fix: typing, add pyrefly, migrate to pixi

[johanneskoester]

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.

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📝 Walkthrough

Walkthrough

Migrates CI from Poetry to pixi, updates workflow checkout actions, adds module-detection and extensive identity/hash APIs to EnvSpecBase and refactors EnvBase field declarations to runtime assignments, and removes the TestRegistry test class from tests/tests.py.

Changes

Cohort / File(s)	Summary
CI/CD Workflow Tooling Migration .github/workflows/release-please.yml, .github/workflows/test.yml	Replaced Poetry/Python setup and poetry-run commands with pixi-based setup and pixi run ... commands; bumped checkout action versions (v3→v6, v4→v5) and updated publish step to use pypa/gh-action-pypi-publish@release/v1 with __token__ authentication.
Build Configuration .gitignore	Added pixi.lock to ignore and normalized newline at end of file.
Core Library API Expansion and Refactor snakemake_interface_software_deployment_plugins/__init__.py	Added module() classmethod to EnvSpecBase, new TSettings TypeVar, multiple abstract/public methods (identity_attributes, source_path_attributes, has_source_paths, modify_source_paths, __or__, managed_identity_attributes, __hash__, __eq__, __str__) and adjusted usages to rely on module(). Refactored EnvBase to remove class-level annotated public fields and assign them at runtime in __init__; initialized internal hash/deployment stores. Added imports for getmodule and ModuleType.
Tests Removal tests/tests.py	Removed TestRegistry test class and its helper/validation methods (plugin registry testing and related helpers deleted).

Estimated code review effort

🎯 4 (Complex) | ⏱️ ~45 minutes

Possibly related PRs

• fix: streamline inheritance annotation #23: Modifies the same core types (EnvBase / EnvSpecBase) and overlaps with API/initialization changes in this module.

🚥 Pre-merge checks | ✅ 2 | ❌ 2

❌ Failed checks (1 warning, 1 inconclusive)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 25.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.
Title check	❓ Inconclusive	The title encompasses multiple distinct changes: typing fixes, pyrefly addition, and pixi migration, but emphasizes the tooling migration as the primary focus without clearly indicating the typing/API changes to EnvSpecBase and EnvBase.	Consider refining the title to better reflect the primary change; for example, 'refactor: migrate to pixi and modernize type annotations' would be more descriptive of the actual scope.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Merge Conflict Detection	✅ Passed	✅ No merge conflicts detected when merging into main

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing touches

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• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch fix/types

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Caution

Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (1)

snakemake_interface_software_deployment_plugins/__init__.py (1)

274-283: ⚠️ Potential issue | 🟡 Minor

Pre-existing: _managed_generic_hash never persists the computed hash back to self.

The computed hash is assigned to the local store variable but never written back to the instance attribute via setattr(self, f"_managed_{kind}_store", store). This means hash() and deployment_hash() recompute the MD5 on every call instead of caching. Not introduced by this PR, but worth fixing while you're in this area.

Proposed fix

     def _managed_generic_hash(self, kind: str) -> str:
-        store = getattr(self, f"_managed_{kind}_store")
-        if store is None:
+        attr = f"_managed_{kind}_store"
+        store = getattr(self, attr)
+        if store is None:
             record_hash = f"record_{kind}"
             hash_object = hashlib.md5()
             if self.within is not None:
                 getattr(self.within, record_hash)(hash_object)
             getattr(self, record_hash)(hash_object)
             store = hash_object.hexdigest()
+            setattr(self, attr, store)
         return store

🧹 Nitpick comments (3)

.github/workflows/release-please.yml (1)

14-16: Inconsistent checkout action versions across workflows.

This file uses actions/checkout@v6 (line 25), while .github/workflows/test.yml uses @v5 for the formatting and linting jobs (lines 15, 27) but @v6 for the testing job (line 38). Consider aligning all checkout steps to the same version for consistency.

.github/workflows/test.yml (1)

15-15: Inconsistent actions/checkout versions within the same workflow.

The formatting and linting jobs use actions/checkout@v5 (lines 15, 27) while the testing job uses actions/checkout@v6 (line 38). Pick one version consistently.

Proposed fix

       - name: Check out the code
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6

...

       - name: Check out the code
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6

Also applies to: 27-27, 38-38

snakemake_interface_software_deployment_plugins/__init__.py (1)

160-161: TSettings TypeVar is unused in this file but exported as part of the public API.

Confirmed that TSettings is not referenced within this file or elsewhere in the repository. However, since this is a plugin interface library, it appears to be intentionally exported for plugin implementations to use in their own type annotations. Consider adding a brief comment explaining its purpose as a TypeVar for plugin developers (e.g., # TypeVar for plugin implementations to annotate Settings-compatible types).