snakemake-software-deployment-plugin-container 0.7.1__tar.gz → 0.7.3__tar.gz

{snakemake_software_deployment_plugin_container-0.7.1 → snakemake_software_deployment_plugin_container-0.7.3}/CHANGELOG.md

@@ -1,5 +1,19 @@
 # Changelog
 
+## [0.7.3](https://github.com/snakemake/snakemake-software-deployment-plugin-container/compare/v0.7.2...v0.7.3) (2026-09-10)
+
+
+### Bug Fixes
+
+* add quiet flag to udocker execution ([fcb5780](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/fcb57800287a59cee68c1ec87a47d17a304ce207))
+
+## [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)
 
 

{snakemake_software_deployment_plugin_container-0.7.1 → snakemake_software_deployment_plugin_container-0.7.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: snakemake-software-deployment-plugin-container
-Version: 0.7.1
+Version: 0.7.3
 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>

{snakemake_software_deployment_plugin_container-0.7.1 → snakemake_software_deployment_plugin_container-0.7.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "snakemake-software-deployment-plugin-container"
-version = "0.7.1"
+version = "0.7.3"
 authors = [
     { name = "Ben Carrillo", email = "ben.uzh@pm.me" },
     { name = "Johannes Köster", email = "johannes.koester@uni-due.de" }

{snakemake_software_deployment_plugin_container-0.7.1 → snakemake_software_deployment_plugin_container-0.7.3}/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 +162,65 @@ 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 pre_subcommand_options(self) -> str:
+        return ""
+
     def options(self) -> str:
         return "--rm"
 
@@ -202,7 +259,9 @@ class RuntimeManager:
     def decorate_shellcmd(self, cmd: str) -> str:
         mountpoints = self.get_mountpoint_args()
         return (
-            f"{self.env.settings.runtime} {self.subcommand()}"
+            f"{self.env.settings.runtime}"
+            f" {self.pre_subcommand_options()}"
+            f" {self.subcommand()}"
             f" {self.options()}"
             f" {self.workdir_option()} {getcwd()!r}"  # Working directory inside container
             f" {mountpoints}"
@@ -234,6 +293,14 @@ 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:
@@ -248,11 +315,27 @@ class RuntimeManagerDocker(RuntimeManager):
             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 pre_subcommand_options(self) -> str:
+        return "--quiet"
+
     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()}"