fix: warn on non-file-modification-date changes like params, code, or input files

snakemake/dag.py

@@ -27,7 +27,7 @@
 from snakemake.exceptions import RemoteFileException, WorkflowError, ChildIOException
 from snakemake.exceptions import InputFunctionException
 from snakemake.logging import logger
-from snakemake.common import DYNAMIC_FILL, group_into_chunks
+from snakemake.common import DYNAMIC_FILL, ON_WINDOWS, group_into_chunks
 from snakemake.deployment import conda, singularity
 from snakemake.output_index import OutputIndex
 from snakemake import workflow
@@ -2199,6 +2199,32 @@ def stats(self):
         yield tabulate(rows, headers="keys")
         yield ""
 
+    def get_outputs_with_changes(self, change_type):
+        is_changed = lambda job: (
+            getattr(self.workflow.persistence, f"{change_type}_changed")(job)
+            if not job.is_group()
+            else []
+        )
+        changed = list(chain(*map(is_changed, self.jobs)))
+        if change_type == "code":
+            for job in self.jobs:
+                if not job.is_group():
+                    changed.extend(list(job.outputs_older_than_script_or_notebook()))
+        return changed
+
+    def warn_about_changes(self):
+        for change_type in ["code", "input", "params"]:
+            changed = self.get_outputs_with_changes(change_type)
+            if changed:
+                rerun_trigger = ""
+                if not ON_WINDOWS:
+                    rerun_trigger = f"\n    To trigger a re-run, use 'snakemake -R $(snakemake --list-{change_type}-changes)'."
+                logger.warning(
+                    f"The {change_type} used to generate one or several output files has changed:\n"
+                    f"    To inspect which output files have changes, run 'snakemake --list-{change_type}-changes'."
+                    f"{rerun_trigger}"
+                )
+
     def __str__(self):
         return self.dot()
 

snakemake/jobs.py

@@ -246,8 +246,7 @@ def outputs_older_than_script_or_notebook(self):
         if self.rule.basedir:
             # needed if rule is included from another subdirectory
             path = self.rule.basedir.join(path).get_path_or_uri()
-        if is_local_file(path):
-            assert os.path.exists(path), "cannot find {0}".format(path)
+        if is_local_file(path) and os.path.exists(path):
             script_mtime = os.lstat(path).st_mtime
             for f in self.expanded_output:
                 if f.exists:

snakemake/logging.py

@@ -30,7 +30,7 @@ class ColorizingStreamHandler(_logging.StreamHandler):
         "WARNING": YELLOW,
         "INFO": GREEN,
         "DEBUG": BLUE,
-        "CRITICAL": RED,
+        "CRITICAL": MAGENTA,
         "ERROR": RED,
     }
 
@@ -542,7 +542,7 @@ def job_error():
             if level == "info" and not self.quiet:
                 self.logger.warning(msg["msg"])
             if level == "warning":
-                self.logger.warning(msg["msg"])
+                self.logger.critical(msg["msg"])
             elif level == "error":
                 self.logger.error(msg["msg"])
             elif level == "debug":

snakemake/workflow.py

@@ -926,24 +926,22 @@ def files(items):
             dag.clean(only_temp=True, dryrun=dryrun)
             return True
         elif list_version_changes:
-            items = list(chain(*map(self.persistence.version_changed, dag.jobs)))
+            items = dag.get_outputs_with_changes("version")
             if items:
                 print(*items, sep="\n")
             return True
         elif list_code_changes:
-            items = list(chain(*map(self.persistence.code_changed, dag.jobs)))
-            for j in dag.jobs:
-                items.extend(list(j.outputs_older_than_script_or_notebook()))
+            items = dag.get_outputs_with_changes("code")
             if items:
                 print(*items, sep="\n")
             return True
         elif list_input_changes:
-            items = list(chain(*map(self.persistence.input_changed, dag.jobs)))
+            items = dag.get_outputs_with_changes("input")
             if items:
                 print(*items, sep="\n")
             return True
         elif list_params_changes:
-            items = list(chain(*map(self.persistence.params_changed, dag.jobs)))
+            items = dag.get_outputs_with_changes("params")
             if items:
                 print(*items, sep="\n")
             return True
@@ -1027,6 +1025,7 @@ def files(items):
         )
 
         if not dryrun:
+            dag.warn_about_changes()
             if len(dag):
                 shell_exec = shell.get_executable()
                 if shell_exec is not None:
@@ -1072,6 +1071,7 @@ def files(items):
                 logger.info(NOTHING_TO_BE_DONE_MSG)
         else:
             # the dryrun case
+            dag.warn_about_changes()
             if len(dag):
                 logger.run_info("\n".join(dag.stats()))
             else:
@@ -1093,21 +1093,24 @@ def files(items):
             if dryrun:
                 if len(dag):
                     logger.run_info("\n".join(dag.stats()))
-                logger.info(
-                    "This was a dry-run (flag -n). The order of jobs "
-                    "does not reflect the order of execution."
-                )
+                    logger.info(
+                        "This was a dry-run (flag -n). The order of jobs "
+                        "does not reflect the order of execution."
+                    )
+                dag.warn_about_changes()
                 logger.remove_logfile()
             else:
                 if stats:
                     self.scheduler.stats.to_json(stats)
+                dag.warn_about_changes()
                 logger.logfile_hint()
             if not dryrun and not no_hooks:
                 self._onsuccess(logger.get_logfile())
             return True
         else:
             if not dryrun and not no_hooks:
                 self._onerror(logger.get_logfile())
+            dag.warn_about_changes()
             logger.logfile_hint()
             return False