Added handling of cache in both cli.py and inference.py

[jimmymcheung]

This is a putative fix to add handling of custom caching directory as intended in the hint of download_fasta_utilities function in fasta_utils.py. See more on issue #13

[jimmymcheung]

Additionally, in commit 51b1e18 I solve a reference problem causing FileNotFoundError when simplefold is called outside of the directory where these python scripts resides. However, from a quick test with protein 7NJS (named in PDB, 445aa), it seems the performance is decreased by ~12%. Validation on this decrease is needed, and potentially further improvements.

[jimmymcheung]

I've updated the recent patches from the main.

[jimmymcheung]

In a latest test-run to predict Hsp90 (PDB: 3Q6M, 90aa), this change actually becomes faster than without adding the Path(__file__).parents[2], after change in #31. Here's the sampling time with 3B model, mlx backend, and plddt option:

• Running at project's root, without the path fix: 10:21
• Running with Path(__file__).parents[2] set at each occurrence: 08:15
• Running with str(Path(__file__).parents[2]) as a variable, and reference at each occurrence: 08:18