fix: Prevent binary log files to crash snakemake execution with show-failed-logs

snakemake/logging.py

@@ -506,6 +506,9 @@ def show_logs(logs):
                 except FileNotFoundError:
                     yield f"Logfile {f} not found."
                     return
+                except UnicodeDecodeError:
+                    yield f"Logfile {f} is not a text file."
+                    return
                 lines = content.splitlines()
                 logfile_header = f"Logfile {f}:"
                 if not lines:

tests/test_issue2826_failed_binary_logs/Snakefile

@@ -0,0 +1,12 @@
+rule:
+    log:
+        'log.bin'
+    run:
+        import pickle
+        with open(log[0], 'wb') as f:
+            # Write anything binary to the file
+            # that cannot be interpreted as unicode
+            # dumping the log object was an easy way to do this 
+            pickle.dump(log, f)
+        # make this test fail
+        a

tests/tests.py

@@ -616,6 +616,18 @@ def test_dup_out_patterns():
     run(dpath("test_dup_out_patterns"), shouldfail=True)
 
 
+def test_issue2826_failed_binary_logs():
+    """Show how a binary log file crushes `show_logs`
+
+    The log file in this test is a binary file.
+    The `show_failed_logs` is activated by default using `run`,
+    thus `show_logs` will be called at the end of the test.
+    Thus this test will check if `show_logs` is able to handle
+    the binary log file.
+    """
+    run(dpath("test_issue2826_failed_binary_logs"), shouldfail=True)
+
+
 # TODO reactivate once generic cluster executor is properly released
 # @skip_on_windows
 # def test_restartable_job_cmd_exit_1_no_restart():