snakemake-software-deployment-plugin-container 0.5.1__tar.gz → 0.5.2__tar.gz

{snakemake_software_deployment_plugin_container-0.5.1 → snakemake_software_deployment_plugin_container-0.5.2}/CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+## [0.5.2](https://github.com/snakemake/snakemake-software-deployment-plugin-container/compare/v0.5.1...v0.5.2) (2026-03-10)
+
+
+### Bug Fixes
+
+* fix mount point handling ([d42e16a](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/d42e16a8ba547897d976a3fa5b98ec9389cc4ab8))
+
 ## [0.5.1](https://github.com/snakemake/snakemake-software-deployment-plugin-container/compare/v0.5.0...v0.5.1) (2026-03-09)
 
 

{snakemake_software_deployment_plugin_container-0.5.1 → snakemake_software_deployment_plugin_container-0.5.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: snakemake-software-deployment-plugin-container
-Version: 0.5.1
+Version: 0.5.2
 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-0.5.1 → snakemake_software_deployment_plugin_container-0.5.2}/pixi.lock

@@ -36,7 +36,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/00/27/5ec3deed103817f19e8bd53298e724aab0b62900b3663cdd516ba3ea5b66/configargparse-1.7.3-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/20/12/38679034af332785aac8774540895e234f4d07f7545804097de4b666afd8/packaging-25.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/28/90/a4a3652e832667917383f8d34112bdb37b78a6d14efc049e22a2c8192524/snakemake_interface_common-1.23.0-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/b3/39/3ec3982e83f4474d536157df7a63483cfe0a0d7878a3ef2f8c688b7afbe0/snakemake_interface_software_deployment_plugins-0.16.3-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/99/e4/73def54a8259bb2f9dde1426af41796bfdd5c36c71989dc7cf43f1e7c5af/snakemake_interface_software_deployment_plugins-0.16.5-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/55/d6/caafad263b0e2375c2a8c586ac8b91fb7d3e363e6d1ab1e35a365d684254/udocker-1.3.17-py2.py3-none-any.whl
       - pypi: ./
       osx-arm64:
@@ -61,7 +61,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/00/27/5ec3deed103817f19e8bd53298e724aab0b62900b3663cdd516ba3ea5b66/configargparse-1.7.3-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/20/12/38679034af332785aac8774540895e234f4d07f7545804097de4b666afd8/packaging-25.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/28/90/a4a3652e832667917383f8d34112bdb37b78a6d14efc049e22a2c8192524/snakemake_interface_common-1.23.0-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/b3/39/3ec3982e83f4474d536157df7a63483cfe0a0d7878a3ef2f8c688b7afbe0/snakemake_interface_software_deployment_plugins-0.16.3-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/99/e4/73def54a8259bb2f9dde1426af41796bfdd5c36c71989dc7cf43f1e7c5af/snakemake_interface_software_deployment_plugins-0.16.5-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/55/d6/caafad263b0e2375c2a8c586ac8b91fb7d3e363e6d1ab1e35a365d684254/udocker-1.3.17-py2.py3-none-any.whl
       - pypi: ./
   dev:
@@ -126,7 +126,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/80/b4/bb7263e12aade3842b938bc5c6958cae79c5ee18992f9b9349019579da0f/pytest_cov-6.3.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/ca/71/37daa46f89475f8582b7762ecd2722492df26421714a33e72ccc9a84d7a5/ruff-0.14.14-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/28/90/a4a3652e832667917383f8d34112bdb37b78a6d14efc049e22a2c8192524/snakemake_interface_common-1.23.0-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/b3/39/3ec3982e83f4474d536157df7a63483cfe0a0d7878a3ef2f8c688b7afbe0/snakemake_interface_software_deployment_plugins-0.16.3-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/99/e4/73def54a8259bb2f9dde1426af41796bfdd5c36c71989dc7cf43f1e7c5af/snakemake_interface_software_deployment_plugins-0.16.5-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/55/d6/caafad263b0e2375c2a8c586ac8b91fb7d3e363e6d1ab1e35a365d684254/udocker-1.3.17-py2.py3-none-any.whl
       - pypi: ./
       osx-arm64:
@@ -159,7 +159,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/80/b4/bb7263e12aade3842b938bc5c6958cae79c5ee18992f9b9349019579da0f/pytest_cov-6.3.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/b8/7c/3c1db59a10e7490f8f6f8559d1db8636cbb13dccebf18686f4e3c9d7c772/ruff-0.14.14-py3-none-macosx_11_0_arm64.whl
       - pypi: https://files.pythonhosted.org/packages/28/90/a4a3652e832667917383f8d34112bdb37b78a6d14efc049e22a2c8192524/snakemake_interface_common-1.23.0-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/b3/39/3ec3982e83f4474d536157df7a63483cfe0a0d7878a3ef2f8c688b7afbe0/snakemake_interface_software_deployment_plugins-0.16.3-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/99/e4/73def54a8259bb2f9dde1426af41796bfdd5c36c71989dc7cf43f1e7c5af/snakemake_interface_software_deployment_plugins-0.16.5-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/55/d6/caafad263b0e2375c2a8c586ac8b91fb7d3e363e6d1ab1e35a365d684254/udocker-1.3.17-py2.py3-none-any.whl
       - pypi: ./
   publish:
@@ -224,7 +224,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/14/25/b208c5683343959b670dc001595f2f3737e051da617f66c31f7c4fa93abc/rich-14.3.3-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/b7/46/f5af3402b579fd5e11573ce652019a67074317e18c1935cc0b4ba9b35552/secretstorage-3.5.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/28/90/a4a3652e832667917383f8d34112bdb37b78a6d14efc049e22a2c8192524/snakemake_interface_common-1.23.0-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/b3/39/3ec3982e83f4474d536157df7a63483cfe0a0d7878a3ef2f8c688b7afbe0/snakemake_interface_software_deployment_plugins-0.16.3-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/99/e4/73def54a8259bb2f9dde1426af41796bfdd5c36c71989dc7cf43f1e7c5af/snakemake_interface_software_deployment_plugins-0.16.5-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/3a/7a/882d99539b19b1490cac5d77c67338d126e4122c8276bf640e411650c830/twine-6.2.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/55/d6/caafad263b0e2375c2a8c586ac8b91fb7d3e363e6d1ab1e35a365d684254/udocker-1.3.17-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/39/08/aaaad47bc4e9dc8c725e68f9d04865dbcb2052843ff09c97b08904852d84/urllib3-2.6.3-py3-none-any.whl
@@ -272,7 +272,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/ff/9a/9afaade874b2fa6c752c36f1548f718b5b83af81ed9b76628329dab81c1b/rfc3986-2.0.0-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/14/25/b208c5683343959b670dc001595f2f3737e051da617f66c31f7c4fa93abc/rich-14.3.3-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/28/90/a4a3652e832667917383f8d34112bdb37b78a6d14efc049e22a2c8192524/snakemake_interface_common-1.23.0-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/b3/39/3ec3982e83f4474d536157df7a63483cfe0a0d7878a3ef2f8c688b7afbe0/snakemake_interface_software_deployment_plugins-0.16.3-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/99/e4/73def54a8259bb2f9dde1426af41796bfdd5c36c71989dc7cf43f1e7c5af/snakemake_interface_software_deployment_plugins-0.16.5-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/3a/7a/882d99539b19b1490cac5d77c67338d126e4122c8276bf640e411650c830/twine-6.2.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/55/d6/caafad263b0e2375c2a8c586ac8b91fb7d3e363e6d1ab1e35a365d684254/udocker-1.3.17-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/39/08/aaaad47bc4e9dc8c725e68f9d04865dbcb2052843ff09c97b08904852d84/urllib3-2.6.3-py3-none-any.whl
@@ -1326,18 +1326,18 @@ packages:
   - configargparse>=1.7
   - packaging>=24.0,<26.0
   requires_python: '>=3.8'
-- pypi: https://files.pythonhosted.org/packages/b3/39/3ec3982e83f4474d536157df7a63483cfe0a0d7878a3ef2f8c688b7afbe0/snakemake_interface_software_deployment_plugins-0.16.3-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/99/e4/73def54a8259bb2f9dde1426af41796bfdd5c36c71989dc7cf43f1e7c5af/snakemake_interface_software_deployment_plugins-0.16.5-py3-none-any.whl
   name: snakemake-interface-software-deployment-plugins
-  version: 0.16.3
-  sha256: 06cf68074540eefb9d8a899b51713f94d2a92c40d1f1dc761dd17c0b64a8d650
+  version: 0.16.5
+  sha256: 84599f7c5d87932d2a89fdd741c6a3a94e02c0b0a66fb2f6c5cda1d319199f6d
   requires_dist:
   - argparse-dataclass>=2.0.0,<3.0
   - snakemake-interface-common>=1.23.0,<2.0.0
   requires_python: '>=3.11,<4.0'
 - pypi: ./
   name: snakemake-software-deployment-plugin-container
-  version: 0.5.1
-  sha256: 0f1915aa8eeba9ac9d81b81ba79943aa30c5276083d502a46ce83615dba5162f
+  version: 0.5.2
+  sha256: ee1dab514017eaa893aa93b7a07a7aa76d015c50001fa559b5db0d9f8200dacb
   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-0.5.1 → snakemake_software_deployment_plugin_container-0.5.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "snakemake-software-deployment-plugin-container"
-version = "0.5.1"
+version = "0.5.2"
 authors = [
     { name = "Ben Carrillo", email = "ben.uzh@pm.me" },
     { name = "Johannes Köster", email = "johannes.koester@uni-due.de" }

{snakemake_software_deployment_plugin_container-0.5.1 → snakemake_software_deployment_plugin_container-0.5.2}/src/snakemake_software_deployment_plugin_container/__init__.py

@@ -161,21 +161,25 @@ class RuntimeManager:
     def subcommand(self) -> str:
         return "run"
 
-    def mountpoints(self) -> str:
-        mountpoints = ""
-        # always mount the temporary directory
-        for source, mountpoint in [
-            (self.env.tempdir, "/tmp"),
+    def get_mountpoint_args(self) -> str:
+        mountpoint_specs = [
             (self.env.tempdir, self.env.tempdir),
             (getcwd(), getcwd()),
-        ]:
+        ] + [(mountpoint, mountpoint) for mountpoint in self.env.mountpoints]
+
+        mountpoints = ""
+        # always mount the temporary directory
+        for source, mountpoint in mountpoint_specs:
             mountpoints += f" {self.mount_option()} {str(source)!r}:{str(mountpoint)!r}"
         for mountpoint in self.env.settings.mountpoints:
             mountpoints += f" {self.mount_option()} {mountpoint!r}"
         return mountpoints
 
+    # TODO add TEMPDIR env vars, ensure that in addition /tmp is writable
+    # in case it is not the same as self.tempdir
+
     def decorate_shellcmd(self, cmd: str) -> str:
-        mountpoints = self.mountpoints()
+        mountpoints = self.get_mountpoint_args()
         return (
             f"{self.env.settings.runtime} {self.subcommand()}"
             f" {self.options()}"