snakemake-executor-plugin-slurm 1.6.1__py3-none-any.whl → 1.8.0__py3-none-any.whl

snakemake_executor_plugin_slurm/__init__.py

@@ -140,6 +140,14 @@ class ExecutorSettings(ExecutorSettingsBase):
             "This flag has no effect, if not set.",
         },
     )
+    qos: Optional[str] = field(
+        default=None,
+        metadata={
+            "help": "If set, the given QoS will be used for job submission.",
+            "env_var": False,
+            "required": False,
+        },
+    )
     reservation: Optional[str] = field(
         default=None,
         metadata={
@@ -299,7 +307,7 @@ class Executor(RemoteExecutor):
             "run_uuid": self.run_uuid,
             "slurm_logfile": slurm_logfile,
             "comment_str": comment_str,
-            "account": self.get_account_arg(job),
+            "account": next(self.get_account_arg(job)),
             "partition": self.get_partition_arg(job),
             "workdir": self.workflow.workdir_init,
         }
@@ -309,6 +317,9 @@ class Executor(RemoteExecutor):
         if self.workflow.executor_settings.requeue:
             call += " --requeue"
 
+        if self.workflow.executor_settings.qos:
+            call += f" --qos={self.workflow.executor_settings.qos}"
+
         if self.workflow.executor_settings.reservation:
             call += f" --reservation={self.workflow.executor_settings.reservation}"
 
@@ -657,10 +668,21 @@ We leave it to SLURM to resume your job(s)"""
         else raises an error - implicetly.
         """
         if job.resources.get("slurm_account"):
-            # here, we check whether the given or guessed account is valid
-            # if not, a WorkflowError is raised
-            self.test_account(job.resources.slurm_account)
-            return f" -A '{job.resources.slurm_account}'"
+            # split the account upon ',' and whitespace, to allow
+            # multiple accounts being given
+            accounts = [
+                a for a in re.split(r"[,\s]+", job.resources.slurm_account) if a
+            ]
+            for account in accounts:
+                # here, we check whether the given or guessed account is valid
+                # if not, a WorkflowError is raised
+                self.test_account(account)
+            # sbatch only allows one account per submission
+            # yield one after the other, if multiple were given
+            # we have to quote the account, because it might
+            # contain build-in shell commands - see issue #354
+            for account in accounts:
+                yield f" -A {shlex.quote(account)}"
         else:
             if self._fallback_account_arg is None:
                 self.logger.warning("No SLURM account given, trying to guess.")
@@ -668,7 +690,7 @@ We leave it to SLURM to resume your job(s)"""
                 if account:
                     self.logger.warning(f"Guessed SLURM account: {account}")
                     self.test_account(f"{account}")
-                    self._fallback_account_arg = f" -A {account}"
+                    self._fallback_account_arg = f" -A {shlex.quote(account)}"
                 else:
                     self.logger.warning(
                         "Unable to guess SLURM account. Trying to proceed without."
@@ -676,7 +698,7 @@ We leave it to SLURM to resume your job(s)"""
                     self._fallback_account_arg = (
                         ""  # no account specific args for sbatch
                     )
-            return self._fallback_account_arg
+            yield self._fallback_account_arg
 
     def get_partition_arg(self, job: JobExecutorInterface):
         """
@@ -691,7 +713,9 @@ We leave it to SLURM to resume your job(s)"""
                 self._fallback_partition = self.get_default_partition(job)
             partition = self._fallback_partition
         if partition:
-            return f" -p {partition}"
+            # we have to quote the partition, because it might
+            # contain build-in shell commands
+            return f" -p {shlex.quote(partition)}"
         else:
             return ""
 
@@ -719,32 +743,35 @@ 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%256 --noheader"
+        # first we need to test with sacctmgr because sshare might not
+        # work in a multicluster environment
+        cmd = f'sacctmgr -n -s list user "{os.environ["USER"]}" format=account%256'
+        sacctmgr_report = sshare_report = ""
         try:
             accounts = subprocess.check_output(
                 cmd, shell=True, text=True, stderr=subprocess.PIPE
             )
         except subprocess.CalledProcessError as e:
-            sshare_report = (
+            sacctmgr_report = (
                 "Unable to test the validity of the given or guessed"
-                f" SLURM account '{account}' with sshare: {e.stderr}."
+                f" SLURM account '{account}' with sacctmgr: {e.stderr}."
             )
             accounts = ""
 
         if not accounts.strip():
-            cmd = f'sacctmgr -n -s list user "{os.environ["USER"]}" format=account%256'
+            cmd = "sshare -U --format Account%256 --noheader"
             try:
                 accounts = subprocess.check_output(
                     cmd, shell=True, text=True, stderr=subprocess.PIPE
                 )
             except subprocess.CalledProcessError as e:
-                sacctmgr_report = (
+                sshare_report = (
                     "Unable to test the validity of the given or guessed "
-                    f"SLURM account '{account}' with sacctmgr: {e.stderr}."
+                    f"SLURM account '{account}' with sshare: {e.stderr}."
                 )
                 raise WorkflowError(
-                    f"The 'sshare' reported: '{sshare_report}' "
-                    f"and likewise 'sacctmgr' reported: '{sacctmgr_report}'."
+                    f"The 'sacctmgr' reported: '{sacctmgr_report}' "
+                    f"and likewise 'sshare' reported: '{sshare_report}'."
                 )
 
         # The set() has been introduced during review to eliminate
@@ -753,7 +780,7 @@ We leave it to SLURM to resume your job(s)"""
 
         if not accounts:
             self.logger.warning(
-                f"Both 'sshare' and 'sacctmgr' returned empty results for account "
+                f"Both 'sacctmgr' and 'sshare' returned empty results for account "
                 f"'{account}'. Proceeding without account validation."
             )
             return ""

snakemake_executor_plugin_slurm/submit_string.py

@@ -1,5 +1,18 @@
 from snakemake_executor_plugin_slurm_jobstep import get_cpu_setting
 from types import SimpleNamespace
+import shlex
+
+
+def safe_quote(value):
+    """
+    Safely quote a parameter value using shlex.quote.
+    Handles None values and converts to string if needed.
+    Returns empty quotes for empty strings.
+    """
+    str_value = str(value)
+    if str_value == "":
+        return "''"
+    return shlex.quote(str_value)
 
 
 def get_submit_command(job, params):
@@ -10,37 +23,41 @@ def get_submit_command(job, params):
     params = SimpleNamespace(**params)
 
     call = (
-        f"sbatch "
-        f"--parsable "
-        f"--job-name {params.run_uuid} "
-        f'--output "{params.slurm_logfile}" '
-        f"--export=ALL "
-        f'--comment "{params.comment_str}"'
+        "sbatch "
+        "--parsable "
+        f"--job-name {safe_quote(params.run_uuid)} "
+        f"--output {safe_quote(params.slurm_logfile)} "
+        "--export=ALL "
+        f"--comment {safe_quote(params.comment_str)}"
     )
 
     # No accout or partition checking is required, here.
     # Checking is done in the submit function.
 
     # here, only the string is used, as it already contains
-    # '-A {account_name}'
+    # "-A '{account_name}'"
     call += f" {params.account}"
     # here, only the string is used, as it already contains
-    # '- p {partition_name}'
+    # "- p '{partition_name}'"
     call += f" {params.partition}"
 
     if job.resources.get("clusters"):
-        call += f" --clusters {job.resources.clusters}"
+        call += f" --clusters {safe_quote(job.resources.clusters)}"
 
     if job.resources.get("runtime"):
-        call += f" -t {job.resources.runtime}"
+        call += f" -t {safe_quote(job.resources.runtime)}"
 
-    if job.resources.get("constraint") or isinstance(
-        job.resources.get("constraint"), str
-    ):
-        call += f" -C '{job.resources.get('constraint')}'"
+    # Both, constraint and qos are optional.
+    # If not set, they will not be added to the sbatch call.
+    # If explicitly set to an empty string,
+    # `--constraint ''` or `--qos ''` will be added.
+    constraint = job.resources.get("constraint")
+    if constraint is not None:
+        call += f" -C {safe_quote(constraint)}"
 
-    if job.resources.get("qos") or isinstance(job.resources.get("qos"), str):
-        call += f" --qos='{job.resources.qos}'"
+    qos = job.resources.get("qos")
+    if qos is not None:
+        call += f" --qos={safe_quote(qos)}"
 
     if job.resources.get("mem_mb_per_cpu"):
         call += f" --mem-per-cpu {job.resources.mem_mb_per_cpu}"
@@ -77,6 +94,7 @@ def get_submit_command(job, params):
     # ensure that workdir is set correctly
     # use short argument as this is the same in all slurm versions
     # (see https://github.com/snakemake/snakemake/issues/2014)
-    call += f" -D '{params.workdir}'"
+    if params.workdir:
+        call += f" -D {safe_quote(params.workdir)}"
 
     return call

{snakemake_executor_plugin_slurm-1.6.1.dist-info → snakemake_executor_plugin_slurm-1.8.0.dist-info}/METADATA

@@ -1,8 +1,9 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: snakemake-executor-plugin-slurm
-Version: 1.6.1
+Version: 1.8.0
 Summary: A Snakemake executor plugin for submitting jobs to a SLURM cluster.
 License: MIT
+License-File: LICENSE
 Keywords: snakemake,plugin,executor,cluster,slurm
 Author: Christian Meesters
 Author-email: meesters@uni-mainz.de
@@ -12,6 +13,7 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Requires-Dist: numpy (>=1.26.4,<3)
 Requires-Dist: pandas (>=2.2.3,<3.0.0)
 Requires-Dist: snakemake-executor-plugin-slurm-jobstep (>=0.3.0,<0.4.0)

snakemake_executor_plugin_slurm-1.8.0.dist-info/RECORD

@@ -0,0 +1,8 @@
+snakemake_executor_plugin_slurm/__init__.py,sha256=G40Rbm62GFQF7bo38OJBFEFAxa4BLYeNO66wPQuki-c,34755
+snakemake_executor_plugin_slurm/efficiency_report.py,sha256=crPfJDK4NojfRbu_wEw3ZmC3suMRABr5r-1rO5q3WEo,7429
+snakemake_executor_plugin_slurm/submit_string.py,sha256=12DaJ9BIqEMC19dKuViPU8W5mZRjBRtNDQQu7M-iEjM,3448
+snakemake_executor_plugin_slurm/utils.py,sha256=7XVXtzu7bg_89wWZisW-Zk7TNQyEgK4v_y4Y3F9uOwc,4491
+snakemake_executor_plugin_slurm-1.8.0.dist-info/METADATA,sha256=8-ktC0sGhHDPOAyxpFl1LwWc7wPueZ2PxREKrQguhME,1507
+snakemake_executor_plugin_slurm-1.8.0.dist-info/WHEEL,sha256=M5asmiAlL6HEcOq52Yi5mmk9KmTVjY2RDPtO4p9DMrc,88
+snakemake_executor_plugin_slurm-1.8.0.dist-info/licenses/LICENSE,sha256=YVc4xTLWMqGfFL36120k7rzXtsT6e4RkJsh68VVn12s,1076
+snakemake_executor_plugin_slurm-1.8.0.dist-info/RECORD,,

{snakemake_executor_plugin_slurm-1.6.1.dist-info → snakemake_executor_plugin_slurm-1.8.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.1.3
+Generator: poetry-core 2.2.0
 Root-Is-Purelib: true
 Tag: py3-none-any

snakemake_executor_plugin_slurm-1.6.1.dist-info/RECORD

@@ -1,8 +0,0 @@
-snakemake_executor_plugin_slurm/__init__.py,sha256=gQA7SwXAcpXAovDC7jlCKczjd6L3gLb-n37rGSm1MY8,33570
-snakemake_executor_plugin_slurm/efficiency_report.py,sha256=crPfJDK4NojfRbu_wEw3ZmC3suMRABr5r-1rO5q3WEo,7429
-snakemake_executor_plugin_slurm/submit_string.py,sha256=Cn9qopyQwBqs1MvZFxSyRR_7mZzCVj8_vO_JNzbiqew,2896
-snakemake_executor_plugin_slurm/utils.py,sha256=7XVXtzu7bg_89wWZisW-Zk7TNQyEgK4v_y4Y3F9uOwc,4491
-snakemake_executor_plugin_slurm-1.6.1.dist-info/LICENSE,sha256=YVc4xTLWMqGfFL36120k7rzXtsT6e4RkJsh68VVn12s,1076
-snakemake_executor_plugin_slurm-1.6.1.dist-info/METADATA,sha256=12IQgnU3tuz2cQ6N6iqhyzSmR7BD_mt9HWfenEse2r4,1434
-snakemake_executor_plugin_slurm-1.6.1.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-snakemake_executor_plugin_slurm-1.6.1.dist-info/RECORD,,