Update python to 3.9

[samtygier-stfc]

Issue

Closes #1341

Description

Update python to 3.9

No code changes needed

Testing & Acceptance Criteria

Tests should pass.

python ./setup.py create_dev_env

You might need to update the precommit hooks for the new python version:
pre-commit install

I have tested installing and running locally (linux) and IDAaaS.

Documentation

Release notes

[rbauststfc]

Have you been able to create the environment on Windows? It failed for me with error:

- nothing provides openssl >=1.1.1m,<1.1.2a needed by python-3.9.10-h6cc024a_1

I haven't had a look through to try and narrow down where the problem might be, but let me know if it would help for me to take a look.

Everything seems good on Linux, though.

[samtygier-stfc]

I'd not tested on windows. I'll see if I can work out the issue.

[samtygier-stfc]

The clash seems to be with astra-toolbox. On windows an environment with just python=3.8.* and astra-toolbox=1.9.9 is fine. But with python=3.9.* and astra-toolbox=1.9.9 gives the openssl error.

python=3.9.* and astra-toolbox=2.0.0 also works.

We'll need to wait for a cil-astra which allows astra-toolbox=2.0.0

TomographicImaging/CIL-ASTRA#104

[coveralls]

Coverage remained the same at 76.602% when pulling f88c6f4 on 1341-update-python into c82ef74 on main.

[samtygier-stfc]

CIL 21.4.0 and Astra 2.0 allow the all the conda packages to resolve on WIndows.

Next issue is installing pyqt with pip. Looks like it is attempting to build so missing a wheel?

[samtygier-stfc]

Updating the PyQt version fixes install but changes the spacing is several layouts. Looks like it is just removing unneeded white space, so an improvement.

[samtygier-stfc]

Splitting out the CIL and Qt parts into #1449 and #1452

[samtygier-stfc]

During testing I spotted some new warnings, but they are due to TomographicImaging/CIL#1253 so don't need to block this PR.