Upgrade to python 3.12

[MikeSullivan7]

Issue

Closes #2267
Requires #2280 and #2291

Description

This PR upgrades MI to be built with Python 3.12, the latest version of Python.
This PR will need to be rebased after #2280 is merged!

Testing

make check
make test-system

Acceptance Criteria

Run all tests and check that MI runs as normal without any issues or warnings, this transition should be seemless.

Documentation

Release note

[coveralls]

coverage: 74.316% (+1.3%) from 73.051%
when pulling 3b21da6 on 2267_python_3.12_upgrade
into 4370485 on main.

[MikeSullivan7]

In the Github Actions we get the following error

Run python -m pytest --cov --cov-report=xml -n auto -o log_cli=true --ignore=mantidimaging/eyes_tests --durations=10
##[debug]C:\Program Files\Git\bin\bash.EXE -l D:\a\_temp\d44cfc21-81ce-4ac6-89d0-faf82ec53d38.sh
C:\Users\runneradmin\miniconda3\envs\mantidimaging-dev\Lib\site-packages\_pytest\config\__init__.py:331: PluggyTeardownRaisedWarning: A plugin raised an exception during an old-style hookwrapper teardown.
Plugin: helpconfig, Hook: pytest_cmdline_parse
ConftestImportFailure: ImportError: DLL load failed while importing astra_c: The specified module could not be found. (from D:\a\mantidimaging\mantidimaging\conftest.py)
For more information see https://pluggy.readthedocs.io/en/stable/api_reference.html#pluggy.PluggyTeardownRaisedWarning
  config = pluginmanager.hook.pytest_cmdline_parse(
ImportError while loading conftest 'D:\a\mantidimaging\mantidimaging\conftest.py'.
conftest.py:11: in <module>
    from mantidimaging.core.utility.leak_tracker import leak_tracker
mantidimaging\core\__init__.py:5: in <module>
    from . import operations, io, parallel, utility  # noqa: F401
mantidimaging\core\io\__init__.py:5: in <module>
    from . import (  # noqa: F401
mantidimaging\core\io\saver.py:[20](https://github.com/mantidproject/mantidimaging/actions/runs/10096299143/job/27918470051#step:12:21): in <module>
    from ..operations.rescale import RescaleFilter
mantidimaging\core\operations\rescale\__init__.py:5: in <module>
    from .rescale import RescaleFilter  # noqa:F401
mantidimaging\core\operations\rescale\rescale.py:11: in <module>
    from mantidimaging.gui.utility.qt_helpers import Type
mantidimaging\gui\__init__.py:5: in <module>
    from .gui import execute  # noqa: F401  # noqa:F8[21](https://github.com/mantidproject/mantidimaging/actions/runs/10096299143/job/27918470051#step:12:22)
mantidimaging\gui\gui.py:13: in <module>
    from mantidimaging.gui.windows.main import MainWindowView
mantidimaging\gui\windows\main\__init__.py:6: in <module>
    from .view import MainWindowView  # noqa: F401
mantidimaging\gui\windows\main\view.py:39: in <module>
    from mantidimaging.gui.windows.recon import ReconstructWindowView
mantidimaging\gui\windows\recon\__init__.py:5: in <module>
    from .model import ReconstructWindowModel  # noqa: F401
mantidimaging\gui\windows\recon\model.py:12: in <module>
    from mantidimaging.core.reconstruct import get_reconstructor_for
mantidimaging\core\reconstruct\__init__.py:7: in <module>
    from .astra_recon import AstraRecon
mantidimaging\core\reconstruct\astra_recon.py:10: in <module>
    import astra
C:\Users\runneradmin\miniconda3\envs\mantidimaging-dev\Lib\site-packages\astra\__init__.py:[26](https://github.com/mantidproject/mantidimaging/actions/runs/10096299143/job/27918470051#step:12:27): in <module>
    from . import matlab as m
C:\Users\runneradmin\miniconda3\envs\mantidimaging-dev\Lib\site-packages\astra\matlab.py:38: in <module>
    from . import astra_c
E   ImportError: DLL load failed while importing astra_c: The specified module could not be found.

However when looking in C:/Users/runneradmin/miniconda3/envs/mantidimaging-dev/Lib/site-packages/astra we have the following files:

__init__.py
__pycache__
algorithm.py
algorithm_c.cp311-win_amd64.pyd
astra.py
astra_c.cp311-win_amd64.pyd
creators.py
data2d.py
data2d_c.cp311-win_amd64.pyd
data3d.py
data3d_c.cp311-win_amd64.pyd
experimental.cp311-win_amd64.pyd
extrautils.cp311-win_amd64.pyd
functions.py
log.py
log_c.cp311-win_amd64.pyd
matlab.py
matrix.py
matrix_c.cp311-win_amd64.pyd
optomo.py
plugin.py
plugin_c.cp311-win_amd64.pyd
plugins
projector.py
projector_c.cp311-win_amd64.pyd
projector3d.py
projector3d_c.cp311-win_amd64.pyd
pythonutils.py
tests.py
utils.cp311-win_amd64.pyd

Where we can see the file astra_c.cp311-win_amd64.pyd exists, so it is confusing as to why we get the import error.....

[samtygier-stfc]

Does it make any difference if you remove astra-toolbox from the channels in the environment files?

[MikeSullivan7]

Does it make any difference if you remove astra-toolbox from the channels in the environment files?

I tried this locally in environment-dev.yaml and it didn't seem to have much of an effect, but will try again to make sure as I may have changed other things since then

[MikeSullivan7]

So after running pytest on a fresh install of Windows 10 on a virtual machine, I get the same error as the Github actions:

Could potentially be Cuda related then

[MikeSullivan7]

So in version Astra 2.0.0 there is an astra_c.py file which is not in version 2.1.0, which may be causing the problems

[MikeSullivan7]

I noticed that between the package builds on my machine and a fresh install, some of the astra dependencies are different builds, i.e. for libastra we have build cuda11.2hb8489e9_0 on a fresh install vs cuda11.8hb8fb34d_111 on my local machine.

When attempting to match the builds on the virtual machine, I get this:

Therefore it seems that it is not possible to run this version of Astra unless you have a full CUDA install and therefore need a GPU.

NOTE: This is also the case for python 3.10

[MikeSullivan7]

Ive set the env variable at the stage just before building the dev environment and it seems to do the job!

[samtygier-stfc]

Looks good from some quick local testing, but lets wait until the pyinstaller thing is understood.

[MikeSullivan7]

PyInstaller now builds without CUDA errors, worked out that some files were being missed in cupy_backends after the cupy upgrade, so these have now been added explicitly as a submodule in PackagingWithPyInstaller.py :)

[samtygier-stfc]

Looks good. I've run system and unit tests locally. Run operations and reconstruction loclaly. Built a pyinstaller and tested it.