snakemake-software-deployment-plugin-container 0.5.2__tar.gz → 0.6.0__tar.gz

{snakemake_software_deployment_plugin_container-0.5.2 → snakemake_software_deployment_plugin_container-0.6.0}/CHANGELOG.md

@@ -1,5 +1,17 @@
 # Changelog
 
+## [0.6.0](https://github.com/snakemake/snakemake-software-deployment-plugin-container/compare/v0.5.2...v0.6.0) (2026-03-10)
+
+
+### Features
+
+* support for docker ([#14](https://github.com/snakemake/snakemake-software-deployment-plugin-container/issues/14)) ([1ccee66](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/1ccee662f69a60b4a3afa300c4ec3c70da96bc6a))
+
+
+### Bug Fixes
+
+* properly handle docker:// urls for non-apptainer runtimes ([2b8323d](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/2b8323d0a1731d75393ca9d5c1c2b362358ab6ba))
+
 ## [0.5.2](https://github.com/snakemake/snakemake-software-deployment-plugin-container/compare/v0.5.1...v0.5.2) (2026-03-10)
 
 

{snakemake_software_deployment_plugin_container-0.5.2 → snakemake_software_deployment_plugin_container-0.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: snakemake-software-deployment-plugin-container
-Version: 0.5.2
+Version: 0.6.0
 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-0.5.2 → snakemake_software_deployment_plugin_container-0.6.0}/pixi.lock

@@ -1336,8 +1336,8 @@ packages:
   requires_python: '>=3.11,<4.0'
 - pypi: ./
   name: snakemake-software-deployment-plugin-container
-  version: 0.5.2
-  sha256: ee1dab514017eaa893aa93b7a07a7aa76d015c50001fa559b5db0d9f8200dacb
+  version: 0.6.0
+  sha256: 18daca129554e3467d78b71f17c2e1e0d84d0ab4610be60276629e12a6cb5309
   requires_dist:
   - snakemake-interface-common>=1.23.0,<2.0.0
   - snakemake-interface-software-deployment-plugins>=0.16.0,<1.0

{snakemake_software_deployment_plugin_container-0.5.2 → snakemake_software_deployment_plugin_container-0.6.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "snakemake-software-deployment-plugin-container"
-version = "0.5.2"
+version = "0.6.0"
 authors = [
     { name = "Ben Carrillo", email = "ben.uzh@pm.me" },
     { name = "Johannes Köster", email = "johannes.koester@uni-due.de" }

{snakemake_software_deployment_plugin_container-0.5.2 → snakemake_software_deployment_plugin_container-0.6.0}/src/snakemake_software_deployment_plugin_container/__init__.py

@@ -5,6 +5,7 @@ __copyright__ = "Copyright 2025, ben carrillo"
 __email__ = "ben.uzh@pm.me"
 __license__ = "MIT"
 
+import os
 import shlex
 from dataclasses import dataclass, field
 from os import getcwd
@@ -33,6 +34,7 @@ class Runtime(SettingsEnumBase):
     UDOCKER = 0
     PODMAN = 1
     APPTAINER = 2
+    DOCKER = 3
 
 
 @dataclass
@@ -54,6 +56,16 @@ class Settings(SoftwareDeploymentSettingsBase):
             "Current working directory and the system tmpdir are always mounted.",
         },
     )
+    use_user_namespaces: bool = field(
+        default=False,
+        metadata={
+            "help": "Whether to use user namespaces (if supported by the runtime). "
+            "This can be useful to avoid permission issues, but is not always "
+            "supported. For non-docker runtimes, this is not needed. "
+            "For docker, the fallback option is to set the user and group id via "
+            "--user. This happens automatically if this flag here is not used.",
+        },
+    )
 
 
 common_settings = CommonSettings(provides="container")
@@ -92,6 +104,8 @@ class Env(EnvBase):
         self.runtime_manager = RuntimeManager(self)
         if self.settings.runtime == Runtime.APPTAINER:
             self.runtime_manager = RuntimeManagerApptainer(self)
+        elif self.settings.runtime == Runtime.DOCKER:
+            self.runtime_manager = RuntimeManagerDocker(self)
 
     # The decorator ensures that the decorated method is only called once
     # in case multiple environments of the same kind are created.
@@ -156,7 +170,10 @@ class RuntimeManager:
         return "-v"
 
     def image_uri(self) -> str:
-        return self.env.spec.image_uri
+        image_uri = self.env.spec.image_uri
+        if image_uri.startswith("docker://"):
+            return image_uri[9:]
+        return image_uri
 
     def subcommand(self) -> str:
         return "run"
@@ -208,3 +225,15 @@ class RuntimeManagerApptainer(RuntimeManager):
         if re.match(r"[a-z\.]+://", super().image_uri()):
             return super().image_uri()
         return f"docker://{super().image_uri()}"
+
+
+class RuntimeManagerDocker(RuntimeManager):
+    def options(self) -> str:
+        options = super().options()
+        if self.env.settings.use_user_namespaces:
+            options += " --userns keep-id"
+        else:
+            uid = os.getuid()
+            gid = os.getgid()
+            options += f" --user {uid}:{gid}"
+        return options

{snakemake_software_deployment_plugin_container-0.5.2 → snakemake_software_deployment_plugin_container-0.6.0}/tests/test_plugin.py

@@ -87,18 +87,33 @@ class TestUDockerContainer(TestBase):
         return Settings(runtime=Runtime.UDOCKER)
 
 
-# Helper function to check if podman is available
 def is_podman_available():
     return shutil.which("podman") is not None
 
 
+def is_docker_available():
+    return shutil.which("docker") is not None
+
+
 @pytest.mark.skipif(
     not is_podman_available(), reason="podman not available on the system"
 )
 class TestPodmanContainer(TestBase):
     __test__ = True  # activate automatic testing
 
-    def get_software_deployment_provider_settings(
+    def get_settings(
         self,
     ) -> Optional[SoftwareDeploymentSettingsBase]:
         return Settings(runtime=Runtime.PODMAN)
+
+
+@pytest.mark.skipif(
+    not is_docker_available(), reason="docker not available on the system"
+)
+class TestDockerContainer(TestBase):
+    __test__ = True  # activate automatic testing
+
+    def get_settings(
+        self,
+    ) -> Optional[SoftwareDeploymentSettingsBase]:
+        return Settings(runtime=Runtime.DOCKER)