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chore: Update pyproject & ci tasks to current SnakeDeploy template #28

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f9432f8
refactor: Move plugin module to src dir
jonasfreimuth Mar 16, 2026
e77f45a
chore: Use pixi infra from current scaffold
jonasfreimuth Mar 16, 2026
9f683aa
style: Format with ruff
jonasfreimuth Mar 16, 2026
e0d18f0
ci: Rename actions for consistency
jonasfreimuth Mar 16, 2026
40c24c2
ci: Use checkout action v6
jonasfreimuth Mar 16, 2026
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2 changes: 2 additions & 0 deletions .gitattributes
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Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
# SCM syntax highlighting & preventing 3-way merges
pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff
84 changes: 25 additions & 59 deletions .github/workflows/ci.yml
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Expand Up @@ -7,86 +7,52 @@ on:
pull_request:

jobs:
formatting:
format:
runs-on: ubuntu-latest
steps:
- name: Check out the code
uses: actions/checkout@v4
uses: actions/checkout@v6

- uses: actions/setup-python@v5
with:
python-version: "3.11"

- name: Install poetry
run: pip install poetry

- name: Determine dependencies
run: poetry lock

- uses: actions/setup-python@v5
with:
python-version: "3.11"
cache: poetry

- name: Install Dependencies using Poetry
run: poetry install
- name: Setup pixi
uses: prefix-dev/setup-pixi@v0

- name: Check formatting
run: poetry run black --check .
run: pixi run format --check
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linting:
lint:
runs-on: ubuntu-latest
steps:
- name: Check out the code
uses: actions/checkout@v3

- uses: actions/setup-python@v4
with:
python-version: "3.11"

- name: Install poetry
run: pip install poetry

- name: Determine dependencies
run: poetry lock
uses: actions/checkout@v6

- uses: actions/setup-python@v4
with:
python-version: "3.11"
cache: poetry

- name: Install Dependencies using Poetry
run: poetry install
- name: Setup pixi
uses: prefix-dev/setup-pixi@v0

- name: Check code
run: poetry run flake8
run: pixi run lint

testing:
typecheck:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4

- uses: actions/setup-python@v5
with:
python-version: "3.11"
- name: Check out the code
uses: actions/checkout@v6

- name: Install poetry
run: pip install poetry
- name: Setup pixi
uses: prefix-dev/setup-pixi@v0

- name: Determine dependencies
run: poetry lock
- name: Check code
run: pixi run typecheck

- uses: actions/setup-python@v5
with:
python-version: "3.11"
cache: poetry
test:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v6

- name: Install dependencies
run: |
poetry install
- name: Setup pixi
uses: prefix-dev/setup-pixi@v0

- name: Run pytest
run: poetry run coverage run -m pytest tests/tests.py
run: pixi run test -v

- name: Run Coverage
run: poetry run coverage report -m
run: pixi run coverage-report
39 changes: 18 additions & 21 deletions .github/workflows/release-please.yml
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Expand Up @@ -5,45 +5,42 @@ on:

name: release-please

env:
PYTHON_VERSION: "3.11"

jobs:
release-please:
runs-on: ubuntu-latest
outputs:
release_created: ${{ steps.release.outputs.release_created }}
steps:
- uses: googleapis/release-please-action@v4
- uses: GoogleCloudPlatform/release-please-action@v3
id: release
with:
release-type: python
package-name: snakemake-executor-plugin-cluster-generic
token: ${{ secrets.RELEASE_PLEASE_PR_CI_TOKEN }}
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publish:
runs-on: ubuntu-latest
needs: release-please
if: ${{ needs.release-please.outputs.release_created }}
steps:
- uses: actions/checkout@v4
- name: Check out the code
uses: actions/checkout@v4

- uses: actions/setup-python@v5
- name: Setup pixi
uses: prefix-dev/setup-pixi@v0
with:
python-version: "3.11"

- name: Install poetry
run: pip install poetry
cache: true
python-version: ${{ env.PYTHON_VERSION }}
Comment on lines +32 to +36
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@coderabbitai coderabbitai Bot Mar 16, 2026

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⚠️ Potential issue | 🟡 Minor

🧩 Analysis chain

🌐 Web query:

Does prefix-dev/setup-pixi action support python-version parameter?

💡 Result:

No. prefix-dev/setup-pixi does not have a python-version input—its supported inputs are defined in action.yml, and python-version is not one of them. [1]

If you want a specific Python version, set it in your Pixi environment (e.g., python = ">=3.11" in pixi.toml/pyproject.toml) and let pixi install resolve it. [2]

Sources: [1], [2]

Remove the unsupported python-version parameter from setup-pixi.

The prefix-dev/setup-pixi action does not support a python-version input parameter. Python version should be managed through your pixi.toml or pyproject.toml configuration instead (e.g., python = ">=3.11"). The parameter at lines 35–36 will be silently ignored and should be removed.

🤖 Prompt for AI Agents 
Verify each finding against the current code and only fix it if needed.

In @.github/workflows/release-please.yml around lines 32 - 36, Remove the
unsupported python-version input from the "Setup pixi" step using the
prefix-dev/setup-pixi action: locate the job step that uses
prefix-dev/setup-pixi (named "Setup pixi") and delete the python-version: ${{
env.PYTHON_VERSION }} line (and its key if present) so only supported inputs
like cache remain; manage Python versions via pixi.toml or pyproject.toml
instead.


- name: Determine dependencies
run: poetry lock
- name: Build source and wheel distribution + check build
run: |
pixi run -e dev check-build

- uses: actions/setup-python@v5
- name: Publish to PyPI
uses: pypa/gh-action-pypi-publish@release/v1
with:
python-version: "3.11"
cache: poetry

- name: Install Dependencies using Poetry
run: poetry install

- name: Publish to PyPi
env:
PYPI_USERNAME: __token__
PYPI_PASSWORD: ${{ secrets.PYPI_TOKEN }}
run: poetry publish --build --username $PYPI_USERNAME --password $PYPI_PASSWORD
user: __token__
password: ${{ secrets.PYPI_TOKEN }}
4 changes: 3 additions & 1 deletion .gitignore
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Expand Up @@ -159,4 +159,6 @@ cython_debug/
# option (not recommended) you can uncomment the following to ignore the entire idea folder.
#.idea/

poetry.lock
# pixi environments
.pixi/*
!.pixi/config.toml
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