Problem with pip-installing from requirements.txt about scikit-fmm HOT 11 CLOSED

What FMM based app are you trying to build?

scikit-fmm builds on TravisCI in my experience. When I last looked into it you had to do some stuff to get numpy installed onto the TravisCI build VMs. see: https://github.com/scikit-fmm/scikit-fmm/blob/master/.travis.yml

Hope that helps.

from scikit-fmm.

I am going to close this issue because it seems this is not an issue with scikit-fmm. Reopen if there is still a problem.

from scikit-fmm.

It's a Gradle-based because part of it uses Java and Kotlin. My .travis.yml is

language: java

jdk:
- oraclejdk8
python: '3.6'

cache:
  directories:
  - .gradle

install:
- pyenv shell 3.6
- pip3 install --user -r requirements.txt

script:
- whoami
- gradle build -q

so I actually only use pip in the VM.

The full requirements.txt is

numpy>=1.14
numba>=0.35
requests>=2.14
scikit-fmm==0.0.9
websockets==4.0.1
pillow==5.0.0
matplotlib==2.1.0

from scikit-fmm.

I just tried building in a locally created virtual environment (again, pip only) on my machine. I get the same traceback when it tried to build scikit-fmm.

I'm looking at a way this can be fixed

from scikit-fmm.

The issue still persists. You can clearly see the bug in setup.py from numpy.distutils.core import setup. The import will fail during running setup.py (!) which is needed to determine what to install. pip would not know that numpy is required because it would fail on parsing setup.py. The solution seem to be specifying build dependencies (see discussion here)

from scikit-fmm.

Thanks for the message. I thought this was fixed by @ManifoldFR in 3053a97 but I guess not? I will reopen the issue. Can you give more context of how the problem is occurring? (Python version, scikit-fmm version, os, commands, specific error messages, etc.) It would be great if you could make a PR that addresses the problem.

from scikit-fmm.

@jkfurtney sure!
python2.7 (pip 19.2.1) or 3.6 (pip 8.1.1)
You can see the error, but I'm confused now - it seems that at the end installation was successful and I can import it. I'm trying to reproduce the case when it failed for good but I already went through multiple pip versions and I don't remember which one I used before

virtualenv venv 
source venv/bin/activate
printf "numpy==1.16.0\nscikit-fmm==2019.1.30\n" > requirements.txt
pip install -r requirements.txt

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==1.16.0 (from -r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/9f/85/163127d3fb0573deb9eca947cfc73aa3618eaaf8656501460574471d114a/numpy-1.16.0-cp27-cp27mu-manylinux1_x86_64.whl (17.0MB)
     |████████████████████████████████| 17.0MB 13.0MB/s 
Collecting scikit-fmm==2019.1.30 (from -r requirements.txt (line 2))
  Downloading https://files.pythonhosted.org/packages/9a/a5/2bacbdbbde95598fdc36ded7968a2e590f51fcfcd81a68e5c783db131d80/scikit-fmm-2019.1.30.tar.gz (418kB)
     |████████████████████████████████| 419kB 25.5MB/s 
Building wheels for collected packages: scikit-fmm
  Building wheel for scikit-fmm (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/sinyavskiy/venv/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-xjZvl8/scikit-fmm/setup.py'"'"'; __file__='"'"'/tmp/pip-install-xjZvl8/scikit-fmm/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-eIL7fF --python-tag cp27
       cwd: /tmp/pip-install-xjZvl8/scikit-fmm/
  Complete output (7 lines):
  Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "/tmp/pip-install-xjZvl8/scikit-fmm/setup.py", line 121, in <module>
      setup_package()
    File "/tmp/pip-install-xjZvl8/scikit-fmm/setup.py", line 115, in setup_package
      from numpy.distutils.core import setup
  ImportError: No module named numpy.distutils.core
  ----------------------------------------
  ERROR: Failed building wheel for scikit-fmm
  Running setup.py clean for scikit-fmm
Failed to build scikit-fmm
Installing collected packages: numpy, scikit-fmm
  Running setup.py install for scikit-fmm ... done
Successfully installed numpy-1.16.0 scikit-fmm-2019.1.30

Even if it succeeds in the end, I think error message should not be there anyway

from scikit-fmm.

Isn't numpy.distutils.core installed along with NumPy?

from scikit-fmm.

Isn't numpy.distutils.core installed along with NumPy?

yes, I think its included into a standard numpy packaging

from scikit-fmm.

Is this still a problem? I will close this for now.

from scikit-fmm.

@jkfurtney, unfortunately I'm still seeing this with version 2019.1.30 of scikit-fmm. It tries to build the wheel before numpy is installed.

I'm on Python 3.7.9 and pip 20.3.1 on MacOS 11, and for me this can be reproduced easily on a fresh Python installation/virtualenv:

$ pip install wheel
$ pip install scikit-fmm==2019.1.30 numpy==1.15.0

This will give the above error (seen in #23 (comment)). The installation will then continue successfully, but with this deprecation warning:

DEPRECATION: scikit-fmm was installed using the legacy 'setup.py install' method, because a wheel could not be built for it. pip 21.0 will remove support for this functionality. A possible replacement is to fix the wheel build issue reported above. You can find discussion regarding this at pypa/pip#8368.

from scikit-fmm.