chore: use Pixi for improved CI/CD and update project configuration

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.github/workflows/release-please.yml

@@ -17,34 +17,27 @@ jobs:
           release-type: python
           package-name: snakemake-interface-executor-plugins
 
-  publish:
+  publish-pypi:
     runs-on: ubuntu-latest
     needs: release-please
     if: ${{ needs.release-please.outputs.release_created }}
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: actions/setup-python@v2
-        with:
-          python-version: "3.11"
 
-      - name: Install poetry
-        run: pip install poetry
-
-      - name: Determine dependencies
-        run: poetry lock
+    steps:
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v4
+      - name: Install Pixi
+        uses: prefix-dev/setup-pixi@v0.8.3
         with:
-          python-version: "3.11"
-          cache: poetry
+          environments: publish
+          pixi-version: v0.42.1
 
-      - name: Install Dependencies using Poetry
+      - name: Build source and wheel distribution + check build
+        # this will build the source and wheel into the dist/ directory
         run: |
-          poetry install
+          pixi run --environment publish check-build
 
-      - name: Publish to PyPi
+      - name: Publish distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
         env:
           PYPI_USERNAME: __token__
           PYPI_PASSWORD: ${{ secrets.PYPI_TOKEN }}
-        run: poetry publish --build --username $PYPI_USERNAME --password $PYPI_PASSWORD

.github/workflows/test.yml

@@ -7,88 +7,54 @@ on:
   pull_request:
     branches-ignore: []
 
+permissions:
+  contents: read
+  checks: write
+  issues: write
+  pull-requests: write
+
 jobs:
-  formatting:
+  quality-control:
     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/setup-python@v4
-        with:
-          python-version: "3.11"
-          cache: poetry
+        uses: actions/checkout@v4
 
-      - name: Install Dependencies using Poetry
-        run: poetry install
-
-      - name: Check formatting
-        run: poetry run black --check .
-
-  linting:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check out the code
-        uses: actions/checkout@v3
-
-      - uses: actions/setup-python@v4
+      - name: Install Pixi
+        uses: prefix-dev/setup-pixi@v0.8.3
         with:
-          python-version: "3.11"
-
-      - name: Install poetry
-        run: pip install poetry
+          environments: dev
+          pixi-version: v0.42.1
+          cache: true
 
-      - name: Determine dependencies
-        run: poetry lock
-
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-          cache: poetry
+      - name: Ruff Format
+        if: always()
+        run: |
+          pixi run --environment dev format --check
 
-      - name: Install Dependencies using Poetry
-        run: poetry install
+      - name: Ruff lint
+        if: always()
+        run: |
+          pixi run --environment dev lint --diff
+      # - name: Mypy
+      #   if: always()
+      #   run: |
+      #     pixi run --environment dev type-check
 
-      - name: Check code
-        run: poetry run flake8
+      - name: Collect QC
+        run: echo "All quality control checks passed"
 
   testing:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v4
+      - name: Install Pixi
+        uses: prefix-dev/setup-pixi@v0.8.3
         with:
-          python-version: "3.11"
-
-      - name: Install poetry
-        run: pip install poetry
-
-      - name: Determine dependencies
-        run: poetry lock
-
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-          cache: poetry
-
-      - name: Install dependencies
-        run: |
-          pip install connection-pool # because it is incompatible with poetry
-          poetry install
-
-      - name: Run pytest
-        run: poetry run coverage run -m pytest tests/tests.py
+          environments: dev
+          pixi-version: v0.42.1
+          cache: true
 
-      - name: Run Coverage
-        run: poetry run coverage report -m
+      - name: Run tests
+        run: pixi run --environment dev test --show-capture=all -s -vv

.gitignore

@@ -159,4 +159,7 @@ cython_debug/
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
 
-poetry.lock
+poetry.lock
+# pixi environments
+.pixi
+*.egg-info