snakemake-software-deployment-plugin-container 0.6.3__tar.gz → 0.7.2__tar.gz

{snakemake_software_deployment_plugin_container-0.6.3 → snakemake_software_deployment_plugin_container-0.7.2}/CHANGELOG.md

@@ -1,5 +1,26 @@
 # Changelog
 
+## [0.7.2](https://github.com/snakemake/snakemake-software-deployment-plugin-container/compare/v0.7.1...v0.7.2) (2026-09-08)
+
+
+### Performance Improvements
+
+* explicit handling of deployment ([#25](https://github.com/snakemake/snakemake-software-deployment-plugin-container/issues/25)) ([127dff9](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/127dff9b49f81a0fd55504676e1385b1dea977f7))
+
+## [0.7.1](https://github.com/snakemake/snakemake-software-deployment-plugin-container/compare/v0.7.0...v0.7.1) (2026-09-07)
+
+
+### Bug Fixes
+
+* bump twine ([6a5fcdf](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/6a5fcdf33ff93101266551449e090f3a13d569b7))
+
+## [0.7.0](https://github.com/snakemake/snakemake-software-deployment-plugin-container/compare/v0.6.3...v0.7.0) (2026-09-07)
+
+
+### Features
+
+* auto-pass workflow environment variables into container ([#21](https://github.com/snakemake/snakemake-software-deployment-plugin-container/issues/21)) ([3083669](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/3083669e9e250053508099d26cfef93ec4fa8432))
+
 ## [0.6.3](https://github.com/snakemake/snakemake-software-deployment-plugin-container/compare/v0.6.2...v0.6.3) (2026-07-24)
 
 

{snakemake_software_deployment_plugin_container-0.6.3 → snakemake_software_deployment_plugin_container-0.7.2}/PKG-INFO

@@ -1,13 +1,13 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: snakemake-software-deployment-plugin-container
-Version: 0.6.3
+Version: 0.7.2
 Project-URL: repository, https://github.com/snakemake/snakemake-software-deployment-plugin-container
 Project-URL: documentation, https://snakemake.github.io/snakemake-plugin-catalog/plugins/software-deployment/container.html
 Author-email: Ben Carrillo <ben.uzh@pm.me>, Johannes Köster <johannes.koester@uni-due.de>
 License-File: LICENSE
 Requires-Python: <4.0,>=3.11
 Requires-Dist: snakemake-interface-common<2.0.0,>=1.23.0
-Requires-Dist: snakemake-interface-software-deployment-plugins<1.0,>=0.16.0
+Requires-Dist: snakemake-interface-software-deployment-plugins<1.0,>=0.19.2
 Requires-Dist: udocker<2.0.0,>=1.3.17
 Description-Content-Type: text/markdown
 

{snakemake_software_deployment_plugin_container-0.6.3 → snakemake_software_deployment_plugin_container-0.7.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "snakemake-software-deployment-plugin-container"
-version = "0.6.3"
+version = "0.7.2"
 authors = [
     { name = "Ben Carrillo", email = "ben.uzh@pm.me" },
     { name = "Johannes Köster", email = "johannes.koester@uni-due.de" }
@@ -10,7 +10,7 @@ readme = "README.md"
 requires-python = ">=3.11,<4.0"
 dependencies = [
     "snakemake-interface-common (>=1.23.0,<2.0.0)",
-    "snakemake-interface-software-deployment-plugins (>=0.16.0,<1.0)",
+    "snakemake-interface-software-deployment-plugins (>=0.19.2,<1.0)",
     "udocker (>=1.3.17,<2.0.0)",
 ]
 
@@ -63,7 +63,7 @@ exclude_lines = ["pass", "\\.\\.\\."]
 fail_under = 86.0
 
 [tool.pixi.feature.publish.pypi-dependencies]
-twine = ">=6.1.0,<7"
+twine = ">=7.0,<8"
 build = ">=1.2.2,<2"
 
 

{snakemake_software_deployment_plugin_container-0.6.3 → snakemake_software_deployment_plugin_container-0.7.2}/src/snakemake_software_deployment_plugin_container/__init__.py

@@ -1,3 +1,6 @@
+from pathlib import Path
+from abc import abstractmethod
+from snakemake_interface_software_deployment_plugins import DeployableEnvBase
 import re
 
 __author__ = "ben carrillo"
@@ -91,7 +94,7 @@ class EnvSpec(EnvSpecBase):
 
 
 # All errors should be wrapped with snakemake-interface-common.errors.WorkflowError
-class Env(EnvBase):
+class Env(DeployableEnvBase, EnvBase):
     # image_repo is the de-referenced repository from where the image was obtained
     image_repo: str
     settings: Settings
@@ -159,11 +162,62 @@ class Env(EnvBase):
         # Return an empty tuple () if no software can be reported.
         return [SoftwareReport(name=self.spec.image_uri)]
 
+    def is_deployment_path_portable(self) -> bool:
+        """Return whether the deployment path matters for the environment, i.e.
+        whether the environment is portable. If this returns False, the deployment
+        path is considered for the deployment hash. For example, conda environments are not
+        portable because they hardcode the path in binaries, while containers are
+        portable.
+        """
+        return True
+
+    async def deploy(self) -> None:
+        """Deploy the environment to self.deployment_path.
+
+        When issuing shell commands, the environment should use
+        self.run_cmd(cmd: str) in order to ensure that it runs within eventual
+        parent environments (e.g. a container or an env module).
+        """
+        deploy_cmd = self.runtime_manager.deploy_cmd()
+        assert deploy_cmd is not None
+        self.deployment_path.mkdir(parents=True, exist_ok=True)
+        self.run_cmd(
+            deploy_cmd,
+            check=True,
+        )
+
+    def remove(self) -> None:
+        """Remove the deployed environment."""
+        if (
+            self.is_deployable()
+            and self.runtime_manager.deployed_image_path() is not None
+        ):
+            self.runtime_manager.deployed_image_path.unlink(missing_ok=True)
+
+    def is_deployable(self) -> bool:
+        return (
+            self.settings.runtime is Runtime.UDOCKER
+            or self.settings.runtime is Runtime.APPTAINER
+        )
+
 
 @dataclass
 class RuntimeManager:
     env: Env
 
+    def deployed_image_name(self) -> str:
+        return (
+            self.env.spec.image_uri.replace("/", "_")
+            .replace(":", "_")
+            .replace("#", "_")
+        )
+
+    @abstractmethod
+    def deployed_image_path(self) -> Path | None: ...
+
+    @abstractmethod
+    def deploy_cmd(self) -> str | None: ...
+
     def options(self) -> str:
         return "--rm"
 
@@ -217,7 +271,11 @@ class RuntimeManagerApptainer(RuntimeManager):
         return "exec"
 
     def options(self) -> str:
-        return ""
+        options = ""
+        envvars = [f"{env_var}={os.environ[env_var]}" for env_var in self.env.envvars]
+        if envvars:
+            options += f" --env {','.join(envvars)}"
+        return options
 
     def workdir_option(self) -> str:
         return "--cwd"
@@ -230,6 +288,14 @@ class RuntimeManagerApptainer(RuntimeManager):
             return super().image_uri()
         return f"docker://{super().image_uri()}"
 
+    def deployed_image_path(self) -> Path | None:
+        return (self.env.deployment_path / self.deployed_image_name()).with_suffix(
+            ".sif"
+        )
+
+    def deploy_cmd(self) -> str | None:
+        return f"apptainer pull {self.deployed_image_path()} {self.image_uri()}"
+
 
 class RuntimeManagerDocker(RuntimeManager):
     def options(self) -> str:
@@ -240,11 +306,28 @@ class RuntimeManagerDocker(RuntimeManager):
             uid = os.getuid()
             gid = os.getgid()
             options += f" --user {uid}:{gid}"
+        for env_var in self.env.envvars:
+            options += f" --env {env_var}"
         return options
 
+    def deployed_image_path(self) -> Path | None:
+        return None
+
+    def deploy_cmd(self) -> str | None:
+        # No need to deploy anything in docker, the daemon handles that on the fly.
+        return None
+
 
 class RuntimeManagerUdocker(RuntimeManager):
     def options(self) -> str:
         options = super().options()
         options += " --nobanner --env TINI_SUBREAPER=1"
+        for env_var in self.env.envvars:
+            options += f" --env {env_var}={os.environ[env_var]}"
         return options
+
+    def deployed_image_path(self) -> Path | None:
+        return None
+
+    def deploy_cmd(self) -> str | None:
+        return f"UDOCKER_DIR={self.env.deployment_path} udocker pull {self.image_uri()}"

{snakemake_software_deployment_plugin_container-0.6.3 → snakemake_software_deployment_plugin_container-0.7.2}/tests/test_plugin.py

@@ -1,7 +1,9 @@
+from collections.abc import Set
 from typing import Optional, Type
+import shutil
+import os
 
 import pytest
-import shutil
 
 from snakemake_interface_software_deployment_plugins.tests import (
     TestSoftwareDeploymentBase,
@@ -22,6 +24,10 @@ from snakemake_software_deployment_plugin_container import (
 )
 
 
+os.environ["TESTVAR1"] = "testvalue"
+os.environ["TESTVAR2"] = "testvalue2"
+
+
 class TestBase(TestSoftwareDeploymentBase):
     test_container = "quay.io/biocontainers/samtools:1.23.1--ha83d96e_0"
 
@@ -47,6 +53,9 @@ class TestBase(TestSoftwareDeploymentBase):
         # with exit code 0 (i.e. without error).
         return "samtools --version"
 
+    def get_envvars(self) -> Set[str]:
+        return {"TESTVAR1", "TESTVAR2"}
+
 
 class TestApptainerContainer(TestBase):
     __test__ = True