INRA-Tropolink

WIKI

INRA Tropolink project : A web-tool to infer graphs of tropospheric connectivity from archived meteorological data.

First clone

Add the ForgeMIA upstream:

git remote add forgemia git@forgemia.inra.fr:tropo-group/notebook.git

And don't forget to also push your code on it:

git push forgemia

Run

Update the tropolink_env Conda environment (if dependencies have changed):

sudo /opt/tljh/user/bin/conda env update -n tropolink_env --file tropolink_env.yml

Activate the conda environnement :

conda activate tropolink_env

Trust the notebook, so that it can be run automatically:

jupyter trust Connectivities\ Analysis.ipynb

Launch Jupyter :

jupyter notebook

Run all cells :

In the notebook menu, select Kernel > Restart and Run All.

Quit

Close the conda environnement :

conda deactivate

Developper's documentation

Tropolink Design documentation

API configuration

The urls used to get connectivities can be configured in the file nbconnectivity/settings.py.

Admin documentation

To install TLJH or upgrade an existing installation, run:

# curl -L https://tljh.jupyter.org/bootstrap.py | python3 - --admin makina

To add new admin users from the CLI:

# useradd -m -u 21XXX -s /bin/bash -G jupyterhub-admins,jupyterhub-users jupyter-$USER 
# passwd jupyter-$USER
# tljh-config add-item users.admin makina
# tljh-config reload

Deploiement

1. Se connecter au serveur du projet : ssh -J rde@ssh-proxy tropolink3@staging-tropolink.fr

2. cd notebook : dépôt git synchronisé sur forgemia et notre gitlab

3. git status pour vérifier qu'il n'y a pas de modif en local puis git pull pour mettre à jour le contenu

4. Si besoin de mettre à jour le noyau, regénérer le noyau conda:

# sudo /opt/tljh/user/bin/conda env update -n tropolink_env --file tropolink_env.yml

5. Si besoin d'activer des extensions Jupyter requises :

# /opt/tljh/user/bin/pip install jupyter_contrib_nbextensions
# /opt/tljh/user/bin/jupyter contrib nbextension install --sys-prefix
# /opt/tljh/user/bin/jupyter nbextension enable init_cell/main --sys-prefix
# /opt/tljh/user/bin/jupyter nbextension enable hide_input/main --sys-prefix