fix: make identity_attributes/source_path_attributes classmethods

[jiangyun-fun]

Problem

EnvSpec.identity_attributes and EnvSpec.source_path_attributes are defined as instance methods (self), but the interface base (snakemake_interface_software_deployment_plugins.EnvSpecBase) and the sibling plugins (conda, container) declare them as @classmethod (cls).

Impact

EnvSpecBase.__hash__ -> managed_identity_attributes() (a classmethod) calls cls.identity_attributes(). Because this plugin's identity_attributes is an instance method, that call raises:

TypeError: EnvSpec.identity_attributes() missing 1 required positional argument: 'self'

So every envmodules spec is unhashable. Anywhere a spec is used as a dict key or set member it crashes — in particular SoftwareDeploymentManager.get_env() does if env_spec in self.specs_to_envs:, which hashes the spec. This breaks standalone envmodules(...) usage and the fallback chain envmodules(...) or conda(...) (the headline composition form).

Fix

Make both methods @classmethod, matching the interface and the other plugins:

@classmethod
def identity_attributes(cls) -> Iterable[str]:
    yield "names"

@classmethod
def source_path_attributes(cls) -> Iterable[str]:
    return ()

Neither body uses self, so this is a drop-in fix.

Verification

After the change, envmodules specs are hashable (hash(spec) succeeds) and get_env() no longer crashes on the fallback path.

Context: snakemake/snakemake#4209; related interface fix: snakemake/snakemake-interface-software-deployment-plugins#58.

Summary by CodeRabbit

• Bug Fixes
  • Improved environment identity and source-path attribute handling, making environment identification and hashing more consistent.
  • Fixed shell command generation to correctly load and quote module names containing unsafe characters (e.g., spaces).
  • Ensured environment specifications implement correct equality and hashing, including reliable dictionary-key usage.
• Tests
  • Added unit tests to cover environment identity attributes, string formatting, hashing/record hashing, and decorated shell command behavior.

[coderabbitai]

Caution

Review failed

Pull request was closed or merged during review

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: 7b3cfd53-757b-4de0-8988-611451c81bbc

📥 Commits

Reviewing files that changed from the base of the PR and between 7b3bc51 and f33739a.

📒 Files selected for processing (1)

• tests/test_plugin.py

💤 Files with no reviewable changes (1)

• tests/test_plugin.py

---

📝 Walkthrough

Walkthrough

EnvSpec attribute providers were converted to class methods. Tests were added for EnvSpec formatting, identity, hashing, shell command decoration, hash recording, and software reporting.

Changes

EnvSpec and Env behavior

Layer / File(s)	Summary
EnvSpec attribute providers src/snakemake_software_deployment_plugin_envmodules/__init__.py	EnvSpec.identity_attributes and EnvSpec.source_path_attributes are class methods and keep returning names and no source-path attributes.
EnvSpec and Env tests tests/test_plugin.py	Adds imports, helpers, and assertions for EnvSpec formatting, identity, hashing, dictionary-key use, Env.decorate_shellcmd, Env.record_hash, and Env.report_software.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

🚥 Pre-merge checks | ✅ 2 | ❌ 3

❌ Failed checks (3 warnings)

Check name	Status	Explanation	Resolution
Linked Issues check	⚠️ Warning	This PR fixes EnvSpec classmethods and hashability in envmodules, but it does not implement #58's concrete Env/EnvSpec loading in load_plugin().	Update SoftwareDeploymentPluginRegistry.load_plugin() to use module.Env and module.EnvSpec, and verify plugin.env_spec_cls resolves to the concrete class.
Out of Scope Changes check	⚠️ Warning	The patch centers on envmodules hashability and test coverage, which is outside #58's concrete plugin-loading requirement.	Split the hashability regression fix into a separate PR, or change the patch to address the plugin registry's concrete class loading.
Docstring Coverage	⚠️ Warning	Docstring coverage is 13.33% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately summarizes the main code change: converting EnvSpec methods to classmethods.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{Comment @coderabbitai help to get the list of available commands.}

[johanneskoester]

@jiangyun-fun do you want to add some additional tests to raise the coverage?

[jiangyun-fun]

Thanks, @johanneskoester! Done as requested — coverage is now ~84% (clears the gate); the hash tests guard the classmethod fix.

[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@tests/test_plugin.py`:
- Around line 99-108: The test in test_envspec_hash_and_equality_use_names is
asserting a stronger hash contract than Python guarantees by checking hash(a) !=
hash(c) for unequal objects. Remove that assertion and update the test to
validate distinctness through the existing equality semantics in _spec and
EnvSpec hashing, for example by asserting the set size for a, b, and c instead
of requiring different hash values for non-equal instances.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 1d1fde9e-4aba-4bb7-850b-cb2aa54d3b7c

📥 Commits

Reviewing files that changed from the base of the PR and between 195f695 and 7b3bc51.

📒 Files selected for processing (2)

• src/snakemake_software_deployment_plugin_envmodules/__init__.py
• tests/test_plugin.py