snakemake-software-deployment-plugin-container 0.7.2__tar.gz → 0.7.4__tar.gz

{snakemake_software_deployment_plugin_container-0.7.2 → snakemake_software_deployment_plugin_container-0.7.4}/CHANGELOG.md

@@ -1,5 +1,19 @@
 # Changelog
 
+## [0.7.4](https://github.com/snakemake/snakemake-software-deployment-plugin-container/compare/v0.7.3...v0.7.4) (2026-09-10)
+
+
+### Bug Fixes
+
+* handle runtime setup (for now needed by udocker) ([78cc3ac](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/78cc3ace79c5a6305ae2676a82d46b83f30a2347))
+
+## [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)
 
 

{snakemake_software_deployment_plugin_container-0.7.2 → snakemake_software_deployment_plugin_container-0.7.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: snakemake-software-deployment-plugin-container
-Version: 0.7.2
+Version: 0.7.4
 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-0.7.2 → snakemake_software_deployment_plugin_container-0.7.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "snakemake-software-deployment-plugin-container"
-version = "0.7.2"
+version = "0.7.4"
 authors = [
     { name = "Ben Carrillo", email = "ben.uzh@pm.me" },
     { name = "Johannes Köster", email = "johannes.koester@uni-due.de" }

{snakemake_software_deployment_plugin_container-0.7.2 → snakemake_software_deployment_plugin_container-0.7.4}/src/snakemake_software_deployment_plugin_container/__init__.py

@@ -1,3 +1,4 @@
+from typing import ClassVar
 from pathlib import Path
 from abc import abstractmethod
 from snakemake_interface_software_deployment_plugins import DeployableEnvBase
@@ -114,6 +115,13 @@ class Env(DeployableEnvBase, EnvBase):
         elif self.settings.runtime == Runtime.UDOCKER:
             self.runtime_manager = RuntimeManagerUdocker(self)
 
+        # Handle runtime manager setup if needed.
+        # This is only done once per runtime manager type, not per environment.
+        if not self.runtime_manager.is_setup:
+            if self.runtime_manager.setup_cmd() is not None:
+                self.run_cmd(self.runtime_manager.setup_cmd(), check=True)
+            self.runtime_manager.is_setup = True
+
     # The decorator ensures that the decorated method is only called once
     # in case multiple environments of the same kind are created.
     @EnvBase.once
@@ -204,6 +212,10 @@ class Env(DeployableEnvBase, EnvBase):
 @dataclass
 class RuntimeManager:
     env: Env
+    is_setup: ClassVar[bool] = False
+
+    def setup_cmd(self) -> str | None:
+        return None
 
     def deployed_image_name(self) -> str:
         return (
@@ -218,6 +230,9 @@ class RuntimeManager:
     @abstractmethod
     def deploy_cmd(self) -> str | None: ...
 
+    def pre_subcommand_options(self) -> str:
+        return ""
+
     def options(self) -> str:
         return "--rm"
 
@@ -256,7 +271,9 @@ 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}"
@@ -319,6 +336,12 @@ class RuntimeManagerDocker(RuntimeManager):
 
 
 class RuntimeManagerUdocker(RuntimeManager):
+    def setup_cmd(self) -> str | None:
+        return "udocker install"
+
+    def pre_subcommand_options(self) -> str:
+        return "--quiet"
+
     def options(self) -> str:
         options = super().options()
         options += " --nobanner --env TINI_SUBREAPER=1"