_b/q30qg_l50b5gvqd8y4_wb9h00000gn/T/pip-install-MCTUmd/scipy/setup.py", line 414, in setup_package
        setup(**metadata)
      File "/usr/local/var/pyenv/versions/2.7.16/envs/issue/lib/python2.7/site-packages/setuptools/__init__.py", line 144, in setup
        _install_setup_requires(attrs)
      File "/usr/local/var/pyenv/versions/2.7.16/envs/issue/lib/python2.7/site-packages/setuptools/__init__.py", line 139, in _install_setup_requires
        dist.fetch_build_eggs(dist.setup_requires)
      File "/usr/local/var/pyenv/versions/2.7.16/envs/issue/lib/python2.7/site-packages/setuptools/dist.py", line 719, in fetch_build_eggs
        replace_conflicting=True,
      File "/usr/local/var/pyenv/versions/2.7.16/envs/issue/lib/python2.7/site-packages/pkg_resources/__init__.py", line 782, in resolve
        replace_conflicting=replace_conflicting
      File "/usr/local/var/pyenv/versions/2.7.16/envs/issue/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1065, in best_match
        return self.obtain(req, installer)
      File "/usr/local/var/pyenv/versions/2.7.16/envs/issue/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1077, in obtain
        return installer(requirement)
      File "/usr/local/var/pyenv/versions/2.7.16/envs/issue/lib/python2.7/site-packages/setuptools/dist.py", line 786, in fetch_build_egg
        return cmd.easy_install(req)
      File "/usr/local/var/pyenv/versions/2.7.16/envs/issue/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 "/usr/local/var/pyenv/versions/2.7.16/envs/issue/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 705, in install_item
        dists = self.install_eggs(spec, download, tmpdir)
      File "/usr/local/var/pyenv/versions/2.7.16/envs/issue/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 "/usr/local/var/pyenv/versions/2.7.16/envs/issue/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 "/usr/local/var/pyenv/versions/2.7.16/envs/issue/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1144, in run_setup
        run_setup(setup_script, args)
      File "/usr/local/var/pyenv/versions/2.7.16/envs/issue/lib/python2.7/site-packages/setuptools/sandbox.py", line 253, in run_setup
        raise
      File "/usr/local/var/pyenv/versions/2.7.16/lib/python2.7/contextlib.py", line 35, in __exit__
        self.gen.throw(type, value, traceback)
      File "/usr/local/var/pyenv/versions/2.7.16/envs/issue/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
        yield
      File "/usr/local/var/pyenv/versions/2.7.16/lib/python2.7/contextlib.py", line 35, in __exit__
        self.gen.throw(type, value, traceback)
      File "/usr/local/var/pyenv/versions/2.7.16/envs/issue/lib/python2.7/site-packages/setuptools/sandbox.py", line 166, in save_modules
        saved_exc.resume()
      File "/usr/local/var/pyenv/versions/2.7.16/envs/issue/lib/python2.7/site-packages/setuptools/sandbox.py", line 141, in resume
        six.reraise(type, exc, self._tb)
      File "/usr/local/var/pyenv/versions/2.7.16/envs/issue/lib/python2.7/site-packages/setuptools/sandbox.py", line 154, in save_modules
        yield saved
      File "/usr/local/var/pyenv/versions/2.7.16/envs/issue/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
        yield
      File "/usr/local/var/pyenv/versions/2.7.16/envs/issue/lib/python2.7/site-packages/setuptools/sandbox.py", line 250, in run_setup
        _execfile(setup_script, ns)
      File "/usr/local/var/pyenv/versions/2.7.16/envs/issue/lib/python2.7/site-packages/setuptools/sandbox.py", line 45, in _execfile
        exec(code, globals, locals)
      File "/var/folders/_b/q30qg_l50b5gvqd8y4_wb9h00000gn/T/easy_install-o9MJ5E/numpy-1.17.1/setup.py", line 31, in <module>
        if sys.version_info[0] < 3:
    RuntimeError: Python version >= 3.5 required.
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

About Check the logs for full command output, where to find the logs?

[pradyunsg]

Thanks for the detailed bug report @1fish2! Much appreciated!

You're hitting this issue, due to the use of setup_requires in scipy 1.0.1 -- it's trying to install numpy before allowing further execution, which doesn't work well with pip. The use of setup_requires is not compatible with pip.

where to find the logs?

The logs are the results/output of the command executed -- they're shown prior to that sentence, above the "-------"-style separator.

---

The easiest workaround here, is the one you've already found -- install numpy before scipy, so that when scipy's setup_requires looks, it would find numpy installed and not take any action.

[pradyunsg]

Relevant docs: https://pip.pypa.io/en/latest/reference/pip_install/#controlling-setup-requires

[1fish2]

Thanks, Pradyun. I appreciate the quick analysis.

Unless I'm mistaken, it used to work with the same SciPy release. Does this mean the SciPy 1.0.1 installer must've changed? I guess I should file an Issue there.

[1fish2]

* Debugging question: What changed to make this stop working? * Could pip issue a helpful error message so people could quickly figure out what to do? The current error message is a head scratcher. Between these two factors, we spent a bunch of time on it. Thanks for all the contributions to this central tool!

[1fish2]

I tested this on pip back to 8.1.2, then pip 9.0.3 with wheel back to 0.31.1, then setuptools back to 38.3.0, six back to 1.11.0, and pbr back to 4.0.2. In all cases I got RuntimeError: Python version >= 3.5 required.

I'm OK with the workaround but the error message is misleading. Also I'm sure it used to work...

[pradyunsg]

Does this mean the SciPy 1.0.1 installer must've changed?

Nope. What changed is that the newest version of numpy no longer supports Python 2.

scipy 1.0.1 likely has setup_requires="numpy" or something along those lines. Thus, when installing, easy_install will try to install the latest version that matches that requirement, which no longer supports Python 2, as the error message suggests.

easy_install does not understand newer metadata (like python_requires) which means it chooses a version that is incompatible with the running interpreter.

---

Honestly, the best option here IMO is to install numpy prior to installing scipy.

[1fish2]

Aha. Thank you for figuring that out!

It also turns out that pip install numpy==1.14.6 scipy==1.0.1 without --no-binary numpy,scipy successfully installs both and links them to the brew-installed OpenBLAS, at least on my Mac. The point of the --no-binary numpy,scipy and ~/.numpy-site.cfg was to link them to a specific OpenBLAS instead of the Accelerate framework on Mac or an old OpenBLAS on Linux. Maybe we only need to do that on some Linux machines...

[rgommers]

nice catch, thanks @pradyunsg! easy_install being invoked under the hood explains a few other issues like this we've been having.

[xavfernandez]

I don't think there is anything actionable on pip side here ?