snakemake-software-deployment-plugin-container 0.2.1__tar.gz → 0.4.0__tar.gz

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Files changed (13) hide show
  1. {snakemake_software_deployment_plugin_container-0.2.1 → snakemake_software_deployment_plugin_container-0.4.0}/CHANGELOG.md +19 -0
  2. {snakemake_software_deployment_plugin_container-0.2.1 → snakemake_software_deployment_plugin_container-0.4.0}/PKG-INFO +2 -2
  3. {snakemake_software_deployment_plugin_container-0.2.1 → snakemake_software_deployment_plugin_container-0.4.0}/pixi.lock +98 -98
  4. {snakemake_software_deployment_plugin_container-0.2.1 → snakemake_software_deployment_plugin_container-0.4.0}/pyproject.toml +3 -3
  5. {snakemake_software_deployment_plugin_container-0.2.1 → snakemake_software_deployment_plugin_container-0.4.0}/src/snakemake_software_deployment_plugin_container/__init__.py +18 -6
  6. {snakemake_software_deployment_plugin_container-0.2.1 → snakemake_software_deployment_plugin_container-0.4.0}/.github/workflows/ci.yml +0 -0
  7. {snakemake_software_deployment_plugin_container-0.2.1 → snakemake_software_deployment_plugin_container-0.4.0}/.github/workflows/conventional-prs.yml +0 -0
  8. {snakemake_software_deployment_plugin_container-0.2.1 → snakemake_software_deployment_plugin_container-0.4.0}/.github/workflows/release-please.yml +0 -0
  9. {snakemake_software_deployment_plugin_container-0.2.1 → snakemake_software_deployment_plugin_container-0.4.0}/.gitignore +0 -0
  10. {snakemake_software_deployment_plugin_container-0.2.1 → snakemake_software_deployment_plugin_container-0.4.0}/LICENSE +0 -0
  11. {snakemake_software_deployment_plugin_container-0.2.1 → snakemake_software_deployment_plugin_container-0.4.0}/README.md +0 -0
  12. {snakemake_software_deployment_plugin_container-0.2.1 → snakemake_software_deployment_plugin_container-0.4.0}/setup.cfg +0 -0
  13. {snakemake_software_deployment_plugin_container-0.2.1 → snakemake_software_deployment_plugin_container-0.4.0}/tests/test_plugin.py +0 -0
{snakemake_software_deployment_plugin_container-0.2.1 → 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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+ ### 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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{snakemake_software_deployment_plugin_container-0.2.1 → 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: 0.2.1
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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: snakemake-interface-software-deployment-plugins<1.0,>=0.12.0
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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-0.2.1 → snakemake_software_deployment_plugin_container-0.4.0}/pixi.lock RENAMED
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  license: GPL-3.0-only WITH GCC-exception-3.1
956
956
  license_family: GPL
957
957
  purls: []
958
- size: 603334
959
- timestamp: 1770252441199
958
+ size: 603262
959
+ timestamp: 1771378117851
960
960
  - conda: https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.18-h3b78370_2.conda
961
961
  sha256: c467851a7312765447155e071752d7bf9bf44d610a5687e32706f480aad2833f
962
962
  md5: 915f5995e94f60e9a4826e0b0920ee88
@@ -1034,19 +1034,19 @@ packages:
1034
1034
  purls: []
1035
1035
  size: 909777
1036
1036
  timestamp: 1768148320535
1037
- - conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_17.conda
1038
- sha256: 50c48cd3716a2e58e8e2e02edc78fef2d08fffe1e3b1ed40eb5f87e7e2d07889
1039
- md5: 24c2fe35fa45cd71214beba6f337c071
1037
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_18.conda
1038
+ sha256: 78668020064fdaa27e9ab65cd2997e2c837b564ab26ce3bf0e58a2ce1a525c6e
1039
+ md5: 1b08cd684f34175e4514474793d44bcb
1040
1040
  depends:
1041
1041
  - __glibc >=2.17,<3.0.a0
1042
- - libgcc 15.2.0 he0feb66_17
1042
+ - libgcc 15.2.0 he0feb66_18
1043
1043
  constrains:
1044
- - libstdcxx-ng ==15.2.0=*_17
1044
+ - libstdcxx-ng ==15.2.0=*_18
1045
1045
  license: GPL-3.0-only WITH GCC-exception-3.1
1046
1046
  license_family: GPL
1047
1047
  purls: []
1048
- size: 5852406
1049
- timestamp: 1770252584235
1048
+ size: 5852330
1049
+ timestamp: 1771378262446
1050
1050
  - conda: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.3-h5347b49_0.conda
1051
1051
  sha256: 1a7539cfa7df00714e8943e18de0b06cceef6778e420a5ee3a2a145773758aee
1052
1052
  md5: db409b7c1720428638e7c0d509d3e1b5
@@ -1516,9 +1516,9 @@ packages:
1516
1516
  - pkg:pypi/rfc3986?source=hash-mapping
1517
1517
  size: 38028
1518
1518
  timestamp: 1733921806657
1519
- - conda: https://conda.anaconda.org/conda-forge/noarch/rich-14.3.2-pyhcf101f3_0.conda
1520
- sha256: ed17985cec5a0540002c6cabe67848f7cc17e5f4019c0e2a40534e9b7c0b38de
1521
- md5: 33950a076fd589a7655c6888cc3d2b34
1519
+ - conda: https://conda.anaconda.org/conda-forge/noarch/rich-14.3.3-pyhcf101f3_0.conda
1520
+ sha256: b06ce84d6a10c266811a7d3adbfa1c11f13393b91cc6f8a5b468277d90be9590
1521
+ md5: 7a6289c50631d620652f5045a63eb573
1522
1522
  depends:
1523
1523
  - markdown-it-py >=2.2.0
1524
1524
  - pygments >=2.13.0,<3.0.0
@@ -1529,8 +1529,8 @@ packages:
1529
1529
  license_family: MIT
1530
1530
  purls:
1531
1531
  - pkg:pypi/rich?source=compressed-mapping
1532
- size: 208269
1533
- timestamp: 1769971520792
1532
+ size: 208472
1533
+ timestamp: 1771572730357
1534
1534
  - conda: https://conda.anaconda.org/conda-forge/linux-64/ruff-0.14.14-h40fa522_1.conda
1535
1535
  noarch: python
1536
1536
  sha256: 0c6c9825ff88195fd13936d63872213d6c88c1fe795d136881c0753c3037c5ff
@@ -1600,21 +1600,21 @@ packages:
1600
1600
  - configargparse>=1.7
1601
1601
  - packaging>=24.0,<26.0
1602
1602
  requires_python: '>=3.8'
1603
- - pypi: https://files.pythonhosted.org/packages/2c/16/cae29057073ff0108a7bf4c699a3f258ffa9e530300548c015a0404ed7b0/snakemake_interface_software_deployment_plugins-0.10.0-py3-none-any.whl
1603
+ - pypi: https://files.pythonhosted.org/packages/c0/09/946f1fad9abd7b1fc18386bd77d98ba6f78ce049e1265966a78754d9bbcd/snakemake_interface_software_deployment_plugins-0.13.0-py3-none-any.whl
1604
1604
  name: snakemake-interface-software-deployment-plugins
1605
- version: 0.10.0
1606
- sha256: af5e6946a8cd846d45dff995c58dd14eea4105b172b7de45b856a52a99c854aa
1605
+ version: 0.13.0
1606
+ sha256: ad2711e3bc6b10445931fc491cde10a2d9488331facc3b6abb7d710cb114383b
1607
1607
  requires_dist:
1608
1608
  - argparse-dataclass>=2.0.0,<3.0
1609
1609
  - snakemake-interface-common>=1.17.4,<2.0.0
1610
1610
  requires_python: '>=3.11,<4.0'
1611
1611
  - pypi: ./
1612
1612
  name: snakemake-software-deployment-plugin-container
1613
- version: 0.2.1
1614
- sha256: a2494a8414f9ab599bbf11c99bcf20e57ab10251a797d2e924cbe3ade6f16732
1613
+ version: 0.4.0
1614
+ sha256: f2c88bae3529fc99faa876666fc571614891836ca94b6715fee70c2bf7b07922
1615
1615
  requires_dist:
1616
1616
  - snakemake-interface-common>=1.17.4,<2.0.0
1617
- - snakemake-interface-software-deployment-plugins>=0.9.1,<1.0
1617
+ - snakemake-interface-software-deployment-plugins>=0.12.0,<1.0
1618
1618
  - udocker>=1.3.17,<2.0.0
1619
1619
  requires_python: '>=3.11,<4.0'
1620
1620
  - conda: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h366c992_103.conda
@@ -1735,7 +1735,7 @@ packages:
1735
1735
  license: MIT
1736
1736
  license_family: MIT
1737
1737
  purls:
1738
- - pkg:pypi/zipp?source=compressed-mapping
1738
+ - pkg:pypi/zipp?source=hash-mapping
1739
1739
  size: 24194
1740
1740
  timestamp: 1764460141901
1741
1741
  - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
{snakemake_software_deployment_plugin_container-0.2.1 → 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 = "0.2.1"
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-0.2.1 → snakemake_software_deployment_plugin_container-0.4.0}/src/snakemake_software_deployment_plugin_container/__init__.py RENAMED
@@ -46,7 +46,8 @@ class Settings(SoftwareDeploymentSettingsBase):
46
46
  default_factory=list,
47
47
  metadata={
48
48
  "nargs": "+",
49
- "help": "Additional mount points (format: hostpath:containerpath)",
49
+ "help": "Additional mount points (format: hostpath:containerpath). "
50
+ "Current working directory and the system tmpdir are always mounted.",
50
51
  },
51
52
  )
52
53
 
@@ -74,8 +75,8 @@ class EnvSpec(EnvSpecBase):
74
75
  class Env(EnvBase):
75
76
  # image_repo is the de-referenced repository from where the image was obtained
76
77
  image_repo: str
77
- settings: Settings # type: ignore
78
- spec: EnvSpec # type: ignore
78
+ settings: Settings
79
+ spec: EnvSpec
79
80
 
80
81
  # image_hash is a hash of the image that can be used to identify it
81
82
  # TODO: populate it *after* fetching/execution
@@ -109,12 +110,13 @@ class Env(EnvBase):
109
110
  raise WorkflowError(f"{cmd} is not available in PATH")
110
111
 
111
112
  def decorate_shellcmd(self, cmd: str) -> str:
112
- # TODO pass more options here (user etc)
113
+ # TODO pass more options here (user etc)?
113
114
 
114
115
  mountpoints = (
115
- f" -v {getcwd()!r}:{getcwd()!r}" # Mount host directory to container
116
- f" -v {str(self.source_cache)!r}:{str(self.source_cache)!r}" # Mount host cache to container
116
+ f" -v {str(self.tempdir)!r}:/tmp" # always mount the temporary directory
117
117
  )
118
+ for mountpoint in self.mountpoints:
119
+ mountpoints += f" -v {str(mountpoint)!r}:{str(mountpoint)!r}"
118
120
  for mountpoint in self.settings.mountpoints:
119
121
  mountpoints += f" -v {mountpoint!r}"
120
122
 
@@ -130,6 +132,16 @@ class Env(EnvBase):
130
132
 
131
133
  return decorated_cmd
132
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
+
133
145
  def record_hash(self, hash_object) -> None:
134
146
  # Update given hash such that it changes whenever the environment
135
147
  # could potentially contain a different set of software (in terms of versions or