fix: load concrete Env/EnvSpec classes instead of abstract bases

[jiangyun-fun]

Problem

SoftwareDeploymentPluginRegistry.load_plugin() populated the Plugin with:

_env_cls=module.EnvBase,
_env_spec_cls=module.EnvSpecBase,

Each plugin module imports EnvBase/EnvSpecBase as the abstract base classes for its own Env/EnvSpec subclasses, so module.EnvBase / module.EnvSpecBase resolve to those abstract bases — not the concrete classes the plugin defines. As a result plugin.env_spec_cls was always EnvSpecBase (and _env_cls always EnvBase) for every plugin.

This is inconsistent with expected_attributes(), which already correctly requires the concrete Env and EnvSpec attributes.

Impact

Because plugin.env_spec_cls was the abstract EnvSpecBase, methods like source_path_attributes() (abstract body ...) returned None. Snakemake's software-deployment directive factory iterates plugin.env_spec_cls.source_path_attributes() and crashed:

TypeError: 'NoneType' object is not iterable

This broke every software: <kind>(...) directive at parse time (conda/container/envmodules), so the whole generic software-deployment feature was unusable with the published plugin versions.

Fix

Read the concrete classes that plugins actually expose:

_env_cls=module.Env,
_env_spec_cls=module.EnvSpec,

Verification

With this change plus the corresponding snakemake-side fixes, the software: conda(envfile=...) path works end-to-end (the conda env is created and the rule runs); before this, any software: directive crashed in the factory. plugin.env_spec_cls now resolves to the concrete class for all plugins, e.g.:

conda:      env_spec_cls=EnvSpec, source_path_attributes=['envfile', 'pinfile']
container:  env_spec_cls=EnvSpec, source_path_attributes=[]
envmodules: env_spec_cls=EnvSpec

Context: snakemake/snakemake#4209.

Summary by CodeRabbit

• Bug Fixes
  • Improved plugin loading so deployment plugins now use the correct environment classes during initialization.
  • This helps ensure plugins are recognized and configured properly without changing their public interface.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: fdff41bb-72f8-44c4-8b5a-596f8c869989

📥 Commits

Reviewing files that changed from the base of the PR and between 4f0156a and b021cb0.

📒 Files selected for processing (1)

• snakemake_interface_software_deployment_plugins/registry/__init__.py

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📝 Walkthrough

Walkthrough

The plugin registry now constructs Plugin using module.Env and module.EnvSpec for environment classes instead of module.EnvBase and module.EnvSpecBase.

Changes

Plugin registry environment classes

Layer / File(s)	Summary
Environment class sources snakemake_interface_software_deployment_plugins/registry/__init__.py	load_plugin passes module.Env and module.EnvSpec into Plugin instead of module.EnvBase and module.EnvSpecBase.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~2 minutes

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 50.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and accurately summarizes the main change: loading concrete Env/EnvSpec classes instead of abstract bases.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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