fix: fixed code change detection when using modules

.github/workflows/conventional-prs.yml

@@ -13,4 +13,6 @@ jobs:
     steps:
       - uses: amannn/action-semantic-pull-request@v3.4.0
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          validateSingleCommit: true

snakemake/jobs.py

@@ -244,13 +244,15 @@ def outputs_older_than_script_or_notebook(self):
             return
         if self.rule.basedir:
             # needed if rule is included from another subdirectory
-            path = os.path.relpath(os.path.join(self.rule.basedir, path))
-        assert os.path.exists(path), "cannot find {0}".format(path)
-        script_mtime = os.lstat(path).st_mtime
-        for f in self.expanded_output:
-            if f.exists:
-                if not f.is_newer(script_mtime):
-                    yield f
+            path = self.rule.basedir.join(path).get_path_or_uri()
+        if is_local_file(path):
+            assert os.path.exists(path), "cannot find {0}".format(path)
+            script_mtime = os.lstat(path).st_mtime
+            for f in self.expanded_output:
+                if f.exists:
+                    if not f.is_newer(script_mtime):
+                        yield f
+        # TODO also handle remote file case here.
 
     @property
     def threads(self):

snakemake/sourcecache.py

@@ -150,12 +150,14 @@ class HostingProviderFile(SourceFile):
 
     def __init__(
         self,
-        repo: str,
-        path: str,
+        repo: str = None,
+        path: str = None,
         tag: str = None,
         branch: str = None,
         commit: str = None,
     ):
+        if repo is None:
+            raise SourceFileError("repo must be given")
         if not self.__class__.valid_repo.match(repo):
             raise SourceFileError(
                 "repo {} is not a valid repo specification (must be given as owner/name)."