feat: suffix replacement

[johanneskoester]

Summary by CodeRabbit

• New Features

  • Added support for suffix-substitution configuration in source files.

• Bug Fixes

  • Removed unintended debugger breakpoint that was interrupting hash operations during runtime.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 2cdf0cdb-1db9-4c3b-8924-784c52d109ae

📥 Commits

Reviewing files that changed from the base of the PR and between 8f81191 and 5d5c27b.

📒 Files selected for processing (1)

• snakemake_interface_software_deployment_plugins/__init__.py

📝 Walkthrough

Walkthrough

This PR extends the environment specification interface with suffix replacement configuration for source files and inserts a debugging breakpoint in the hash computation method. The SuffixReplacement dataclass and replace_suffix() method on EnvSpecSourceFile enable callers to configure suffix substitution, while a breakpoint() call is added to EnvBase._managed_generic_hash().

Changes

Environment Specification Enhancements

Layer / File(s)	Summary
Suffix replacement support snakemake_interface_software_deployment_plugins/__init__.py	Introduced SuffixReplacement dataclass with old_suffixes: List[str] and new_suffix: str fields. Extended EnvSpecSourceFile with optional suffix_replacement field. Added replace_suffix(suffixes, new_suffix) method that returns a new EnvSpecSourceFile instance with the replacement configured, raising ValueError if already set.
Debug breakpoint in hash method snakemake_interface_software_deployment_plugins/__init__.py	Inserted breakpoint() statement inside EnvBase._managed_generic_hash() to pause execution during hash computation.

🎯 2 (Simple) | ⏱️ ~8 minutes

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% 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 'feat: suffix replacement' directly corresponds to the main changes: adding a SuffixReplacement dataclass and suffix_replacement functionality to EnvSpecSourceFile.
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
• Commit unit tests in branch feat/suffix-replacement

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[coderabbitai]

Actionable comments posted: 1

🧹 Nitpick comments (1)

snakemake_interface_software_deployment_plugins/__init__.py (1)

56-65: 💤 Low value

The cached field is not propagated to the new instance.

When creating the new EnvSpecSourceFile, self.cached is not copied over and will default to None. If this is intentional (e.g., because suffix replacement invalidates the cache), consider adding a brief comment. If the cache should be preserved, include it:

         return EnvSpecSourceFile(
             path_or_uri=self.path_or_uri,
             suffix_replacement=SuffixReplacement(
                 old_suffixes=suffixes, new_suffix=new_suffix
             ),
+            cached=self.cached,
         )

🤖 Prompt for 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.

In `@snakemake_interface_software_deployment_plugins/__init__.py` around lines 56
- 65, The replace_suffix method creates a new EnvSpecSourceFile but doesn't
propagate self.cached, causing the cached field to be lost; update
replace_suffix to pass cached=self.cached into the new EnvSpecSourceFile
construction (or, if cache invalidation is intended, add a short comment in
replace_suffix explaining why suffix replacement must drop the cache) so the
behavior is explicit; reference the replace_suffix method, EnvSpecSourceFile
constructor call, and the cached attribute when making the change.

🤖 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`:
- Line 326: Remove the stray debug breakpoint() call that halts execution during
hash computation; locate the breakpoint() invocation (shown in the diff) and
delete it before merging, or replace it with a non-interactive log statement
(e.g., using the module's logger or debug facility) if you need to record the
event without stopping the process.

---

Nitpick comments:
In `@snakemake_interface_software_deployment_plugins/__init__.py`:
- Around line 56-65: The replace_suffix method creates a new EnvSpecSourceFile
but doesn't propagate self.cached, causing the cached field to be lost; update
replace_suffix to pass cached=self.cached into the new EnvSpecSourceFile
construction (or, if cache invalidation is intended, add a short comment in
replace_suffix explaining why suffix replacement must drop the cache) so the
behavior is explicit; reference the replace_suffix method, EnvSpecSourceFile
constructor call, and the cached attribute when making the change.

🪄 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: c8fb18d1-077a-4054-9fcf-921c0f23ad0d

📥 Commits

Reviewing files that changed from the base of the PR and between 58c5322 and 8f81191.

📒 Files selected for processing (1)

• snakemake_interface_software_deployment_plugins/__init__.py