Jenkins tests are failing because install-devel.sh creates a cgat-flow conda environment in several stages:
add cgat-core deps
add cgat-apps deps
add a minimum set of cgat-flow deps
... and more...
The problem is that conda env upgrade -f env.yml statements may modify the version of Python in cgat-flow so you right now python setup.py develop is run in the cgat-flow environment with a version of Python, and after a conda env upgrade -f env.yml, the version of Python changes and therefore cgat-core and co. are not found in the testing part of install-devel.sh
This PR tries to solve that issue by reordering the installation of conda environments and the installation of CGAT code.
Jenkins tests are failing because
install-devel.shcreates acgat-flowconda environment in several stages:The problem is that
conda env upgrade -f env.ymlstatements may modify the version of Python incgat-flowso you right nowpython setup.py developis run in thecgat-flowenvironment with a version of Python, and after aconda env upgrade -f env.yml, the version of Python changes and thereforecgat-coreand co. are not found in the testing part ofinstall-devel.shThis PR tries to solve that issue by reordering the installation of conda environments and the installation of CGAT code.