Installing Bokeh - Package Suggestion

ossacris · May 7, 2019, 3:17pm

Dear SWAN team,

Thanks a lot for putting in place such a great tool.

I tried to install bokeh and got the following:

bash-4.2$ pip install bokeh
Collecting bokeh
Requirement already satisfied: PyYAML>=3.10 in /cvmfs/sft.cern.ch/lcg/views/LCG_95apython3/x86_64-centos7-gcc7-opt/lib/python3.6/site-packages (from bokeh) (3.13)
Requirement already satisfied: six>=1.5.2 in /cvmfs/sft.cern.ch/lcg/views/LCG_95apython3/x86_64-centos7-gcc7-opt/lib/python3.6/site-packages (from bokeh) (1.11.0)
Requirement already satisfied: Jinja2>=2.7 in /cvmfs/sft.cern.ch/lcg/views/LCG_95apython3/x86_64-centos7-gcc7-opt/lib/python3.6/site-packages (from bokeh) (2.10)
Requirement already satisfied: tornado>=4.3 in /cvmfs/sft.cern.ch/lcg/views/LCG_95apython3/x86_64-centos7-gcc7-opt/lib/python3.6/site-packages (from bokeh) (5.1)
Requirement already satisfied: numpy>=1.7.1 in /cvmfs/sft.cern.ch/lcg/views/LCG_95apython3/x86_64-centos7-gcc7-opt/lib/python3.6/site-packages (from bokeh) (1.14.2)
Collecting packaging>=16.8 (from bokeh)
Using cached https://files.pythonhosted.org/packages/91/32/58bc30e646e55eab8b21abf89e353f59c0cc02c417e42929f4a9546e1b1d/packaging-19.0-py2.py3-none-any.whl
Requirement already satisfied: python-dateutil>=2.1 in /cvmfs/sft.cern.ch/lcg/views/LCG_95apython3/x86_64-centos7-gcc7-opt/lib/python3.6/site-packages (from bokeh) (2.7.3)
Collecting pillow>=4.0 (from bokeh)
Using cached https://files.pythonhosted.org/packages/d2/c2/f84b1e57416755e967236468dcfb0fad7fd911f707185efc4ba8834a1a94/Pillow-6.0.0-cp36-cp36m-manylinux1_x86_64.whl
Requirement already satisfied: MarkupSafe>=0.23 in /cvmfs/sft.cern.ch/lcg/views/LCG_95apython3/x86_64-centos7-gcc7-opt/lib/python3.6/site-packages (from Jinja2>=2.7->bokeh) (1.0)
Requirement already satisfied: pyparsing>=2.0.2 in /cvmfs/sft.cern.ch/lcg/views/LCG_95apython3/x86_64-centos7-gcc7-opt/lib/python3.6/site-packages (from packaging>=16.8->bokeh) (2.2.0)
py2neo 4.0.0 requires colorama, which is not installed.
py2neo 4.0.0 requires neo4j-driver>=1.6.0, which is not installed.
paramiko 2.4.0 requires bcrypt>=3.1.3, which is not installed.
paramiko 2.4.0 requires cryptography>=1.5, which is not installed.
paramiko 2.4.0 requires pyasn1>=0.1.7, which is not installed.
paramiko 2.4.0 requires pynacl>=1.0.1, which is not installed.
keras 2.2.0 has requirement keras_applications==1.0.2, but you’ll have keras-applications 1.0.6 which is incompatible.
keras 2.2.0 has requirement keras_preprocessing==1.0.1, but you’ll have keras-preprocessing 1.0.5 which is incompatible.
Installing collected packages: packaging, pillow, bokeh
Could not install packages due to an EnvironmentError: [Errno 30] Read-only file system: ‘/cvmfs/sft.cern.ch/lcg/releases/Python/3.6.5-54b64/x86_64-centos7-gcc7-opt/lib/python3.6/site-packages/packaging’

You are using pip version 10.0.1, however version 19.1.1 is available.
You should consider upgrading via the ‘pip install --upgrade pip’ command.

I wonder if you could please lend me a hand to correctly install the package.

Moreover, I think this can be a handy package for visualization and it could be included in LCG.

Again thank you very much.

Cheers!

Oscar

etejedor · May 7, 2019, 3:30pm

Dear Oscar,

Please follow the instructions here:

github.com

swan-cern/help/blob/master/advanced/install_packages.md

# Install packages in CERNBox

LCG releases on CVMFS incorporate new packages quite frequently, so if you think there is a missing package that can be 
potentially useful for a significant number of users, please [let the SWAN team know](mailto:swan-talk@cern.ch) and 
[contact the librarians directly](https://sft.its.cern.ch/jira/projects/SPI).

On the other hand, you can install packages on your CERNBox and, if necessary, configure your environment to pick them 
up in SWAN. A typical case is the installation of Python packages, which requires to run pip from a SWAN terminal:

   `pip install --user package_name`

If this fails because you are trying to install an updated version of a package that already exists in CVMFS, you will need to add the `--upgrade` flag.

Then, it would be necessary to add the local installation path to `PYTHONPATH`, by creating a bash startup script that configures that variable (don't forget to call this startup script in the session configuration menu):

    export PYTHONPATH=$CERNBOX_HOME/.local/lib/python3.5/site-packages:$PYTHONPATH

As a result of performing the aforementioned steps, the package will be installed on your CERNBox and it will be picked by 
any notebook you open after that. Since the package is on your CERNBox, it will be also available in any new session 
you start in SWAN.

You can also find them in the help panel, in SWAN. Note the required --user flag.

ossacris · May 8, 2019, 9:48am

Thanks a lot! It worked perfectly.