snakemake-software-deployment-plugin-container 0.1.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- snakemake_software_deployment_plugin_container-0.1.0/.github/workflows/ci.yml +54 -0
- snakemake_software_deployment_plugin_container-0.1.0/.github/workflows/conventional-prs.yml +16 -0
- snakemake_software_deployment_plugin_container-0.1.0/.github/workflows/release-please.yml +45 -0
- snakemake_software_deployment_plugin_container-0.1.0/.gitignore +7 -0
- snakemake_software_deployment_plugin_container-0.1.0/CHANGELOG.md +24 -0
- snakemake_software_deployment_plugin_container-0.1.0/LICENSE +21 -0
- snakemake_software_deployment_plugin_container-0.1.0/PKG-INFO +42 -0
- snakemake_software_deployment_plugin_container-0.1.0/README.md +29 -0
- snakemake_software_deployment_plugin_container-0.1.0/pixi.lock +1826 -0
- snakemake_software_deployment_plugin_container-0.1.0/pyproject.toml +71 -0
- snakemake_software_deployment_plugin_container-0.1.0/setup.cfg +7 -0
- snakemake_software_deployment_plugin_container-0.1.0/src/snakemake_software_deployment_plugin_container/__init__.py +146 -0
- snakemake_software_deployment_plugin_container-0.1.0/tests/test_plugin.py +75 -0
|
@@ -0,0 +1,54 @@
|
|
|
1
|
+
name: CI
|
|
2
|
+
|
|
3
|
+
on:
|
|
4
|
+
push:
|
|
5
|
+
branches:
|
|
6
|
+
- main
|
|
7
|
+
pull_request:
|
|
8
|
+
|
|
9
|
+
jobs:
|
|
10
|
+
formatting:
|
|
11
|
+
runs-on: ubuntu-latest
|
|
12
|
+
steps:
|
|
13
|
+
- name: Check out the code
|
|
14
|
+
uses: actions/checkout@v5
|
|
15
|
+
|
|
16
|
+
- name: Setup pixi
|
|
17
|
+
uses: prefix-dev/setup-pixi@v0
|
|
18
|
+
|
|
19
|
+
- name: Check formatting
|
|
20
|
+
run: pixi run format --check .
|
|
21
|
+
|
|
22
|
+
linting:
|
|
23
|
+
runs-on: ubuntu-latest
|
|
24
|
+
steps:
|
|
25
|
+
- name: Check out the code
|
|
26
|
+
uses: actions/checkout@v5
|
|
27
|
+
|
|
28
|
+
- name: Setup pixi
|
|
29
|
+
uses: prefix-dev/setup-pixi@v0
|
|
30
|
+
|
|
31
|
+
- name: Check code
|
|
32
|
+
run: pixi run lint
|
|
33
|
+
|
|
34
|
+
testing:
|
|
35
|
+
runs-on: ubuntu-latest
|
|
36
|
+
steps:
|
|
37
|
+
- uses: actions/checkout@v5
|
|
38
|
+
|
|
39
|
+
- name: Setup pixi
|
|
40
|
+
uses: prefix-dev/setup-pixi@v0
|
|
41
|
+
|
|
42
|
+
- name: Setup envmodules
|
|
43
|
+
run: |
|
|
44
|
+
sudo apt-get update
|
|
45
|
+
sudo apt-get install -y environment-modules
|
|
46
|
+
|
|
47
|
+
- name: Run pytest
|
|
48
|
+
shell: bash -el {0}
|
|
49
|
+
run: |
|
|
50
|
+
command -v module
|
|
51
|
+
pixi run test -v
|
|
52
|
+
|
|
53
|
+
- name: Run Coverage
|
|
54
|
+
run: pixi run coverage-report
|
|
@@ -0,0 +1,16 @@
|
|
|
1
|
+
name: PR
|
|
2
|
+
on:
|
|
3
|
+
pull_request_target:
|
|
4
|
+
types:
|
|
5
|
+
- opened
|
|
6
|
+
- reopened
|
|
7
|
+
- edited
|
|
8
|
+
- synchronize
|
|
9
|
+
|
|
10
|
+
jobs:
|
|
11
|
+
title-format:
|
|
12
|
+
runs-on: ubuntu-latest
|
|
13
|
+
steps:
|
|
14
|
+
- uses: amannn/action-semantic-pull-request@v3.4.0
|
|
15
|
+
env:
|
|
16
|
+
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
|
|
@@ -0,0 +1,45 @@
|
|
|
1
|
+
on:
|
|
2
|
+
push:
|
|
3
|
+
branches:
|
|
4
|
+
- main
|
|
5
|
+
|
|
6
|
+
name: release-please
|
|
7
|
+
|
|
8
|
+
env:
|
|
9
|
+
PYTHON_VERSION: 3.11
|
|
10
|
+
|
|
11
|
+
permissions:
|
|
12
|
+
contents: write
|
|
13
|
+
pull-requests: write
|
|
14
|
+
|
|
15
|
+
jobs:
|
|
16
|
+
release-please:
|
|
17
|
+
runs-on: ubuntu-latest
|
|
18
|
+
outputs:
|
|
19
|
+
release_created: ${{ steps.release.outputs.release_created }}
|
|
20
|
+
steps:
|
|
21
|
+
- uses: googleapis/release-please-action@v4
|
|
22
|
+
id: release
|
|
23
|
+
with:
|
|
24
|
+
release-type: python
|
|
25
|
+
token: ${{ secrets.RELEASE_PLEASE_PR_CI_TOKEN }}
|
|
26
|
+
|
|
27
|
+
publish:
|
|
28
|
+
runs-on: ubuntu-latest
|
|
29
|
+
needs: release-please
|
|
30
|
+
if: ${{ needs.release-please.outputs.release_created }}
|
|
31
|
+
steps:
|
|
32
|
+
- uses: actions/checkout@v5
|
|
33
|
+
|
|
34
|
+
- name: Setup pixi
|
|
35
|
+
uses: prefix-dev/setup-pixi@v0
|
|
36
|
+
|
|
37
|
+
- name: Build source and wheel distribution + check build
|
|
38
|
+
run: |
|
|
39
|
+
pixi run check-build
|
|
40
|
+
|
|
41
|
+
- name: Publish to PyPI
|
|
42
|
+
uses: pypa/gh-action-pypi-publish@release/v1
|
|
43
|
+
with:
|
|
44
|
+
user: __token__
|
|
45
|
+
password: ${{ secrets.PYPI_TOKEN }}
|
|
@@ -0,0 +1,24 @@
|
|
|
1
|
+
# Changelog
|
|
2
|
+
|
|
3
|
+
## 0.1.0 (2026-02-13)
|
|
4
|
+
|
|
5
|
+
|
|
6
|
+
### Bug Fixes
|
|
7
|
+
|
|
8
|
+
* do not mount a folder that does not exist ([1e78c0b](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/1e78c0bb0ff3c4066c99b6a0cdb29873f1094e76))
|
|
9
|
+
* mount cache folder inside container ([9a2ff7b](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/9a2ff7b4f95cb491a84f11d722381c0de7d810cd))
|
|
10
|
+
* typing and class naming, migrate to pixi ([6be2502](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/6be25021166cc610eeb74f4c8a0b6c9b09052a58))
|
|
11
|
+
* use ContainerType enum ([b2964fe](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/b2964fe5b224a3dd1e917d7f31a5dca51fe0fb0b))
|
|
12
|
+
* use shlex for more robust shell escaping ([1f650db](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/1f650db150bb4d80a7ab73c65ff0a9fdfd4820f4))
|
|
13
|
+
* use shlex for more robust shell escaping ([ea77d4a](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/ea77d4a637cc2057d606d63d743fac3b7aa925b5))
|
|
14
|
+
|
|
15
|
+
|
|
16
|
+
### Dependencies
|
|
17
|
+
|
|
18
|
+
* bump deps to latest stable snakemake release ([a4f3187](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/a4f3187a0a5d66c4d26013c3bbb7e707e8def674))
|
|
19
|
+
|
|
20
|
+
|
|
21
|
+
### Documentation
|
|
22
|
+
|
|
23
|
+
* add comment about tag in container URI ([e777fd7](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/e777fd78a7ba55386276ad3dce91b94fa8879f56))
|
|
24
|
+
* add TODO in README ([6d461e5](https://github.com/snakemake/snakemake-software-deployment-plugin-container/commit/6d461e5d94ecb20e98d13460e93bd6fa2b6b4a88))
|
|
@@ -0,0 +1,21 @@
|
|
|
1
|
+
MIT License
|
|
2
|
+
|
|
3
|
+
Copyright (c) 2025 btraven
|
|
4
|
+
|
|
5
|
+
Permission is hereby granted, free of charge, to any person obtaining a copy
|
|
6
|
+
of this software and associated documentation files (the "Software"), to deal
|
|
7
|
+
in the Software without restriction, including without limitation the rights
|
|
8
|
+
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
|
9
|
+
copies of the Software, and to permit persons to whom the Software is
|
|
10
|
+
furnished to do so, subject to the following conditions:
|
|
11
|
+
|
|
12
|
+
The above copyright notice and this permission notice shall be included in all
|
|
13
|
+
copies or substantial portions of the Software.
|
|
14
|
+
|
|
15
|
+
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
|
16
|
+
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
|
17
|
+
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
|
18
|
+
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
|
19
|
+
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
|
20
|
+
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
|
|
21
|
+
SOFTWARE.
|
|
@@ -0,0 +1,42 @@
|
|
|
1
|
+
Metadata-Version: 2.4
|
|
2
|
+
Name: snakemake-software-deployment-plugin-container
|
|
3
|
+
Version: 0.1.0
|
|
4
|
+
Project-URL: repository, https://github.com/snakemake/snakemake-software-deployment-plugin-container
|
|
5
|
+
Project-URL: documentation, https://snakemake.github.io/snakemake-plugin-catalog/plugins/software-deployment/container.html
|
|
6
|
+
Author-email: Ben Carrillo <ben.uzh@pm.me>, Johannes Köster <johannes.koester@uni-due.de>
|
|
7
|
+
License-File: LICENSE
|
|
8
|
+
Requires-Python: <4.0,>=3.11
|
|
9
|
+
Requires-Dist: snakemake-interface-common<2.0.0,>=1.17.4
|
|
10
|
+
Requires-Dist: snakemake-interface-software-deployment-plugins<1.0,>=0.9.1
|
|
11
|
+
Requires-Dist: udocker<2.0.0,>=1.3.17
|
|
12
|
+
Description-Content-Type: text/markdown
|
|
13
|
+
|
|
14
|
+
# snakemake-software-deployment-plugin-container
|
|
15
|
+
|
|
16
|
+
A generic container plugin implementing snakemake's software-deployment interface.
|
|
17
|
+
|
|
18
|
+
* It executes the given commands within a rootless container.
|
|
19
|
+
* It currently supports both `udocker` and `podman`.
|
|
20
|
+
|
|
21
|
+
## Usage
|
|
22
|
+
|
|
23
|
+
The `kind` parameter specifies valid values for the container runtime to use.
|
|
24
|
+
|
|
25
|
+
The `container` directive (should be) used to specify the container image to use
|
|
26
|
+
for the software deployment. This string should be a valid container image name,
|
|
27
|
+
including the tag; e.g., `biocontainers/example:1.0`.
|
|
28
|
+
|
|
29
|
+
By default, the plugin will attemtp to use 'latest' tag if no tag is provided.
|
|
30
|
+
However, be aware that some registries may not support this, for [good
|
|
31
|
+
reasons](https://github.com/BioContainers/containers/issues/297#issuecomment-439055879)
|
|
32
|
+
having to do with reproducibility. So, it's a good idea to specify a tag.
|
|
33
|
+
|
|
34
|
+
## Status
|
|
35
|
+
|
|
36
|
+
- Work in progress. The plugin conforms to the current software-deployment interface specification, and it has passing tests.
|
|
37
|
+
- Will revisit when further work is done in snakemake core to allow a more reusable integration of deployment plugins.
|
|
38
|
+
|
|
39
|
+
## TODO
|
|
40
|
+
|
|
41
|
+
- [ ] Add support for apptainer
|
|
42
|
+
- [ ] Implement repot_sofware method with container URI *and* the resolved hash of the image.
|
|
@@ -0,0 +1,29 @@
|
|
|
1
|
+
# snakemake-software-deployment-plugin-container
|
|
2
|
+
|
|
3
|
+
A generic container plugin implementing snakemake's software-deployment interface.
|
|
4
|
+
|
|
5
|
+
* It executes the given commands within a rootless container.
|
|
6
|
+
* It currently supports both `udocker` and `podman`.
|
|
7
|
+
|
|
8
|
+
## Usage
|
|
9
|
+
|
|
10
|
+
The `kind` parameter specifies valid values for the container runtime to use.
|
|
11
|
+
|
|
12
|
+
The `container` directive (should be) used to specify the container image to use
|
|
13
|
+
for the software deployment. This string should be a valid container image name,
|
|
14
|
+
including the tag; e.g., `biocontainers/example:1.0`.
|
|
15
|
+
|
|
16
|
+
By default, the plugin will attemtp to use 'latest' tag if no tag is provided.
|
|
17
|
+
However, be aware that some registries may not support this, for [good
|
|
18
|
+
reasons](https://github.com/BioContainers/containers/issues/297#issuecomment-439055879)
|
|
19
|
+
having to do with reproducibility. So, it's a good idea to specify a tag.
|
|
20
|
+
|
|
21
|
+
## Status
|
|
22
|
+
|
|
23
|
+
- Work in progress. The plugin conforms to the current software-deployment interface specification, and it has passing tests.
|
|
24
|
+
- Will revisit when further work is done in snakemake core to allow a more reusable integration of deployment plugins.
|
|
25
|
+
|
|
26
|
+
## TODO
|
|
27
|
+
|
|
28
|
+
- [ ] Add support for apptainer
|
|
29
|
+
- [ ] Implement repot_sofware method with container URI *and* the resolved hash of the image.
|