Wellies

A set of tools to build consistent pyflow suites.

The Wellies documentation can be found https://pyflow-wellies.readthedocs.io

Installation

with pip

First you need to assure you have ecFlow installed on your system. The simplest way is to create a conda environment. We recommend using mamba to speed up the environment creation process:

$ mamba create -c conda-forge -n wellies-env python=3.10 ecflow
$ conda activate wellies-env

Then, wellies can be installed directly with pip

$ python -m pip pyflow-wellies

from source

First, build a conda environment with all the dependencies

mamba env create -f ./environment.yml -n wellies-env
conda activate wellies-env

Then, install wellies in your environment:

pip install .

Quickstart

Create empty suite

To create an empty suite with the default wellies structure, simply run

wellies-quickstart /path/to/project -p mysuite

Once created the suite can be build this:

cd /path/to/project
./mysuite.py configs/*.yaml

which is equivalent to

./mysuite.py configs/config.yaml config/tools.yaml configs/data.yaml config/execution_contexts.yaml

You can also cherry pick your configuration files following your needs:

cd /path/to/project
./mysuite.py configs/config.yaml config/tools.yaml

Contributing

Building package

To build source distributions, build is required. With that the source distribution can be built from any environment with

git clone https://github.com/ecmwf/pyflow-wellies.git
cd pyflow-wellies
python -m build

Testing

To run tests, first install testing dependencies:

git clone https://github.com/ecmwf/pyflow-wellies.git
cd pyflow-wellies
pip install .[test]

Then to run all tests

python -m pytest

To run individual tests:

python -m pytest tests/test_data.py::test_rsync_data

Documentation

To build your own local documentation you need mkdocs and a few entra plugins. As there are many auto-generated parts in the documentation, you will need a environment with wellies and all of its dependencies installed to build the documentation. To install the documentation-only dependencies:

git clone https://github.com/ecmwf/pyflow-wellies.git
cd pyflow-wellies
pip install .[docs]

Then to build it

mkdocs build

To build and make it available in a local server

mkdocs serve