378 Convert source tree to python-copier-template

[rtuck99]

This moves the project to the python-copier-template project style

Fixes #378

Notes

Documentation

• Documentation from the template has been changed from .rst Restructured Text to .md Markdown style, and the folder hierarchy has been flattened to remove the separation between user and developer sections. This is probably a good move for dodal as the distinction between users and developers is somewhat blurred anyway. I have attempted to retain customisation of the documentation where appropriate.
• The API documentation should still work

Development environment

• Building standalone containers is no longer supported and relevant documentation removed, but there is now support for devcontainers (but I haven't tried it yet)

CI

• Github workflows are now refactored out into reusable workflows prefixed by an underscore _ called from the main workflows.
• Warnings in Pytest are now errors and this has resulted in a number of fixes to both production and test code:
  • Where async tasks were not awaited and outlived the lifespan of the test
  • Where file resources were not closed after being opened (notably in various logging tests)
  • Where deprecated methods were being called
  • Some warnings generated by code in our dependencies have been suppressed in pyproject.toml
• There have been some changes to linter flags in pyproject.toml which add various additional checks

Dependencies

• Nb python-copier-template has a dependency on pydantic >= 2.0 which conflicts with the rest of dodal dependencies so cannot be included in the list of development dependencies; you have to uninstall it after running it

Developer Portal

• When merged, the project should appear on the Developer Portal Software Catalog
  https://dev-portal.diamond.ac.uk

TODO

• Pypi uploads on release (The option appeared partway through the upgrade and I left at the default)

Checks for reviewer

• Would the PR title make sense to a scientist on a set of release notes
• If a new device has been added does it follow the standards
• If changing the API for a pre-existing device, ensure that any beamlines using this device have updated their Bluesky plans accordingly
• Have the connection tests for the relevant beamline(s) been run via dodal connect ${BEAMLINE}

[codecov]

Codecov Report

Attention: Patch coverage is 96.99248% with 4 lines in your changes missing coverage. Please review.

Project coverage is 94.17%. Comparing base (5ff36da) to head (473765a).
Report is 27 commits behind head on main.

Files	Patch %	Lines
src/dodal/devices/areadetector/adaravis.py	75.00%	1 Missing ⚠️
src/dodal/devices/areadetector/adsim.py	0.00%	1 Missing ⚠️
src/dodal/devices/oav/oav_parameters.py	75.00%	1 Missing ⚠️
src/dodal/utils.py	87.50%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #667      +/-   ##
==========================================
+ Coverage   93.55%   94.17%   +0.61%     
==========================================
  Files         105      108       +3     
  Lines        4114     4306     +192     
==========================================
+ Hits         3849     4055     +206     
+ Misses        265      251      -14     

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[dperl-dls]

This all looks fine, probably too complicated to inspect every individual line - since warnings are now errors I can only assume things are on average better than they were

[dperl-dls]

:(