snakemake-executor-plugin-slurm 0.4.1__tar.gz → 0.4.3__tar.gz

{snakemake_executor_plugin_slurm-0.4.1 → snakemake_executor_plugin_slurm-0.4.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: snakemake-executor-plugin-slurm
-Version: 0.4.1
+Version: 0.4.3
 Summary: A Snakemake executor plugin for submitting jobs to a SLURM cluster.
 Home-page: https://github.com/snakemake/snakemake-executor-plugin-slurm
 License: MIT
@@ -14,7 +14,7 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Requires-Dist: snakemake-executor-plugin-slurm-jobstep (>=0.1.10,<0.2.0)
 Requires-Dist: snakemake-interface-common (>=1.13.0,<2.0.0)
-Requires-Dist: snakemake-interface-executor-plugins (>=8.2.0,<9.0.0)
+Requires-Dist: snakemake-interface-executor-plugins (>=9.0.0,<10.0.0)
 Requires-Dist: throttler (>=1.2.2,<2.0.0)
 Project-URL: Documentation, https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/slurm.html
 Project-URL: Repository, https://github.com/snakemake/snakemake-executor-plugin-slurm
@@ -22,4 +22,6 @@ Description-Content-Type: text/markdown
 
 # Snakemake executor plugin: slurm
 
+[![Open in Gitpod](https://gitpod.io/button/open-in-gitpod.svg)](https://gitpod.io/#https://github.com/snakemake/snakemake-executor-plugin-slurm)
+
 For documentation, see the [Snakemake plugin catalog](https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/slurm.html).

{snakemake_executor_plugin_slurm-0.4.1 → snakemake_executor_plugin_slurm-0.4.3}/README.md

@@ -1,3 +1,5 @@
 # Snakemake executor plugin: slurm
 
+[![Open in Gitpod](https://gitpod.io/button/open-in-gitpod.svg)](https://gitpod.io/#https://github.com/snakemake/snakemake-executor-plugin-slurm)
+
 For documentation, see the [Snakemake plugin catalog](https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/slurm.html).

{snakemake_executor_plugin_slurm-0.4.1 → snakemake_executor_plugin_slurm-0.4.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "snakemake-executor-plugin-slurm"
-version = "0.4.1"
+version = "0.4.3"
 description = "A Snakemake executor plugin for submitting jobs to a SLURM cluster."
 authors = [
     "Christian Meesters <meesters@uni-mainz.de>",
@@ -16,7 +16,7 @@ keywords = ["snakemake", "plugin", "executor", "cluster", "slurm"]
 [tool.poetry.dependencies]
 python = "^3.11"
 snakemake-interface-common = "^1.13.0"
-snakemake-interface-executor-plugins = "^8.2.0"
+snakemake-interface-executor-plugins = "^9.0.0"
 snakemake-executor-plugin-slurm-jobstep = "^0.1.10"
 throttler = "^1.2.2"
 

{snakemake_executor_plugin_slurm-0.4.1 → snakemake_executor_plugin_slurm-0.4.3}/snakemake_executor_plugin_slurm/__init__.py

@@ -65,7 +65,7 @@ class Executor(RemoteExecutor):
         # with job_info being of type
         # snakemake_interface_executor_plugins.executors.base.SubmittedJobInfo.
 
-        log_folder = f"group_{job.name}" if job.is_group() else f"rule_{job.name}"
+        group_or_rule = f"group_{job.name}" if job.is_group() else f"rule_{job.name}"
 
         try:
             wildcard_str = f"_{'_'.join(job.wildcards)}" if job.wildcards else ""
@@ -73,9 +73,17 @@ class Executor(RemoteExecutor):
             wildcard_str = ""
 
         slurm_logfile = os.path.abspath(
-            f".snakemake/slurm_logs/{log_folder}/%j{wildcard_str}.log"
+            f".snakemake/slurm_logs/{group_or_rule}/{wildcard_str}/%j.log"
         )
-        os.makedirs(os.path.dirname(slurm_logfile), exist_ok=True)
+        logdir = os.path.dirname(slurm_logfile)
+        # this behavior has been fixed in slurm 23.02, but there might be plenty of
+        # older versions around, hence we should rather be conservative here.
+        assert "%j" not in logdir, (
+            "bug: jobid placeholder in parent dir of logfile. This does not work as "
+            "we have to create that dir before submission in order to make sbatch "
+            "happy. Otherwise we get silent fails without logfiles being created."
+        )
+        os.makedirs(logdir, exist_ok=True)
 
         # generic part of a submission string:
         # we use a run_uuid as the job-name, to allow `--name`-based