feat: Allow to mark all output files as temp with --all-temp (#1097)

* mark all output as temp

* move logic into rule

* fixes

snakemake/__init__.py

@@ -116,6 +116,7 @@ def snakemake(
     print_compilation=False,
     debug=False,
     notemp=False,
+    all_temp=False,
     keep_remote_local=False,
     nodeps=False,
     keep_target_files=False,
@@ -242,8 +243,8 @@ def snakemake(
         list_untracked (bool):      list files in the workdir that are not used in the workflow (default False)
         summary (bool):             list summary of all output files and their status (default False)
         archive (str):              archive workflow into the given tarball
-        delete_all_output (bool)    remove all files generated by the workflow (default False)
-        delete_temp_output (bool)   remove all temporary files generated by the workflow (default False)
+        delete_all_output (bool):    remove all files generated by the workflow (default False)
+        delete_temp_output (bool):   remove all temporary files generated by the workflow (default False)
         latency_wait (int):         how many seconds to wait for an output file to appear after the execution of a job, e.g. to handle filesystem latency (default 3)
         wait_for_files (list):      wait for given files to be present before executing the workflow
         list_resources (bool):      list resources used in the workflow (default False)
@@ -585,6 +586,7 @@ def snakemake(
             scheduler_solver_path=scheduler_solver_path,
             conda_base_path=conda_base_path,
             check_envvars=not lint,  # for linting, we do not need to check whether requested envvars exist
+            all_temp=all_temp,
         )
         success = True
 
@@ -645,6 +647,7 @@ def snakemake(
                     latency_wait=latency_wait,
                     verbose=verbose,
                     notemp=notemp,
+                    all_temp=all_temp,
                     keep_remote_local=keep_remote_local,
                     nodeps=nodeps,
                     jobscript=jobscript,
@@ -1857,6 +1860,12 @@ def get_argument_parser(profile=None):
         "a part of the workflow, since temp() would lead to deletion of "
         "probably needed files by other parts of the workflow.",
     )
+    group_behavior.add_argument(
+        "--all-temp",
+        action="store_true",
+        help="Mark all output files as temp files. This can be useful for CI testing, "
+        "in order to save space.",
+    )
     group_behavior.add_argument(
         "--keep-remote",
         action="store_true",
@@ -2815,6 +2824,7 @@ def open_browser():
             debug=args.debug,
             jobscript=args.jobscript,
             notemp=args.notemp,
+            all_temp=args.all_temp,
             keep_remote_local=args.keep_remote,
             greediness=args.greediness,
             no_hooks=args.no_hooks,

snakemake/rules.py

@@ -56,6 +56,7 @@
 )
 from snakemake.logging import logger
 from snakemake.common import Mode, ON_WINDOWS, lazy_property, TBDString
+import snakemake.io
 
 
 class Rule:
@@ -543,8 +544,14 @@ def _set_inoutput_item(self, item, output=False, name=None):
                             self
                         )
                     )
+
+            if self.workflow.all_temp and output:
+                # mark as temp if all output files shall be marked as temp
+                item = snakemake.io.flag(item, "temp")
+
             # record rule if this is an output file output
             _item = IOFile(item, rule=self)
+
             if is_flagged(item, "temp"):
                 if output:
                     self.temp_output.add(_item)

snakemake/workflow.py

@@ -136,6 +136,7 @@ def __init__(
         conda_base_path=None,
         check_envvars=True,
         max_threads=None,
+        all_temp=False,
     ):
         """
         Create the controller.
@@ -215,6 +216,7 @@ def __init__(
         self._conda_base_path = conda_base_path
         self.check_envvars = check_envvars
         self.max_threads = max_threads
+        self.all_temp = all_temp
 
         _globals = globals()
         _globals["workflow"] = self

tests/test_all_temp/Snakefile

@@ -0,0 +1,23 @@
+rule all:
+    input:
+        "test2.txt"
+    run:
+        import os
+        if os.path.exists("test1.txt"):
+            raise ValueError("test1.txt still present!")
+
+
+rule a:
+    output:
+        "test1.txt"
+    shell:
+        "touch {output}"
+
+
+rule b:
+    input:
+        "test1.txt"
+    output:
+        "test2.txt"
+    shell:
+        "touch {output}"

tests/tests.py

@@ -1282,3 +1282,7 @@ def test_github_issue1069():
 def test_touch_pipeline_with_temp_dir():
     # Issue #1028
     run(dpath("test_touch_pipeline_with_temp_dir"), forceall=True, touch=True)
+
+
+def test_all_temp():
+    run(dpath("test_all_temp"), all_temp=True)