Automatically set AMBERHOME so Amber executables produce output files

[jkalayan]

Summary

This PR updates the way AmberTools executables are configured and tested in both the main code and the tests. The main improvement is that the AMBERHOME environment variable is now set automatically based on the location of each Amber executable. This results in aiida_* executables and tests run locally to now return outputs/pass.

AmberTools environment configuration:

• In aiida_amber/helpers.py, the get_code function now sets the AMBERHOME environment variable automatically.

Test fixtures improvements:

• In conftest.py, all code fixtures for AmberTools executables (sander, tleap, antechamber, pdb4amber, parmed) now:
  • Use shutil.which to determine the absolute path to each executable.
  • Set the AMBERHOME environment variable dynamically for each fixture, mirroring the change in the main code.

• Include in-process cli tests alongside sub-process tests to improve coverage.

Impact

• These changes allow local AmberTools executables to be found, run to completion and return output files as expected.

[coveralls]

Coverage Report for CI Build 36761563662

Coverage increased (+24.4%) to 81.405%

Details

• Coverage increased (+24.4%) from the base build.
• Patch coverage: No coverable lines changed in this PR.
• 5 coverage regressions across 1 file.

Uncovered Changes

No uncovered changes found.

Coverage Regressions

5 previously-covered lines in 1 file lost coverage.

File	Lines Losing Coverage	Coverage
helpers.py	5	68.57%

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Coverage Stats

Relevant Lines:	1253
Covered Lines:	1020
Line Coverage:	81.4%
Coverage Strength:	4.88 hits per line

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💛 - Coveralls

[harryswift01]

This looks like a good fix that will ensure that the aiida_* executables can locate their AMBERHOME data files and reliably produce output. Happy to see this merged in.