[Code scan] Preserve older backups in file_safe_backup

[njzjz]

This issue is a result of a Codex global repository scan.

file_safe_backup() is documented to rotate existing backups so that the latest file becomes *.bak.0 and older backups move to higher indices. The current rename loop computes j = len(fbak) - i + 1, then replaces f'.{j}' in the filename. For existing STRU.bak.0 and STRU.bak.1, this starts at j == 3, so no filename changes. The subsequent rename of the live file to STRU.bak.0 can overwrite the previous backup instead of preserving it.

abacus-develop/interfaces/ASE_interface/abacuslite/io/generalio.py

Lines 70 to 100 in 84ca04b

	def file_safe_backup(fn: Path, suffix: str = 'bak'):
	'''for the case where there are already files with the same name,
	add a suffix to the file name, like `STRU.bak.0`. If there are
	already `STRU.bak.0`, rename the elder to `STRU.bak.1` and let
	the latest one be `STRU.bak.0`.
	Parameters
	----------
	fn : Path
	The path to the file to backup. Note: it must be provided
	as the Path object so that its folder is accessible by this
	function.
	suffix : str, optional
	The suffix to add to the file name. Default is 'bak'
	'''
	assert isinstance(fn, Path)
	where = fn.parent
	# get the backup files
	fbak = sorted(list(where.glob(f'{fn.name}.{suffix}.*')),
	key=lambda p: int(p.name.split('.')[-1]))
	if fbak:
	# rename the elder by adding 1 to the suffix
	for i, f in enumerate(fbak[::-1]): # reverse order, to avoid overwrite
	j = len(fbak) - i + 1 #: STRU.bak.i -> STRU.bak.i+1
	fname = f.name.replace(f'.{j}', f'.{j+1}')
	f.rename(f.parent / fname)
	# backup the latest file, if there is one
	if fn.exists():
	fn.rename(fn.parent / f'{fn.name}.{suffix}.0')

Relevant code:

fbak = sorted(list(where.glob(f'{fn.name}.{suffix}.*')),
              key=lambda p: int(p.name.split('.')[-1]))
if fbak:
    for i, f in enumerate(fbak[::-1]):
        j = len(fbak) - i + 1 #: STRU.bak.i -> STRU.bak.i+1
        fname = f.name.replace(f'.{j}', f'.{j+1}')
        f.rename(f.parent / fname)

if fn.exists():
    fn.rename(fn.parent / f'{fn.name}.{suffix}.0')

Suggested fix:

Parse each backup index from the filename and rename in descending index order, e.g. old_idx -> old_idx + 1, before moving the current file to index 0. Also consider ignoring or handling non-integer backup suffixes explicitly.

[kirk0830]

@njzjz hi, thanks for pointing out this issue. @QuantumMisaka has some update on abacuslite, after his PR I will check again if this issue can be closed.

Regards,
Yike