fix: --delete-all-output ignores --dry-run (snakemake#3265)

GaspardR · bayraktar1 · web-flow · commit 23fef829c5ac · 2025-03-13T11:38:06.000+01:00
Fixes snakemake#3264 ### QC  * [ ] 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). Should I add a test case for this?  ## Summary by CodeRabbit - **New Features** - Added a dry run option for output deletion, allowing users to simulate deletions before execution. - Enhanced workflow commands to improve file and directory management during output operations. - **Bug Fixes** - Corrected a file path reference in deletion validation to ensure more reliable output handling.  --------- Co-authored-by: bayraktar1 <bayraktar.d@protonmail.com>
diff --git a/src/snakemake/cli.py b/src/snakemake/cli.py
@@ -2093,7 +2093,7 @@ def args_to_api(args, parser):
                     elif args.archive:
                         dag_api.archive(args.archive)
                     elif args.delete_all_output:
-                        dag_api.delete_output()
+                        dag_api.delete_output(dryrun=args.dryrun)
                     elif args.delete_temp_output:
                         dag_api.delete_output(only_temp=True, dryrun=args.dryrun)
                     else:
diff --git a/tests/test_delete_all_output/Snakefile b/tests/test_delete_all_output/Snakefile
@@ -13,7 +13,7 @@ rule delete_all_output:
         python -m snakemake --cores 1 -s Snakefile_inner all && \
         rm nothere && \
         python -m snakemake --cores 1 -s Snakefile_inner --delete-all-output all && \
-        test -f infile && test ! -f intermediate && test ! -f somedir/final && \
+        test -f infile && test ! -f intermediate && test ! -f some_dir/final && \
         test ! -d empty_dir && test ! -L dangling && test ! -d full_dir
         """
 
diff --git a/tests/test_github_issue_3265_respect_dryrun_delete_all/Snakefile b/tests/test_github_issue_3265_respect_dryrun_delete_all/Snakefile
@@ -0,0 +1,36 @@
+shell.executable("bash")
+
+
+rule all:
+    input:
+        "delete_all_output",
+        "delete_temp_output",
+    output:
+        touch("all_ok"),
+
+
+rule delete_all_output:
+    output:
+        touch("delete_all_output"),
+    shell:
+        """
+        echo $PATH
+        ls
+        python -m snakemake --cores 1 -s Snakefile_inner all && \
+        rm nothere && \
+        python -m snakemake --cores 1 -s Snakefile_inner --dry-run --delete-all-output all && \
+        test -f infile && test -f intermediate && test -f some_dir/final && \
+        test -d empty_dir && test -L dangling && test -d full_dir
+        """
+
+
+rule delete_temp_output:
+    output:
+        touch("delete_temp_output"),
+    shell:
+        """
+        python -m snakemake --cores 1 -s Snakefile_inner --notemp temp && \
+        python -m snakemake --cores 1 -s Snakefile_inner --dry-run  --delete-temp-output temp && \
+        test -f infile && test -f temp_intermediate && \
+        test -d temp_empty_dir && test -d temp_full_dir && test -f temp_keep
+        """
diff --git a/tests/test_github_issue_3265_respect_dryrun_delete_all/Snakefile_inner b/tests/test_github_issue_3265_respect_dryrun_delete_all/Snakefile_inner
@@ -0,0 +1,75 @@
+shell.executable("bash")
+
+
+rule all:
+    input:
+        "some_dir/final",
+        "empty_dir",
+        "full_dir",
+
+
+rule a:
+    input:
+        "infile",
+    output:
+        "intermediate",
+        "dangling",
+        touch(protected("protected")),
+    shell:
+        "ln -s {input} {output[0]} && touch nothere && ln -s nothere {output[1]}"
+
+
+rule b:
+    input:
+        "intermediate",
+    output:
+        touch("some_dir/final"),
+
+
+rule c:
+    output:
+        directory("empty_dir"),
+    shell:
+        "mkdir empty_dir"
+
+
+rule d:
+    output:
+        directory("full_dir"),
+    shell:
+        "mkdir full_dir && touch full_dir/somefile"
+
+
+rule e:
+    input:
+        "infile",
+    output:
+        temp("temp_intermediate"),
+    shell:
+        "touch {output}"
+
+
+rule f:
+    input:
+        "temp_intermediate",
+    output:
+        directory(temp("temp_empty_dir")),
+    shell:
+        "mkdir temp_empty_dir"
+
+
+rule g:
+    input:
+        "temp_intermediate",
+    output:
+        directory(temp("temp_full_dir")),
+    shell:
+        "mkdir temp_full_dir && touch temp_full_dir/somefile"
+
+
+rule temp:
+    input:
+        "temp_empty_dir",
+        "temp_full_dir",
+    output:
+        touch("temp_keep"),
diff --git a/tests/test_github_issue_3265_respect_dryrun_delete_all/expected-results/all_ok b/tests/test_github_issue_3265_respect_dryrun_delete_all/expected-results/all_ok
diff --git a/tests/test_github_issue_3265_respect_dryrun_delete_all/infile b/tests/test_github_issue_3265_respect_dryrun_delete_all/infile
diff --git a/tests/tests.py b/tests/tests.py
@@ -44,6 +44,11 @@ def test_delete_all_output():
     run(dpath("test_delete_all_output"))
 
 
+@skip_on_windows
+def test_github_issue_3265_respect_dryrun_delete_all():
+    run(dpath("test_github_issue_3265_respect_dryrun_delete_all"))
+
+
 def test_github_issue_14():
     """Add cleanup_scripts argument to allow the user to keep scripts"""
     # Return temporary directory for inspection - we should keep scripts here
