fix: address mypy issues

.github/workflows/test.yml

@@ -35,10 +35,11 @@ jobs:
         if: always()
         run: |
           pixi run --environment dev lint --diff
-      # - name: Mypy
-      #   if: always()
-      #   run: |
-      #     pixi run --environment dev type-check
+
+      - name: Mypy
+        if: always()
+        run: |
+          pixi run --environment dev type-check
 
       - name: Collect QC
         run: echo "All quality control checks passed"

snakemake_interface_executor_plugins/executors/base.py

@@ -21,13 +21,18 @@ class SubmittedJobInfo:
 
 
 class AbstractExecutor(ABC):
+    workflow: WorkflowExecutorInterface
+    logger: LoggerExecutorInterface
+
     def __init__(
         self,
         workflow: WorkflowExecutorInterface,
         logger: LoggerExecutorInterface,
     ):
         self.workflow = workflow
-        self.dag = workflow.dag
+        self.dag = (
+            workflow.dag
+        )  # we cant type annotate this because dag type is in snakemake
         self.logger = logger
 
     def get_resource_declarations_dict(self, job: JobExecutorInterface):

snakemake_interface_executor_plugins/executors/real.py

@@ -4,15 +4,15 @@
 __license__ = "MIT"
 
 from abc import abstractmethod
-from typing import Dict
+from typing import Mapping
 
 from snakemake_interface_common import at_least_snakemake_version
 from snakemake_interface_executor_plugins.executors.base import (
     AbstractExecutor,
     SubmittedJobInfo,
 )
 from snakemake_interface_executor_plugins.logging import LoggerExecutorInterface
-from snakemake_interface_executor_plugins.settings import ExecMode
+from snakemake_interface_executor_plugins.settings import ExecMode, ExecutorSettingsBase
 from snakemake_interface_executor_plugins.utils import (
     encode_target_jobs_cli_args,
     format_cli_arg,
@@ -23,6 +23,12 @@
 
 
 class RealExecutor(AbstractExecutor):
+    # Class attributes with type annotations
+    workflow: WorkflowExecutorInterface
+    logger: LoggerExecutorInterface
+    executor_settings: ExecutorSettingsBase
+    snakefile: str
+
     def __init__(
         self,
         workflow: WorkflowExecutorInterface,
@@ -179,5 +185,5 @@ def format_job_exec(self, job: JobExecutorInterface) -> str:
         )
         return args
 
-    def envvars(self) -> Dict[str, str]:
+    def envvars(self) -> Mapping[str, str]:
         return self.workflow.spawned_job_args_factory.envvars()

snakemake_interface_executor_plugins/executors/remote.py

@@ -12,7 +12,7 @@
 import sys
 import tempfile
 import threading
-from typing import Generator, List
+from typing import Generator, List, Optional
 from snakemake_interface_common.exceptions import WorkflowError
 from snakemake_interface_executor_plugins.executors.base import SubmittedJobInfo
 from snakemake_interface_executor_plugins.executors.real import RealExecutor
@@ -36,7 +36,20 @@ class RemoteExecutor(RealExecutor, ABC):
     also for the cloud.
     """
 
-    default_jobscript = "jobscript.sh"
+    # Class attributes with type annotations
+    default_jobscript: str = "jobscript.sh"
+    _next_seconds_between_status_checks: Optional[int]
+    max_status_checks_per_second: float
+    jobname: str
+    snakefile: str
+    is_default_jobscript: bool
+    jobscript: str
+    _tmpdir: Optional[str]
+    active_jobs: List[SubmittedJobInfo]
+    lock: threading.Lock
+    wait: bool
+    wait_thread: threading.Thread
+    status_rate_limiter: Throttler
 
     def __init__(
         self,
@@ -118,7 +131,7 @@ def cancel_jobs(self, active_jobs: List[SubmittedJobInfo]):
         ...
 
     def get_exec_mode(self) -> ExecMode:
-        return ExecMode.REMOTE
+        return ExecMode.REMOTE  # type: ignore
 
     def get_python_executable(self):
         return (
@@ -128,7 +141,7 @@ def get_python_executable(self):
             else "python"
         )
 
-    def get_job_args(self, job: JobExecutorInterface):
+    def get_job_args(self, job: JobExecutorInterface, **kwargs):
         waitfiles_parameter = ""
         if SharedFSUsage.INPUT_OUTPUT in self.workflow.storage_settings.shared_fs_usage:
             wait_for_files = []
@@ -148,7 +161,7 @@ def get_job_args(self, job: JobExecutorInterface):
             else:
                 waitfiles_parameter = format_cli_arg("--wait-for-files", wait_for_files)
 
-        return f"{super().get_job_args(job)} {waitfiles_parameter}"
+        return f"{super().get_job_args(job, **kwargs)} {waitfiles_parameter}"
 
     def report_job_submission(
         self, job_info: SubmittedJobInfo, register_job: bool = True

snakemake_interface_executor_plugins/jobs.py

@@ -5,9 +5,10 @@
 
 from abc import ABC, abstractmethod
 import sys
-from typing import Any, Iterable, Mapping, Optional, Sequence, Union
+from typing import Any, Iterable, Mapping, Optional, Sequence, Union, List
 
 from snakemake_interface_common.rules import RuleInterface
+from snakemake_interface_executor_plugins.utils import TargetSpec
 
 
 class JobExecutorInterface(ABC):
@@ -58,7 +59,7 @@ def output(self) -> Iterable[str]: ...
     def register(self, external_jobid: Optional[str] = None) -> None: ...
 
     @abstractmethod
-    def get_target_spec(self) -> str: ...
+    def get_target_spec(self) -> List[TargetSpec]: ...
 
     @abstractmethod
     def rules(self) -> Iterable[RuleInterface]: ...

snakemake_interface_executor_plugins/scheduler.py

@@ -4,8 +4,14 @@
 __license__ = "MIT"
 
 from abc import ABC, abstractmethod
+from typing import Callable
+from snakemake_interface_executor_plugins.jobs import JobExecutorInterface
 
 
 class JobSchedulerExecutorInterface(ABC):
+    submit_callback: Callable[[JobExecutorInterface], None]
+    finish_callback: Callable[[JobExecutorInterface], None]
+    error_callback: Callable[[JobExecutorInterface], None]
+
     @abstractmethod
     def executor_error_callback(self, exception: Exception) -> None: ...

snakemake_interface_executor_plugins/settings.py

@@ -1,8 +1,12 @@
 from abc import ABC, abstractmethod
 from dataclasses import dataclass
-from typing import List, Sequence, Set
+from typing import Callable, Iterable, List, Sequence, Set
 
-from snakemake_interface_common.settings import SettingsEnumBase, TSettingsEnumBase
+from snakemake_interface_common.settings import (
+    SettingsEnumBase,
+    TContainer,
+    TSettingsEnumBase,
+)
 
 
 import snakemake_interface_common.plugin_registry.plugin
@@ -149,15 +153,18 @@ def choices(cls) -> List[str]:
         return super().choices() + ["none"]
 
     @classmethod
-    def _parse_choices_into(cls, choices: str, container) -> List[TSettingsEnumBase]:
+    def _parse_choices_into(
+        cls,
+        choices: List[str],
+        container: Callable[[Iterable[TSettingsEnumBase]], TContainer],
+    ) -> TContainer:
         if "none" in choices:
             if len(choices) > 1:
                 raise ValueError(
                     "Cannot specify 'none' together with other shared filesystem usages."
                 )
             return container([])
-        else:
-            return container(cls.parse_choice(choice) for choice in choices)
+        return super()._parse_choices_into(choices, container)
 
 
 class StorageSettingsExecutorInterface(ABC):

snakemake_interface_executor_plugins/workflow.py

@@ -21,6 +21,7 @@
     GroupSettingsExecutorInterface,
     RemoteExecutionSettingsExecutorInterface,
     StorageSettingsExecutorInterface,
+    ExecutorSettingsBase,
 )
 
 
@@ -53,6 +54,10 @@ def group_settings(self) -> GroupSettingsExecutorInterface: ...
     @abstractmethod
     def executor_plugin(self) -> Optional[Plugin]: ...
 
+    @property
+    @abstractmethod
+    def executor_settings(self) -> ExecutorSettingsBase: ...
+
     @property
     @abstractmethod
     def resource_scopes(self): ...
@@ -72,3 +77,7 @@ def workdir_init(self): ...
     @property
     @abstractmethod
     def scheduler(self) -> JobSchedulerExecutorInterface: ...
+
+    @property
+    @abstractmethod
+    def dag(self): ...

tests/tests.py

@@ -1,9 +1,15 @@
 from typing import List
+from types import SimpleNamespace
+from unittest.mock import Mock, patch
+import pytest
+from snakemake_interface_executor_plugins.executors.real import RealExecutor
+from snakemake_interface_executor_plugins.executors.remote import RemoteExecutor
 from snakemake_interface_executor_plugins.registry import ExecutorPluginRegistry
 from snakemake_interface_common.plugin_registry.tests import TestRegistryBase
 from snakemake_interface_common.plugin_registry.plugin import PluginBase, SettingsBase
 from snakemake_interface_common.plugin_registry import PluginRegistryBase
 from snakemake_interface_executor_plugins.utils import format_cli_arg
+from snakemake_interface_executor_plugins.settings import SharedFSUsage
 
 
 class TestRegistry(TestRegistryBase):
@@ -54,3 +60,39 @@ def test_format_cli_arg_expr():
 def test_format_cli_arg_list():
     fmt = format_cli_arg("--config", ["foo={'bar': 1}"])
     assert fmt == "--config \"foo={'bar': 1}\""
+
+
+def test_shared_fs_usage_parses_none_and_regular_choices():
+    assert SharedFSUsage.parse_choices_list(["none"]) == []
+    assert SharedFSUsage.parse_choices_set(["none"]) == set()
+    assert SharedFSUsage.parse_choices_list(["input-output"]) == [
+        SharedFSUsage.INPUT_OUTPUT
+    ]
+    assert SharedFSUsage.parse_choices_set(["input-output"]) == {
+        SharedFSUsage.INPUT_OUTPUT
+    }
+    with pytest.raises(ValueError, match="Cannot specify 'none'"):
+        SharedFSUsage.parse_choices_set(["none", "input-output"])
+
+
+def test_remote_job_args_forward_cores_to_real_executor():
+    class StubRemote(RemoteExecutor):
+        def run_job(self, job):
+            pass
+
+        def cancel_jobs(self, active_jobs):
+            pass
+
+        async def check_active_jobs(self, active_jobs):
+            pass
+
+    remote = object.__new__(StubRemote)
+    remote.workflow = SimpleNamespace(
+        storage_settings=SimpleNamespace(shared_fs_usage=set())
+    )
+    job = Mock()
+    with patch.object(RealExecutor, "get_job_args", return_value="--cores 2") as parent:
+        result = remote.get_job_args(job, cores=2)
+
+    parent.assert_called_once_with(job, cores=2)
+    assert "--cores 2" in result