Develop Reference

Installing OpenCV fails because it cannot find "skbuild"

I have a docker image that I need to install openCV in it and from yesterday it started to fail because it cannot find the "skbuild" module:
Step 12/24 : RUN pip install opencv-python opencv-contrib-python
---> Running in a0f746a23aed
Collecting opencv-python
Downloading https://files.pythonhosted.org/packages/77/f5/49f034f8d109efcf9b7e98fbc051878b83b2f02a1c73f92bbd37f317288e/opencv-python-4.4.0.42.tar.gz (88.9MB)
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-build-cciracwm/opencv-python/setup.py", line 9, in <module>
import skbuild
ModuleNotFoundError: No module named 'skbuild'
And on the host also I cannot find that module and pip search is either return nothing or returns a server error:
sudo pip3 search skbuild
WARNING: The directory '/home/ali/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
ERROR: Exception:
Traceback (most recent call last):
File "/usr/local/lib/python3.6/dist-packages/pip/_internal/cli/base_command.py", line 216, in _main
status = self.run(options, args)
File "/usr/local/lib/python3.6/dist-packages/pip/_internal/commands/search.py", line 60, in run
pypi_hits = self.search(query, options)
File "/usr/local/lib/python3.6/dist-packages/pip/_internal/commands/search.py", line 80, in search
hits = pypi.search({'name': query, 'summary': query}, 'or')
File "/usr/lib/python3.6/xmlrpc/client.py", line 1112, in __call__
return self.__send(self.__name, args)
File "/usr/lib/python3.6/xmlrpc/client.py", line 1452, in __request
verbose=self.__verbose
File "/usr/local/lib/python3.6/dist-packages/pip/_internal/network/xmlrpc.py", line 45, in request
return self.parse_response(response.raw)
File "/usr/lib/python3.6/xmlrpc/client.py", line 1342, in parse_response
return u.close()
File "/usr/lib/python3.6/xmlrpc/client.py", line 656, in close
raise Fault(**self._stack[0])
xmlrpc.client.Fault: <Fault -32403: 'server error; service unavailable'>
Is this because their server has some problems or it is related to my pip?
Update
I tried it on different python and pip versions, python versions 3.6 and 3.7 and pip version 19.12 and 20.2.2 and 9.0.1 (the one inside image).
Update 2
I added pip install scikit-build one step before opencv installation but I get another error related to cmake:
Step 12/25 : RUN pip install scikit-build
---> Running in afe0c5c0fca0
Collecting scikit-build
Downloading https://files.pythonhosted.org/packages/78/c9/7c2c7397ea64e36ebb292446896edcdecbb8c1aa6b9a1a32f6f67984c3df/scikit_build-0.11.1-py2.py3-none-any.whl (72kB)
Collecting packaging (from scikit-build)
Downloading https://files.pythonhosted.org/packages/46/19/c5ab91b1b05cfe63cccd5cfc971db9214c6dd6ced54e33c30d5af1d2bc43/packaging-20.4-py2.py3-none-any.whl
Requirement already satisfied: wheel>=0.29.0 in /usr/lib/python3/dist-packages (from scikit-build)
Collecting distro (from scikit-build)
Downloading https://files.pythonhosted.org/packages/25/b7/b3c4270a11414cb22c6352ebc7a83aaa3712043be29daa05018fd5a5c956/distro-1.5.0-py2.py3-none-any.whl
Requirement already satisfied: setuptools>=28.0.0; python_version >= "3" in /usr/lib/python3/dist-packages (from scikit-build)
Requirement already satisfied: six in /usr/lib/python3/dist-packages (from packaging->scikit-build)
Collecting pyparsing>=2.0.2 (from packaging->scikit-build)
Downloading https://files.pythonhosted.org/packages/8a/bb/488841f56197b13700afd5658fc279a2025a39e22449b7cf29864669b15d/pyparsing-2.4.7-py2.py3-none-any.whl (67kB)
Installing collected packages: pyparsing, packaging, distro, scikit-build
Successfully installed distro-1.5.0 packaging-20.4 pyparsing-2.4.7 scikit-build-0.11.1
Removing intermediate container afe0c5c0fca0
---> 533658ddf26d
Step 13/25 : RUN pip install opencv-python opencv-contrib-python
---> Running in 0f2c03bc042a
Collecting opencv-python
Downloading https://files.pythonhosted.org/packages/77/f5/49f034f8d109efcf9b7e98fbc051878b83b2f02a1c73f92bbd37f317288e/opencv-python-4.4.0.42.tar.gz (88.9MB)
Collecting opencv-contrib-python
Downloading https://files.pythonhosted.org/packages/48/98/05bd8e00c71b66c4e7847cc051cac404191d904df58b51a7dcc3767ff747/opencv_contrib_python-4.2.0.34-cp37-cp37m-manylinux1_x86_64.whl (34.2MB)
Collecting numpy>=1.14.5 (from opencv-python)
Downloading https://files.pythonhosted.org/packages/3d/d1/90cd7e0b27ee86d77f5386d38b74520486100286d50772377791b6ef22ff/numpy-1.19.1-cp37-cp37m-manylinux1_x86_64.whl (13.4MB)
Building wheels for collected packages: opencv-python
Running setup.py bdist_wheel for opencv-python: started
Running setup.py bdist_wheel for opencv-python: finished with status 'error'
Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-w49xv99a/opencv-python/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/tmpycj03zlwpip-wheel- --python-tag cp37:
/usr/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'long_description_content_type'
warnings.warn(msg)
Traceback (most recent call last):
File "/usr/local/lib/python3.7/dist-packages/skbuild/setuptools_wrap.py", line 560, in setup
cmkr = cmaker.CMaker(cmake_executable)
File "/usr/local/lib/python3.7/dist-packages/skbuild/cmaker.py", line 95, in __init__
self.cmake_version = get_cmake_version(self.cmake_executable)
File "/usr/local/lib/python3.7/dist-packages/skbuild/cmaker.py", line 82, in get_cmake_version
"Problem with the CMake installation, aborting build. CMake executable is %s" % cmake_executable)
Problem with the CMake installation, aborting build. CMake executable is cmake
----------------------------------------
Failed building wheel for opencv-python
Running setup.py clean for opencv-python
Failed to build opencv-python
Installing collected packages: numpy, opencv-python, opencv-contrib-python
Found existing installation: numpy 1.13.3
Not uninstalling numpy at /usr/lib/python3/dist-packages, outside environment /usr
Running setup.py install for opencv-python: started
Running setup.py install for opencv-python: finished with status 'error'
Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-w49xv99a/opencv-python/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-maky1uyw-record/install-record.txt --single-version-externally-managed --compile:
/usr/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'long_description_content_type'
warnings.warn(msg)
Traceback (most recent call last):
File "/usr/local/lib/python3.7/dist-packages/skbuild/setuptools_wrap.py", line 560, in setup
cmkr = cmaker.CMaker(cmake_executable)
File "/usr/local/lib/python3.7/dist-packages/skbuild/cmaker.py", line 95, in __init__
self.cmake_version = get_cmake_version(self.cmake_executable)
File "/usr/local/lib/python3.7/dist-packages/skbuild/cmaker.py", line 82, in get_cmake_version
"Problem with the CMake installation, aborting build. CMake executable is %s" % cmake_executable)
Problem with the CMake installation, aborting build. CMake executable is cmake

If you read the opencv-python package FAQ in PyPI, it clearly provides an answer for this specific issue: you must run pip install --upgrade pip. Check pip version afterwards with pip -V.
This is because your pip is too old to understand the new manylinux2014 package format and tries to compile from source. That will also fail because pip is too old to understand how to use pyproject.toml to install build dependencies such as scikit-build.
Another issue I'm spotting is that you install both opencv-python and opencv-contrib-python. You should not do this. It's also explained in the PyPI page of the packages. Most likely you should be using just opencv-contrib-python-headless package since you are using Docker and I assume you do not use the GUI functionalities of OpenCV.

just update the pip and it will work
python -m pip install --upgrade pip

Just update pip.
If you use python3 then:
pip3 install --upgrade pip
pip3 install opencv-python

skbuild is for Scikit-build.
Install it using pip:
As for windows: pip install scikit-build
After the succesfull installation:
pip install cmake

Since I have python3 installed, I had to use
python3 -m pip install --upgrade pip

11/may/2021: faced same issue on a fresh ubuntu18 virtualbox image. this worked for me
sudo -H pip3 install --upgrade pip
pip3 install opencv-python

I also had the error, in my case when executing
python3.7 -m pip install --user opencv-python in order to get catkin_make -j8 working again in a ROS project. Thus, Docker is not needed to get the error.
First the details:
Collecting opencv-python
Cache entry deserialization failed, entry ignored
Downloading https://files.pythonhosted.org/packages/30/46/821920986c7ce5bae5518c1d490e520a9ab4cef51e3e54e35094dadf0d68/opencv-python-4.4.0.46.tar.gz (88.9MB)
100% |████████████████████████████████| 88.9MB 17kB/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-8jky5692/opencv-python/setup.py", line 9, in <module>
import skbuild
ModuleNotFoundError: No module named 'skbuild'
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-8jky5692/opencv-python/
Just documenting what I did to solve it:
python -m pip install --user opencv-python gives me /usr/bin/python: No module named pip
sudo apt install python-pip (in addition to the already existing sudo apt install python3-pip installation for pip3)
python -m pip -V now gives me pip 9.0.1 from /usr/lib/python2.7/dist-packages (python 2.7)
pip -V gives me pip 20.3.3 from /home/MYUSERNAME/.local/lib/python3.6/site-packages/pip (python 3.6) (because apt-get installs a standard 3.6, independently from existing python versions)
sudo apt-get update && sudo apt-get install cmake libopenmpi-dev python3.7-dev zlib1g-dev (not sure if this step is needed)
pip install opencv-python WORKING
catkin_make -j8 in my catkin workspace in the Python base environment WORKING
Additional hints for the cmake error that is mentioned in the Update 2
This cmake error is perhaps due to a corrupted workspace during or after catkin_make install:
I had a similar cmake error when I executed the catkin_make command inside my Python virtual environment. When I changed back to the base environment (using deactivate), catkin_make ran through. This is probably due to dependency issues in the virtual environment, perhaps also because of the version that is used when you use standard python -m that is used by some internal scripts, see one of the bullet points above. I had to assign python2.7 to the python -m pip -V pip version, probably because ROS gazebo needed 2.7.
Most promising (if this is a catkin issue): simply remove catkin and install it again, see Error 2 Invoking "make -j4 -l4" failed.
Perhaps also see Invoking "cmake" failed.

I had a similar problem and what finally worked was to change from python:3-alpine to python:3.8-slim and install python and openCV similar to what has been done in the selected answer here: Minimal SciPy Dockerfile

If non of these answers works for you try:
pip3 install opencv-python-headless

with python3 you need to use pip3

Wrong pip3 python location

I'm in Ubuntu / Linux
I try to install python3.8.2 with the latest version.
before i install i had Version 3.5.2, and that works very well.
but now pip and pip3 is the same linked location:
pip -V
pip 20.0.2 from /usr/local/lib/python3.8/site-packages/pip (python 3.8)
pip3 -V
pip 20.0.2 from /usr/local/lib/python3.8/site-packages/pip (python 3.8)
the problem is why i can't install any packages with the new version error message says:
**
sudo pip3 install nltk
**
WARNING: The directory '/home/fredy/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
Collecting nltk
Downloading nltk-3.4.5.zip (1.5 MB)
|████████████████████████████████| 1.5 MB 2.3 MB/s
ERROR: Command errored out with exit status 1:
command: /usr/local/bin/python3.8 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-d0mx8gb1/nltk/setup.py'"'"'; __file__='"'"'/tmp/pip-install-d0mx8gb1/nltk/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 /tmp/pip-install-d0mx8gb1/nltk/pip-egg-info
cwd: /tmp/pip-install-d0mx8gb1/nltk/
Complete output (11 lines):
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/home/fredy/.local/lib/python3.8/site-packages/setuptools/__init__.py", line 19, in <module>
from setuptools.dist import Distribution
File "/home/fredy/.local/lib/python3.8/site-packages/setuptools/dist.py", line 34, in <module>
from setuptools import windows_support
File "/home/fredy/.local/lib/python3.8/site-packages/setuptools/windows_support.py", line 2, in <module>
import ctypes
File "/usr/local/lib/python3.8/ctypes/__init__.py", line 7, in <module>
from _ctypes import Union, Structure, Array
ModuleNotFoundError: No module named '_ctypes'
----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
(pip list)
Package Version
---------- -------
pip 20.0.2
setuptools 46.1.1
(pip3 list)
Package Version
---------- -------
pip 20.0.2
setuptools 46.1.1
step1:
how can i come back to python3 with pip3. ?
step2:
how can i fix the error so i can work with 3.8.2 ?
What will you do ? :)
Thanks for your time !

pip install wheel randomly fails

I have a python project that I have packaged locally as a wheel, and I want to install this wheel in a virtual environment in a docker container, based off python:alpine3.7. My problem is that sometimes i works, and sometimes it fails to resolve the dependencies in the wheel, seemingly at random.
The dependencies for the wheel is:
_install_requires = [
'numpy>=1.15.0',
'pandas>=0.21.0',
'scipy>=1.0.0',
'scikit-learn>=0.19.2'
]
And my dockerfile is as follows:
FROM python:alpine3.7
# install dependencies
# the lapack package is only in the community repository
RUN echo "http://dl-4.alpinelinux.org/alpine/edge/community" >> /etc/apk/repositories
RUN apk --update add --no-cache --virtual .build-deps \
gcc \
freetype-dev
RUN apk add --update lapack-dev python py-pip python-dev &&\
apk add --update linux-headers
# Install dependencies
RUN apk add --no-cache --virtual .build-deps \
gfortran \
musl-dev \
g++ \
make &&\
ln -s /usr/include/locale.h /usr/include/xlocale.h
RUN pip install --upgrade pip && pip install virtualenv
RUN virtualenv -p python3 ./venv
ADD dist/project-as-wheel-py3-none-any.whl .
RUN . ./venv/bin/activate && pip install ./project-as-wheel-py3-none-any.whl
When building the docker container, sometimes it fails, with a typical log being:
Processing /project-as-wheel-py3-none-any.whl
Collecting scikit-learn>=0.19.2 (from project-as-wheel==0.2.6)
Downloading https://files.pythonhosted.org/packages/25/b6/454cf208be93efa3db50ce06b732328c57ede005d1dcfa71d9a1548530b0/scikit-learn-0.19.2.tar.gz (9.7MB)
Collecting pandas>=0.21.0 (from project-as-wheel==0.2.6)
Downloading https://files.pythonhosted.org/packages/3e/56/82c4d4c049294f87ebd05b65fdcbc9ed68bd23fb0a7e4469caf9a75d199f/pandas-0.23.3.tar.gz (10.5MB)
Collecting numpy>=1.15.0 (from project-as-wheel==0.2.6)
Downloading https://files.pythonhosted.org/packages/3a/20/c81632328b1a4e1db65f45c0a1350a9c5341fd4bbb8ea66cdd98da56fe2e/numpy-1.15.0.zip (4.5MB)
Collecting scipy>=1.0.0 (from project-as-wheel==0.2.6)
Downloading https://files.pythonhosted.org/packages/07/76/7e844757b9f3bf5ab9f951ccd3e4a8eed91ab8720b0aac8c2adcc2fdae9f/scipy-1.1.0.tar.gz (15.6MB)
Collecting python-dateutil>=2.5.0 (from pandas>=0.21.0->project-as-wheel==0.2.6)
Downloading https://files.pythonhosted.org/packages/cf/f5/af2b09c957ace60dcfac112b669c45c8c97e32f94aa8b56da4c6d1682825/python_dateutil-2.7.3-py2.py3-none-any.whl (211kB)
Collecting pytz>=2011k (from pandas>=0.21.0->project-as-wheel==0.2.6)
Downloading https://files.pythonhosted.org/packages/30/4e/27c34b62430286c6d59177a0842ed90dc789ce5d1ed740887653b898779a/pytz-2018.5-py2.py3-none-any.whl (510kB)
Collecting six>=1.5 (from python-dateutil>=2.5.0->pandas>=0.21.0->project-as-wheel==0.2.6)
Downloading https://files.pythonhosted.org/packages/67/4b/141a581104b1f6397bfa78ac9d43d8ad29a7ca43ea90a2d863fe3056e86a/six-1.11.0-py2.py3-none-any.whl
Building wheels for collected packages: scikit-learn, pandas, numpy, scipy
Running setup.py bdist_wheel for scikit-learn: started
Running setup.py bdist_wheel for scikit-learn: finished with status 'error'
Complete output from command /venv/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-439jjmrz/scikit-learn/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-ogmdp3dv --python-tag cp37:
Partial import of sklearn during the build process.
Traceback (most recent call last):
File "/tmp/pip-install-439jjmrz/scikit-learn/setup.py", line 168, in get_numpy_status
import numpy
ModuleNotFoundError: No module named 'numpy'
Traceback (most recent call last):
File "/tmp/pip-install-439jjmrz/scikit-learn/setup.py", line 148, in get_scipy_status
import scipy
ModuleNotFoundError: No module named 'scipy'
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-install-439jjmrz/scikit-learn/setup.py", line 269, in <module>
setup_package()
File "/tmp/pip-install-439jjmrz/scikit-learn/setup.py", line 249, in setup_package
.format(numpy_req_str, instructions))
ImportError: Numerical Python (NumPy) is not installed.
scikit-learn requires NumPy >= 1.8.2.
Installation instructions are available on the scikit-learn website: http://scikit-learn.org/stable/install.html
----------------------------------------
Failed building wheel for scikit-learn
Running setup.py clean for scikit-learn
Running setup.py bdist_wheel for pandas: started
Running setup.py bdist_wheel for pandas: still running...
Running setup.py bdist_wheel for pandas: still running...
Running setup.py bdist_wheel for pandas: still running...
Running setup.py bdist_wheel for pandas: still running...
Running setup.py bdist_wheel for pandas: still running...
Running setup.py bdist_wheel for pandas: still running...
Running setup.py bdist_wheel for pandas: finished with status 'done'
Stored in directory: /root/.cache/pip/wheels/8d/e7/58/7a882c73419e95e6709d925abb4b56c719c9be59ef826fe01c
Running setup.py bdist_wheel for numpy: started
Running setup.py bdist_wheel for numpy: still running...
Running setup.py bdist_wheel for numpy: finished with status 'done'
Stored in directory: /root/.cache/pip/wheels/77/d2/00/03180c22fc40b6f17f6a5c6ea0fa1689734a9cf4cf54179a1c
Running setup.py bdist_wheel for scipy: started
Running setup.py bdist_wheel for scipy: finished with status 'error'
Complete output from command /venv/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-439jjmrz/scipy/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-83ktidr8 --python-tag cp37:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-install-439jjmrz/scipy/setup.py", line 474, in <module>
setup_package()
File "/tmp/pip-install-439jjmrz/scipy/setup.py", line 450, in setup_package
from numpy.distutils.core import setup
ModuleNotFoundError: No module named 'numpy'
----------------------------------------
Failed building wheel for scipy
Running setup.py clean for scipy
Complete output from command /venv/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-439jjmrz/scipy/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" clean --all:
`setup.py clean` is not supported, use one of the following instead:
- `git clean -xdf` (cleans all files)
- `git clean -Xdf` (cleans all versioned files, doesn't touch
files that aren't checked into the git repo)
Add `--force` to your command to use it anyway if you must (unsupported).
----------------------------------------
Failed cleaning build dir for scipy
Successfully built pandas numpy
Failed to build scikit-learn scipy
Installing collected packages: scikit-learn, six, python-dateutil, pytz, numpy, pandas, scipy, project-as-wheel
Running setup.py install for scikit-learn: started
Running setup.py install for scikit-learn: finished with status 'error'
Complete output from command /venv/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-439jjmrz/scikit-learn/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-dwajrs1d/install-record.txt --single-version-externally-managed --compile --install-headers /venv/include/site/python3.7/scikit-learn:
Partial import of sklearn during the build process.
Traceback (most recent call last):
File "/tmp/pip-install-439jjmrz/scikit-learn/setup.py", line 168, in get_numpy_status
import numpy
ModuleNotFoundError: No module named 'numpy'
Traceback (most recent call last):
File "/tmp/pip-install-439jjmrz/scikit-learn/setup.py", line 148, in get_scipy_status
import scipy
ModuleNotFoundError: No module named 'scipy'
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-install-439jjmrz/scikit-learn/setup.py", line 269, in <module>
setup_package()
File "/tmp/pip-install-439jjmrz/scikit-learn/setup.py", line 249, in setup_package
.format(numpy_req_str, instructions))
ImportError: Numerical Python (NumPy) is not installed.
scikit-learn requires NumPy >= 1.8.2.
Installation instructions are available on the scikit-learn website: http://scikit-learn.org/stable/install.html
----------------------------------------
Command "/venv/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-439jjmrz/scikit-learn/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-dwajrs1d/install-record.txt --single-version-externally-managed --compile --install-headers /venv/include/site/python3.7/scikit-learn" failed with error code 1 in /tmp/pip-install-439jjmrz/scikit-learn/
What confuses me is that pip manages to install numpy and pandas, then fails to install scipy claiming there's "No module named 'numpy'".
Edit: A TL;DR on the log is:
pip tries to install scikit-learn, fails as numpy is not installed.
pip tries to install pandas, succeeds.
pip tries to install numpy, succeeds.
pip tries to install scipy, fail as numpy is not installed (however it was successfully installed in step 3 above!).
pip declares that it succeeded in installing pandas and numpy, but failed to install scikit-learn and scipy.
pip tries again to install scipy, fails again, complaining that numpy is not installed.
pip gives up.
Edit2: Based on Nuts suggestion I changed the relevant line in the dockerfile to
RUN . ./venv/bin/activate && pip install numpy && pip install scipy && pip install ./project-as-wheel-py3-none-any.whl
Not very satisfactory, as I can't get the version requirements out of setup.py, but it works.

Change requirements to this
_install_requires = [
'numpy>= 1.8.2',
'pandas>=0.21.0',
'scipy>=1.0.0',
'scikit-learn>=0.19.2'
]

Scikit install asks for Scipy even though it is installed

I am trying to install Scikit by running:
pip install scikit-learn
When I run it, I get this message:
Collecting scikit-learn
Using cached scikit-learn-0.18.1.tar.gz
Installing collected packages: scikit-learn
Running setup.py install for scikit-learn ... error
Complete output from command c:\python36\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\USER\\AppData\\Local\\Temp\\pip-build-3080ikpy\\scikit-learn\\setup.py';f=getatt
r(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\USER\AppData\Local\Temp\pip-04zx4iu6-record\i
nstall-record.txt --single-version-externally-managed --compile:
Partial import of sklearn during the build process.
Traceback (most recent call last):
File "C:\Users\USER\AppData\Local\Temp\pip-build-3080ikpy\scikit-learn\setup.py", line 149, in get_scipy_status
import scipy
File "c:\python36\lib\site-packages\scipy\__init__.py", line 61, in <module>
from numpy._distributor_init import NUMPY_MKL # requires numpy+mkl
ImportError: cannot import name 'NUMPY_MKL'
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "C:\Users\USER\AppData\Local\Temp\pip-build-3080ikpy\scikit-learn\setup.py", line 270, in <module>
setup_package()
File "C:\Users\USER\AppData\Local\Temp\pip-build-3080ikpy\scikit-learn\setup.py", line 260, in setup_package
.format(scipy_req_str, instructions))
ImportError: Scientific Python (SciPy) is not installed.
scikit-learn requires SciPy >= 0.9.
Installation instructions are available on the scikit-learn website: http://scikit-learn.org/stable/install.html
Which seems to ask me to install Scipy, however I already have Scipy installed, and indeed if I run
pip install scipy
I get
Requirement already satisfied: scipy in c:\python36\lib\site-packages
Requirement already satisfied: numpy>=1.8.2 in c:\python36\lib\site-packages (from scipy)

Your install shows this: from numpy._distributor_init import NUMPY_MKL # requires numpy+mkl ImportError: cannot import name 'NUMPY_MKL'
So you need to do a few things. Get the right SciPy: http://www.lfd.uci.edu/~gohlke/pythonlibs/#scipy
Get the right NumPy: http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy
Get the right SciKit Learn: http://www.lfd.uci.edu/~gohlke/pythonlibs/#sci-kitlearn
Now do pip uninstall each of your other packages. Then do pip install the wheels you downloaded at those links provided - NumPy 1st, SciPy 2nd, then Ski-kitlearn last. That should then solve your issue. Note at those links you're downloading the files with cp36‑cp36m‑win32.whlor cp36‑cp36m‑win_amd64.whl depending on if you have 32bit or 64bit Python installed.

Python script not executing (No module named APNSWrapper)

In the terminal I run this command:
Python pnot.py
I get the following error:
Traceback (most recent call last):
File "pnot.py", line 1, in <module>
from APNSWrapper import *
ImportError: No module named APNSWrapper
I have tried to install the module:
pip install APNSWrapper==0.6.1
Requirement already satisfied (use --upgrade to upgrade): APNSWrapper==0.6.1 in /Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages
Requirement already satisfied (use --upgrade to upgrade): docutils>=0.3 in /Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages (from APNSWrapper==0.6.1)
Cleaning up...
I have tried to install APNS:
Pip install apns
I get the following error:
Downloading/unpacking apns
Downloading apns-1.1.2.tar.gz
Running setup.py egg_info for package apns
Installing collected packages: apns
Running setup.py install for apns
error: /Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/__pycache__/apns.cpython-33.pyc: Permission denied
Complete output from command /Library/Frameworks/Python.framework/Versions/3.3/bin/python3.3 -c "import setuptools;__file__='/private/var/folders/8g/6w73vzqs04b6f1cq8m8pyswc0000gn/T/pip_build_samiesyed/apns/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/8g/6w73vzqs04b6f1cq8m8pyswc0000gn/T/pip-3yfn_n-record/install-record.txt --single-version-externally-managed:
running install
running build
running build_py
creating build
creating build/lib
copying apns.py -> build/lib
running install_lib
copying build/lib/apns.py -> /Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages
byte-compiling /Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/apns.py to apns.cpython-33.pyc
error: /Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/__pycache__/apns.cpython-33.pyc: Permission denied
----------------------------------------
Cleaning up...
Command /Library/Frameworks/Python.framework/Versions/3.3/bin/python3.3 -c "import setuptools;__file__='/private/var/folders/8g/6w73vzqs04b6f1cq8m8pyswc0000gn/T/pip_build_samiesyed/apns/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/8g/6w73vzqs04b6f1cq8m8pyswc0000gn/T/pip-3yfn_n-record/install-record.txt --single-version-externally-managed failed with error code 1 in /private/var/folders/8g/6w73vzqs04b6f1cq8m8pyswc0000gn/T/pip_build_s/apns
Storing complete log in /Users/s/.pip/pip.log
script code:
from APNSWrapper import *
wrapper = APNSNotificationWrapper('cert.pem', True)
for token in ['xxxxxxx']:
token = binascii.unhexlify(token)
apn = APNSNotification()
apn.token(token)
alert = APNSAlert()
alert.body('hello world')
apn.alert(alert)
apn.sound()
wrapper.append(apn)
wrapper.notify()
This is really frustrating me, not sure why the script is not executing.

Most likely pip and python point to different Python installations. One might be from package manager, one might be from the system defaults.
You can find this out by doing commands
which python
which pip
Probably pip installs packages against some other python installation you are trying to use.
The solution to the problem, no matter how it has manifested itself, is to use virtualenv environments for your Python package installations. virtualenv creates a self-contained folder containing the python interpreter and package installations, which you can wipe clean and rebuild in the case of problems.
First install virtualenv.
Then do:
virtualenv venv # Create virtualenv installation in folder called venv
source venv/bin/activate # Modify your shell and PATH to use python from venv/bin/python
pip install apns # Installs apns in venv/lib
python pnot.py # Now it runs your script using venv/bin/python interpreter
# and packages installed in venv/lib/python2.7
More information about python and virtualenv installations
http://opensourcehacker.com/2012/09/16/recommended-way-for-sudo-free-installation-of-python-software-with-virtualenv/