Skip to content

Commit 820404d

Browse files
H-KwonH-Kwon
committed
Initial commit
0 parents  commit 820404d

13 files changed

Lines changed: 706 additions & 0 deletions

File tree

‎.gitattributes‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,2 @@
1+
# SCM syntax highlighting & preventing 3-way merges
2+
pixi.lock merge=binary linguist-language=YAML linguist-generated=true

‎.github/workflows/ci.yml‎

Lines changed: 70 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,70 @@
1+
name: CI
2+
3+
on:
4+
push:
5+
branches:
6+
- main
7+
pull_request:
8+
9+
env:
10+
PYTHON_VERSION: 3.11
11+
12+
jobs:
13+
linting:
14+
runs-on: ubuntu-latest
15+
steps:
16+
- name: Check out the code
17+
uses: actions/checkout@v3
18+
19+
- uses: actions/setup-python@v4
20+
with:
21+
python-version: ${{ env.PYTHON_VERSION }}
22+
23+
- name: Install poetry
24+
run: pip install poetry
25+
26+
- name: Determine dependencies
27+
run: poetry lock
28+
29+
- uses: actions/setup-python@v4
30+
with:
31+
python-version: ${{ env.PYTHON_VERSION }}
32+
cache: poetry
33+
34+
- name: Install Dependencies using Poetry
35+
run: poetry install
36+
37+
- name: Check formatting
38+
run: poetry run ruff format --check .
39+
40+
- name: Lint
41+
run: poetry run ruff check .
42+
43+
testing:
44+
runs-on: ubuntu-latest
45+
steps:
46+
- uses: actions/checkout@v3
47+
48+
- uses: actions/setup-python@v4
49+
with:
50+
python-version: ${{ env.PYTHON_VERSION }}
51+
52+
- name: Install poetry
53+
run: pip install poetry
54+
55+
- name: Determine dependencies
56+
run: poetry lock
57+
58+
- uses: actions/setup-python@v4
59+
with:
60+
python-version: ${{ env.PYTHON_VERSION }}
61+
cache: poetry
62+
63+
- name: Install dependencies
64+
run: poetry install
65+
66+
- name: Run pytest
67+
run: poetry run coverage run -m pytest
68+
69+
- name: Run Coverage
70+
run: poetry run coverage report -m

‎.github/workflows/conventional-prs.yml‎

Lines changed: 16 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -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 }}

‎.github/workflows/release-please.yml‎

Lines changed: 45 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -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+
jobs:
12+
release-please:
13+
runs-on: ubuntu-latest
14+
outputs:
15+
release_created: ${{ steps.release.outputs.release_created }}
16+
steps:
17+
- uses: GoogleCloudPlatform/release-please-action@v3
18+
id: release
19+
with:
20+
release-type: python
21+
package-name: snakemake-storage-plugin-git
22+
23+
publish:
24+
runs-on: ubuntu-latest
25+
needs: release-please
26+
if: ${{ needs.release-please.outputs.release_created }}
27+
steps:
28+
- name: Check out the code
29+
uses: actions/checkout@v4
30+
31+
- name: Setup pixi
32+
uses: prefix-dev/setup-pixi@v0
33+
with:
34+
cache: true
35+
python-version: ${{ env.PYTHON_VERSION }}
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 }}

‎.gitignore‎

Lines changed: 206 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,206 @@
1+
# Byte-compiled / optimized / DLL files
2+
__pycache__/
3+
*.py[codz]
4+
*$py.class
5+
6+
# C extensions
7+
*.so
8+
9+
# Distribution / packaging
10+
.Python
11+
build/
12+
develop-eggs/
13+
dist/
14+
downloads/
15+
eggs/
16+
.eggs/
17+
lib/
18+
lib64/
19+
parts/
20+
sdist/
21+
var/
22+
wheels/
23+
share/python-wheels/
24+
*.egg-info/
25+
.installed.cfg
26+
*.egg
27+
MANIFEST
28+
29+
# PyInstaller
30+
# Usually these files are written by a python script from a template
31+
# before PyInstaller builds the exe, so as to inject date/other infos into it.
32+
*.manifest
33+
*.spec
34+
35+
# Installer logs
36+
pip-log.txt
37+
pip-delete-this-directory.txt
38+
39+
# Unit test / coverage reports
40+
htmlcov/
41+
.tox/
42+
.nox/
43+
.coverage
44+
.coverage.*
45+
.cache
46+
nosetests.xml
47+
coverage.xml
48+
*.cover
49+
*.py.cover
50+
.hypothesis/
51+
.pytest_cache/
52+
cover/
53+
54+
# Translations
55+
*.mo
56+
*.pot
57+
58+
# Django stuff:
59+
*.log
60+
local_settings.py
61+
db.sqlite3
62+
db.sqlite3-journal
63+
64+
# Flask stuff:
65+
instance/
66+
.webassets-cache
67+
68+
# Scrapy stuff:
69+
.scrapy
70+
71+
# Sphinx documentation
72+
docs/_build/
73+
74+
# PyBuilder
75+
.pybuilder/
76+
target/
77+
78+
# Jupyter Notebook
79+
.ipynb_checkpoints
80+
81+
# IPython
82+
profile_default/
83+
ipython_config.py
84+
85+
# pyenv
86+
# For a library or package, you might want to ignore these files since the code is
87+
# intended to run in multiple environments; otherwise, check them in:
88+
# .python-version
89+
90+
# pipenv
91+
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
92+
# However, in case of collaboration, if having platform-specific dependencies or dependencies
93+
# having no cross-platform support, pipenv may install dependencies that don't work, or not
94+
# install all needed dependencies.
95+
Pipfile.lock
96+
97+
# UV
98+
# Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
99+
# This is especially recommended for binary packages to ensure reproducibility, and is more
100+
# commonly ignored for libraries.
101+
#uv.lock
102+
103+
# poetry
104+
# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
105+
# This is especially recommended for binary packages to ensure reproducibility, and is more
106+
# commonly ignored for libraries.
107+
# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
108+
poetry.lock
109+
poetry.toml
110+
111+
# pdm
112+
# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
113+
# pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
114+
# https://pdm-project.org/en/latest/usage/project/#working-with-version-control
115+
#pdm.lock
116+
#pdm.toml
117+
.pdm-python
118+
.pdm-build/
119+
120+
# pixi
121+
# Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
122+
pixi.lock
123+
# Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
124+
# in the .venv directory. It is recommended not to include this directory in version control.
125+
.pixi
126+
127+
# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
128+
__pypackages__/
129+
130+
# Celery stuff
131+
celerybeat-schedule
132+
celerybeat.pid
133+
134+
# SageMath parsed files
135+
*.sage.py
136+
137+
# Environments
138+
.env
139+
.envrc
140+
.venv
141+
env/
142+
venv/
143+
ENV/
144+
env.bak/
145+
venv.bak/
146+
147+
# Spyder project settings
148+
.spyderproject
149+
.spyproject
150+
151+
# Rope project settings
152+
.ropeproject
153+
154+
# mkdocs documentation
155+
/site
156+
157+
# mypy
158+
.mypy_cache/
159+
.dmypy.json
160+
dmypy.json
161+
162+
# Pyre type checker
163+
.pyre/
164+
165+
# pytype static type analyzer
166+
.pytype/
167+
168+
# Cython debug symbols
169+
cython_debug/
170+
171+
# PyCharm
172+
# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
173+
# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
174+
# and can be added to the global gitignore or merged into this file. For a more nuclear
175+
# option (not recommended) you can uncomment the following to ignore the entire idea folder.
176+
#.idea/
177+
178+
# Abstra
179+
# Abstra is an AI-powered process automation framework.
180+
# Ignore directories containing user credentials, local state, and settings.
181+
# Learn more at https://abstra.io/docs
182+
.abstra/
183+
184+
# Visual Studio Code
185+
# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
186+
# that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
187+
# and can be added to the global gitignore or merged into this file. However, if you prefer,
188+
# you could uncomment the following to ignore the entire vscode folder
189+
# .vscode/
190+
191+
# Ruff stuff:
192+
.ruff_cache/
193+
194+
# PyPI configuration file
195+
.pypirc
196+
197+
# Marimo
198+
marimo/_static/
199+
marimo/_lsp/
200+
__marimo__/
201+
202+
# Streamlit
203+
.streamlit/secrets.toml
204+
205+
# Custom
206+
workflow/

‎CHANGELOG.md‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
# Changelog

‎CODE_OF_CONDUCT.md‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,3 @@
1+
# Code of Conduct
2+
3+
This project has adopted the [Snakemake Code of Conduct](https://github.com/snakemake/snakemake/blob/main/CODE_OF_CONDUCT.md)

‎LICENSE‎

Lines changed: 21 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,21 @@
1+
MIT License
2+
3+
Copyright (c) 2025 University of Potsdam, Software Engineering Group
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.

‎README.md‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,3 @@
1+
# snakemake-storage-plugin-git
2+
3+
Snakemake storage plugin for downloading remote git repositories as input files.

0 commit comments

Comments
 (0)