Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

fix: fix source cache handling for remote source files retrieved via github() or gitlab() tags. #1322

Merged
merged 2 commits into from Jan 11, 2022
Merged

fix: fix source cache handling for remote source files retrieved via github() or gitlab() tags. #1322

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
0e56bde
fix: fix source cache handling for remote source files retrieved via …
johanneskoester Jan 8, 2022
40fc4b2
fix: convert to url separators in windows case.
johanneskoester Jan 11, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
14 changes: 12 additions & 2 deletions snakemake/sourcecache.py
View file
Open in desktop
Expand Up @@ -13,7 +13,13 @@
from abc import ABC, abstractmethod


from snakemake.common import is_local_file, get_appdirs, parse_uri, smart_join
from snakemake.common import (
ON_WINDOWS,
is_local_file,
get_appdirs,
parse_uri,
smart_join,
)
from snakemake.exceptions import WorkflowError, SourceFileError
from snakemake.io import git_content, split_git_path
from snakemake.logging import logger
Expand Down Expand Up @@ -202,6 +208,10 @@ def get_basedir(self):

def join(self, path):
path = os.path.normpath("{}/{}".format(self.path, path))
if ON_WINDOWS:
# convert back to URL separators
# (win specific separators are introduced by normpath above)
path = path.replace("\\", "/")
return self.__class__(
repo=self.repo,
path=path,
Expand Down Expand Up @@ -237,7 +247,7 @@ def get_path_or_uri(self):

def infer_source_file(path_or_uri, basedir: SourceFile = None):
if isinstance(path_or_uri, SourceFile):
if basedir is None:
if basedir is None or isinstance(path_or_uri, HostingProviderFile):
return path_or_uri
else:
path_or_uri = path_or_uri.get_path_or_uri()
Expand Down