snakemake-executor-plugin-finished 0.1.0__py3-none-any.whl

snakemake_executor_plugin_finished/__init__.py

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+from snakemake_interface_executor_plugins.settings import CommonSettings
+
+from .executor import Executor
+
+common_settings = CommonSettings(
+    non_local_exec=False,
+    dryrun_exec=False,
+    implies_no_shared_fs=False,
+    job_deploy_sources=False,
+    touch_exec=True,
+    pass_envvar_declarations_to_cmd=False,
+    auto_deploy_default_storage_provider=False,
+)
+
+__all__ = ["Executor", "common_settings"]

snakemake_executor_plugin_finished/executor.py

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+from __future__ import annotations
+
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Iterable, Set
+
+from snakemake_interface_common.exceptions import WorkflowError
+from snakemake_interface_executor_plugins.executors.base import (
+    AbstractExecutor,
+    SubmittedJobInfo,
+)
+from snakemake_interface_executor_plugins.jobs import JobExecutorInterface
+from snakemake_interface_executor_plugins.logging import LoggerExecutorInterface
+from snakemake_interface_executor_plugins.workflow import WorkflowExecutorInterface
+
+
+@dataclass
+class FinishedTargets:
+    """Tracks requested targets and which remain unmatched."""
+
+    requested: Set[str]
+    remaining: Set[str]
+
+
+class Executor(AbstractExecutor):
+    """Mark targets as finished without executing jobs."""
+
+    _targets: FinishedTargets
+
+    def __init__(
+        self, workflow: WorkflowExecutorInterface, logger: LoggerExecutorInterface
+    ) -> None:
+        super().__init__(workflow, logger)
+        targets = self._resolve_targets()
+        if not targets:
+            raise WorkflowError(
+                "No targets specified for finished executor. "
+                "Provide targets as positional arguments."
+            )
+        self._targets = FinishedTargets(requested=targets, remaining=set(targets))
+
+    def _normalize_targets(self, targets: Iterable[str]) -> Set[str]:
+        return {str(target) for target in targets}
+
+    def _resolve_targets(self) -> Set[str]:
+        dag = self.workflow.dag
+        targets = getattr(dag, "derived_targetfiles", None)
+        if targets is None:
+            targets = getattr(dag, "targetfiles", None)
+        if not targets:
+            return set()
+        return self._normalize_targets(targets)
+
+    def _job_target(self, job: JobExecutorInterface) -> str | None:
+        target = getattr(job, "targetfile", None)
+        if target is None:
+            return None
+        return str(target)
+
+    def _job_outputs(self, job: JobExecutorInterface) -> Set[str]:
+        return {str(output) for output in job.output}
+
+    def _touch_target(self, target: str) -> None:
+        target_path = Path(target)
+        target_path.touch()
+        if target_path.is_dir():
+            (target_path / ".snakemake_timestamp").touch()
+
+    def run_job(self, job: JobExecutorInterface) -> None:
+        job_info = SubmittedJobInfo(job=job)
+        self.report_job_submission(job_info)
+
+        job_targets = set()
+        target = self._job_target(job)
+        if target is not None:
+            job_targets.add(target)
+        job_targets.update(self._job_outputs(job))
+        matches = self._targets.remaining.intersection(job_targets)
+        if matches:
+            missing = sorted(match for match in matches if not Path(match).exists())
+            if missing:
+                raise WorkflowError("Target files do not exist: " + ", ".join(missing))
+            self.workflow.async_run(self.workflow.persistence.finished(job))
+            for match in sorted(matches):
+                self._touch_target(match)
+            self.logger.info(
+                f"Job '{job.name}' marked as finished for: {', '.join(sorted(matches))}"
+            )
+            self._targets.remaining.difference_update(matches)
+
+        self.report_job_success(job_info)
+
+    def shutdown(self) -> None:
+        if self._targets.remaining:
+            missing = sorted(self._targets.remaining)
+            raise WorkflowError(
+                f"Something went wrong, the following targets were not found: {missing}"
+            )
+
+    def cancel(self) -> None:
+        pass
+
+    def handle_job_success(self, job: JobExecutorInterface) -> None:
+        pass
+
+    def handle_job_error(self, job: JobExecutorInterface) -> None:
+        pass

snakemake_executor_plugin_finished-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: snakemake-executor-plugin-finished
+Version: 0.1.0
+Summary: Snakemake executor plugin that marks targets as finished
+Project-URL: Repository, https://github.com/alephreish/snakemake-executor-plugin-finished
+Project-URL: Documentation, https://snakemake.github.io/snakemake-plugin-catalog/plugins/executor/finished.html
+Author-email: Andrey Rozenberg <alephreish@gmail.com>
+License-File: LICENSE
+Requires-Python: <4.0,>=3.11
+Requires-Dist: snakemake-interface-common<2,>=1.23.0
+Requires-Dist: snakemake-interface-executor-plugins<10,>=9.0.0

snakemake_executor_plugin_finished-0.1.0.dist-info/RECORD

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+snakemake_executor_plugin_finished/__init__.py,sha256=Eqn49aSkdqvWoxT02J1r-NwCKE446_PG9qDS23DZ2cY,408
+snakemake_executor_plugin_finished/executor.py,sha256=_-sgdpAXK23ROLcoYN5vTntnlYfdcVJqSBaEKYWiwdM,3749
+snakemake_executor_plugin_finished-0.1.0.dist-info/METADATA,sha256=YqqYO0mvHc3OwHiTdxJ2VzykrEl61XeaF5AkZpG0E78,567
+snakemake_executor_plugin_finished-0.1.0.dist-info/WHEEL,sha256=mffPy8wBnZQn2VnJUU5jE99KsxaSfiyMHV9Yt0aLVxs,87
+snakemake_executor_plugin_finished-0.1.0.dist-info/licenses/LICENSE,sha256=0KHw8Fby7qS29jRRdKIuOCXE3Dkj1hZatJZrDuRIKYM,1073
+snakemake_executor_plugin_finished-0.1.0.dist-info/RECORD,,

snakemake_executor_plugin_finished-0.1.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: hatchling 1.30.1
+Root-Is-Purelib: true
+Tag: py3-none-any

snakemake_executor_plugin_finished-0.1.0.dist-info/licenses/LICENSE

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+MIT License
+
+Copyright (c) 2026 Andrey Rozenberg
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.