fix: patch LocalSourceFile to work with containerize

snakemake/deployment/containerize.py

@@ -59,7 +59,7 @@ def containerize(workflow):
             "\n".join(map("#   {}".format, env.content.decode().strip().split("\n")))
         )
         get_env_cmds.append("RUN mkdir -p {}".format(prefix))
-        if env.file.startswith("https://"):
+        if env.file.get_path_or_uri().startswith("https://"):
             # get_env_cmds.append("RUN curl -sSL {} > {}".format(env.file, env_target_path))
             get_env_cmds.append("ADD {} {}".format(env.file, env_target_path))
         else:

snakemake/sourcecache.py

@@ -87,6 +87,9 @@ class LocalSourceFile(SourceFile):
     def __init__(self, path):
         self.path = path
 
+    def __fspath__(self):
+        return self.path
+
     def get_path_or_uri(self):
         return self.path
 

tests/test_github_issue1210/Snakefile

@@ -0,0 +1,10 @@
+rule all:
+  input: "python-version.txt"
+
+rule py_emit_version:
+  output: "python-version.txt"
+  conda: "envs/py39.yaml"
+  shell:
+    """
+    python -VV > {output}
+    """

tests/test_github_issue1210/envs/py39.yaml

@@ -0,0 +1,6 @@
+name: py39
+channels:
+  - conda-forge
+  - nodefaults
+dependencies:
+  - python=3.9

tests/tests.py

@@ -1320,3 +1320,9 @@ def test_github_issue1158():
         dpath("test_github_issue1158"),
         cluster="./qsub.py",
     )
+
+def test_github_issue1210():
+    run(
+        dpath("test_github_issue1210"),
+        containerize=True
+    )