Standardizing Python project setup using uv

[mauvais2]

Build and packaging

• Switched Python dependency and virtual environment management to uv, which makes environment setup faster and more consistent across local development and CI.
• Added pyproject.toml support for platform-specific installs on cpu, cuda, rocm, and mchip, giving us a cleaner and more maintainable way to manage platform differences.
• Updated packaging configuration so the project is ready for publishing to PyPI, which will make installation easier for users and reduce the need for local builds.
• Added Dockerfiles for cpu, cuda, rocm, and mchip to support reproducible container builds across supported platforms.

CI and testing

• Updated CI to use the CPU build configuration defined in pyproject.toml, helping keep CI aligned with the new environment and packaging setup.
• Refactored the CI pipeline to remove duplicate jobs and replace them with reusable common jobs, which reduces maintenance and makes the pipeline easier to extend.
• Added pytest profiling to surface the longest-running tests, making it easier to spot bottlenecks and improve test suite performance over time.
• Updated affected source and test code to work with the new dependency and build structure.

Documentation and release workflow

• Updated the README and Read the Docs documentation with instructions for using uv and for installing atomsci-ampl from PyPI.
• Updated the Confluence release documentation to include the package publish package step.
• Defined the publish pipeline and left it manual for now, so the workflow is in place while still allowing controlled rollout.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

@@            Coverage Diff             @@
##            1.8.0     #429      +/-   ##
==========================================
+ Coverage   51.61%   52.90%   +1.29%     
==========================================
  Files          38       38              
  Lines       11982    12205     +223     
==========================================
+ Hits         6184     6457     +273     
+ Misses       5798     5748      -50     

Flag	Coverage Δ
unittests	52.90% <100.00%> (+1.29%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
atomsci/ddm/__init__.py	100.00% <ø> (ø)
atomsci/ddm/pipeline/model_wrapper.py	68.73% <100.00%> (-0.13%)	⬇️
atomsci/ddm/pipeline/parameter_parser.py	92.52% <100.00%> (-0.09%)	⬇️

... and 3 files with indirect coverage changes

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