Propagate enable_profiling through ProcessedContainerSettings

Snakefile

@@ -273,14 +273,26 @@ def get_algorithm_image(wildcards):
     return None
 
 # Run the pathway reconstruction algorithm
+# When profiling is enabled, each reconstruct job writes a 'usage-profile.tsv' alongside its raw-pathway.txt.
+# Declare it as a rule output so that Snakemake tracks it and, critically, transfers it back from the execute
+# node in environments without a shared filesystem (e.g. HTCondor with shared-fs-usage: none). This is only
+# produced when profiling is actually performed, which requires the singularity/apptainer container framework
+# (see run_container_singularity), so we gate on the same condition to avoid declaring an output that is never
+# created (which would fail the rule).
+profiling_outputs = {}
+if container_settings.enable_profiling and container_settings.framework.is_singularity_family:
+    profiling_outputs['profile_file'] = SEP.join([out_dir, '{dataset}-{algorithm}-{params}', 'usage-profile.tsv'])
+
 rule reconstruct:
     input: collect_prepared_input
     # Each reconstruct call should be in a separate output subdirectory that is unique for the parameter combination so
     # that multiple instances of the container can run simultaneously without overwriting the output files
     # Overwriting files can happen because the pathway reconstruction algorithms often generate output files with the
     # same name regardless of the inputs or parameters, and these aren't renamed until after the container command
     # terminates
-    output: pathway_file = SEP.join([out_dir, '{dataset}-{algorithm}-{params}', 'raw-pathway.txt'])
+    output:
+        pathway_file = SEP.join([out_dir, '{dataset}-{algorithm}-{params}', 'raw-pathway.txt']),
+        **profiling_outputs
     resources:
         htcondor_transfer_input_files=get_algorithm_image
     run:

spras/config/container_schema.py

@@ -95,6 +95,7 @@ def from_container_settings(settings: ContainerSettings, hash_length: int) -> "P
             unpack_singularity=unpack_singularity,
             base_url=container_base_url,
             prefix=container_prefix,
+            enable_profiling=settings.enable_profiling,
             hash_length=hash_length,
             images=dict(settings.images),
         )

spras/containers.py

@@ -553,7 +553,7 @@ def run_container_singularity(resolved: ResolvedImage, command: List[str], volum
         # as `containers.py`.
         wrapper = os.path.join(os.path.dirname(__file__), "cgroup_wrapper.sh")
         cmd = [wrapper, my_cgroup] + singularity_cmd
-        proc = subprocess.run(cmd, capture_output=True, text=True, stderr=subprocess.STDOUT)
+        proc = subprocess.run(cmd, text=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 
         print("Reading memory and CPU stats from cgroup")
         create_apptainer_container_stats(my_cgroup, out_dir)

test/test_config.py

@@ -251,6 +251,22 @@ def test_config_container_images_invalid_algorithm(self):
         with pytest.raises(ValueError, match="Unknown algorithm name 'typo_algo'"):
             config.init_global(test_config)
 
+    def test_config_container_enable_profiling(self):
+        # enable_profiling must survive the ContainerSettings -> ProcessedContainerSettings
+        # conversion in from_container_settings(). containers.py reads it off the processed
+        # settings at runtime, so if it isn't propagated the profiling code path never runs.
+        # Regression test for the field being silently dropped during that conversion.
+        test_config = get_test_config()
+
+        # Default: absent from config --> False
+        config.init_global(test_config)
+        assert config.config.container_settings.enable_profiling is False
+
+        # Explicitly enabled --> must propagate to the processed settings as True
+        test_config["containers"]["enable_profiling"] = True
+        config.init_global(test_config)
+        assert config.config.container_settings.enable_profiling is True
+
     def test_error_dataset_label(self):
         test_config = get_test_config()
         error_test_dicts = [{"label": "test$"}, {"label": "@test'"}, {"label": "[test]"}, {"label": "test-test"},