fix: logdir misconstruct when leading slash in wildcard (#220)

This is a minor fix, which addresses issue #214: A slurm logdirectory
will start with `/` if a wildcard starts with `/`. After discussing with
@johanneskoester , allowing for slashes in wildcards should not be an
issue. Hence, the escape in this PR. Also,
snakemake/snakemake#3318 can be considered
solved.

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
- Introduced functionality for requesting GPU resources in SLURM jobs,
with detailed documentation on methods for specifying GPUs and
associated CPU settings.

- **Bug Fixes**
- Improved handling of job resource specifications to enforce clarity
between GRES and GPU inputs, preventing potential conflicts.

- **Dependencies**
- Updated the version of the `snakemake-executor-plugin-slurm-jobstep`
dependency from `^0.2.0` to `^0.3.0`, which may include enhancements and
bug fixes.

- **Documentation**
- Added a new section on "GPU Jobs" outlining how to request GPU
resources with examples and clarifications on resource specifications.

- **Tests**
- Removed unnecessary import from test files, streamlining the test code
without affecting functionality.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Author: cmeesters

snakemake_executor_plugin_slurm/__init__.py

@@ -180,7 +180,9 @@ def run_job(self, job: JobExecutorInterface):
         group_or_rule = f"group_{job.name}" if job.is_group() else f"rule_{job.name}"
 
         try:
-            wildcard_str = "_".join(job.wildcards) if job.wildcards else ""
+            wildcard_str = (
+                "_".join(job.wildcards).replace("/", "_") if job.wildcards else ""
+            )
         except AttributeError:
             wildcard_str = ""
 
@@ -264,10 +266,10 @@ def run_job(self, job: JobExecutorInterface):
                     "specified. Assuming 'tasks_per_node=1'."
                     "Probably not what you want."
                 )
+
         # we need to set cpus-per-task OR cpus-per-gpu, the function
         # will return a string with the corresponding value
         call += f" {get_cpu_setting(job, gpu_job)}"
-
         if job.resources.get("slurm_extra"):
             self.check_slurm_extra(job)
             call += f" {job.resources.slurm_extra}"

tests/tests.py

@@ -16,12 +16,12 @@ def get_executor(self) -> str:
         return "slurm"
 
     def get_executor_settings(self) -> Optional[ExecutorSettingsBase]:
-        return ExecutorSettings()
+        return ExecutorSettings(init_seconds_before_status_checks=1)
 
 
 class TestWorkflowsRequeue(TestWorkflows):
     def get_executor_settings(self) -> Optional[ExecutorSettingsBase]:
-        return ExecutorSettings(requeue=True)
+        return ExecutorSettings(requeue=True, init_seconds_before_status_checks=1)
 
 
 class TestGresString:
@@ -110,3 +110,38 @@ def test_both_gres_and_gpu_set(self, mock_job):
             WorkflowError, match="GRES and GPU are set. Please only set one of them."
         ):
             set_gres_string(job)
+
+
+class TestWildcardsWithSlashes(snakemake.common.tests.TestWorkflowsLocalStorageBase):
+    """
+    Test handling of wildcards with slashes to ensure log directories are
+    correctly constructed.
+    """
+
+    __test__ = True
+
+    def get_executor(self) -> str:
+        return "slurm"
+
+    def get_executor_settings(self) -> Optional[ExecutorSettingsBase]:
+        return ExecutorSettings(
+            logdir="test_logdir", init_seconds_before_status_checks=1
+        )
+
+    def test_wildcard_slash_replacement(self):
+        """
+        Test that slashes in wildcards are correctly replaced with
+        underscores in log directory paths.
+        """
+
+    # Just test the wildcard sanitization logic directly
+    wildcards = ["/leading_slash", "middle/slash", "trailing/"]
+
+    # This is the actual logic from the Executor.run_job method
+    wildcard_str = "_".join(wildcards).replace("/", "_") if wildcards else ""
+
+    # Assert that slashes are correctly replaced with underscores
+    assert wildcard_str == "_leading_slash_middle_slash_trailing_"
+
+    # Verify no slashes remain in the wildcard string
+    assert "/" not in wildcard_str