fix: apply modify func on all attributes, not only in case of source path attributes

[johanneskoester]

Summary by CodeRabbit

• Bug Fixes
  • Improved environment specification handling when applying attribute-based modifications.
  • Preserved original specifications when no attributes require changes.
  • Ensured nested fallback and scoped specifications are processed consistently.

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Review details

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: 93d72c5e-a19f-4fd0-9fc8-b16a60665aa6

📥 Commits

Reviewing files that changed from the base of the PR and between 3ae9389 and b7cae69.

📒 Files selected for processing (1)

• snakemake_interface_software_deployment_plugins/__init__.py

📝 Walkthrough

Walkthrough

EnvSpecBase._modify_attributes now selects the requested attributes before copying. It preserves unchanged objects and recursively processes nested within and fallback specifications when modifications exist.

Changes

Environment specification updates

Layer / File(s)	Summary
Attribute selection and conditional copying snakemake_interface_software_deployment_plugins/__init__.py	_modify_attributes now copies the specification only when selected attributes exist. It no longer relies on has_source_paths() for this decision.

Estimated code review effort: 2 (Simple) | ~10 minutes

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly describes applying the modification function to all attributes instead of only source path attributes.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
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.

✨ Finishing Touches 💡 1

🛠️ Fix failing CI checks 💡

• Create stacked PR
• Commit on current branch

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch fix/source-path-modification-all-attributes

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[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 `@snakemake_interface_software_deployment_plugins/__init__.py`:
- Around line 129-135: The attribute-copying logic around self_or_copied must
also copy the parent when a nested within or fallback specification is modified,
even if the current attributes list is empty. Update the relevant
nested-replacement flow to detect descendant changes and preserve the original
parent unchanged, then add regression coverage for a parent with no local
selected attributes and a matching nested within or fallback.

🪄 Autofix

Fix all unresolved CodeRabbit comments on this PR:

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

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: 1b2f7669-acce-432d-a47c-766698308b93

📥 Commits

Reviewing files that changed from the base of the PR and between 74eb072 and 3ae9389.

📒 Files selected for processing (1)

• snakemake_interface_software_deployment_plugins/__init__.py