openghg 0.3.1

OpenGHG - a cloud platform for greenhouse gas data analysis and collaboration

OpenGHG is a project based on the prototype HUGS platform which aims to be a platform for collaboration and analysis of greenhouse gas (GHG) data.

The platform will be built on open-source technologies and will allow researchers to collaborate on large datasets by harnessing the power and scalability of the cloud.

For more information please see our documentation.

Cloud

You can login to our OpenGHG Cloud JupyterHub and use OpenGHG in the cloud. This will allow you to use the full power of OpenGHG from your local device. Once you're logged in please checkout some of our tutorials to help you get started.

Install locally

To run OpenGHG locally you'll need Python 3.7 or later on Linux or MacOS, we don't currently support Windows.

Install OpenGHG

You can install OpenGHG using pip or conda, though conda allows the complete functionality to be accessed at once.

If using pip or conda, we recommend creating a virtual environment first and installing openghg into this environment.

pip

To use pip, first create a virtual environment using the following

$ python -m venv openghg_env

Then activate the environment

$ source openghg_env/bin/activate

Then install OpenGHG

$ pip install openghg

This will allow the majority of functionality to be accessed but see below for more details on accessing optional regridding (tranform) functionality introduced in v.x.x.

Additional functionality

Some optional functionality is available within OpenGHG to allow for multi-dimensional regridding of map data (openghg.tranform sub-module). This makes use of the xesmf package. This Python library is built upon underlying FORTRAN and C libraries (ESMF) which cannot be installed directly within a Python virtual environment.

To use this functionality these libraries must be installed separately. One suggestion for how to do this is as follows.

If still within the created virtual environment, exit this using

$ deactivate

We will need to create a conda environment to contain just the additional C and FORTRAN libraries necessary for the xesmf module (and dependencies) to run. This can be done by installing the esmf package using conda

$ conda create --name openghg_add esmf -c conda-forge

Then activate the Python virtual environment in the same way as above:

$ source openghg_env/bin/activate

Run the following lines to link the Python virtual environment to the installed dependencies, doing so by installing the esmpy Python wrapper (a dependency of xesmf):

$ ESMFVERSION='v'$(conda list -n openghg_add esmf | tail -n1 | awk '{print $2}')
$ export ESMFMKFILE="$(conda env list | grep openghg_add | awk '{print $2}')/lib/esmf.mk"
$ pip install "git+https://github.com/esmf-org/esmf.git@${ESMFVERSION}#subdirectory=src/addon/ESMPy/"

Note: The pip install command above for esmf module may produce an AttributeError. At present (19/07/2022) an error of this type is expected and may not mean the xesmf module cannot be installed. This error will be fixed if PR #49 is merged.

Now the dependencies have all been installed, the xesmf library can be installed within the virtual environment

$ pip install xesmf

conda

Create a conda environment called openghg_env and enable the use of conda-forge

$ conda create --name openghg_env

Activate the environment

$ conda activate openghg_env

Then install OpenGHG and its dependencies from our conda channel and conda-forge.

$ conda install --channel conda-forge --channel openghg openghg

Note: the xesmf library is already incorporated into the conda install from vx.x onwards and so does not need to be installed separately.

Set environment variable

OpenGHG expects an environment variable OPENGHG_PATH to be set. This tells OpenGHG where to place the local object store.

Please add the following line to your shell profile (~/.bashrc, ~/.profile, ...).

OPENGHG_PATH=/your/selected/path

We recommend a path such as /home/your_username/openghg_store.

Developers

If you'd like to contribute to OpenGHG please see the contributing section of our documentation. If you'd like to take a look at the source and run the tests follow the steps below.

Clone

$ git clone https://github.com/openghg/openghg.git

Install dependencies

We recommend you create a virtual environment first

$ python -m venv openghg_env

Then activate the environment

$ source openghg_env/bin/activate

Then install the dependencies

$ cd openghg
$ pip install --upgrade pip wheel
$ pip install -r requirements-dev.txt

See above for additional steps to install the xesmf library as required.

Run the tests

To run the tests

$ pytest -v tests/

NOTE: Some of the tests require the udunits2 library to be installed.

The udunits package is not pip installable so we've added a separate flag to specifically run these tests. If you're on Debian / Ubuntu you can do

$ sudo apt-get install libudunits2-0

You can then run the cfchecks marked tests using

$ pytest -v --run-cfchecks tests/

If all the tests pass then you're good to go. If they don't please open an issue and let us know some details about your setup.

Documentation

For further documentation and tutorials please visit our documentation.

Community

If you'd like further help or would like to talk to one of the developers of this project, please join our Gitter at gitter.im/openghg/lobby.