fix: cache wrapper files and wait for them in case of shared filesystem for sources by johanneskoester · Pull Request #3809 · snakemake/snakemake

johanneskoester · 2025-10-23T21:54:46Z

Description

QC

The PR contains a test case for the changes or the changes are already covered by an existing test case.
The documentation (docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).

Summary by CodeRabbit

Refactor
- Improved job dependency handling with an option to skip input files when building wait lists.
- Jobs now ensure wrapper scripts and their runtime environments are available before running.
- Grouped-job dependency resolution now aggregates per-job wait lists consistently (skipping inputs where appropriate).
New Features
- Added a CLI option to specify a runtime source-cache path and wired it into workflow settings.
Tests
- Added a qsub wrapper script and corresponding test to broaden wrapper coverage.

…em for sources

coderabbitai · 2025-10-23T21:54:56Z

📝 Walkthrough

Walkthrough

Added optional skipping of input files in Job.get_wait_for_files and extended wait-listing for wrapper jobs to include wrapper script and conda env files. Wired a new runtime_source_cache_path through CLI, WorkflowSettings, SourceCache, spawn_jobs, and workflow initialization. Added qsub wrapper test and script; small wrapper error-message tweak.

Changes

Cohort / File(s)	Summary
Job wait-for-files & wrapper handling `src/snakemake/jobs.py`	Added parameter `get_wait_for_files(self, skip_input_files: bool = False)` and conditional logic to skip local/storage inputs when requested. When `is_wrapper` is true, compute wrapper script and conda env paths (via `from snakemake import wrapper`) and append corresponding `IOFile` entries to the wait list. `GroupJob.get_wait_for_files` now extends by calling `job.get_wait_for_files(skip_input_files=True)` for each child.
Runtime source-cache wiring (CLI → settings → sourcecache → spawn) `src/snakemake/cli.py`, `src/snakemake/settings/types.py`, `src/snakemake/sourcecache.py`, `src/snakemake/spawn_jobs.py`, `src/snakemake/workflow.py`	Added CLI option `--runtime-source-cache-path` and threaded `runtime_source_cache_path: Optional[Path] = None` into `WorkflowSettings`. `SourceCache.__init__` now accepts an optional `runtime_cache_path` parameter. Workflow post-init now creates `SourceCache` with `runtime_cache_path=self.workflow_settings.runtime_source_cache_path`. `spawn_jobs` now exposes/forwards the runtime-source-cache-path to spawned jobs (gated by shared_source_cache flag).
Wrapper error message `src/snakemake/wrapper.py`	Tweaked error message to show the wrapper location as `prefix+path` (uses "at {prefix}{path}") when a wrapper script cannot be located; no functional changes.
Tests and test helper `tests/tests_using_conda.py`, `tests/test_wrapper/qsub/*`	Added `test_wrapper_qsub()` (skipped on Windows, conda-marked) invoking cluster `./qsub` and added a qsub shell wrapper script for tests (`tests/test_wrapper/qsub` files).

Sequence Diagram(s)

sequenceDiagram
  autonumber
  participant Caller as Caller
  participant Job as Job.get_wait_for_files
  participant Wrapper as snakemake.wrapper
  participant Group as GroupJob.get_wait_for_files

  Caller->>Job: call get_wait_for_files(skip_input_files)
  alt skip_input_files == False
    Job->>Job: include local & storage inputs
  else skip_input_files == True
    Job->>Job: skip input files
  end
  alt is_wrapper == True
    Job->>Wrapper: resolve script_path & conda_env_path
    Wrapper-->>Job: script_path, conda_env_path
    Job->>Job: append IOFile(script_path), IOFile(conda_env_path)
  end
  Job-->>Caller: return wait-for-files list

  Note right of Group: aggregates child jobs with inputs skipped
  Caller->>Group: call get_wait_for_files()
  Group->>Job: job.get_wait_for_files(skip_input_files=True) [for each child]
  Job-->>Group: child wait lists
  Group-->>Caller: combined wait-for-files list

sequenceDiagram
  autonumber
  participant CLI as CLI
  participant Settings as WorkflowSettings
  participant Workflow as Workflow.__init__/post_init
  participant SourceCache as SourceCache

  CLI->>Settings: set runtime_source_cache_path (from --runtime-source-cache-path)
  Settings-->>Workflow: workflow_settings contains runtime_source_cache_path
  Workflow->>SourceCache: init SourceCache(cache_path, runtime_cache_path=workflow_settings.runtime_source_cache_path)
  SourceCache-->>Workflow: SourceCache instance (aware of runtime path)
  Workflow->>Spawn: spawn_jobs receives sourcecache.runtime_cache_path (via spawn args)

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~25 minutes

Areas to focus:
- Correctness of new skip_input_files logic and interactions with GroupJob aggregation.
- Wrapper path resolution and IOFile creation (ensure path existence/format expectations).
- Propagation of runtime_source_cache_path across CLI → WorkflowSettings → SourceCache → spawn_jobs and gating logic in spawn_jobs (shared_source_cache flag).
- Tests: new qsub wrapper script and added test to ensure it behaves as intended on CI (non-Windows).

Possibly related PRs

feat: Add --cache to general_args for jobscripts #3080 — Related changes to spawn_jobs' general_args for passing cache-related CLI args to spawned jobs; likely overlaps with runtime-source-cache argument handling.

Pre-merge checks and finishing touches

❌ Failed checks (2 warnings)

Check name	Status	Explanation	Resolution
Description Check	⚠️ Warning	The PR description fails to meet the template requirements because the main description section is entirely empty—it contains only the placeholder comment "" with no substantive content. While the author has properly completed both QC checklist items, the template explicitly requires a description section that should explain the changes, and this section is absent. This is a significant structural gap that prevents reviewers from understanding the motivation, approach, and impact of the changes within the PR description itself.	The author should add a substantive description explaining the purpose, implementation approach, and rationale for the wrapper file caching changes. This section should elaborate on why caching wrapper files is necessary for shared filesystem scenarios and what problem this PR solves. Additionally, the QC section would benefit from brief explanations of which test cases were added and how they verify the fix, rather than leaving the checklist items as standalone checks.
Docstring Coverage	⚠️ Warning	Docstring coverage is 41.67% which is insufficient. The required threshold is 80.00%.	You can run `@coderabbitai generate docstrings` to improve docstring coverage.

✅ Passed checks (1 passed)

Check name	Status	Explanation
Title Check	✅ Passed	The PR title "fix: cache wrapper files and wait for them in case of shared filesystem for sources" directly and comprehensively describes the core changes in the changeset. The title accurately reflects the addition of wrapper file caching logic to the `get_wait_for_files` method, the extension of wait-for-files logic for wrapper-enabled jobs, and the new runtime source cache path configuration for shared filesystem scenarios. The title is concise, specific, and provides sufficient detail for a teammate scanning history to understand the primary objective of this PR.

✨ 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 fix/cache-wrapper-files

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github-actions · 2025-10-23T21:55:57Z

Please format your code with pixi run format

coderabbitai

Actionable comments posted: 1

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src/snakemake/wrapper.py (1 hunks)

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src/snakemake/wrapper.py (1)

src/snakemake/shell.py (1)

prefix (133-134)

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coderabbitai · 2025-10-24T19:48:01Z

    if script_source is None:
        raise WorkflowError(
-            f"Unable to locate wrapper script for wrapper {path}. "
+            f"Unable to locate wrapper script at {prefix}{path}. "


⚠️ Potential issue | 🟡 Minor

Handle None prefix in error message.

The error message improvement is good, but if prefix is None, it will display "at None{path}". The get_path() function defaults None to PREFIX (lines 28-29), but this doesn't affect the prefix variable here.

Apply this diff to handle the None case consistently:

- f"Unable to locate wrapper script at {prefix}{path}. " + f"Unable to locate wrapper script at {prefix if prefix is not None else PREFIX}{path}. "

📝 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

f"Unable to locate wrapper script at {prefix}{path}. "

f"Unable to locate wrapper script at {prefix if prefix is not None else PREFIX}{path}. "

🤖 Prompt for AI Agents

In src/snakemake/wrapper.py around line 107, the error message concatenates prefix directly and can render "None{path}" if prefix is None; coerce prefix to the same default used by get_path (e.g., PREFIX or an empty string) before formatting the message so None is not shown. Update the code to set prefix = prefix if prefix is not None else PREFIX (or call get_path() to obtain the resolved prefix) and use that variable in the f-string.

coderabbitai

Actionable comments posted: 0

🧹 Nitpick comments (4)

tests/test_wrapper/qsub (1)
1-6: Harden the test wrapper: quote args and use bash consistently.

Quote "$1" to avoid globbing/word-splitting.

Use bash to run the jobscript (shebang is bash).

Add strict mode to fail fast.

Apply:
 #!/bin/bash
-echo `date` >> qsub.log
-tail -n1 $1 >> qsub.log
+set -euo pipefail
+printf '%s\n' "$(date)" >> qsub.log
+tail -n1 -- "$1" >> qsub.log
 # simulate printing of job id by a random number
-echo $RANDOM
-sh $1
+echo "$RANDOM"
+bash "$1"
src/snakemake/settings/types.py (1)

136-137: LGTM: new WorkflowSettings runtime_source_cache_path.

Matches downstream usage and defaulting semantics. Consider documenting it's for internal plumbing to avoid user confusion.

src/snakemake/cli.py (1)

1349-1353: New flag placement OK; optionally move to INTERNAL group.

Flag is marked “internal use” but sits in BEHAVIOR. Optional: move to the INTERNAL group for help clarity.
src/snakemake/spawn_jobs.py (1)
277-279: Also gate on spawned_jobs_assume_shared_fs to ensure consistency.

If an executor assumes shared FS for spawned jobs, we should pass the runtime source cache path regardless of the local shared_fs_usage. Align the gating with get_shared_fs_usage_arg.

Apply:
-        shared_source_cache = (
-            SharedFSUsage.SOURCE_CACHE in self.workflow.storage_settings.shared_fs_usage
-        )
+        if executor_common_settings.spawned_jobs_assume_shared_fs:
+            shared_source_cache = True
+        else:
+            shared_source_cache = (
+                SharedFSUsage.SOURCE_CACHE
+                in self.workflow.storage_settings.shared_fs_usage
+            )
Optional: base64-encode the path like other path args if you foresee spaces/odd chars:
-            format_cli_arg(
+            format_cli_arg(
                 "--runtime-source-cache-path",
                 self.workflow.sourcecache.runtime_cache_path,
-                skip=not shared_source_cache,
+                skip=not shared_source_cache,
+                # base64_encode=True,  # optional
             ),
Also applies to: 351-355

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src/snakemake/settings/types.py (1 hunks)
src/snakemake/sourcecache.py (1 hunks)
src/snakemake/spawn_jobs.py (2 hunks)
src/snakemake/workflow.py (1 hunks)
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Files:

src/snakemake/settings/types.py
src/snakemake/spawn_jobs.py
src/snakemake/workflow.py
src/snakemake/sourcecache.py
src/snakemake/cli.py
tests/tests_using_conda.py

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src/snakemake/spawn_jobs.py (3)

src/snakemake/api.py (1)

workflow (114-168)

src/snakemake/workflow.py (1)

sourcecache (500-501)

src/snakemake/sourcecache.py (1)

runtime_cache_path (370-371)

src/snakemake/workflow.py (1)

src/snakemake/sourcecache.py (2)

SourceCache (349-458)

runtime_cache_path (370-371)

tests/tests_using_conda.py (3)

src/snakemake/workflow.py (2)

conda (2148-2153)

run (2346-2347)

src/snakemake/deployment/conda.py (1)

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🔇 Additional comments (5)

src/snakemake/workflow.py (1)

211-214: LGTM: SourceCache now respects runtime cache path.

Wiring looks correct; SourceCache will create a TemporaryDirectory when unset and use the provided path otherwise.

tests/tests_using_conda.py (1)

137-146: LGTM: qsub wrapper test adds valuable coverage.

Mirrors existing wrapper test with cluster submission; no issues spotted.

src/snakemake/cli.py (1)

2066-2071: LGTM: value flows into WorkflowSettings.

Correctly threads args.runtime_source_cache_path into WorkflowSettings.

src/snakemake/sourcecache.py (1)

354-367: LGTM: optional runtime cache path is handled correctly.

Constructor and property semantics make sense; lazy directory creation via cache_entry.parent.mkdir ensures path exists when needed.

src/snakemake/spawn_jobs.py (1)

381-383: All SourceCache instantiations are correctly updated. Verification confirms all 4 SourceCache constructor callsites in the codebase properly pass the runtime_cache_path parameter (wrapper.py, workflow.py, script/init.py, notebook.py). Debug logging of args is acceptable as you noted; no blocking concerns found.

🤖 I have created a release *beep* *boop* --- ## [9.13.5](v9.13.4...v9.13.5) (2025-11-04) ### Bug Fixes * cache wrapper files and wait for them in case of shared filesystem for sources ([#3809](#3809)) ([498fff7](498fff7)) * correctly handle meta-wrapper tag replacement depending on the used snakemake-wrapper release ([#3826](#3826)) ([8d46a4a](8d46a4a)) * ensure that flags are properly considered for input files before applying path modifiers (i.e. default storage providers) ([#3813](#3813)) ([d3bfe32](d3bfe32)) * ensure that tokens are not leaked when paths or uris of source files are logged ([#3821](#3821)) ([a217e50](a217e50)) * print secs as numeric in jsonl benchmark format ([#3814](#3814)) ([395a5e6](395a5e6)) * revert breaking change in 9.11.9 disallowing empty input files even when unused ([#3810](#3810)) ([83c05cc](83c05cc)) * shorten report ids (thus dir names) in order to avoid issues with path length on windows ([#3822](#3822)) ([b24d971](b24d971)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

…em for sources (snakemake#3809) ### Description  ### QC  * [x] The PR contains a test case for the changes or the changes are already covered by an existing test case. * [x] The documentation (`docs/`) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).  ## Summary by CodeRabbit * **Refactor** * Improved job dependency handling with an option to skip input files when building wait lists. * Jobs now ensure wrapper scripts and their runtime environments are available before running. * Grouped-job dependency resolution now aggregates per-job wait lists consistently (skipping inputs where appropriate). * **New Features** * Added a CLI option to specify a runtime source-cache path and wired it into workflow settings. * **Tests** * Added a qsub wrapper script and corresponding test to broaden wrapper coverage.

🤖 I have created a release *beep* *boop* --- ## [9.13.5](snakemake/snakemake@v9.13.4...v9.13.5) (2025-11-04) ### Bug Fixes * cache wrapper files and wait for them in case of shared filesystem for sources ([snakemake#3809](snakemake#3809)) ([498fff7](snakemake@498fff7)) * correctly handle meta-wrapper tag replacement depending on the used snakemake-wrapper release ([snakemake#3826](snakemake#3826)) ([8d46a4a](snakemake@8d46a4a)) * ensure that flags are properly considered for input files before applying path modifiers (i.e. default storage providers) ([snakemake#3813](snakemake#3813)) ([d3bfe32](snakemake@d3bfe32)) * ensure that tokens are not leaked when paths or uris of source files are logged ([snakemake#3821](snakemake#3821)) ([a217e50](snakemake@a217e50)) * print secs as numeric in jsonl benchmark format ([snakemake#3814](snakemake#3814)) ([395a5e6](snakemake@395a5e6)) * revert breaking change in 9.11.9 disallowing empty input files even when unused ([snakemake#3810](snakemake#3810)) ([83c05cc](snakemake@83c05cc)) * shorten report ids (thus dir names) in order to avoid issues with path length on windows ([snakemake#3822](snakemake#3822)) ([b24d971](snakemake@b24d971)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

fix: cache wrapper files and wait for them in case of shared filesyst…

c260069

…em for sources

johanneskoester added 3 commits October 23, 2025 18:56

fmt

4137578

fix, convert cache paths to iofile

1c73b9e

error handling

d67cbbf

coderabbitai Bot reviewed Oct 24, 2025

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fix: pass runtime cache path to spawned jobs

99b33c8

coderabbitai Bot reviewed Oct 28, 2025

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johanneskoester merged commit 498fff7 into main Oct 30, 2025
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johanneskoester deleted the fix/cache-wrapper-files branch October 30, 2025 14:45

snakemake-bot mentioned this pull request Oct 30, 2025

chore(main): release 9.13.5 #3818

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fix: cache wrapper files and wait for them in case of shared filesystem for sources#3809

fix: cache wrapper files and wait for them in case of shared filesystem for sources#3809
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	f"Unable to locate wrapper script at {prefix}{path}. "
	f"Unable to locate wrapper script at {prefix if prefix is not None else PREFIX}{path}. "

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johanneskoester commented Oct 23, 2025 •

edited by coderabbitai Bot

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coderabbitai Bot commented Oct 23, 2025 •

edited

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