Install.sh for pip install

[ruben]

Hi,

Can anybody show me an install.sh file that works for installing python packages?
The suggestion in the README

#!/bin/bash
python3.6 -m pip install --sytem --target . numpy
python3.6 -m pip install --sytem --target . scipy
python3.6 -m pip install --sytem --target . networkx

gives the error

End of install.sh stdout. stderr as follows:
Usage:   
  /usr/bin/python3.6 -m pip install [options] <requirement specifier> [package-index-options] ...
  /usr/bin/python3.6 -m pip install [options] -r <requirements file> [package-index-options] ...
  /usr/bin/python3.6 -m pip install [options] [-e] <vcs project url> ...
  /usr/bin/python3.6 -m pip install [options] [-e] <local project path> ...
  /usr/bin/python3.6 -m pip install [options] <archive url/path> ...

no such option: --system 

and the the example on The Halite III Server Environment also gives an error.
What is the command that does work?

[samamiller]

Try removing --system and see what happens.

no such option: --system

[ruben]

That is the example on

The Halite III Server Environment

We hope this listing of our server environment, compute and memory limits, and installed languages and libraries helps you navigate the Halite III ! Hardware The Halite III game servers are run in Google Cloud Compute Engine instances with 4 vCPU and 6 GB of memory. The servers are running Ubuntu 18.04 Bots are given 1GB of RAM and are pinned to a CPU. Threads: you may spawn additional threads, but due to the restriction of the game environment, your code will not do extra work in the…

and also gives an error

Error chmoding ./decorator.py - [Errno 1] Operation not permitted: './decorator.py'

Error chmoding ./share/doc/networkx-2.2/examples/graph/plot_roget.py - [Errno 1] Operation not permitted: './share/doc/networkx-2.2/examples/graph/plot_roget.py'

Error chmoding ./share/doc/networkx-2.2/examples/graph/plot_football.py - [Errno 1] Operation not permitted: './share/doc/networkx-2.2/examples/graph/plot_football.py'

Error chmoding ./share/doc/networkx-2.2/examples/graph/plot_erdos_renyi.py - [Errno 1] Operation not permitted: './share/doc/networkx-2.2/examples/graph/plot_erdos_renyi.py'

Error chmoding ./share/doc/networkx-2.2/examples/graph/expected_degree_sequence.py - [Errno 1] Operation not permitted: './share/doc/networkx-2.2/examples/graph/expected_degree_sequence.py'

[samamiller]

try replacing --system with --user or --system-site-packages

[ruben]

For --system-site-packages I get the same error as for --system : no such option: --system-site-packages

and for the --user option I get the following error
Exception: Traceback (most recent call last): File "/usr/local/lib/python3.6/dist-packages/pip/_internal/cli/base_command.py", line 143, in main status = self.run(options, args) File "/usr/local/lib/python3.6/dist-packages/pip/_internal/commands/install.py", line 366, in run use_user_site=options.use_user_site, File "/usr/local/lib/python3.6/dist-packages/pip/_internal/req/__init__.py", line 49, in install_given_reqs **kwargs File "/usr/local/lib/python3.6/dist-packages/pip/_internal/req/req_install.py", line 760, in install use_user_site=use_user_site, pycompile=pycompile, File "/usr/local/lib/python3.6/dist-packages/pip/_internal/req/req_install.py", line 382, in move_wheel_files warn_script_location=warn_script_location, File "/usr/local/lib/python3.6/dist-packages/pip/_internal/wheel.py", line 215, in move_wheel_files prefix=prefix, File "/usr/local/lib/python3.6/dist-packages/pip/_internal/locations.py", line 165, in distutils_scheme i.finalize_options() File "/usr/lib/python3.6/distutils/command/install.py", line 274, in finalize_options raise DistutilsOptionError("can't combine user with prefix, " distutils.errors.DistutilsOptionError: can't combine user with prefix, exec_prefix/home, or install_(plat)base

[ruben]

Btw, just found out that scipy and numpy are already installed. So, basically the question is, how do I get networkx to work?

[samamiller]

maybe try conda instead nevermind, I tried it doesn’t work even though server environment says conda is installed

#!bin/bash

conda install networkx

[ruben]

Nope…
Possible errors running install.sh. stdout output as follows: End of install.sh stdout. stderr as follows: ./install.sh: line 2: conda: command not found End of install.sh output.

[samamiller]

I just tried

#bin/bash

python3.6 -m pip install --target . networkx

and it worked for me.

[ruben]

What the ****, I thought I tried that a lot of times already.
No idea what happened there, but it works now, thanks for the help!!

[bogdandm]

Have the same issue with scikit-image.
install.sh

#!/bin/sh
python3.6 -m pip install --target . scikit-image==0.14.*

Log:

Possible errors running install.sh. stdout output as follows:
Collecting scikit-image==0.14.*
... usual pip output ...
Successfully installed PyWavelets-1.0.1 cloudpickle-0.6.1 cycler-0.10.0 dask-0.20.1 decorator-4.3.0 kiwisolver-1.0.1 matplotlib-3.0.2 networkx-2.2 numpy-1.15.4 pillow-5.3.0 pyparsing-2.3.0 python-dateutil-2.7.5 scikit-image-0.14.1 scipy-1.1.0 setuptools-40.5.0 six-1.11.0 toolz-0.9.0
End of install.sh stdout. stderr as follows:
tensorflow 1.11.0 has requirement setuptools<=39.1.0, but you'll have setuptools 40.5.0 which is incompatible.
End of install.sh output.
Error chmoding ./pyparsing.py - [Errno 1] Operation not permitted: './pyparsing.py'
...

Maybe there is something with reinstalling already preinstalled packages. The only solution atm I think is to list all dependencies manually (skipping already installed at server) and add --no-deps flag. But The Halite III Server Environment does not listed all packages (no setuptools, six, etc) so it is pretty hard to debug.

[lidavidm]

Any output on stderr is treated as a ‘failure’ - you can suppress this by redirecting stderr.

python3.6 -m pip install --target . scikit-image==0.14.* 2>/dev/null

[bogdandm]

Possible errors running install.sh. stdout output as follows:
End of install.sh stdout. stderr as follows:
./install.sh: line 2: /dev/null
: Permission denied
End of install.sh output.

did not know that you can set permssions for /dev/null

update:
Ok, this works but requires manually check dependencies.

python3.6 -m pip install --no-deps --target . scikit-image pywt

[alexander-mol]

I’m having a similar problem trying to install networkx. All of the solutions recommended above don’t work for me.

Error log:
Possible errors running install.sh. stdout output as follows: Collecting networkx Downloading https://files.pythonhosted.org/packages/f3/f4/7e20ef40b118478191cec0b58c3192f822cace858c19505c7670961b76b2/networkx-2.2.zip (1.7MB) Collecting decorator>=4.3.0 (from networkx) Downloading https://files.pythonhosted.org/packages/bc/bb/a24838832ba35baf52f32ab1a49b906b5f82fb7c76b2f6a7e35e140bac30/decorator-4.3.0-py2.py3-none-any.whl Building wheels for collected packages: networkx Running setup.py bdist_wheel for networkx: started Running setup.py bdist_wheel for networkx: finished with status ‘done’ Stored in directory: /home/bot_compilation/.cache/pip/wheels/68/f8/29/b53346a112a07d30a5a84d53f19aeadaa1a474897c0423af91 Successfully built networkx Installing collected packages: decorator, networkx Successfully installed decorator-4.3.0 networkx-2.2 End of install.sh stdout. stderr as follows: ./install.sh: line 2: $’\r’: command not found End of install.sh output.

Any help would be greatly appreciated!