chore: use Pixi for improved CI/CD and update project configuration (#82)

Co-authored-by: Johannes Köster <[email protected]>

Author: jjjermiah

.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/[email protected]
         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 +7,52 @@ 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/[email protected]
         with:
-          python-version: "3.11"
-
-      - name: Install poetry
-        run: pip install poetry
+          environments: dev
+          pixi-version: v0.42.1
 
-      - 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/[email protected]
         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
 
-      - 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 +159,8 @@ 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
+pixi.lock

pyproject.toml

@@ -1,26 +1,16 @@
-[tool.poetry]
-authors = ["Johannes Köster <[email protected]>"]
-description = "This package provides a stable interface for interactions between Snakemake and its executor plugins."
-license = "MIT"
+[project]
 name = "snakemake-interface-executor-plugins"
-packages = [{include = "snakemake_interface_executor_plugins"}]
-readme = "README.md"
 version = "9.3.3"
-
-[tool.poetry.dependencies]
-argparse-dataclass = "^2.0.0"
-python = "^3.11"
-throttler = "^1.2.2"
-snakemake-interface-common = "^1.17.4"
-
-[tool.poetry.dev-dependencies]
-black = "^24.0.0"
-coverage = {extras = ["toml"], version = "^6.3.1"}
-flake8 = "^4.0.1"
-flake8-bugbear = "^22.1.11"
-pytest = "^7.0"
-snakemake = {git="https://github.com/snakemake/snakemake.git"}
-snakemake-executor-plugin-cluster-generic = {git = "https://github.com/snakemake/snakemake-executor-plugin-cluster-generic.git"}
+description = "This package provides a stable interface for interactions between Snakemake and its executor plugins."
+authors = [{ name = "Johannes Köster", email = "[email protected]" }]
+license = { text = "MIT" }
+readme = "README.md"
+requires-python = ">=3.11"
+dependencies = [
+  "snakemake-interface-common>=1.17.4",
+  "throttler>=1.2.2",
+  "argparse-dataclass>=2.0.0",
+]
 
 [tool.coverage.run]
 omit = [".*", "*/site-packages/*"]
@@ -31,3 +21,57 @@ fail_under = 63
 [build-system]
 build-backend = "poetry.core.masonry.api"
 requires = ["poetry-core"]
+
+[tool.pixi.project]
+channels = ["conda-forge"]
+platforms = ["osx-arm64", "linux-64"]
+
+[tool.pixi.pypi-dependencies]
+
+[tool.pixi.tasks]
+
+[tool.pixi.environments]
+dev = { features = ["dev"] }
+publish = { features = ["publish"] }
+
+[tool.pixi.feature.dev.pypi-dependencies]
+snakemake-interface-executor-plugins = { path = ".", editable = true }
+snakemake = { git = "https://github.com/snakemake/snakemake.git" }
+snakemake-executor-plugin-cluster-generic = { git = "https://github.com/snakemake/snakemake-executor-plugin-cluster-generic.git" }
+
+[tool.pixi.feature.dev.tasks.test]
+cmd = [
+  "pytest",
+  "--cov=snakemake_interface_executor_plugins",
+  "--cov-report=xml:coverage-report/coverage.xml",
+  "--cov-report=term-missing",
+  "tests/tests.py"
+]
+description = "Run tests and generate coverage report"
+
+
+[tool.pixi.feature.dev.dependencies]
+pytest = ">=8.3.5,<9"
+ruff = ">=0.10.0,<0.11"
+mypy = ">=1.15.0,<2"
+pytest-cov = ">=6.0.0,<7"
+
+[tool.pixi.feature.dev.tasks]
+format = "ruff format snakemake_interface_executor_plugins"
+lint = "ruff check"
+type-check = "mypy snakemake_interface_executor_plugins/"
+qc = { depends-on = ["format", "lint", "type-check"] }
+
+[tool.mypy]
+ignore_missing_imports = true
+
+# Publish
+[tool.pixi.feature.publish.dependencies]
+twine = ">=6.1.0,<7"
+python-build = ">=1.2.2,<2"
+
+[tool.pixi.feature.publish.tasks]
+build = { cmd = "python -m build", description = "Build the package into the dist/ directory" }
+check-build = { cmd = "python -m twine check dist/*", depends-on = [
+  "build",
+], description = "Check that the package can be uploaded" }

snakemake_interface_executor_plugins/executors/base.py

@@ -46,7 +46,8 @@ def isdigit(i):
             for resource, value in job.resources.items()
             if isinstance(value, int)
             # need to check bool seperately because bool is a subclass of int
-            and isdigit(value) and resource not in excluded_resources
+            and isdigit(value)
+            and resource not in excluded_resources
         }
 
     def get_resource_declarations(self, job: JobExecutorInterface):