snakemake-executor-plugin-slurm 1.2.1__py3-none-any.whl → 1.2.3__py3-none-any.whl

snakemake_executor_plugin_slurm/__init__.py

@@ -653,7 +653,7 @@ We leave it to SLURM to resume your job(s)"""
         """
         tests whether the given account is registered, raises an error, if not
         """
-        cmd = "sshare -U --format Account --noheader"
+        cmd = "sshare -U --format Account%256 --noheader"
         try:
             accounts = subprocess.check_output(
                 cmd, shell=True, text=True, stderr=subprocess.PIPE

snakemake_executor_plugin_slurm/utils.py

@@ -58,6 +58,9 @@ def set_gres_string(job: JobExecutorInterface) -> str:
     gres_re = re.compile(r"^[a-zA-Z0-9_]+(:[a-zA-Z0-9_]+)?:\d+$")
     # gpu model arguments can be of type "string"
     gpu_model_re = re.compile(r"^[a-zA-Z0-9_]+$")
+    # any arguments should not start and end with ticks or
+    # quotation marks:
+    string_check = re.compile(r"^[^'\"].*[^'\"]$")
     # The Snakemake resources can be only be of type "int",
     # hence no further regex is needed.
 
@@ -81,20 +84,36 @@ def set_gres_string(job: JobExecutorInterface) -> str:
         # Validate GRES format (e.g., "gpu:1", "gpu:tesla:2")
         gres = job.resources.gres
         if not gres_re.match(gres):
-            raise WorkflowError(
-                f"Invalid GRES format: {gres}. Expected format: "
-                "'<name>:<number>' or '<name>:<type>:<number>' "
-                "(e.g., 'gpu:1' or 'gpu:tesla:2')"
-            )
+            if not string_check.match(gres):
+                raise WorkflowError(
+                    "GRES format should not be a nested string (start "
+                    "and end with ticks or quotation marks). "
+                    "Expected format: "
+                    "'<name>:<number>' or '<name>:<type>:<number>' "
+                    "(e.g., 'gpu:1' or 'gpu:tesla:2')"
+                )
+            else:
+                raise WorkflowError(
+                    f"Invalid GRES format: {gres}. Expected format: "
+                    "'<name>:<number>' or '<name>:<type>:<number>' "
+                    "(e.g., 'gpu:1' or 'gpu:tesla:2')"
+                )
         return f" --gres={job.resources.gres}"
 
     if gpu_model and gpu_string:
         # validate GPU model format
         if not gpu_model_re.match(gpu_model):
-            raise WorkflowError(
-                f"Invalid GPU model format: {gpu_model}."
-                " Expected format: '<name>' (e.g., 'tesla')"
-            )
+            if not string_check.match(gpu_model):
+                raise WorkflowError(
+                    "GPU model format should not be a nested string (start "
+                    "and end with ticks or quotation marks). "
+                    "Expected format: '<name>' (e.g., 'tesla')"
+                )
+            else:
+                raise WorkflowError(
+                    f"Invalid GPU model format: {gpu_model}."
+                    " Expected format: '<name>' (e.g., 'tesla')"
+                )
         return f" --gpus={gpu_model}:{gpu_string}"
     elif gpu_model and not gpu_string:
         raise WorkflowError("GPU model is set, but no GPU number is given")

{snakemake_executor_plugin_slurm-1.2.1.dist-info → snakemake_executor_plugin_slurm-1.2.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: snakemake-executor-plugin-slurm
-Version: 1.2.1
+Version: 1.2.3
 Summary: A Snakemake executor plugin for submitting jobs to a SLURM cluster.
 License: MIT
 Keywords: snakemake,plugin,executor,cluster,slurm

snakemake_executor_plugin_slurm-1.2.3.dist-info/RECORD

@@ -0,0 +1,7 @@
+snakemake_executor_plugin_slurm/__init__.py,sha256=M90YYpeg4KPj_ebf7uR6JvBiRPwmYtABr6FoUChfswM,31476
+snakemake_executor_plugin_slurm/submit_string.py,sha256=sXzMm5SVNQ4upIOcsIZjUqj7khnG-lieo5yJSSus5sc,2483
+snakemake_executor_plugin_slurm/utils.py,sha256=7XVXtzu7bg_89wWZisW-Zk7TNQyEgK4v_y4Y3F9uOwc,4491
+snakemake_executor_plugin_slurm-1.2.3.dist-info/LICENSE,sha256=YVc4xTLWMqGfFL36120k7rzXtsT6e4RkJsh68VVn12s,1076
+snakemake_executor_plugin_slurm-1.2.3.dist-info/METADATA,sha256=RzbmGjPq104voS-X1drzNBAfsUgcNaNcqZ-T0zSmneQ,1360
+snakemake_executor_plugin_slurm-1.2.3.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+snakemake_executor_plugin_slurm-1.2.3.dist-info/RECORD,,

{snakemake_executor_plugin_slurm-1.2.1.dist-info → snakemake_executor_plugin_slurm-1.2.3.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.1.2
+Generator: poetry-core 2.1.3
 Root-Is-Purelib: true
 Tag: py3-none-any

snakemake_executor_plugin_slurm-1.2.1.dist-info/RECORD

@@ -1,7 +0,0 @@
-snakemake_executor_plugin_slurm/__init__.py,sha256=QFAmMAvEkBg6BuEtZIFFrh8IY0C0lxZksEd_WwiCyCU,31472
-snakemake_executor_plugin_slurm/submit_string.py,sha256=sXzMm5SVNQ4upIOcsIZjUqj7khnG-lieo5yJSSus5sc,2483
-snakemake_executor_plugin_slurm/utils.py,sha256=ZzXiXFDVLs15PLJnDP0eq98fNCtzlLbhtT03ec8Ou34,3578
-snakemake_executor_plugin_slurm-1.2.1.dist-info/LICENSE,sha256=YVc4xTLWMqGfFL36120k7rzXtsT6e4RkJsh68VVn12s,1076
-snakemake_executor_plugin_slurm-1.2.1.dist-info/METADATA,sha256=3l9RutnMcL44MmGTqKEOzfAkSMD8EJwyvRO3yYiGtPc,1360
-snakemake_executor_plugin_slurm-1.2.1.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
-snakemake_executor_plugin_slurm-1.2.1.dist-info/RECORD,,