feat: add source cache path attribute for mounting in e.g. containers

[johanneskoester]

Summary by CodeRabbit

• New Features
  • Added an optional configuration to specify a source cache path during environment initialization, enabling cached sources for improved reuse. Existing behavior remains unchanged if not provided.
• Tests
  • Expanded test coverage to include scenarios using the new source cache path, ensuring correct handling and integration in typical workflows.

[coderabbitai]

📝 Walkthrough

Walkthrough

Adds a new source_cache parameter to EnvBase.init and stores it on the instance. Updates tests to create and pass a source_cache directory during environment setup.

Changes

Cohort / File(s)	Summary of changes
Core API: EnvBase constructor snakemake_interface_software_deployment_plugins/__init__.py	Adds source_cache: Path parameter to EnvBase.init; assigns to self.source_cache.
Tests: environment setup snakemake_interface_software_deployment_plugins/tests.py	Creates tmp source_cache directory and passes source_cache argument to constructor.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

• feat: pass tempdir to EnvBase #16: Also modifies EnvBase.init to add/store a new Path-backed parameter (tempdir), similar constructor expansion.
• fix: streamline inheritance annotation #23: Reworks EnvBase’s constructor/signature and attributes, overlapping with adding a new field like source_cache.

Pre-merge checks and finishing touches

❌ 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%.	You can run @coderabbitai generate docstrings to improve docstring coverage.

✅ 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 succinctly conveys the primary change of adding a source cache path attribute and uses clear conventional commit formatting, making it both concise and specific to the main feature introduced without extraneous details.

✨ Finishing touches

• 📝 Generate Docstrings

🧪 Generate unit tests

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch feat/source-cache

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[coderabbitai]

Actionable comments posted: 1

🧹 Nitpick comments (1)

snakemake_interface_software_deployment_plugins/__init__.py (1)

182-182: Consider adding documentation for the new parameter.

While the implementation is correct, adding a docstring to the __init__ method or inline comment explaining that source_cache is intended for mounting in containers (per the PR title) would improve maintainability.

📜 Review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 8e453b2 and 505a611.

📒 Files selected for processing (2)

• snakemake_interface_software_deployment_plugins/__init__.py (2 hunks)
• snakemake_interface_software_deployment_plugins/tests.py (1 hunks)

🧰 Additional context used

📓 Path-based instructions (1)

**/*.py

⚙️ CodeRabbit configuration file

**/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

Files:

• snakemake_interface_software_deployment_plugins/__init__.py
• snakemake_interface_software_deployment_plugins/tests.py

🔇 Additional comments (2)

snakemake_interface_software_deployment_plugins/tests.py (2)

155-160: LGTM! Test setup correctly supports the new parameter.

The source_cache directory setup follows the same pattern as other test directories (tempdir, deployment_prefix, etc.), ensuring consistency in the test infrastructure.

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168-168: LGTM! Constructor call updated correctly.

The source_cache parameter is passed in the correct position matching the updated __init__ signature.

[coderabbitai]

⚠️ Potential issue | 🔴 Critical

🧩 Analysis chain

Verify usage of source_cache across the codebase.

The parameter is added but not visibly used within this file. Confirm that plugins or downstream code will consume this attribute.

---

🏁 Script executed:

#!/bin/bash
# Search for usages of source_cache in the codebase
rg -n -C3 'source_cache' --type=py

Length of output: 3482

---

Remove or implement usage of source_cache.
The source_cache parameter is assigned but never referenced elsewhere. Remove it or add the intended functionality and document its purpose.

🤖 Prompt for AI Agents

In snakemake_interface_software_deployment_plugins/__init__.py around line 172,
the function signature includes a source_cache: Path parameter that is assigned
but never used; either remove the parameter from the signature and any callers
and update docs/tests accordingly, or implement its intended behavior by adding
logic to use source_cache for caching downloaded/processed source artifacts
(e.g., check for an existing cached file there, read from it when present, and
write newly fetched sources into it) and add a docstring comment explaining its
purpose and format; update unit tests and call sites to reflect the chosen
change.