feat: additional mountpoints

[johanneskoester]

Summary by CodeRabbit

• New Features

  • Configurable container mount points allowing users to add custom volume bindings and storage locations
  • Automatic mounting of the working directory and source cache into container executions

• Improvements

  • Dynamic assembly of container mount configuration to include user-specified mounts
  • Safer command invocation with improved shell-escaping to reduce injection or parsing errors

[coderabbitai]

Caution

Review failed

The pull request is closed.

📝 Walkthrough

Walkthrough

Adds a public mountpoints: List[str] setting (CLI-enabled) and imports List. Env.decorate_shellcmd now assembles container mount flags from the working dir, source-cache, and user-provided settings.mountpoints, replacing the previous hard-coded host/cache mount entries in the generated command.

Changes

Cohort / File(s)	Summary
Container mountpoints src/snakemake_software_deployment_plugin_container/__init__.py	Added mountpoints: List[str] to Settings with CLI metadata; imported List. Updated Env.decorate_shellcmd to build an assembled mountpoints string including existing hostdir and source-cache mounts plus user-specified mounts from settings.mountpoints, and to use that assembled string in the final container command (replacing prior hard-coded host/cache mount entries).

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

🚥 Pre-merge checks | ✅ 2 | ❌ 2

❌ Failed checks (2 warnings)

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.
Merge Conflict Detection	⚠️ Warning	❌ Merge conflicts detected (1 file): ⚔️ src/snakemake_software_deployment_plugin_container/__init__.py (content) These conflicts must be resolved before merging into main.	Resolve conflicts locally and push changes to this branch.

✅ 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 'feat: additional mountpoints' clearly and concisely describes the main change: adding support for user-configurable container mount points via a new mountpoints setting.

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✨ Finishing touches

• 📝 Generate docstrings

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch feat/mountpoints

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[coderabbitai]

Actionable comments posted: 2

🤖 Fix all issues with AI agents

In `@src/snakemake_software_deployment_plugin_container/__init__.py`:
- Around line 49-55: The dataclass field "mountpoints: List[str] = field(...)"
uses a mutable default list (default=[]), which triggers dataclasses import-time
errors; change the field to use default_factory=list instead of default so
replace the default=[] with default_factory=list in the field() call for
mountpoints (preserving metadata like "nargs" and "help") to ensure safe
initialization of List[str] instances per dataclass instance.
- Around line 121-126: Replace the use of Python repr(!r) when building the
mountpoints string with shlex.quote to ensure POSIX shell-safe quoting for
getcwd(), SNAKEMAKE_MOUNTPOINT, self.source_cache and containercache (e.g., use
shlex.quote(getcwd()) and shlex.quote(SNAKEMAKE_MOUNTPOINT) instead of !r); for
the loop over self.settings.mountpoints, call shlex.quote on each mountpoint but
first validate the user-provided string contains a ':' separator (raise
ValueError with a clear message if missing) to avoid generating malformed -v
arguments; keep using the existing shlex import.

[coderabbitai]

⚠️ Potential issue | 🟠 Major

Use shlex.quote() instead of !r for shell-safe quoting.

!r produces Python repr() output, not POSIX shell quoting. For paths containing both quote types (e.g., /home/it's "here"), repr can emit backslash-escaped single-quoted strings which are invalid in POSIX shell. Since shlex is already imported and used on line 136, use it consistently here as well.

Additionally, user-provided mountpoints on line 126 are interpolated without any format validation — a value missing the : separator will produce a confusing container-runtime error.

🔒 Proposed fix

         mountpoints = (
-            f" -v {getcwd()!r}:{SNAKEMAKE_MOUNTPOINT!r}"  # Mount host directory to container
-            f" -v {str(self.source_cache)!r}:{containercache!r}"  # Mount host cache to container
+            f" -v {shlex.quote(getcwd())}:{shlex.quote(SNAKEMAKE_MOUNTPOINT)}"  # Mount host directory to container
+            f" -v {shlex.quote(str(self.source_cache))}:{shlex.quote(containercache)}"  # Mount host cache to container
         )
         for mountpoint in self.settings.mountpoints:
-            mountpoints += f" -v {mountpoint!r}"
+            if ":" not in mountpoint:
+                raise WorkflowError(
+                    f"Invalid mountpoint format {mountpoint!r}, expected hostpath:containerpath"
+                )
+            mountpoints += f" -v {shlex.quote(mountpoint)}"

📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change

	mountpoints = (
	f" -v {getcwd()!r}:{SNAKEMAKE_MOUNTPOINT!r}" # Mount host directory to container
	f" -v {str(self.source_cache)!r}:{containercache!r}" # Mount host cache to container
	)
	for mountpoint in self.settings.mountpoints:
	mountpoints += f" -v {mountpoint!r}"
	mountpoints = (
	f" -v {shlex.quote(getcwd())}:{shlex.quote(SNAKEMAKE_MOUNTPOINT)}" # Mount host directory to container
	f" -v {shlex.quote(str(self.source_cache))}:{shlex.quote(containercache)}" # Mount host cache to container
	)
	for mountpoint in self.settings.mountpoints:
	if ":" not in mountpoint:
	raise WorkflowError(
	f"Invalid mountpoint format {mountpoint!r}, expected hostpath:containerpath"
	)
	mountpoints += f" -v {shlex.quote(mountpoint)}"

🤖 Prompt for AI Agents

In `@src/snakemake_software_deployment_plugin_container/__init__.py` around lines
121 - 126, Replace the use of Python repr(!r) when building the mountpoints
string with shlex.quote to ensure POSIX shell-safe quoting for getcwd(),
SNAKEMAKE_MOUNTPOINT, self.source_cache and containercache (e.g., use
shlex.quote(getcwd()) and shlex.quote(SNAKEMAKE_MOUNTPOINT) instead of !r); for
the loop over self.settings.mountpoints, call shlex.quote on each mountpoint but
first validate the user-provided string contains a ':' separator (raise
ValueError with a clear message if missing) to avoid generating malformed -v
arguments; keep using the existing shlex import.