fix: source_path not mounted by GaspardR · Pull Request #3738 · snakemake/snakemake

GaspardR · 2025-09-10T19:05:00Z

fixes #3737

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

Bug Fixes
- Source cache is now mounted in Singularity/Apptainer runs whenever the cache directory exists, even if extra container arguments are provided; a debug message is logged when the cache is missing.
Tests
- Added an integration test validating source-cache binding alongside custom bind arguments.
- Added a sample workflow rule to verify copying a source file to an output inside a container.

Fixes snakemake source-cache not being bind mounted to container when using additional apptainer-args.

coderabbitai · 2025-09-10T19:05:08Z

📝 Walkthrough

Walkthrough

Always compute the Snakemake source-cache path and, if it exists, add it as a quoted bind mount to Apptainer/Singularity invocations; add a test Snakefile and a test function exercising source-cache mounting with apptainer bind args.

Changes

Cohort / File(s)	Summary of edits
Singularity source-cache binding logic `src/snakemake/deployment/singularity.py`	Removed the `len(args) == 0` guard; always compute `source_cache_path` and, if `os.path.exists(source_cache_path)`, append a quoted `--bind` argument to `args`; otherwise log a debug message. Command construction unchanged otherwise.
Source-cache test workflow `tests/test_singularity_source_cache/Snakefile`	Added rule `a` that uses `workflow.source_path("test.txt")`, runs in `docker://bash:5.3.3`, and copies the source file to `test.out`.
Source-cache test runner `tests/tests.py`	Added `test_singularity_source_cache()` decorated with `@skip_on_windows`, `@apptainer`, and `@connected`, invoking the test data path with APPTAINER deployment and `apptainer_args="--bind /tmp:/tmp"`.

Sequence Diagram(s)

sequenceDiagram
  autonumber
  participant User as User
  participant SM as Snakemake
  participant Cont as Apptainer/Singularity

  User->>SM: Run workflow (rule uses workflow.source_path)
  SM->>SM: Compute source_cache_path
  alt source_cache_path exists
    SM->>SM: Append quoted --bind '<source_cache_path>' to args
  else
    SM->>SM: Log debug: source-cache not found
  end
  SM->>Cont: Launch container with assembled args (including any user apptainer-args)
  Cont-->>SM: Container runs and returns result
  SM-->>User: Rule completes

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

Possibly related PRs

feat: files added in rule params with workflow.source_path will be available in used containers #3385 — Also modifies src/snakemake/deployment/singularity.py to ensure the Snakemake source-cache is mounted into containers.

Suggested reviewers

johanneskoester

Pre-merge checks and finishing touches

❌ Failed checks (2 warnings)

Check name	Status	Explanation	Resolution
Description Check	⚠️ Warning	The pull request description only contains a reference to the linked issue and the QC checklist but lacks the required descriptive summary of the changes, motivations, or implementation details as specified by the repository’s template.	Please add a concise description of the pull request’s purpose and the key changes made above the QC section to match the repository’s description template.
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 (3 passed)

Check name	Status	Explanation
Title Check	✅ Passed	The title succinctly describes the primary change, which is fixing the mounting of source_path in containers, and it clearly conveys the bug being addressed without extraneous detail.
Linked Issues Check	✅ Passed	The changes in singularity.py remove the conditional guard on additional apptainer args to always bind the source-cache when it exists, and the new test in tests/tests.py alongside the Snakefile under tests/test_singularity_source_cache verifies that workflow.source_path is mounted inside containers when extra --apptainer-args are supplied, fully satisfying the coding requirements of issue #3737.
Out of Scope Changes Check	✅ Passed	All modified files are directly related to the fix for mounting the source-cache under extra apptainer args and the corresponding tests; no unrelated or out-of-scope changes were detected.

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Actionable comments posted: 1

🧹 Nitpick comments (1)

tests/test_singularity_source_cache/Snakefile (1)
1-9: Minor: name the param for clarity and future-proof formatting

Explicitly naming the param avoids relying on the implicit {params} expansion and reads clearer.
 rule a:
     output:
         "test.out"
     params:
-        workflow.source_path("test.txt")
+        src=workflow.source_path("test.txt")
     singularity:
         "docker://bash:5.3.3"
     shell:
-        "cp {params} {output}"
+        "cp {params.src} {output}"

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🔇 Additional comments (1)

tests/tests.py (1)

861-870: LGTM: test exercises source-cache bind with explicit apptainer args

Covers the regression path where user-provided binds previously disabled the source-cache mount.

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

coderabbitai

Actionable comments posted: 0

♻️ Duplicate comments (1)

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

132-139: Unconditional source-cache bind and fixed spacing/quoting — LGTM

This addresses the bug (bind now added regardless of extra args) and resolves the earlier whitespace/quoting issue when appending --bind.

🧹 Nitpick comments (3)

src/snakemake/deployment/singularity.py (3)
136-136: Use f-string conversion flag instead of repr() (RUF010)

Satisfy Ruff and align with common style.
-        args += f" --bind {repr(source_cache_path)}"
+        args += f" --bind {source_cache_path!r}"
135-135: Prefer isdir() to avoid binding a non-directory path

Slightly safer and semantically tighter.
-    if os.path.exists(source_cache_path):
+    if os.path.isdir(source_cache_path):
138-139: Nit: log the path with !r for clarity/consistency

Matches the quoting used elsewhere.
-        logger.debug(
-            f"Source cache directory {source_cache_path} does not exist, skipping bind mount"
+        logger.debug(
+            f"Source cache directory {source_cache_path!r} does not exist, skipping bind mount"

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coderabbitai

Actionable comments posted: 0

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tests/tests.py (1)
834-843: LGTM! Test correctly exercises the source-cache mounting scenario.

The test follows the established pattern and appropriately reproduces the bug scenario where apptainer_args are provided alongside source-cache usage.

Consider adding an additional test case without apptainer_args to ensure the fix doesn't break the default case. For example:
@skip_on_windows
@apptainer
@connected
def test_singularity_source_cache_no_args():
    run(
        dpath("test_singularity_source_cache"),
        deployment_method={DeploymentMethod.APPTAINER},
    )
This would provide better coverage by testing both scenarios (with and without extra args).

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cademirch

Looks good to me. Its not clear to me why the len(args)==0 check was there in the first place, it seems like that makes it impossible to use the source cache and specify your own apptainer args.

🤖 I have created a release *beep* *boop* --- ## [9.11.7](v9.11.6...v9.11.7) (2025-10-01) ### Bug Fixes * Add type annotations in logging module ([#3757](#3757)) ([63404b2](63404b2)) * source_path not mounted ([#3738](#3738)) ([86e30b3](86e30b3)) ### Documentation * mastodon announcements ([#3723](#3723)) ([7da1b18](7da1b18)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

fixes snakemake#3737 ### 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 * **Bug Fixes** * Source cache is now mounted in Singularity/Apptainer runs whenever the cache directory exists, even if extra container arguments are provided; a debug message is logged when the cache is missing. * **Tests** * Added an integration test validating source-cache binding alongside custom bind arguments. * Added a sample workflow rule to verify copying a source file to an output inside a container.  --------- Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> Co-authored-by: Cade Mirchandani <[email protected]>

🤖 I have created a release *beep* *boop* --- ## [9.11.7](snakemake/snakemake@v9.11.6...v9.11.7) (2025-10-01) ### Bug Fixes * Add type annotations in logging module ([snakemake#3757](snakemake#3757)) ([63404b2](snakemake@63404b2)) * source_path not mounted ([snakemake#3738](snakemake#3738)) ([86e30b3](snakemake@86e30b3)) ### Documentation * mastodon announcements ([snakemake#3723](snakemake#3723)) ([7da1b18](snakemake@7da1b18)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).

fixes source_path not mounted

682df9e

Fixes snakemake source-cache not being bind mounted to container when using additional apptainer-args.

GaspardR requested a review from johanneskoester as a code owner September 10, 2025 19:05

GaspardR changed the title ~~fixes source_path not mounted~~ fix: source_path not mounted Sep 10, 2025

Formatting

6c6d2a8

coderabbitai Bot reviewed Sep 10, 2025

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Comment thread src/snakemake/deployment/singularity.py

GaspardR and others added 2 commits September 10, 2025 15:18

Update src/snakemake/deployment/singularity.py

c439b56

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

Removes trailing parentheses

049cb1a

coderabbitai Bot reviewed Sep 10, 2025

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Create test.txt

383e263

cademirch self-requested a review September 30, 2025 14:08

Merge branch 'main' into fix_snakemake_cache_apptainer_mount

130fabc

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cademirch approved these changes Sep 30, 2025

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johanneskoester approved these changes Sep 30, 2025

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johanneskoester merged commit 86e30b3 into snakemake:main Sep 30, 2025
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snakemake-bot mentioned this pull request Sep 30, 2025

chore(main): release 9.11.7 #3762

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GaspardR deleted the fix_snakemake_cache_apptainer_mount branch September 30, 2025 16:49

coderabbitai Bot mentioned this pull request Nov 13, 2025

fix: mount local storage prefix into containers #3840

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fix: source_path not mounted#3738

fix: source_path not mounted#3738
johanneskoester merged 6 commits intosnakemake:mainfrom
GaspardR:fix_snakemake_cache_apptainer_mount

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GaspardR commented Sep 10, 2025 •

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