The flow (flux) of climate critical gases, such as carbon dioxide (CO2), between the ocean and the atmosphere is a fundamental component of our climate and the biogeochemical development of the oceans. Therefore, the accurate calculation of these air-sea gas fluxes is critical if we are to monitor the health of our oceans and changes to our climate. FluxEngine is an open source software toolbox that allows users to easily perform calculations of air-sea gas fluxes from model, in-situ and Earth observation data. The original development and verification of the toolbox was described in a previous publication and the toolbox is already being used by scientists across multiple disciplines. The toolbox has now been considerably updated to allow its use as a Python library, to enable simplified installation, verification of its installation, to enable the handling of multiple sparingly soluble gases and greatly expanded functionality for supporting in situ dataset analyses. This new functionality for supporting in situ analyses includes user defined grids, time periods and projections, the ability to re-analyse in situ CO2 data to a common temperature dataset and the ability to easily calculate gas fluxes using in situ data from drifting buoys, fixed moorings and research cruises. Here we describe these new capabilities and then demonstrate their application through illustrative case studies. The first case study demonstrates the workflow for accurately calculating CO2 fluxes using in situ data from four research cruises from the Surface Ocean CO2 Atlas (SOCAT) database. The second case study shows that reanalysing an eight month time series of pCO2 data collected from a fixed station in the Baltic Sea can remove errors equal to 35 % of the net air-sea gas flux. The third case study demonstrates that biological surfactants could supress individual nitrous oxide sea-air gas fluxes by up to 13 %. The final case study illustrates how a dissipation-based gas transfer parameterisation can be implemented and used. The updated version of the toolbox (version 3) and all documentation is now freely available.