snakemake-interface-software-deployment-plugins 0.2.1__tar.gz → 0.2.3__tar.gz

{snakemake_interface_software_deployment_plugins-0.2.1 → snakemake_interface_software_deployment_plugins-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: snakemake-interface-software-deployment-plugins
-Version: 0.2.1
+Version: 0.2.3
 Summary: This package provides a stable interface for interactions between Snakemake and its software deployment plugins.
 License: MIT
 Author: Johannes Köster

{snakemake_interface_software_deployment_plugins-0.2.1 → snakemake_interface_software_deployment_plugins-0.2.3}/pyproject.toml

@@ -5,7 +5,7 @@ license = "MIT"
 name = "snakemake-interface-software-deployment-plugins"
 packages = [{include = "snakemake_interface_software_deployment_plugins"}]
 readme = "README.md"
-version = "0.2.1"
+version = "0.2.3"
 
 [tool.poetry.dependencies]
 argparse-dataclass = "^2.0.0"

{snakemake_interface_software_deployment_plugins-0.2.1 → snakemake_interface_software_deployment_plugins-0.2.3}/snakemake_interface_software_deployment_plugins/__init__.py

@@ -45,6 +45,7 @@ class EnvBase:
     spec: EnvSpecBase
     within: Optional["EnvBase"]
     settings: Optional[SoftwareDeploymentSettingsBase]
+    shell_executable: str
     _managed_hash_store: Optional[str] = field(init=False, default=None)
     _managed_deployment_hash_store: Optional[str] = field(init=False, default=None)
     _obj_hash: Optional[int] = field(init=False, default=None)
@@ -64,7 +65,7 @@ class EnvBase:
             key = (self.__class__, self.within)
             if key in self._cache:
                 return self._cache[key]
-            value = func(*args, **kwargs)
+            value = func(self, *args, **kwargs)
             self._cache[key] = value
             return value
 
@@ -93,7 +94,7 @@ class EnvBase:
         """
         if self.within is not None:
             cmd = self.within.managed_decorate_shellcmd(cmd)
-        return sp.run(cmd, shell=True, **kwargs)
+        return sp.run(cmd, shell=True, executable=self.shell_executable, **kwargs)
 
     def managed_decorate_shellcmd(self, cmd: str) -> str:
         cmd = self.decorate_shellcmd(cmd)

{snakemake_interface_software_deployment_plugins-0.2.1 → snakemake_interface_software_deployment_plugins-0.2.3}/snakemake_interface_software_deployment_plugins/tests.py

@@ -20,6 +20,7 @@ _TEST_SDM_NAME = "test-sdm"
 
 class TestSoftwareDeploymentBase(ABC):
     __test__ = False
+    shell_executable = "bash"
 
     @abstractmethod
     def get_env_spec(self) -> EnvSpecBase:
@@ -59,13 +60,18 @@ class TestSoftwareDeploymentBase(ABC):
         cmd = self.get_test_cmd()
         decorated_cmd = env.managed_decorate_shellcmd(cmd)
         assert cmd != decorated_cmd
-        assert sp.run(decorated_cmd, shell=True, executable="bash").returncode == 0
+        assert (
+            sp.run(
+                decorated_cmd, shell=True, executable=self.shell_executable
+            ).returncode
+            == 0
+        )
 
     def test_deploy(self, tmp_path):
         env = self._get_env(tmp_path)
         self._deploy(env, tmp_path)
         cmd = env.managed_decorate_shellcmd(self.get_test_cmd())
-        assert sp.run(cmd, shell=True, executable="bash").returncode == 0
+        assert sp.run(cmd, shell=True, executable=self.shell_executable).returncode == 0
 
     def test_archive(self, tmp_path):
         env = self._get_env(tmp_path)
@@ -85,7 +91,9 @@ class TestSoftwareDeploymentBase(ABC):
             args["deployment_prefix"] = tmp_path / "deployments"
         if issubclass(env_cls, ArchiveableEnvBase):
             args["archive_prefix"] = tmp_path / "archives"
-        return env_cls(spec=spec, within=None, **args)
+        return env_cls(
+            spec=spec, within=None, shell_executable=self.shell_executable, **args
+        )
 
     def _deploy(self, env: DeployableEnvBase, tmp_path):
         if not isinstance(env, DeployableEnvBase):