test: run calc scripts

[kzsigmond]

This pull request introduces several improvements and bug fixes to the PySCF and Gaussian calculation scripts in the fanpy package, focusing on argument parsing, default parameter handling, and test coverage. The main changes include standardizing argument types and defaults, improving script generation for PySCF workflows, and adding comprehensive tests for these scripts.

Argument parsing and default handling improvements:

• Updated the run_calc function in fanpy/scripts/gaussian/run_calc.py to use explicit default values for nuc_nuc, pspace_exc, objective, and solver parameters, improving reliability and usability.
• Changed the --optimize_orbs argument in fanpy/scripts/pyscf/pyscf_parser.py to use action="store_true" for correct boolean flag behavior, and updated --pspace_exc to accept a string for easier CLI parsing.
• Added logic in fanpy/scripts/pyscf/make_fanci_script.py to parse pspace_exc from a string to a list of integers, ensuring correct data types are passed to downstream functions.

Script generation and interface enhancements:

• Refactored write_wfn_py in fanpy/scripts/pyscf/run_calc.py to require explicit geom and basis arguments, clarified docstrings, and replaced the old_fanpy flag with fanpy_only for clearer intent. Improved the way geometry and other arguments are formatted and passed to subprocesses.
• Fixed directory change logic in job submission scripts to ensure correct working directories during batch calculations.

Test coverage:

• Added new test files tests/test_scripts_gaussian_run_calc.py and tests/test_scripts_pyscf_run_calc.py to provide comprehensive testing for the CLI and Python interfaces of the calculation scripts, including error handling and file generation.
• NOTE some features of run_calc.py in the PySCF folder cannot be tested, as they are used to submit calculations to servers. Also, some of the features would require an interface that has the variational approach.