snakemake-software-deployment-plugin-container 0.5.2__tar.gz → 0.6.1__tar.gz

{snakemake_software_deployment_plugin_container-0.5.2 → snakemake_software_deployment_plugin_container-0.6.1}/.github/workflows/ci.yml

@@ -41,6 +41,10 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@v0
 
+      - run: |
+          sudo sysctl -w kernel.apparmor_restrict_unprivileged_unconfined=0
+          sudo sysctl -w kernel.apparmor_restrict_unprivileged_userns=0
+
       - name: Run pytest
         run: pixi run test -v
 

{snakemake_software_deployment_plugin_container-0.5.2 → snakemake_software_deployment_plugin_container-0.6.1}/.gitignore

@@ -5,3 +5,8 @@ __pycache__/
 *$py.class
 *.swp
 *.swo
+
+/.coverage
+/pixi.lock
+/.zed
+coverage.xml

{snakemake_software_deployment_plugin_container-0.5.2 → snakemake_software_deployment_plugin_container-0.6.1}/CHANGELOG.md

@@ -1,5 +1,24 @@
 # Changelog
 
+## [0.6.1](https://github.com/snakemake/snakemake-software-deployment-plugin-container/compare/v0.6.0...v0.6.1) (2026-06-03)
+
+
+### Bug Fixes
+
+* add parse and unparse func for runtime argument ([e4f9a8d](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/e4f9a8df27ea4848b46127f7f88e8045202ed489))
+
+## [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-0.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: snakemake-software-deployment-plugin-container
-Version: 0.5.2
+Version: 0.6.1
 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-0.6.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "snakemake-software-deployment-plugin-container"
-version = "0.5.2"
+version = "0.6.1"
 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-0.6.1}/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
@@ -44,6 +46,8 @@ class Settings(SoftwareDeploymentSettingsBase):
             "env_var": False,
             "required": False,
             "choices": Runtime.choices(),
+            "parse_func": Runtime.parse_choice,
+            "unparse_func": Runtime.item_to_choice,
         },
     )
     mountpoints: List[str] = field(
@@ -54,6 +58,16 @@ 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 +106,10 @@ 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)
+        elif self.settings.runtime == Runtime.UDOCKER:
+            self.runtime_manager = RuntimeManagerUdocker(self)
 
     # The decorator ensures that the decorated method is only called once
     # in case multiple environments of the same kind are created.
@@ -156,7 +174,10 @@ 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"
@@ -186,7 +207,7 @@ class RuntimeManager:
             f" {self.workdir_option()} {getcwd()!r}"  # Working directory inside container
             f" {mountpoints}"
             f" {self.image_uri()}"  # Container image
-            " /bin/sh"  # Shell executable
+            " /bin/bash"  # Shell executable
             f" -c {shlex.quote(cmd)}"  # The command to execute
         )
 
@@ -208,3 +229,22 @@ 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
+
+
+class RuntimeManagerUdocker(RuntimeManager):
+    def options(self) -> str:
+        options = super().options()
+        options += " --nobanner --env TINI_SUBREAPER=1"
+        return options

{snakemake_software_deployment_plugin_container-0.5.2 → snakemake_software_deployment_plugin_container-0.6.1}/tests/test_plugin.py

@@ -21,18 +21,13 @@ from snakemake_software_deployment_plugin_container import (
     Runtime,
 )
 
-# There can be multiple subclasses of SoftwareDeploymentProviderBase here.
-# This way, you can implement multiple test scenarios.
-# For each subclass, the test suite tests the environment activation and execution
-# within, and, if applicable, environment deployment and archiving.
-
 
 class TestBase(TestSoftwareDeploymentBase):
-    test_container = "alpine:latest"
+    test_container = "quay.io/biocontainers/samtools:1.23.1--ha83d96e_0"
 
     def get_contained_executable(self) -> str:
         # just provide something that is available inside of the container
-        return "sh"
+        return "samtools"
 
     def get_env_spec(self) -> EnvSpecBase:
         # If the software deployment provider does not support deployable environments,
@@ -50,27 +45,11 @@ class TestBase(TestSoftwareDeploymentBase):
     def get_test_cmd(self) -> str:
         # Return a test command that should be executed within the environment
         # with exit code 0 (i.e. without error).
-        return "/bin/true"
+        return "samtools --version"
 
 
 class TestApptainerContainer(TestBase):
-    # TODO reactivate apptainer tests, they currently fail in CI with
-    # ERROR  : Could not write info to setgroups: Permission denied
-    # ERROR  : Error while waiting event for user namespace mappings: no event received
-    __test__ = False
-
-    def get_settings(
-        self,
-    ) -> Optional[SoftwareDeploymentSettingsBase]:
-        return Settings(runtime=Runtime.APPTAINER)
-
-
-class TestApptainerContainerWithScheme(TestBase):
-    # TODO reactivate apptainer tests, they currently fail in CI with
-    # ERROR  : Could not write info to setgroups: Permission denied
-    # ERROR  : Error while waiting event for user namespace mappings: no event received
-    __test__ = False
-    test_container = "docker://alpine:latest"
+    __test__ = True
 
     def get_settings(
         self,
@@ -87,18 +66,33 @@ 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)