Include extracted simulation metadata node for MD runs with sander

[jkalayan]

Summary

This pull request adds support for extracting and returning simulation metadata from Amber sander runs, updates dependencies, and expands test coverage for MD workflows.

Simulation Metadata Extraction and Output Enhancements

• Added a new output node simulation_metadata of type Dict to the SanderCalculation.
• Implemented helper methods in SanderParser (copy_repository_file, parse_file_contents, output_parsed_metadata) to support file handling and metadata extraction.
• Introduced a new utility module aiida_amber/utils/fileparsers.py with the extract_amber_files function, using biosim-extractor for metadata parsing.

Dependency and Compatibility Updates

• Updated Python requirement to >=3.12 and replaced MDAnalysis with biosim-extractor as a dependency in both pyproject.toml and conda-recipe/meta.yaml.
• Pinned voluptuous to a compatible version range.
• Updated matrix for Python versions in CI from 3.11-3.13 to 3.12-3.14

Testing Improvements and Coverage

• Added new tests for MD workflows, ensuring that simulation_metadata node is produced.
• Refactored test helpers for clarity and expanded test cases.
• Added a new MD input file for testing (02_md.in).

Minor Code and Input Adjustments

• Fixed input file paths and names in tests for consistency with new input files.
• Cleaned up CLI code by removing unnecessary print statements.

Impact

• These changes improve the plugin's ability to extract, validate, and expose simulation metadata from sander MD runs, modernise its dependencies, and ensure test coverage for MD workflows.

[coveralls]

Coverage Report for CI Build 36900448569

Coverage increased (+0.3%) to 81.699%

Details

• Coverage increased (+0.3%) from the base build.
• Patch coverage: No coverable lines changed in this PR.
• 12 coverage regressions across 2 files.

Uncovered Changes

No uncovered changes found.

Coverage Regressions

12 previously-covered lines in 2 files lost coverage.

File	Lines Losing Coverage	Coverage
parsers/sander.py	8	87.88%
cli/sander.py	4	85.29%

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Coverage Stats

Relevant Lines:	1295
Covered Lines:	1058
Line Coverage:	81.7%
Coverage Strength:	2.45 hits per line

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💛 - Coveralls

[jimboid]

If you address the python 3.12 being in the test matrix twice in stead of 3.12, 3.13, 3.14 then you are good to go.

[jkalayan]

Thanks @jimboid, removed duplicate Python version in CI matrix

[jimboid]

Looks good now. Please go ahead and merge.