Fix the first two MREs from snakemake#823.

- Incorporates @epruesse's fix for MRE snakemake#1
- Adds a fix for MRE snakemake#2 - properly marks group jobs as finished
- Some minor updates to tests

snakemake/dag.py

@@ -617,8 +617,13 @@ def unneeded_files():
                 yield from filterfalse(partial(needed, job_), tempfiles & files)
 
             # temp output
-            if not job.dynamic_output and (
-                job not in self.targetjobs or job.rule.name == self.workflow.first_rule
+            if (
+                not job.dynamic_output
+                and not job.is_checkpoint
+                and (
+                    job not in self.targetjobs
+                    or job.rule.name == self.workflow.first_rule
+                )
             ):
                 tempfiles = (
                     f
@@ -1349,7 +1354,11 @@ def finish(self, job, update_dynamic=True):
         self._running.remove(job)
 
         # turn off this job's Reason
-        self.reason(job).mark_finished()
+        if job.is_group():
+            for j in job:
+                self.reason(j).mark_finished()
+        else:
+            self.reason(job).mark_finished()
 
         try:
             self._ready_jobs.remove(job)

tests/test_issue823_1/Snakefile

@@ -21,7 +21,7 @@ rule b:
     input:
         _checkpoint_output,
     output:
-        temp('b.txt')
+        'b.txt'
     shell:
         "touch {output}"