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Merge pull request #1 from snakemake/feature/working
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feat: working
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johanneskoester authored Nov 26, 2023
2 parents c8746f0 + 5e2b176 commit f13b72b
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27 changes: 18 additions & 9 deletions .github/workflows/ci.yml
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Expand Up @@ -18,7 +18,7 @@ jobs:

- uses: actions/setup-python@v4
with:
python-version: "${{ env.PYTHON_VERSION }}"
python-version: ${{ env.PYTHON_VERSION }}

- name: Install poetry
run: pipx install poetry
Expand All @@ -28,7 +28,7 @@ jobs:

- uses: actions/setup-python@v4
with:
python-version: "${{ env.PYTHON_VERSION }}"
python-version: ${{ env.PYTHON_VERSION }}
cache: poetry

- name: Install Dependencies using Poetry
Expand All @@ -45,17 +45,17 @@ jobs:

- uses: actions/setup-python@v4
with:
python-version: "${{ env.PYTHON_VERSION }}"
python-version: ${{ env.PYTHON_VERSION }}

- name: Install poetry
run: pipx install poetry
run: pip install poetry

- name: Determine dependencies
run: poetry lock

- uses: actions/setup-python@v4
with:
python-version: "${{ env.PYTHON_VERSION }}"
python-version: ${{ env.PYTHON_VERSION }}
cache: poetry

- name: Install Dependencies using Poetry
Expand All @@ -66,22 +66,31 @@ jobs:

testing:
runs-on: ubuntu-latest

services:
azurite:
image: mcr.microsoft.com/azure-storage/azurite
ports:
- 10000:10000
- 10001:10001
- 10002:10002

steps:
- uses: actions/checkout@v3

- uses: actions/setup-python@v4
with:
python-version: "${{ env.PYTHON_VERSION }}"

python-version: ${{ env.PYTHON_VERSION }}
- name: Install poetry
run: pipx install poetry
run: pip install poetry

- name: Determine dependencies
run: poetry lock

- uses: actions/setup-python@v4
with:
python-version: "${{ env.PYTHON_VERSION }}"
python-version: ${{ env.PYTHON_VERSION }}
cache: poetry

- name: Install dependencies
Expand Down
4 changes: 2 additions & 2 deletions .github/workflows/release-please.yml
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Expand Up @@ -29,7 +29,7 @@ jobs:

- uses: actions/setup-python@v4
with:
python-version: "${{ env.PYTHON_VERSION }}"
python-version: ${{ env.PYTHON_VERSION }}

- name: Install poetry
run: pipx install poetry
Expand All @@ -39,7 +39,7 @@ jobs:

- uses: actions/setup-python@v4
with:
python-version: "${{ env.PYTHON_VERSION }}"
python-version: ${{ env.PYTHON_VERSION }}
cache: poetry

- name: Install Dependencies using Poetry
Expand Down
163 changes: 163 additions & 0 deletions .gitignore
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@@ -0,0 +1,163 @@
poetry.lock
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/
cover/

# Translations
*.mo
*.pot

# Django stuff:
*.log
local_settings.py
db.sqlite3
db.sqlite3-journal

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# PyBuilder
.pybuilder/
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
# For a library or package, you might want to ignore these files since the code is
# intended to run in multiple environments; otherwise, check them in:
# .python-version

# pipenv
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
# However, in case of collaboration, if having platform-specific dependencies or dependencies
# having no cross-platform support, pipenv may install dependencies that don't work, or not
# install all needed dependencies.
#Pipfile.lock

# poetry
# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
# This is especially recommended for binary packages to ensure reproducibility, and is more
# commonly ignored for libraries.
# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
#poetry.lock

# pdm
# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
#pdm.lock
# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
# in version control.
# https://pdm.fming.dev/#use-with-ide
.pdm.toml

# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
__pypackages__/

# Celery stuff
celerybeat-schedule
celerybeat.pid

# SageMath parsed files
*.sage.py

# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# Pyre type checker
.pyre/

# pytype static type analyzer
.pytype/

# Cython debug symbols
cython_debug/

# PyCharm
# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
# and can be added to the global gitignore or merged into this file. For a more nuclear
# option (not recommended) you can uncomment the following to ignore the entire idea folder.
#.idea/

poetry.lock
7 changes: 7 additions & 0 deletions .vscode/settings.json
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@@ -0,0 +1,7 @@
{
"[python]": {
"editor.codeActionsOnSave": {
"source.organizeImports": true
}
},
}
16 changes: 15 additions & 1 deletion README.md
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@@ -1,5 +1,19 @@
# Snakemake Storage Plugin Az

Azure Storage plugin for snakemake.
Azure Blob Storage plugin for snakemake.

This plugin is in draft form ! This is scaffolded from snakemake/poetry-snakemake-plugin.

# Testing

Testing this plugin locally require the azurite storage emulator to be running locally.
This can be setup using the following docker run command:

```
docker run -p 10000:10000 mcr.microsoft.com/azure-storage/azurite azurite-blob --blobHost 0.0.0.0
```

Then execute the tests:
```
poetry run coverage run -m pytest tests/tests.py
```
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