snakemake-software-deployment-plugin-container 0.1.0__tar.gz → 0.2.1__tar.gz

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Files changed (13) hide show
  1. {snakemake_software_deployment_plugin_container-0.1.0 → snakemake_software_deployment_plugin_container-0.2.1}/CHANGELOG.md +14 -0
  2. {snakemake_software_deployment_plugin_container-0.1.0 → snakemake_software_deployment_plugin_container-0.2.1}/PKG-INFO +1 -1
  3. {snakemake_software_deployment_plugin_container-0.1.0 → snakemake_software_deployment_plugin_container-0.2.1}/pixi.lock +92 -156
  4. {snakemake_software_deployment_plugin_container-0.1.0 → snakemake_software_deployment_plugin_container-0.2.1}/pyproject.toml +3 -3
  5. {snakemake_software_deployment_plugin_container-0.1.0 → snakemake_software_deployment_plugin_container-0.2.1}/src/snakemake_software_deployment_plugin_container/__init__.py +20 -15
  6. {snakemake_software_deployment_plugin_container-0.1.0 → snakemake_software_deployment_plugin_container-0.2.1}/.github/workflows/ci.yml +0 -0
  7. {snakemake_software_deployment_plugin_container-0.1.0 → snakemake_software_deployment_plugin_container-0.2.1}/.github/workflows/conventional-prs.yml +0 -0
  8. {snakemake_software_deployment_plugin_container-0.1.0 → snakemake_software_deployment_plugin_container-0.2.1}/.github/workflows/release-please.yml +0 -0
  9. {snakemake_software_deployment_plugin_container-0.1.0 → snakemake_software_deployment_plugin_container-0.2.1}/.gitignore +0 -0
  10. {snakemake_software_deployment_plugin_container-0.1.0 → snakemake_software_deployment_plugin_container-0.2.1}/LICENSE +0 -0
  11. {snakemake_software_deployment_plugin_container-0.1.0 → snakemake_software_deployment_plugin_container-0.2.1}/README.md +0 -0
  12. {snakemake_software_deployment_plugin_container-0.1.0 → snakemake_software_deployment_plugin_container-0.2.1}/setup.cfg +0 -0
  13. {snakemake_software_deployment_plugin_container-0.1.0 → snakemake_software_deployment_plugin_container-0.2.1}/tests/test_plugin.py +0 -0
{snakemake_software_deployment_plugin_container-0.1.0 → snakemake_software_deployment_plugin_container-0.2.1}/CHANGELOG.md RENAMED
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  # Changelog
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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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+ ### Features
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+ * additional mountpoints ([#5](https://github.com/snakemake/snakemake-software-deployment-plugin-container/issues/5)) ([29ba897](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/29ba897154bac2082d42048c601a6177e0db0d82))
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  ## 0.1.0 (2026-02-13)
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{snakemake_software_deployment_plugin_container-0.1.0 → snakemake_software_deployment_plugin_container-0.2.1}/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: 0.1.0
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+ Version: 0.2.1
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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-0.1.0 → snakemake_software_deployment_plugin_container-0.2.1}/pixi.lock RENAMED
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- license: Python-2.0
1370
- purls: []
1371
- size: 37364553
1372
- timestamp: 1770272309861
1373
- python_site_packages_path: lib/python3.13/site-packages
1374
1348
  - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.14.3-h32b2ec7_101_cp314.conda
1375
1349
  build_number: 101
1376
1350
  sha256: cb0628c5f1732f889f53a877484da98f5a0e0f47326622671396fb4f2b0cd6bd
@@ -1399,30 +1373,6 @@ packages:
1399
1373
  size: 36702440
1400
1374
  timestamp: 1770675584356
1401
1375
  python_site_packages_path: lib/python3.14/site-packages
1402
- - conda: https://conda.anaconda.org/conda-forge/osx-arm64/python-3.13.12-h20e6be0_100_cp313.conda
1403
- build_number: 100
1404
- sha256: 9a4f16a64def0853f0a7b6a7beb40d498fd6b09bee10b90c3d6069b664156817
1405
- md5: 179c0f5ae4f22bc3be567298ed0b17b9
1406
- depends:
1407
- - __osx >=11.0
1408
- - bzip2 >=1.0.8,<2.0a0
1409
- - libexpat >=2.7.3,<3.0a0
1410
- - libffi >=3.5.2,<3.6.0a0
1411
- - liblzma >=5.8.2,<6.0a0
1412
- - libmpdec >=4.0.0,<5.0a0
1413
- - libsqlite >=3.51.2,<4.0a0
1414
- - libzlib >=1.3.1,<2.0a0
1415
- - ncurses >=6.5,<7.0a0
1416
- - openssl >=3.5.5,<4.0a0
1417
- - python_abi 3.13.* *_cp313
1418
- - readline >=8.3,<9.0a0
1419
- - tk >=8.6.13,<8.7.0a0
1420
- - tzdata
1421
- license: Python-2.0
1422
- purls: []
1423
- size: 12770674
1424
- timestamp: 1770272314517
1425
- python_site_packages_path: lib/python3.13/site-packages
1426
1376
  - conda: https://conda.anaconda.org/conda-forge/osx-arm64/python-3.14.3-h4c637c5_101_cp314.conda
1427
1377
  build_number: 101
1428
1378
  sha256: fccce2af62d11328d232df9f6bbf63464fd45f81f718c661757f9c628c4378ce
@@ -1476,17 +1426,6 @@ packages:
1476
1426
  purls: []
1477
1427
  size: 50062
1478
1428
  timestamp: 1770674497152
1479
- - conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.13-8_cp313.conda
1480
- build_number: 8
1481
- sha256: 210bffe7b121e651419cb196a2a63687b087497595c9be9d20ebe97dd06060a7
1482
- md5: 94305520c52a4aa3f6c2b1ff6008d9f8
1483
- constrains:
1484
- - python 3.13.* *_cp313
1485
- license: BSD-3-Clause
1486
- license_family: BSD
1487
- purls: []
1488
- size: 7002
1489
- timestamp: 1752805902938
1490
1429
  - conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.14-8_cp314.conda
1491
1430
  build_number: 8
1492
1431
  sha256: ad6d2e9ac39751cc0529dd1566a26751a0bf2542adb0c232533d32e176e21db5
@@ -1592,40 +1531,37 @@ packages:
1592
1531
  - pkg:pypi/rich?source=compressed-mapping
1593
1532
  size: 208269
1594
1533
  timestamp: 1769971520792
1595
- - conda: https://conda.anaconda.org/conda-forge/linux-64/ruff-0.10.0-py313hfe82de2_0.conda
1596
- sha256: d8ac711c5e89c4e77678052f6091ddb2934131122735a8a2f32863cc501ae27d
1597
- md5: 356a551336803194c228af2046898d94
1534
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/ruff-0.14.14-h40fa522_1.conda
1535
+ noarch: python
1536
+ sha256: 0c6c9825ff88195fd13936d63872213d6c88c1fe795d136881c0753c3037c5ff
1537
+ md5: d3e1d08b141529c7fce6a13b4d670605
1598
1538
  depends:
1539
+ - python
1599
1540
  - __glibc >=2.17,<3.0.a0
1600
- - libgcc >=13
1601
- - libstdcxx >=13
1602
- - python >=3.13,<3.14.0a0
1603
- - python_abi 3.13.* *_cp313
1541
+ - libgcc >=14
1604
1542
  constrains:
1605
1543
  - __glibc >=2.17
1606
1544
  license: MIT
1607
1545
  license_family: MIT
1608
1546
  purls:
1609
- - pkg:pypi/ruff?source=hash-mapping
1610
- size: 8859214
1611
- timestamp: 1741904923625
1612
- - conda: https://conda.anaconda.org/conda-forge/osx-arm64/ruff-0.10.0-py313h35210b4_0.conda
1613
- sha256: 25fbf2bad97707b740f0461dacb9fcc3a1d641c88ce404b08dd3cf1ee5bda0a9
1614
- md5: 546006878b19dbd667ca28fde4ab3f01
1547
+ - pkg:pypi/ruff?source=compressed-mapping
1548
+ size: 9131490
1549
+ timestamp: 1769520999080
1550
+ - conda: https://conda.anaconda.org/conda-forge/osx-arm64/ruff-0.14.14-h279115b_1.conda
1551
+ noarch: python
1552
+ sha256: 20f93b70375e6ad43ec507611cf28814277be17a2794a2a94e2df13a0b34f8d3
1553
+ md5: bcc5ef166c4de9a225c9ca9cb4fa631e
1615
1554
  depends:
1555
+ - python
1616
1556
  - __osx >=11.0
1617
- - libcxx >=18
1618
- - python >=3.13,<3.14.0a0
1619
- - python >=3.13,<3.14.0a0 *_cp313
1620
- - python_abi 3.13.* *_cp313
1621
1557
  constrains:
1622
1558
  - __osx >=11.0
1623
1559
  license: MIT
1624
1560
  license_family: MIT
1625
1561
  purls:
1626
1562
  - pkg:pypi/ruff?source=hash-mapping
1627
- size: 7802944
1628
- timestamp: 1741905453015
1563
+ size: 8337249
1564
+ timestamp: 1769521105071
1629
1565
  - conda: https://conda.anaconda.org/conda-forge/linux-64/secretstorage-3.4.1-py314hdafbbf9_0.conda
1630
1566
  sha256: f6883925a130126cdbdc62c2f43513db53c9f889cde4abc3bc66542336a87150
1631
1567
  md5: 54452085855583ccc3cc5dcd17b47ffe
@@ -1664,18 +1600,18 @@ packages:
1664
1600
  - configargparse>=1.7
1665
1601
  - packaging>=24.0,<26.0
1666
1602
  requires_python: '>=3.8'
1667
- - pypi: https://files.pythonhosted.org/packages/fc/e7/4a6319039b8bacf07dcfd98f9a7ed3b8b8666bc6713608adc3d0266609bc/snakemake_interface_software_deployment_plugins-0.9.1-py3-none-any.whl
1603
+ - pypi: https://files.pythonhosted.org/packages/2c/16/cae29057073ff0108a7bf4c699a3f258ffa9e530300548c015a0404ed7b0/snakemake_interface_software_deployment_plugins-0.10.0-py3-none-any.whl
1668
1604
  name: snakemake-interface-software-deployment-plugins
1669
- version: 0.9.1
1670
- sha256: b808f4e0cec149d7f18e16b4000ae4cf842ece5d7d4a8891df7f9cbb4a68eb2a
1605
+ version: 0.10.0
1606
+ sha256: af5e6946a8cd846d45dff995c58dd14eea4105b172b7de45b856a52a99c854aa
1671
1607
  requires_dist:
1672
1608
  - argparse-dataclass>=2.0.0,<3.0
1673
1609
  - snakemake-interface-common>=1.17.4,<2.0.0
1674
1610
  requires_python: '>=3.11,<4.0'
1675
1611
  - pypi: ./
1676
1612
  name: snakemake-software-deployment-plugin-container
1677
- version: 0.1.0
1678
- sha256: 2d2ee51657667da18c22a6a7002969fc710605a16a11fbdff8b60d89216247ef
1613
+ version: 0.2.1
1614
+ sha256: a2494a8414f9ab599bbf11c99bcf20e57ab10251a797d2e924cbe3ade6f16732
1679
1615
  requires_dist:
1680
1616
  - snakemake-interface-common>=1.17.4,<2.0.0
1681
1617
  - snakemake-interface-software-deployment-plugins>=0.9.1,<1.0
{snakemake_software_deployment_plugin_container-0.1.0 → snakemake_software_deployment_plugin_container-0.2.1}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
1
1
  [project]
2
2
  name = "snakemake-software-deployment-plugin-container"
3
- version = "0.1.0"
3
+ version = "0.2.1"
4
4
  authors = [
5
5
  { name = "Ben Carrillo", email = "ben.uzh@pm.me" },
6
6
  { name = "Johannes Köster", email = "johannes.koester@uni-due.de" }
@@ -35,7 +35,7 @@ publish = { features = ["publish"] }
35
35
 
36
36
  [tool.pixi.feature.dev.dependencies]
37
37
  pytest = ">=8.3.5,<9"
38
- ruff = ">=0.10.0,<0.11"
38
+ ruff = ">=0.10.0,<0.15"
39
39
  pytest-cov = ">=6.0.0,<7"
40
40
  pyrefly = ">=0.52.0,<0.53"
41
41
 
@@ -57,7 +57,7 @@ cmd = [
57
57
 
58
58
  [tool.coverage.report]
59
59
  exclude_lines = ["pass", "\\.\\.\\."]
60
- fail_under = 94.0
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-0.1.0 → snakemake_software_deployment_plugin_container-0.2.1}/src/snakemake_software_deployment_plugin_container/__init__.py RENAMED
@@ -2,13 +2,12 @@ __author__ = "ben carrillo"
2
2
  __copyright__ = "Copyright 2025, ben carrillo"
3
3
  __email__ = "ben.uzh@pm.me"
4
4
  __license__ = "MIT"
5
- import os.path
6
- import shlex
7
5
 
6
+ import shlex
8
7
  from dataclasses import dataclass, field
9
8
  from os import getcwd
10
9
  from shutil import which
11
- from typing import Iterable
10
+ from typing import Iterable, List
12
11
 
13
12
  from snakemake_interface_software_deployment_plugins.settings import (
14
13
  SoftwareDeploymentSettingsBase,
@@ -25,10 +24,6 @@ from snakemake_interface_common.exceptions import WorkflowError # noqa: F401
25
24
  from snakemake_interface_common.settings import SettingsEnumBase
26
25
 
27
26
 
28
- # The mountpoint for the Snakemake working directory inside the container.
29
- SNAKEMAKE_MOUNTPOINT = "/mnt/snakemake"
30
-
31
-
32
27
  # ContainerType is an enum that defines the different container types we support.
33
28
  # If adding new ones, make sure the choice is the same as the command name.
34
29
  class Runtime(SettingsEnumBase):
@@ -44,6 +39,14 @@ class Settings(SoftwareDeploymentSettingsBase):
44
39
  "help": "Container kind (udocker by default)",
45
40
  "env_var": False,
46
41
  "required": False,
42
+ "choices": Runtime.choices(),
43
+ },
44
+ )
45
+ mountpoints: List[str] = field(
46
+ default_factory=list,
47
+ metadata={
48
+ "nargs": "+",
49
+ "help": "Additional mount points (format: hostpath:containerpath)",
47
50
  },
48
51
  )
49
52
 
@@ -106,18 +109,20 @@ class Env(EnvBase):
106
109
  raise WorkflowError(f"{cmd} is not available in PATH")
107
110
 
108
111
  def decorate_shellcmd(self, cmd: str) -> str:
109
- # TODO pass more options here (extra mount volumes, user etc)
110
- containercache = os.path.join(
111
- SNAKEMAKE_MOUNTPOINT, ".cache/snakemake/source-cache"
112
+ # TODO pass more options here (user etc)
113
+
114
+ 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
112
117
  )
118
+ for mountpoint in self.settings.mountpoints:
119
+ mountpoints += f" -v {mountpoint!r}"
113
120
 
114
121
  decorated_cmd = (
115
122
  f"{self.settings.runtime} run"
116
123
  " --rm" # Remove container after execution
117
- f" -e HOME={SNAKEMAKE_MOUNTPOINT!r}" # Set HOME to working directory
118
- f" -w {SNAKEMAKE_MOUNTPOINT!r}" # Working directory inside container
119
- f" -v {getcwd()!r}:{SNAKEMAKE_MOUNTPOINT!r}" # Mount host directory to container
120
- f" -v {str(self.source_cache)!r}:{containercache!r}" # Mount host cache to container
124
+ f" -w {getcwd()!r}" # Working directory inside container
125
+ f" {mountpoints}"
121
126
  f" {self.spec.image_uri}" # Container image
122
127
  " /bin/sh" # Shell executable
123
128
  f" -c {shlex.quote(cmd)}" # The command to execute
@@ -130,7 +135,7 @@ class Env(EnvBase):
130
135
  # could potentially contain a different set of software (in terms of versions or
131
136
  # packages). Use self.spec (containing the corresponding EnvSpec object)
132
137
  # to determine the hash.
133
- hash_object.update(...)
138
+ hash_object.update(self.spec.image_uri.encode())
134
139
 
135
140
  def report_software(self) -> Iterable[SoftwareReport]:
136
141
  # Report the software contained in the environment. This should be a list of