multiple requirements*.*/environment.*

[KrisThielemans]

At present, we have multiple occurences of installation of Python dependencies:

Docker (uses mamba):

• docker/requirements.* in user_python-ubuntu.sh
• docker/requirements-service.* in user_service-ubuntu.sh
• docker/requirements.* in user_service-ubuntu.sh
• SIRF-Exercises/environment.yml or SIRF-Exercises/requirements.txt in user_service-ubuntu.sh

VM (uses system Python):

• docker/requirements.txt and docker/requirements-service.txt in INSTALL_python_packages.sh
• SIRF-Exercises/requirements.txt in UPDATE.sh

Note that our GitHub Actions workflow uses user_python-ubuntu.sh with system Python (to somewhat mimic the VM) and hence uses docker/requirements.txt, and nothing from SIRF-Exercises.

Moreover, these files are not always consistent regarding what they require, including version restrictions (e.g. docker/requirement.yml still restricts SciPy to 1.7.3.

Some of this is because SIRF-Exercises/environment.yml and requirements.txt are relatively recent. A relevant discussion is in #493.

A temporary solution which doesn't break too many things could be:

• keep docker/requirements-service.* in docker/user_service-ubuntu.sh and VirtualBox/INSTALL_python_packages.sh
• remove docker/requirements.yml and its usage
• keep docker/requirements.txt and its usage in docker/user_service-ubuntu.sh

but it doesn't seem very logical. Easiest seems to remove the SciPy version restriction, which will at least prevent some surprising dependency versions.

I also notice that SIRF-Exercises/requirements.txt installs jupyterlab, but SIRF-Exercises/environment.yml does not. Not sure what best practice for that is, but note that the VM uses requirements.txt to install jupyterlab.