snakemake-software-deployment-plugin-container 0.6.0__tar.gz → 0.6.2__tar.gz

{snakemake_software_deployment_plugin_container-0.6.0 → snakemake_software_deployment_plugin_container-0.6.2}/.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-0.6.0 → snakemake_software_deployment_plugin_container-0.6.2}/.gitignore

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

{snakemake_software_deployment_plugin_container-0.6.0 → snakemake_software_deployment_plugin_container-0.6.2}/CHANGELOG.md

@@ -1,5 +1,19 @@
 # Changelog
 
+## [0.6.2](https://github.com/snakemake/snakemake-software-deployment-plugin-container/compare/v0.6.1...v0.6.2) (2026-06-17)
+
+
+### Bug Fixes
+
+* do not use hardcoded bash path when decorating commands ([#18](https://github.com/snakemake/snakemake-software-deployment-plugin-container/issues/18)) ([394602c](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/394602c53224f82078c3b3a4c104e66ff34503f4))
+
+## [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)
 
 

{snakemake_software_deployment_plugin_container-0.6.0 → snakemake_software_deployment_plugin_container-0.6.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: snakemake-software-deployment-plugin-container
-Version: 0.6.0
+Version: 0.6.2
 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>

{snakemake_software_deployment_plugin_container-0.6.0 → snakemake_software_deployment_plugin_container-0.6.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "snakemake-software-deployment-plugin-container"
-version = "0.6.0"
+version = "0.6.2"
 authors = [
     { name = "Ben Carrillo", email = "ben.uzh@pm.me" },
     { name = "Johannes Köster", email = "johannes.koester@uni-due.de" }

{snakemake_software_deployment_plugin_container-0.6.0 → snakemake_software_deployment_plugin_container-0.6.2}/src/snakemake_software_deployment_plugin_container/__init__.py

@@ -46,6 +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(
@@ -106,6 +108,8 @@ class Env(EnvBase):
             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.
@@ -203,7 +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
+            " bash"  # Shell executable
             f" -c {shlex.quote(cmd)}"  # The command to execute
         )
 
@@ -237,3 +241,10 @@ class RuntimeManagerDocker(RuntimeManager):
             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-0.6.0 → snakemake_software_deployment_plugin_container-0.6.2}/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,