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fix: better handling of allowed rules in combination with snakemake >=9.6.2 #89

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merged 2 commits into from
Jun 23, 2025
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fix: better handling of allowed rules in combination with snakemake >=9.6.2 #89

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fix: better handling of allowed rules in combination with snakemake >…
johanneskoester Jun 23, 2025
73ee7ac
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johanneskoester Jun 23, 2025
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2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ license = { text = "MIT" }
readme = "README.md"
requires-python = ">=3.11"
dependencies = [
"snakemake-interface-common>=1.17.4",
"snakemake-interface-common>=1.19.0",
"throttler>=1.2.2",
"argparse-dataclass>=2.0.0",
]
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56 changes: 30 additions & 26 deletions snakemake_interface_executor_plugins/executors/real.py
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Expand Up @@ -5,6 +5,8 @@

from abc import abstractmethod
from typing import Dict

from snakemake_interface_common import at_least_snakemake_version
from snakemake_interface_executor_plugins.executors.base import (
AbstractExecutor,
SubmittedJobInfo,
Expand Down Expand Up @@ -79,32 +81,34 @@ def additional_general_args(self):

def get_job_args(self, job: JobExecutorInterface, **kwargs):
unneeded_temp_files = list(self.workflow.dag.get_unneeded_temp_files(job))
return join_cli_args(
[
format_cli_arg(
"--target-jobs", encode_target_jobs_cli_args(job.get_target_spec())
),
# Restrict considered rules for faster DAG computation.
# This does not work for updated jobs because they need
# to be updated in the spawned process as well.
format_cli_arg(
"--allowed-rules",
job.rules,
quote=False,
skip=job.is_updated,
),
# Ensure that a group uses its proper local groupid.
format_cli_arg("--local-groupid", job.jobid, skip=not job.is_group()),
format_cli_arg("--cores", kwargs.get("cores", self.cores)),
format_cli_arg("--attempt", job.attempt),
format_cli_arg("--force-use-threads", not job.is_group()),
format_cli_arg(
"--unneeded-temp-files",
unneeded_temp_files,
skip=not unneeded_temp_files,
),
]
)
arg_list = [
format_cli_arg(
"--target-jobs", encode_target_jobs_cli_args(job.get_target_spec())
),
# Restrict considered rules for faster DAG computation.
format_cli_arg(
"--allowed-rules",
job.rules,
quote=False,
# Via this fix: https://github.com/snakemake/snakemake/pull/3640
# --allowed-rules can be always used. The fix is released in
# snakemake 9.6.2. Before, --allowed-rules had to be skipped
# for jobs that have been updated after checkpoint evaluation.
skip=job.is_updated and not at_least_snakemake_version("9.6.2"),
),
# Ensure that a group uses its proper local groupid.
format_cli_arg("--local-groupid", job.jobid, skip=not job.is_group()),
format_cli_arg("--cores", kwargs.get("cores", self.cores)),
format_cli_arg("--attempt", job.attempt),
format_cli_arg("--force-use-threads", not job.is_group()),
format_cli_arg(
"--unneeded-temp-files",
unneeded_temp_files,
skip=not unneeded_temp_files,
),
]

return join_cli_args(arg_list)

@property
def job_specific_local_groupid(self):
Expand Down