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feat: add source cache path attribute for mounting in e.g. containers #33

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Merged
merged 1 commit into from
Oct 1, 2025
Merged

feat: add source cache path attribute for mounting in e.g. containers #33

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2 changes: 2 additions & 0 deletions snakemake_interface_software_deployment_plugins/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -169,6 +169,7 @@ def __init__(
settings: Optional[SoftwareDeploymentSettingsBase],
shell_executable: ShellExecutable,
tempdir: Path,
source_cache: Path,
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@coderabbitai coderabbitai bot Oct 1, 2025

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⚠️ 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.

cache_prefix: Path,
deployment_prefix: Path,
pinfile_prefix: Path,
Expand All @@ -178,6 +179,7 @@ def __init__(
self.settings: Optional[SoftwareDeploymentSettingsBase] = settings
self.shell_executable = shell_executable
self.tempdir = tempdir
self.source_cache: Path = source_cache
self._deployment_prefix: Path = deployment_prefix
self._cache_prefix: Path = cache_prefix
self._pinfile_prefix: Path = pinfile_prefix
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3 changes: 3 additions & 0 deletions snakemake_interface_software_deployment_plugins/tests.py
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Original file line number Diff line number Diff line change
Expand Up @@ -152,17 +152,20 @@ def _get_env(self, tmp_path) -> EnvBase:
deployment_prefix = tmp_path / "deployments"
cache_prefix = tmp_path / "cache"
pinfile_prefix = tmp_path / "pinfiles"
source_cache = tmp_path / "source_cache"
tempdir.mkdir(parents=True, exist_ok=True)
deployment_prefix.mkdir(parents=True, exist_ok=True)
cache_prefix.mkdir(parents=True, exist_ok=True)
pinfile_prefix.mkdir(parents=True, exist_ok=True)
source_cache.mkdir(parents=True, exist_ok=True)

return env_cls(
spec=spec,
within=None,
settings=self.get_settings(),
shell_executable=self.shell_executable,
tempdir=tempdir,
source_cache=source_cache,
deployment_prefix=deployment_prefix,
cache_prefix=cache_prefix,
pinfile_prefix=pinfile_prefix,
Expand Down