fix: fix bugs in --summary and --list-input-changes. Removed outdated…

… statement in tutorial. (#2735)

Thanks to @Horstage!


### 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).

docs/tutorial/advanced.rst

@@ -156,17 +156,6 @@ For the rule ``bwa_map`` this works as follows:
         shell:
             "bwa mem -t {threads} {input} | samtools view -Sb - > {output}"
 
-.. sidebar:: Note
-
-  Snakemake does not automatically rerun jobs when new input files are added as
-  in the exercise below. However, you can get a list of output files that
-  are affected by such changes with ``snakemake --list-input-changes``.
-  To trigger a rerun, this bit of bash magic helps:
-
-  .. code:: console
-
-    snakemake -n --forcerun $(snakemake --list-input-changes)
-
 Any normal function would work as well.
 Input functions take as **single argument** a ``wildcards`` object, that allows to access the wildcards values via attributes (here ``wildcards.sample``).
 They have to **return a string or a list of strings**, that are interpreted as paths to input files (here, we return the path that is stored for the sample in the config file).

snakemake/cli.py

@@ -1081,8 +1081,8 @@ def get_argument_parser(profiles=None):
         "--lc",
         choices=ChangeType.all(),
         type=ChangeType.parse_choice,
-        help="List all output files for which the rule body (run or shell) have "
-        "changed in the Snakefile.",
+        help="List all output files for which the given items (code, input, params) "
+        "have changed since creation.",
     )
     group_utils.add_argument(
         "--list-input-changes",
@@ -1994,6 +1994,10 @@ def args_to_api(args, parser):
                         dag_api.container_cleanup_images()
                     elif args.list_changes:
                         dag_api.list_changes(args.list_changes)
+                    elif args.list_input_changes:
+                        dag_api.list_changes(ChangeType.INPUT)
+                    elif args.list_params_changes:
+                        dag_api.list_changes(ChangeType.PARAMS)
                     elif args.list_untracked:
                         dag_api.list_untracked()
                     elif args.summary:

snakemake/dag.py

@@ -2357,18 +2357,15 @@ def html_node(node_id, node, color):
 
     async def summary(self, detailed=False):
         if detailed:
-            yield "output_file\tdate\trule\tversion\tlog-file(s)\tinput-file(s)\tshellcmd\tstatus\tplan"
+            yield "output_file\tdate\trule\tlog-file(s)\tinput-file(s)\tshellcmd\tstatus\tplan"
         else:
-            yield "output_file\tdate\trule\tversion\tlog-file(s)\tstatus\tplan"
+            yield "output_file\tdate\trule\tlog-file(s)\tstatus\tplan"
 
         for job in self.jobs:
             output = job.output
             for f in output:
                 rule = job.rule.name
 
-                version = self.workflow.persistence.version(f)
-                version = "-" if version is None else str(version)
-
                 date = (
                     time.ctime((await f.mtime()).local_or_storage())
                     if await f.exists()
@@ -2400,8 +2397,6 @@ async def summary(self, detailed=False):
                         status = "missing"
                 elif self.reason(job).updated_input:
                     status = "updated input files"
-                elif self.workflow.persistence.version_changed(job, file=f):
-                    status = f"version changed to {job.rule.version}"
                 elif self.workflow.persistence.code_changed(job, file=f):
                     status = "rule implementation changed"
                 elif self.workflow.persistence.input_changed(job, file=f):
@@ -2410,10 +2405,10 @@ async def summary(self, detailed=False):
                     status = "params changed"
                 if detailed:
                     yield "\t".join(
-                        (f, date, rule, version, log, input, shellcmd, status, pending)
+                        (f, date, rule, log, input, shellcmd, status, pending)
                     )
                 else:
-                    yield "\t".join((f, date, rule, version, log, status, pending))
+                    yield "\t".join((f, date, rule, log, status, pending))
 
     def archive(self, path: Path):
         """Archives workflow such that it can be re-run on a different system.

snakemake/workflow.py

@@ -878,7 +878,12 @@ def summary(self, detailed: bool = False):
         )
         self._build_dag()
 
-        print("\n".join(async_run(self.dag.summary(detailed=detailed))))
+        async def join_summary(detailed):
+            return "\n".join(
+                [line async for line in self.dag.summary(detailed=detailed)]
+            )
+
+        print(async_run(join_summary(detailed)))
 
     def conda_cleanup_envs(self):
         self._prepare_dag(forceall=True, ignore_incomplete=True, lock_warn_only=False)

tests/tests.py

@@ -2033,3 +2033,13 @@ def test_set_resources_human_readable():
 @skip_on_windows
 def test_call_inner():
     run(dpath("test_inner_call"))
+
+
+@skip_on_windows
+def test_list_input_changes():
+    run(dpath("test01"), shellcmd="snakemake --list-input-changes", check_results=False)
+
+
+@skip_on_windows
+def test_summary():
+    run(dpath("test01"), shellcmd="snakemake --summary", check_results=False)