fix: 2142 log directive in default target rule (#2191)

### Description

When the default target rule (e.g `all`) contains a `log` directive,
snakemake deems workflow complete and skips execution. See #2142

This PR fixes this bug by adding a `include_logfiles` flag to
`job.has_product()` method, similar to one used in `job.products()`. In
fact, this flag is simply passed on to `job.products()` internally.

### 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

@@ -1104,7 +1104,7 @@ def update_needrun(job):
                 reason.updated_input.update(updated_subworkflow_input)
             elif job in self.targetjobs:
                 # TODO find a way to handle added/removed input files here?
-                if not job.has_products():
+                if not job.has_products(include_logfiles=False):
                     if job.input:
                         if job.rule.norun:
                             reason.updated_input_run.update(

snakemake/jobs.py

@@ -93,11 +93,11 @@ def reset_params_and_resources(self):
     def get_target_spec(self):
         raise NotImplementedError()
 
-    def products(self):
+    def products(self, include_logfiles=True):
         raise NotImplementedError()
 
-    def has_products(self):
-        for o in self.products():
+    def has_products(self, include_logfiles=True):
+        for o in self.products(include_logfiles=include_logfiles):
             return True
         return False
 

tests/test_github_issue2142/Snakefile

@@ -0,0 +1,8 @@
+rule all:
+    input: "data.txt"
+    log:
+        "logs/all.log"
+
+rule A:
+    output: "data.txt"
+    shell: "touch {output}"

tests/tests.py

@@ -1962,6 +1962,10 @@ def test_github_issue1389():
     run(dpath("test_github_issue1389"), resources={"foo": 4}, shouldfail=True)
 
 
+def test_github_issue2142():
+    run(dpath("test_github_issue2142"))
+
+
 def test_ensure_nonempty_fail():
     run(dpath("test_ensure"), targets=["a"], shouldfail=True)