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[bot] Update shared/vendored #68

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Merged
joverlee521 merged 1 commit into from
Oct 15, 2026
Merged

[bot] Update shared/vendored #68

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4 changes: 2 additions & 2 deletions shared/vendored/.gitrepo
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
[subrepo]
remote = https://github.com/nextstrain/shared
branch = main
commit = 6e82a95b4e1e1a9b2ae42bb9a63c458a0a0ac7c0
parent = d69e5f61ceddb2d39d57a5dcb7c74e3264b09aba
commit = 7a986c3c6c52c51d33dd412800b0bb694030f379
parent = 89b1a481f13aa65c5e722efa3f6abe1cb000e0c4
method = merge
cmdver = 0.4.9
22 changes: 10 additions & 12 deletions shared/vendored/snakemake/remote_files.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@ import socket
from urllib.parse import urlparse
from snakemake.io import get_flag_value, AnnotatedString
from snakemake.logging import logger
from textwrap import dedent


def is_online(host="8.8.8.8", port=53, timeout=3) -> bool:
Expand Down Expand Up @@ -228,17 +229,14 @@ def _local_or_storage(wrapped: AnnotatedString) -> str | AnnotatedString:
)
return wrapped

local = so.local_path()
if not local.exists():
raise Exception(
f"Unable to find local cached file for {so.query!r}. "
"Please make sure you have run the workflow at least once with "
"internet connection and config.use_remote_files set to True to "
"to fetch and save the remote file locally.")
local = str(so.local_path())
logger.warning(dedent(f"""\
Attempting to use the local file for:

logger.warning(
f"Using the cached copy of {so.query} at {local} without revalidation. "
"Set config.use_remote_files to True if you want to force revalidation."
)
remote: {so.query}
local: {local}

return str(local)
Set config.use_remote_files to True if you want to force revalidation of the remote file
or if you run into the MissingInputException with the local file.
"""))
return local
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