install_requires does not work when with packages installed with --no-binary :all:

[mickeyzoox]

In particular, when I use the requirements.txt:

numpy==1.13.3 --no-binary :all:
PyWavelets==0.5.2

pip install -r requirements.txt fails with:

root@6f026802d05f:/# pip install -r requirements.txt
Collecting numpy==1.13.3 (from -r requirements.txt (line 1))
  Downloading numpy-1.13.3.zip (5.0MB)
    100% |████████████████████████████████| 5.0MB 239kB/s
Collecting PyWavelets==0.5.2 (from -r requirements.txt (line 2))
  Downloading PyWavelets-0.5.2.tar.gz (4.4MB)
    100% |████████████████████████████████| 4.4MB 290kB/s
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-build-jmogkb/PyWavelets/setup.py", line 12, in <module>
        from numpy import get_include as get_numpy_include
    ImportError: No module named numpy

BUT, we see that PyWavelets 0.5.2 declares numpy with install_requires (https://github.com/PyWavelets/pywt/blob/master/setup.py#L301), and furthermore removing the --no-binary :all: modifier from numpy installation then this example works.

To reproduce (assuming you have docker):

docker run --rm -it python:2 bash
printf 'numpy==1.13.3 --no-binary :all:\nPyWavelets==0.5.2' > requirements.txt
pip install -r requirements.txt

If this is not the correct place to report this bug, could you direct me to the correct place?

[benoit-pierre]

The problem is with the PyWavelets package:

• numpy is unconditionally imported at the beginning of setup.py
• numpy is missing from setup_requires (it's present in install_requires, but that does not guarantee it will be installed before building/installing from source)

[mickeyzoox]

I see. Thanks!

[mattbennett]

I have the problem described in the issue title, unrelated to PyWavelet.

Example setup.py file and versions in this gist. Reproduced here for convenience:

from setuptools import setup, find_packages

setup(
    name='MyPackageName',
    version='1.0.0',
    url='https://github.com/mypackage.git',
    author='Author Name',
    author_email='[email protected]',
    description='Description of my package',
    packages=[],    
    install_requires=[
       'numpy >= 1.11.3 --no-binary :all:',
    ],
)

$ python
Python 3.7.4 (default, Aug 23 2019, 12:12:50)
[Clang 10.0.1 (clang-1001.0.46.4)] on darwin

$ pip --version
pip 19.2.3 from /Users/mattbennett/.virtualenvs/tmp-1e4ec19d965b2df/lib/python3.7/site-packages/pip (python 3.7)

$ python -c "import pkg_resources; print(pkg_resources.get_distribution('setuptools').version)"
41.2.0

$ pip install .
Processing /Users/mattbennett/.virtualenvs/tmp-1e4ec19d965b2df
    ERROR: Command errored out with exit status 1:
     command: /Users/mattbennett/.virtualenvs/tmp-1e4ec19d965b2df/bin/python3.7 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/jd/c8gwfl2j40990qvpg4fl476h0000gn/T/pip-req-build-w7dcmq0h/setup.py'"'"'; __file__='"'"'/private/var/folders/jd/c8gwfl2j40990qvpg4fl476h0000gn/T/pip-req-build-w7dcmq0h/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/jd/c8gwfl2j40990qvpg4fl476h0000gn/T/pip-req-build-w7dcmq0h/
    Complete output (1 lines):
    error in MyPackageName setup command: 'install_requires' must be a string or list of strings containing valid project/version requirement specifiers; Invalid requirement, parse error at "'--no-bin'"
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

$ python setup.py install
error in MyPackageName setup command: 'install_requires' must be a string or list of strings containing valid project/version requirement specifiers; Invalid requirement, parse error at "'--no-bin'"

---

I can create a requirements file with the same specification

# requirements.txt
numpy >= 1.11.3 --no-binary :all:

And this installs just fine:

$ pip install -r requirements.txt
Collecting numpy>=1.11.3 (from -r reqs.text (line 1))
  Using cached https://files.pythonhosted.org/packages/ac/36/325b27ef698684c38b1fe2e546e2e7ef9cecd7037bcdb35c87efec4356af/numpy-1.17.2.zip
Skipping bdist_wheel for numpy, due to binaries being disabled for it.
Installing collected packages: numpy
  Running setup.py install for numpy ... done
Successfully installed numpy-1.17.2

---

As a workaround I can remove the --no-binary :all: from install_requires and run the following:

pip install . --no-binary numpy

[pganssle]

@mattbennett --no-binary is a pip flag, not a valid way to specify a package. The "workaround" is the correct way to specify this.