snakemake-software-deployment-plugin-container 0.3.0__tar.gz → 0.4.0__tar.gz

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Files changed (13) hide show
  1. {snakemake_software_deployment_plugin_container-0.3.0 → snakemake_software_deployment_plugin_container-0.4.0}/CHANGELOG.md +12 -0
  2. {snakemake_software_deployment_plugin_container-0.3.0 → snakemake_software_deployment_plugin_container-0.4.0}/PKG-INFO +2 -2
  3. {snakemake_software_deployment_plugin_container-0.3.0 → snakemake_software_deployment_plugin_container-0.4.0}/pixi.lock +55 -52
  4. {snakemake_software_deployment_plugin_container-0.3.0 → snakemake_software_deployment_plugin_container-0.4.0}/pyproject.toml +3 -3
  5. {snakemake_software_deployment_plugin_container-0.3.0 → snakemake_software_deployment_plugin_container-0.4.0}/src/snakemake_software_deployment_plugin_container/__init__.py +16 -8
  6. {snakemake_software_deployment_plugin_container-0.3.0 → snakemake_software_deployment_plugin_container-0.4.0}/.github/workflows/ci.yml +0 -0
  7. {snakemake_software_deployment_plugin_container-0.3.0 → snakemake_software_deployment_plugin_container-0.4.0}/.github/workflows/conventional-prs.yml +0 -0
  8. {snakemake_software_deployment_plugin_container-0.3.0 → snakemake_software_deployment_plugin_container-0.4.0}/.github/workflows/release-please.yml +0 -0
  9. {snakemake_software_deployment_plugin_container-0.3.0 → snakemake_software_deployment_plugin_container-0.4.0}/.gitignore +0 -0
  10. {snakemake_software_deployment_plugin_container-0.3.0 → snakemake_software_deployment_plugin_container-0.4.0}/LICENSE +0 -0
  11. {snakemake_software_deployment_plugin_container-0.3.0 → snakemake_software_deployment_plugin_container-0.4.0}/README.md +0 -0
  12. {snakemake_software_deployment_plugin_container-0.3.0 → snakemake_software_deployment_plugin_container-0.4.0}/setup.cfg +0 -0
  13. {snakemake_software_deployment_plugin_container-0.3.0 → snakemake_software_deployment_plugin_container-0.4.0}/tests/test_plugin.py +0 -0
{snakemake_software_deployment_plugin_container-0.3.0 → snakemake_software_deployment_plugin_container-0.4.0}/CHANGELOG.md RENAMED
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  # Changelog
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+ ## [0.4.0](https://github.com/snakemake/snakemake-software-deployment-plugin-container/compare/v0.3.0...v0.4.0) (2026-02-27)
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+ ### Features
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+ * implement check whether given executable is contained in container image ([9edf4a6](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/9edf4a6d4a80cea414bdbc844a58d052e2e8db0a))
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+ ### Bug Fixes
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+ * adapt to latest changes in interface ([3c5fd0b](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/3c5fd0bda99ec3e64dbe0b2b9012e14287759509))
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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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{snakemake_software_deployment_plugin_container-0.3.0 → snakemake_software_deployment_plugin_container-0.4.0}/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: 0.3.0
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+ Version: 0.4.0
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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>
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  License-File: LICENSE
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  Requires-Python: <4.0,>=3.11
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  Requires-Dist: snakemake-interface-common<2.0.0,>=1.17.4
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- Requires-Dist: snakemake-interface-software-deployment-plugins<1.0,>=0.9.1
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  Requires-Dist: udocker<2.0.0,>=1.3.17
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  Description-Content-Type: text/markdown
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{snakemake_software_deployment_plugin_container-0.3.0 → snakemake_software_deployment_plugin_container-0.4.0}/pixi.lock RENAMED
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1735
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1736
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{snakemake_software_deployment_plugin_container-0.3.0 → snakemake_software_deployment_plugin_container-0.4.0}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
1
1
  [project]
2
2
  name = "snakemake-software-deployment-plugin-container"
3
- version = "0.3.0"
3
+ version = "0.4.0"
4
4
  authors = [
5
5
  { name = "Ben Carrillo", email = "ben.uzh@pm.me" },
6
6
  { name = "Johannes Köster", email = "johannes.koester@uni-due.de" }
@@ -10,7 +10,7 @@ readme = "README.md"
10
10
  requires-python = ">=3.11,<4.0"
11
11
  dependencies = [
12
12
  "snakemake-interface-common (>=1.17.4,<2.0.0)",
13
- "snakemake-interface-software-deployment-plugins (>=0.9.1,<1.0)",
13
+ "snakemake-interface-software-deployment-plugins (>=0.12.0,<1.0)",
14
14
  "udocker (>=1.3.17,<2.0.0)",
15
15
  ]
16
16
 
@@ -57,7 +57,7 @@ cmd = [
57
57
 
58
58
  [tool.coverage.report]
59
59
  exclude_lines = ["pass", "\\.\\.\\."]
60
- fail_under = 91.0
60
+ fail_under = 90.0
61
61
 
62
62
  [tool.pixi.feature.publish.dependencies]
63
63
  twine = ">=6.1.0,<7"
{snakemake_software_deployment_plugin_container-0.3.0 → snakemake_software_deployment_plugin_container-0.4.0}/src/snakemake_software_deployment_plugin_container/__init__.py RENAMED
@@ -4,7 +4,6 @@ __email__ = "ben.uzh@pm.me"
4
4
  __license__ = "MIT"
5
5
 
6
6
  import shlex
7
- import tempfile
8
7
  from dataclasses import dataclass, field
9
8
  from os import getcwd
10
9
  from shutil import which
@@ -76,8 +75,8 @@ class EnvSpec(EnvSpecBase):
76
75
  class Env(EnvBase):
77
76
  # image_repo is the de-referenced repository from where the image was obtained
78
77
  image_repo: str
79
- settings: Settings # type: ignore
80
- spec: EnvSpec # type: ignore
78
+ settings: Settings
79
+ spec: EnvSpec
81
80
 
82
81
  # image_hash is a hash of the image that can be used to identify it
83
82
  # TODO: populate it *after* fetching/execution
@@ -111,14 +110,13 @@ class Env(EnvBase):
111
110
  raise WorkflowError(f"{cmd} is not available in PATH")
112
111
 
113
112
  def decorate_shellcmd(self, cmd: str) -> str:
114
- # TODO pass more options here (user etc)
115
- tmpdir = tempfile.gettempdir()
113
+ # TODO pass more options here (user etc)?
116
114
 
117
115
  mountpoints = (
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
116
+ f" -v {str(self.tempdir)!r}:/tmp" # always mount the temporary directory
121
117
  )
118
+ for mountpoint in self.mountpoints:
119
+ mountpoints += f" -v {str(mountpoint)!r}:{str(mountpoint)!r}"
122
120
  for mountpoint in self.settings.mountpoints:
123
121
  mountpoints += f" -v {mountpoint!r}"
124
122
 
@@ -134,6 +132,16 @@ class Env(EnvBase):
134
132
 
135
133
  return decorated_cmd
136
134
 
135
+ def contains_executable(self, executable: str) -> bool:
136
+ return (
137
+ self.run_cmd(
138
+ self.decorate_shellcmd(f"which {executable}"),
139
+ check=True,
140
+ capture_output=True,
141
+ ).returncode
142
+ == 0
143
+ )
144
+
137
145
  def record_hash(self, hash_object) -> None:
138
146
  # Update given hash such that it changes whenever the environment
139
147
  # could potentially contain a different set of software (in terms of versions or