--overwrite should only overwrite if the local and remote md5s differ

[nebfield]

Current overwrite behaviour is fairly dumb:

pygscatalog/pgscatalog.core/src/pgscatalog/core/lib/_download.py

Lines 96 to 131 in 6f226c8

	def https_download(*, url, out_path, directory, overwrite):
	"""Download a file from the PGS Catalog over HTTPS, with automatic retries and
	waiting. md5 checksums are automatically validated."""
	try:
	if Config.FTP_EXCLUSIVE:
	logger.warning("HTTPS downloads disabled by Config.FTP_EXCLUSIVE")
	https_download.retry.wait = tenacity.wait_none()
	https_download.retry.stop = tenacity.stop.stop_after_attempt(1)
	raise ScoreDownloadError("HTTPS disabled")
	if out_path.exists() and not overwrite:
	raise FileExistsError(f"{out_path} already exists")
	checksum_path = url + ".md5"
	checksum = httpx.get(checksum_path, headers=Config.API_HEADER).text
	md5 = hashlib.md5()
	with tempfile.NamedTemporaryFile(dir=directory, delete=False) as f:
	with httpx.stream("GET", url, headers=Config.API_HEADER) as r:
	for data in r.iter_bytes():
	f.write(data)
	md5.update(data)
	if (calc := md5.hexdigest()) != (remote := checksum.split()[0]):
	# will attempt to download again (see decorator)
	raise ScoreChecksumError(
	f"Calculated checksum {calc} doesn't match {remote}"
	)
	except httpx.UnsupportedProtocol as protocol_exc:
	raise ValueError(f"Can't download a local file: {url!r}") from protocol_exc
	except httpx.RequestError as download_exc:
	raise ScoreDownloadError("HTTPS download failed") from download_exc
	else:
	# no exceptions thrown, move the temporary file to the final output path
	os.rename(f.name, out_path)
	logger.info(f"HTTPS download OK, {out_path} checksum validation passed")

Local and remote md5s can differ if there's been an update to the scoring file (e.g. trait update because of an upstream ontology change)