fix: fix premature deletion of temp files in combination with checkpo…

…ints (#2737)

fixes #2732

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [x] The documentation (`docs/`) is updated to reflect the changes or
this is not necessary (e.g. if the change does neither modify the
language nor the behavior or functionalities of Snakemake).

snakemake/dag.py

@@ -1845,8 +1845,13 @@ async def finish(self, job, update_checkpoint_dependencies=True):
                 self.create_conda_envs()
             potential_new_ready_jobs = True
 
-        for job in jobs:
-            await self.handle_temp(job)
+        if not any(self.checkpoint_jobs):
+            # While there are still checkpoint jobs, we cannot safely delete
+            # temp files.
+            # TODO: we maybe could be more accurate and determine whether there is a
+            # checkpoint that depends on the temp file.
+            for job in jobs:
+                await self.handle_temp(job)
 
         return potential_new_ready_jobs
 

tests/test_github_issue2732/Snakefile

@@ -0,0 +1,38 @@
+rule a:
+    output:
+        temp("{name}.txt"),
+    shell:
+        "touch {output}"
+
+rule a1:
+    input:
+        "{name}.txt",
+    output:
+        temp("{name}.a1.out"),
+    shell:
+        "touch {output}"
+
+rule b1:
+    input:
+        "A.txt",
+    output:
+        temp("A.b1.out"),
+    shell:
+        "touch {output}"
+
+checkpoint b2:
+    input:
+        "A.b1.out"
+    output:
+        "A.b2.out"
+    shell:
+        "echo A > {output}"
+
+def in_func1(w):
+    file = checkpoints.b2.get().output[0]
+    return open(file, "r").read().strip()
+
+rule all:
+    input:
+        lambda w: expand(rules.a1.output, name=in_func1(w)),
+    default_target: True

tests/test_github_issue2732/expected-results/A.b2.out

@@ -0,0 +1 @@
+A

tests/tests.py

@@ -2014,32 +2014,37 @@ def test_issue2685():
     run(dpath("test_issue2685"))
 
 
-@skip_on_windows
+@skip_on_windows  # OS agnostic
 def test_set_resources_complex():
     run(
         dpath("test05"),
         shellcmd="snakemake -c1 --set-resources \"compute1:slurm_extra='--nice=10'\"",
     )
 
 
-@skip_on_windows
+@skip_on_windows  # OS agnostic
 def test_set_resources_human_readable():
     run(
         dpath("test05"),
         shellcmd="snakemake -c1 --set-resources \"compute1:runtime='50h'\"",
     )
 
 
-@skip_on_windows
+@skip_on_windows  # OS agnostic
 def test_call_inner():
     run(dpath("test_inner_call"))
 
 
-@skip_on_windows
+@skip_on_windows  # OS agnostic
 def test_list_input_changes():
     run(dpath("test01"), shellcmd="snakemake --list-input-changes", check_results=False)
 
 
-@skip_on_windows
+@skip_on_windows  # OS agnostic
 def test_summary():
     run(dpath("test01"), shellcmd="snakemake --summary", check_results=False)
+
+
+@skip_on_windows  # OS agnostic
+def test_github_issue2732():
+    run(dpath("test_github_issue2732"))