snakemake-software-deployment-plugin-container 0.2.0__tar.gz → 0.3.0__tar.gz

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Files changed (13) hide show
  1. {snakemake_software_deployment_plugin_container-0.2.0 → snakemake_software_deployment_plugin_container-0.3.0}/CHANGELOG.md +14 -0
  2. {snakemake_software_deployment_plugin_container-0.2.0 → snakemake_software_deployment_plugin_container-0.3.0}/PKG-INFO +1 -1
  3. {snakemake_software_deployment_plugin_container-0.2.0 → snakemake_software_deployment_plugin_container-0.3.0}/pixi.lock +55 -58
  4. {snakemake_software_deployment_plugin_container-0.2.0 → snakemake_software_deployment_plugin_container-0.3.0}/pyproject.toml +2 -2
  5. {snakemake_software_deployment_plugin_container-0.2.0 → snakemake_software_deployment_plugin_container-0.3.0}/src/snakemake_software_deployment_plugin_container/__init__.py +10 -15
  6. {snakemake_software_deployment_plugin_container-0.2.0 → snakemake_software_deployment_plugin_container-0.3.0}/.github/workflows/ci.yml +0 -0
  7. {snakemake_software_deployment_plugin_container-0.2.0 → snakemake_software_deployment_plugin_container-0.3.0}/.github/workflows/conventional-prs.yml +0 -0
  8. {snakemake_software_deployment_plugin_container-0.2.0 → snakemake_software_deployment_plugin_container-0.3.0}/.github/workflows/release-please.yml +0 -0
  9. {snakemake_software_deployment_plugin_container-0.2.0 → snakemake_software_deployment_plugin_container-0.3.0}/.gitignore +0 -0
  10. {snakemake_software_deployment_plugin_container-0.2.0 → snakemake_software_deployment_plugin_container-0.3.0}/LICENSE +0 -0
  11. {snakemake_software_deployment_plugin_container-0.2.0 → snakemake_software_deployment_plugin_container-0.3.0}/README.md +0 -0
  12. {snakemake_software_deployment_plugin_container-0.2.0 → snakemake_software_deployment_plugin_container-0.3.0}/setup.cfg +0 -0
  13. {snakemake_software_deployment_plugin_container-0.2.0 → snakemake_software_deployment_plugin_container-0.3.0}/tests/test_plugin.py +0 -0
{snakemake_software_deployment_plugin_container-0.2.0 → snakemake_software_deployment_plugin_container-0.3.0}/CHANGELOG.md RENAMED
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  # Changelog
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+ ## [0.3.0](https://github.com/snakemake/snakemake-software-deployment-plugin-container/compare/v0.2.1...v0.3.0) (2026-02-18)
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+ ### Features
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+ * always mount system tempdir ([60ef0bd](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/60ef0bd3384edffc8816b687b88a321da4b053f3))
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+ ## [0.2.1](https://github.com/snakemake/snakemake-software-deployment-plugin-container/compare/v0.2.0...v0.2.1) (2026-02-17)
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+ ### Bug Fixes
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+ * fix mountpoint handling ([#7](https://github.com/snakemake/snakemake-software-deployment-plugin-container/issues/7)) ([ce2c1c9](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/ce2c1c9cd29820835468ac4b8c808a4b6e114ee9))
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  ## [0.2.0](https://github.com/snakemake/snakemake-software-deployment-plugin-container/compare/v0.1.0...v0.2.0) (2026-02-17)
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{snakemake_software_deployment_plugin_container-0.2.0 → snakemake_software_deployment_plugin_container-0.3.0}/PKG-INFO RENAMED
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  Metadata-Version: 2.4
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  Name: snakemake-software-deployment-plugin-container
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- Version: 0.2.0
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+ Version: 0.3.0
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  Project-URL: repository, https://github.com/snakemake/snakemake-software-deployment-plugin-container
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  Project-URL: documentation, https://snakemake.github.io/snakemake-plugin-catalog/plugins/software-deployment/container.html
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  Author-email: Ben Carrillo <ben.uzh@pm.me>, Johannes Köster <johannes.koester@uni-due.de>
{snakemake_software_deployment_plugin_container-0.2.0 → snakemake_software_deployment_plugin_container-0.3.0}/pixi.lock RENAMED
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318
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421
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432
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1597
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1612
1609
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{snakemake_software_deployment_plugin_container-0.2.0 → snakemake_software_deployment_plugin_container-0.3.0}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
1
1
  [project]
2
2
  name = "snakemake-software-deployment-plugin-container"
3
- version = "0.2.0"
3
+ version = "0.3.0"
4
4
  authors = [
5
5
  { name = "Ben Carrillo", email = "ben.uzh@pm.me" },
6
6
  { name = "Johannes Köster", email = "johannes.koester@uni-due.de" }
@@ -57,7 +57,7 @@ cmd = [
57
57
 
58
58
  [tool.coverage.report]
59
59
  exclude_lines = ["pass", "\\.\\.\\."]
60
- fail_under = 93.0
60
+ fail_under = 91.0
61
61
 
62
62
  [tool.pixi.feature.publish.dependencies]
63
63
  twine = ">=6.1.0,<7"
{snakemake_software_deployment_plugin_container-0.2.0 → snakemake_software_deployment_plugin_container-0.3.0}/src/snakemake_software_deployment_plugin_container/__init__.py RENAMED
@@ -3,8 +3,8 @@ __copyright__ = "Copyright 2025, ben carrillo"
3
3
  __email__ = "ben.uzh@pm.me"
4
4
  __license__ = "MIT"
5
5
 
6
- import os.path
7
6
  import shlex
7
+ import tempfile
8
8
  from dataclasses import dataclass, field
9
9
  from os import getcwd
10
10
  from shutil import which
@@ -25,10 +25,6 @@ from snakemake_interface_common.exceptions import WorkflowError # noqa: F401
25
25
  from snakemake_interface_common.settings import SettingsEnumBase
26
26
 
27
27
 
28
- # The mountpoint for the Snakemake working directory inside the container.
29
- SNAKEMAKE_MOUNTPOINT = "/mnt/snakemake"
30
-
31
-
32
28
  # ContainerType is an enum that defines the different container types we support.
33
29
  # If adding new ones, make sure the choice is the same as the command name.
34
30
  class Runtime(SettingsEnumBase):
@@ -51,7 +47,8 @@ class Settings(SoftwareDeploymentSettingsBase):
51
47
  default_factory=list,
52
48
  metadata={
53
49
  "nargs": "+",
54
- "help": "Additional mount points (format: hostpath:containerpath)",
50
+ "help": "Additional mount points (format: hostpath:containerpath). "
51
+ "Current working directory and the system tmpdir are always mounted.",
55
52
  },
56
53
  )
57
54
 
@@ -114,14 +111,13 @@ class Env(EnvBase):
114
111
  raise WorkflowError(f"{cmd} is not available in PATH")
115
112
 
116
113
  def decorate_shellcmd(self, cmd: str) -> str:
117
- # TODO pass more options here (extra mount volumes, user etc)
118
- containercache = os.path.join(
119
- SNAKEMAKE_MOUNTPOINT, ".cache/snakemake/source-cache"
120
- )
114
+ # TODO pass more options here (user etc)
115
+ tmpdir = tempfile.gettempdir()
121
116
 
122
117
  mountpoints = (
123
- f" -v {getcwd()!r}:{SNAKEMAKE_MOUNTPOINT!r}" # Mount host directory to container
124
- f" -v {str(self.source_cache)!r}:{containercache!r}" # Mount host cache to container
118
+ f" -v {getcwd()!r}:{getcwd()!r}" # Mount host directory to container
119
+ f" -v {str(self.source_cache)!r}:{str(self.source_cache)!r}" # Mount host cache to container
120
+ f" -v {tmpdir!r}:{tmpdir!r}" # always mount the temporary directory
125
121
  )
126
122
  for mountpoint in self.settings.mountpoints:
127
123
  mountpoints += f" -v {mountpoint!r}"
@@ -129,8 +125,7 @@ class Env(EnvBase):
129
125
  decorated_cmd = (
130
126
  f"{self.settings.runtime} run"
131
127
  " --rm" # Remove container after execution
132
- f" -e HOME={SNAKEMAKE_MOUNTPOINT!r}" # Set HOME to working directory
133
- f" -w {SNAKEMAKE_MOUNTPOINT!r}" # Working directory inside container
128
+ f" -w {getcwd()!r}" # Working directory inside container
134
129
  f" {mountpoints}"
135
130
  f" {self.spec.image_uri}" # Container image
136
131
  " /bin/sh" # Shell executable
@@ -144,7 +139,7 @@ class Env(EnvBase):
144
139
  # could potentially contain a different set of software (in terms of versions or
145
140
  # packages). Use self.spec (containing the corresponding EnvSpec object)
146
141
  # to determine the hash.
147
- hash_object.update(...)
142
+ hash_object.update(self.spec.image_uri.encode())
148
143
 
149
144
  def report_software(self) -> Iterable[SoftwareReport]:
150
145
  # Report the software contained in the environment. This should be a list of