snakemake-software-deployment-plugin-container 0.6.2__tar.gz → 0.7.1__tar.gz

{snakemake_software_deployment_plugin_container-0.6.2 → snakemake_software_deployment_plugin_container-0.7.1}/CHANGELOG.md

@@ -1,5 +1,26 @@
 # Changelog
 
+## [0.7.1](https://github.com/snakemake/snakemake-software-deployment-plugin-container/compare/v0.7.0...v0.7.1) (2026-09-07)
+
+
+### Bug Fixes
+
+* bump twine ([6a5fcdf](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/6a5fcdf33ff93101266551449e090f3a13d569b7))
+
+## [0.7.0](https://github.com/snakemake/snakemake-software-deployment-plugin-container/compare/v0.6.3...v0.7.0) (2026-09-07)
+
+
+### Features
+
+* auto-pass workflow environment variables into container ([#21](https://github.com/snakemake/snakemake-software-deployment-plugin-container/issues/21)) ([3083669](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/3083669e9e250053508099d26cfef93ec4fa8432))
+
+## [0.6.3](https://github.com/snakemake/snakemake-software-deployment-plugin-container/compare/v0.6.2...v0.6.3) (2026-07-24)
+
+
+### Bug Fixes
+
+* use shell_executable attribute ([643d62a](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/643d62ad24e9f61187fe870f26ee55fa13134269))
+
 ## [0.6.2](https://github.com/snakemake/snakemake-software-deployment-plugin-container/compare/v0.6.1...v0.6.2) (2026-06-17)
 
 

{snakemake_software_deployment_plugin_container-0.6.2 → snakemake_software_deployment_plugin_container-0.7.1}/PKG-INFO

@@ -1,13 +1,13 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: snakemake-software-deployment-plugin-container
-Version: 0.6.2
+Version: 0.7.1
 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>
 License-File: LICENSE
 Requires-Python: <4.0,>=3.11
 Requires-Dist: snakemake-interface-common<2.0.0,>=1.23.0
-Requires-Dist: snakemake-interface-software-deployment-plugins<1.0,>=0.16.0
+Requires-Dist: snakemake-interface-software-deployment-plugins<1.0,>=0.19.2
 Requires-Dist: udocker<2.0.0,>=1.3.17
 Description-Content-Type: text/markdown
 

{snakemake_software_deployment_plugin_container-0.6.2 → snakemake_software_deployment_plugin_container-0.7.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "snakemake-software-deployment-plugin-container"
-version = "0.6.2"
+version = "0.7.1"
 authors = [
     { name = "Ben Carrillo", email = "ben.uzh@pm.me" },
     { name = "Johannes Köster", email = "johannes.koester@uni-due.de" }
@@ -10,7 +10,7 @@ readme = "README.md"
 requires-python = ">=3.11,<4.0"
 dependencies = [
     "snakemake-interface-common (>=1.23.0,<2.0.0)",
-    "snakemake-interface-software-deployment-plugins (>=0.16.0,<1.0)",
+    "snakemake-interface-software-deployment-plugins (>=0.19.2,<1.0)",
     "udocker (>=1.3.17,<2.0.0)",
 ]
 
@@ -63,7 +63,7 @@ exclude_lines = ["pass", "\\.\\.\\."]
 fail_under = 86.0
 
 [tool.pixi.feature.publish.pypi-dependencies]
-twine = ">=6.1.0,<7"
+twine = ">=7.0,<8"
 build = ">=1.2.2,<2"
 
 

{snakemake_software_deployment_plugin_container-0.6.2 → snakemake_software_deployment_plugin_container-0.7.1}/src/snakemake_software_deployment_plugin_container/__init__.py

@@ -207,7 +207,7 @@ class RuntimeManager:
             f" {self.workdir_option()} {getcwd()!r}"  # Working directory inside container
             f" {mountpoints}"
             f" {self.image_uri()}"  # Container image
-            " bash"  # Shell executable
+            f" {self.env.shell_executable.name}"  # Shell executable
             f" -c {shlex.quote(cmd)}"  # The command to execute
         )
 
@@ -217,7 +217,11 @@ class RuntimeManagerApptainer(RuntimeManager):
         return "exec"
 
     def options(self) -> str:
-        return ""
+        options = ""
+        envvars = [f"{env_var}={os.environ[env_var]}" for env_var in self.env.envvars]
+        if envvars:
+            options += f" --env {','.join(envvars)}"
+        return options
 
     def workdir_option(self) -> str:
         return "--cwd"
@@ -240,6 +244,8 @@ class RuntimeManagerDocker(RuntimeManager):
             uid = os.getuid()
             gid = os.getgid()
             options += f" --user {uid}:{gid}"
+        for env_var in self.env.envvars:
+            options += f" --env {env_var}"
         return options
 
 
@@ -247,4 +253,6 @@ class RuntimeManagerUdocker(RuntimeManager):
     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

{snakemake_software_deployment_plugin_container-0.6.2 → snakemake_software_deployment_plugin_container-0.7.1}/tests/test_plugin.py

@@ -1,7 +1,9 @@
+from collections.abc import Set
 from typing import Optional, Type
+import shutil
+import os
 
 import pytest
-import shutil
 
 from snakemake_interface_software_deployment_plugins.tests import (
     TestSoftwareDeploymentBase,
@@ -22,6 +24,10 @@ from snakemake_software_deployment_plugin_container import (
 )
 
 
+os.environ["TESTVAR1"] = "testvalue"
+os.environ["TESTVAR2"] = "testvalue2"
+
+
 class TestBase(TestSoftwareDeploymentBase):
     test_container = "quay.io/biocontainers/samtools:1.23.1--ha83d96e_0"
 
@@ -47,6 +53,9 @@ class TestBase(TestSoftwareDeploymentBase):
         # with exit code 0 (i.e. without error).
         return "samtools --version"
 
+    def get_envvars(self) -> Set[str]:
+        return {"TESTVAR1", "TESTVAR2"}
+
 
 class TestApptainerContainer(TestBase):
     __test__ = True