fix: typing, add pyrefly, migrate to pixi (#34)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

* **Chores**
* CI/CD updated to use pixi for dependency, build, and publish
workflows; gitignore updated for pixi lock files.

* **New Features**
* Environment specs/base enhanced with improved identity handling,
source-path management, and more reliable hashing/equality.

* **Refactor**
* Simplified environment base initialization and runtime attribute
handling.

* **Tests**
  * Removed legacy registry test class and associated test helpers.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Author: johanneskoester

.github/workflows/release-please.yml

@@ -22,29 +22,17 @@ jobs:
     needs: release-please
     if: ${{ needs.release-please.outputs.release_created }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v6
 
-      - uses: actions/setup-python@v2
-        with:
-          python-version: "3.11"
-
-      - name: Install poetry
-        run: pip install poetry
-
-      - name: Determine dependencies
-        run: poetry lock
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixi@v0
 
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-          cache: poetry
-
-      - name: Install Dependencies using Poetry
+      - name: Build source and wheel distribution + check build
         run: |
-          poetry install
+          pixi run check-build
 
-      - name: Publish to PyPi
-        env:
-          PYPI_USERNAME: __token__
-          PYPI_PASSWORD: ${{ secrets.PYPI_TOKEN }}
-        run: poetry publish --build --username $PYPI_USERNAME --password $PYPI_PASSWORD
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/test.yml

@@ -8,62 +8,40 @@ on:
     branches-ignore: []
 
 jobs:
-  linting:
+  formatting:
     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@v5
 
-      - 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 formatting
-        run: poetry run ruff format --check .
-      
-      - name: Lint
-        run: poetry run ruff check .
+        run: pixi run format --check .
 
-  testing:
+  linting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
+      - name: Check out the code
+        uses: actions/checkout@v5
 
-      - 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 lint
 
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-          cache: poetry
+  testing:
+    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

.gitignore

@@ -3,6 +3,8 @@ __pycache__/
 *.py[cod]
 *$py.class
 
+pixi.lock
+
 # C extensions
 *.so
 
@@ -159,4 +161,4 @@ cython_debug/
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
 
-poetry.lock
+poetry.lock

pyproject.toml

@@ -1,30 +1,72 @@
-[tool.poetry]
-authors = ["Johannes Köster <johannes.koester@uni-due.de>"]
+[project]
+authors = [
+    { name = "Johannes Köster", email = "johannes.koester@uni-due.de" }
+]
 description = "This package provides a stable interface for interactions between Snakemake and its software deployment plugins."
 license = "MIT"
 name = "snakemake-interface-software-deployment-plugins"
-packages = [{include = "snakemake_interface_software_deployment_plugins"}]
 readme = "README.md"
 version = "0.9.0"
+requires-python = ">=3.11,<4.0"
+dependencies = [
+    "argparse-dataclass >=2.0.0,<3.0",
+    "snakemake-interface-common >=1.17.4,<2.0.0"
+]
 
-[tool.poetry.dependencies]
-argparse-dataclass = "^2.0.0"
-python = "^3.11"
-snakemake-interface-common = "^1.17.4"
+[project.urls]
+repository = "https://github.com/snakemake/snakemake-interface-software-deployment-plugins"
 
-[tool.poetry.group.dev.dependencies]
-coverage = {extras = ["toml"], version = "^6.3.1"}
-flake8-bugbear = "^22.1.11"
-pytest = "^7.0"
-ruff = "^0.9.9"
-snakemake-software-deployment-plugin-envmodules = "^0.1.2"
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.pixi.pypi-dependencies]
+snakemake-interface-software-deployment-plugins = { path = ".", editable = true }
+
+[tool.pixi.workspace]
+channels = ["conda-forge"]
+platforms = ["osx-arm64", "linux-64"]
+
+[tool.pixi.environments]
+dev = { features = ["dev"] }
+publish = { features = ["publish"] }
+
+[tool.pixi.feature.dev.dependencies]
+pytest = ">=8.3.5,<9"
+ruff = ">=0.10.0,<0.11"
+pytest-cov = ">=6.0.0,<7"
+pyrefly = ">=0.52.0,<0.53"
 
-[tool.coverage.run]
-omit = [".*", "*/site-packages/*"]
+[tool.pixi.feature.dev.pypi-dependencies]
+snakemake-software-deployment-plugin-envmodules = ">=0.1.2,<1.0"
+
+[tool.pixi.feature.dev.tasks]
+format = "ruff format"
+lint = "ruff check"
+typecheck = "pyrefly check"
+qc = { depends-on = ["format", "lint"] }
+coverage-report = "coverage report -m"
+
+[tool.pixi.feature.dev.tasks.test]
+cmd = [
+    "pytest",
+    "--cov=snakemake_software_deployment_plugin_envmodules",
+    "--cov-report=xml:coverage-report/coverage.xml",
+    "--cov-report=term-missing",
+    "tests/test_interface.py",
+]
 
 [tool.coverage.report]
-fail_under = 60
+exclude_lines = ["pass", "\\.\\.\\."]
+fail_under = 63.0
 
-[build-system]
-build-backend = "poetry.core.masonry.api"
-requires = ["poetry-core"]
+[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_software_deployment_plugins/__init__.py

@@ -5,10 +5,12 @@
 
 from abc import ABC, abstractmethod
 from copy import copy
+from inspect import getmodule
 from dataclasses import dataclass, field
 import hashlib
 from pathlib import Path
 import shutil
+from types import ModuleType
 from typing import (
     Any,
     ClassVar,
@@ -19,6 +21,7 @@
     Self,
     Tuple,
     Type,
+    TypeVar,
     Union,
 )
 import subprocess as sp
@@ -43,16 +46,22 @@ class EnvSpecSourceFile:
 
 
 class EnvSpecBase(ABC):
+    @classmethod
+    def module(cls) -> ModuleType:
+        class_module = getmodule(cls)
+        assert class_module is not None, f"bug: cannot detect class module of {cls}"
+        return class_module
+
     def technical_init(self):
         """This has to be called by Snakemake upon initialization"""
         self.within: Optional["EnvSpecBase"] = None
         self.fallback: Optional["EnvSpecBase"] = None
-        self.kind: str = self.__class__.__module__.common_settings.provides
+        self.kind: str = self.module().common_settings.provides
         self._obj_hash: Optional[int] = None
 
     @classmethod
     def env_cls(cls):
-        return cls.__module__.EnvBase
+        return cls.module().EnvBase
 
     @classmethod
     @abstractmethod
@@ -148,19 +157,11 @@ def run(self, cmd: str, **kwargs) -> sp.CompletedProcess:
         return sp.run([self.executable] + self.args + [self.command_arg, cmd], **kwargs)
 
 
+TSettings = TypeVar("TSettings", bound="SoftwareDeploymentSettingsBase")
+
+
 class EnvBase(ABC):
     _cache: ClassVar[Dict[Tuple[Type["EnvBase"], Optional["EnvBase"]], Any]] = {}
-    spec: EnvSpecBase
-    within: Optional["EnvBase"]
-    settings: Optional[SoftwareDeploymentSettingsBase]
-    shell_executable: ShellExecutable
-    tempdir: Path
-    _cache_prefix: Path
-    _deployment_prefix: Path
-    _pinfile_prefix: Path
-    _managed_hash_store: Optional[str] = None
-    _managed_deployment_hash_store: Optional[str] = None
-    _obj_hash: Optional[int] = None
 
     def __init__(
         self,
@@ -174,15 +175,18 @@ def __init__(
         deployment_prefix: Path,
         pinfile_prefix: Path,
     ):
-        self.spec: EnvSpecBase = spec
-        self.within: Optional["EnvBase"] = within
+        self.spec = spec
+        self.within = within
         self.settings: Optional[SoftwareDeploymentSettingsBase] = settings
         self.shell_executable = shell_executable
         self.tempdir = tempdir
         self.source_cache: Path = source_cache
         self._deployment_prefix: Path = deployment_prefix
         self._cache_prefix: Path = cache_prefix
         self._pinfile_prefix: Path = pinfile_prefix
+        self._managed_hash_store: Optional[str] = None
+        self._managed_deployment_hash_store: Optional[str] = None
+        self._obj_hash: Optional[int] = None
         self.__post_init__()
 
     def __post_init__(self) -> None:  # noqa B027

tests/tests.py tests/test_interface.pytests/tests.py renamed to tests/test_interface.py

@@ -20,8 +20,8 @@ def get_test_plugin_name(self) -> str:
 
     def validate_plugin(self, plugin: PluginBase):
         assert plugin.settings_cls is None
-        assert plugin.env_cls is not None
-        assert plugin.env_spec_cls is not None
+        assert plugin.env_cls is not None  # pyrefly: ignore[missing-attribute]
+        assert plugin.env_spec_cls is not None  # pyrefly: ignore[missing-attribute]
 
     def validate_settings(self, settings: SettingsBase, plugin: PluginBase):
         # assert isinstance(settings, plugin.settings_cls)