I am trying to add read the docs to view our github hosted project's documentation. The project is Calour - an interactive heatmap analysis program for microbiome experiments.
We have a large set of requirements for the project - some are conda installable (such as numpy, scipy, etc.) and some require pip install.
For the sphinx documentation, we need to import the calour module itself, which depends on all these dependencies.
Using the conda: section in readthedocs.yml, we manage to install the conda and pip dependencies, however, when we try to use the python section "python.setup_py_install: true" flag, read the docs does not create the conda environment and instead creates a virtual env without the conda installs.
Is there a way to run setup.py within the conda environment?