fix: Disable Persistence cache for snakemake jobs (#1159)

* Implement test_github_issue1158

* Disable Persistence cache for snakemake jobs

* test_github_issue1158 mark xfail if no strace

* Add tests/test_github_issue1158/expected-results

snakemake/workflow.py

@@ -730,6 +730,9 @@ def files(items):
             or delete_temp_output,
         )
 
+        if self.mode in [Mode.subprocess, Mode.cluster]:
+            self.persistence.deactivate_cache()
+
         if cleanup_metadata:
             for f in cleanup_metadata:
                 self.persistence.cleanup_metadata(f)

tests/conftest.py

@@ -9,6 +9,7 @@
 
 skip_on_windows = pytest.mark.skipif(ON_WINDOWS, reason="Unix stuff")
 only_on_windows = pytest.mark.skipif(not ON_WINDOWS, reason="Windows stuff")
+needs_strace = pytest.mark.xfail(os.system("strace -o /dev/null true") != 0, reason="Missing strace")
 
 
 @pytest.fixture(autouse=True)

tests/test_github_issue1158/Snakefile

@@ -0,0 +1,3 @@
+rule Test:
+    output: "output"
+    shell: "touch {output}"

tests/test_github_issue1158/qsub.py

@@ -0,0 +1,20 @@
+#!/usr/bin/env python3
+import sys
+import os
+import random
+import re
+
+jobscript = sys.argv[1]
+
+os.system("strace -f -o trace {}".format(jobscript))
+
+with open("trace", "r") as fp:
+    lines = fp.readlines()
+
+regex = re.compile('.*openat\(.*.snakemake/incomplete".*')
+matches = list(filter(lambda l: regex.match(l), lines))
+if len(matches) > 0:
+    sys.stderr.write(repr(matches))
+    sys.exit(1)
+
+print(random.randint(1, 100))

tests/tests.py

@@ -12,7 +12,7 @@
 sys.path.insert(0, os.path.dirname(__file__))
 
 from .common import *
-from .conftest import skip_on_windows, only_on_windows, ON_WINDOWS
+from .conftest import skip_on_windows, only_on_windows, ON_WINDOWS, needs_strace
 
 
 def test_list_untracked():
@@ -1306,3 +1306,11 @@ def test_all_temp():
 
 def test_strict_mode():
     run(dpath("test_strict_mode"), shouldfail=True)
+
+
+@needs_strace
+def test_github_issue1158():
+    run(
+        dpath("test_github_issue1158"),
+        cluster="./qsub.py",
+    )