Installation and Setup

As OpenGHG Inversions is dependent on OpenGHG, please ensure that when running locally you are using Python 3.10 or later on Linux or MacOS. Please see the OpenGHG project for further installation instructions of OpenGHG and setting up an object store.

Setup a virtual environment

Check that you have Python 3.10 or greater:

python --version

(Note for Bristol ACRG group: If you are on Blue Pebble, the default anaconda module lang/python/anaconda is Python 3.9. Use module avail to list other options; lang/python/miniconda/3.10.10.cuda-12 or lang/python/miniconda/3.12.2.inc-perl-5.30.0 will work.)

Make a virtual environment

python -m venv openghg_inv

Next activate the environment

source openghg_inv/bin/activate

Installation using pip

First you’ll need to clone the repository

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

Next make sure pip and related install tools are up to date and then install OpenGHG Inversions using the editable install flag (-e)

pip install --upgrade pip setuptools wheel
pip install -e openghg_inversions

Optionally, install the developer requirements (there is more information about this in the “Contributing” section below):

pip install -r requirements-dev.txt

Verify that PyMC is using fast linear algebra libraries

At this point, run

python -c "import pymc"

This should run without printing any messages. If you receive a message about pymc or pytensor using the numpy C-API, then your inversions might run slowly because the fast linear algebra libraries used by numpy haven’t been found.

Solutions to this are: 1. try python -m pip install numpy after upgrading pip, setuptools, wheel 2. create a conda env, install numpy using conda, then use pip to upgrade pip, setuptools, wheel and install openghg_inversions