Tool set up

The cdm tool is a pure Python package, but it has a few dependencies that rely in a specific python and module version. The tool has been tested with Python version 3.7 on Linux and Mac OS systems.

1. Clone the repository

Make sure that you have a designated folder or directory to store the module and clone the latest version via:

$ cd /to_your_designated_folder/
$ git clone git@github.com:glamod/cdm-mapper.git --branch master --single-branch cdm

Warning

Don’t forget to do it as a --single-branch cdm otherwise you wont be able to use it as a python module.

2. Install a python environment

For this you can use and install pyenv and create a new virtual environment with a the python version needed (3.7.3) using pyenv-virtualenv.

If you install pyenv and pyenv-virtualenv you can create an environment with a fix python version:

$ pyenv install 3.7.3
$ pyenv virtualenv 3.7.3 cdm_mapper_env
$ pyenv activate cdm_mapper_env

As another option you can use conda. See the conda docs for more information about how to create an environment from the command line.

Or you can do what I usually do (much faster), install mamba.

Warning

Make sure you activate your environment before continuing

3. Install dependencies

If you used pyenv for your environment, once activated you can install the dependencies using pip:

$ pip install dask==1.1.4 datashader==0.7.0 matplotlib==3.0.3 numpy==1.16.5 pandas==0.24.2 requests==2.21.0 xarray==0.12.1 msgpack==0.5.6 scipy==1.6.0
$ pip install cloudpickle

Check the conda or mamba documentation to install dependencies via those tools.

Warning

The pandas version and the ``cloudpickle`` library are particularly important since these libraries need to be compatible with the way of importing the json module used in the code.

4. Install mdf_reader toolbox

When installing the mdf_reader toolbox you don’t need to create a new python or conda environment, just install the tool by cloning the repository in the same directory where you have stored the cdm toolbox via:

$ cd /to_your_designated_folder/
$ git clone git@github.com:glamod/mdf_reader.git

Warning

Make sure that both repositories cdm and mdf_reader are stored in the same directory

5. Optional step: install jupyter notebooks

Install jupyter notebook and IPython for an easy overview of the tool and to make use of the tutorials under ~/cdm/docs/notebooks:

$ pip install notebook
$ pip install ipykernel

Check the libraries documentation in the links above to install them via conda or mamba.

Add a new kernel to load your notebooks with the right environment (cdm_mapper_env) run:

$ python -m ipykernel install --user --name=cdm_mapper_env
$ jupyter notebook

When you open the notebook, make sure you select the kernel or environment with the name cdm_mapper_env. You can also test the notebook by adding and executing the following code in a jupyter-notebook cell:

from platform import python_version
import sys
print(python_version())
print(sys.executable)
print(sys.version)
print(sys.version_info)

And you should see the following information for your cdm_mapper_env:

/Users/username/.pyenv/versions/3.7.3/envs/cdm_mapper_env/bin/python
3.7.3 (default, Feb  4 2021, 14:32:54)
[Clang 12.0.0 (clang-1200.0.32.28)]
sys.version_info(major=3, minor=7, micro=3, releaselevel='final', serial=0)