Jupyter Guide to Climate Data

Jupyter Books with notebook examples for using climate data

Documentation written with Jupyter Book: https://jupyterbook.org/en/stable/intro.html

Other book examples: https://github.com/bvanderlei/jupyter-guide-to-linear-algebra

Chat: https://gitter.im/ENES-CDI/enes-summer-school

Discussions: https://github.com/IS-ENES-Data/summer-school-2022/discussions/

Material on GitHub: https://github.com/IS-ENES-Data/summer-school-2022

Build from Source

Get Source:

git clone https://github.com/cehbrecht/jupyter-guide-to-climate-data.git

cd jupyter-guide-to-climate-data

Make conda env:

mamba env create
conda activate climate-guide

Build book:

jupyter-book build --all .

... or use make:

make clean build

Show build pages:

firefox _build/html/index.html

Publish book to gh-pages

https://jupyterbook.org/en/stable/publish/gh-pages.html

ghp-import -n -p -f _build/html

... or use make:

make publish

Freeze conda environment

Update conda spec list on levante:

conda list -n summerschool_2022 --explicit > spec-list.txt

You can use this spec-list.txt to create a new environment:

conda env create -f spec-list.txt

Working on Levante at DKRZ

Login to levante ... or use terminal in jupyter.

Get source:

git clone https://github.com/cehbrecht/jupyter-guide-to-climate-data.git

cd jupyter-guide-to-climate-data

To use the jupyter kernel we provide, create a link as follows:

ln -s /work/bm0021/conda-envs-public/kernels/share/jupyter/kernels/summerschool_2022 ${HOME}/.local/share/jupyter/kernels/summerschool_2022

Then, open notebooks in Jupyter and choose kernel "summerschool_2022"

Alternatively, to create your own conda environment and jupyter kernel, follow the steps below:

Init conda:

conda init bash
source ~/.bashrc

Create conda env:

mamba env create

conda activate summerschool_2022

Make kernel:

python -m ipykernel install --user --name="summerschool_2022" --display-name="summerschool_2022"

Set environment variables using one of the following options:

• Option 1) Always add and execute a cell at the top of the current jupyter notebook containing the following code:

  # Set necessary environment variables:
  import conda, os
  conda_file_dir = conda.__file__
  conda_dir = conda_file_dir.split('lib')[0]
  proj_lib = os.path.join(os.path.join(conda_dir, 'share'), 'proj')
  os.environ["PROJ_LIB"] = proj_lib
  os.environ['PATH'] += os.pathsep + os.path.join(conda_dir, 'bin')

• Option 2) Preferably, add the environment variable definition to the kernel.json of your just created jupyter kernel: kernel.json per default located at $HOME/.local/share/jupyter/kernels/summerschool_2022/kernel.json Add the "env" section below:

  {
   "argv": [
    ...
   ],
   "env":
   {
    "PATH":"${PATH}:${HOME}/.conda/envs/summerschool_2022/bin",
    "PROJ_LIB":"${HOME}/.conda/envs/summerschool_2022/share/proj"
   },
   "display_name": "summerschool_2022",
   ...
  }
  

Open notebooks in Jupyter and choose kernel "summerschool_2022"