fix: add curl when containerize with wrapper by GaspardR · Pull Request #4115 · snakemake/snakemake

GaspardR · 2026-03-17T22:14:10Z

--containerize apptainer option from #4030, is used to create apptainer definition file from workflow. When the workflow has rule with wrapper: the image doesn't build, it's missing curl.

Add check for a wrapper rule in workflow and add curl. Add image size optimization if wrapper rule in workflow. Add test for containerize with wrapper.

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).
I, as a human being, have checked each line of code in this pull request

AI-assistance disclosure

I used AI assistance for:

Code generation (e.g., when writing an implementation or fixing a bug)
Test/benchmark generation
Documentation (including examples)
Research and understanding

Summary by CodeRabbit

New Features
- Container images for Apptainer now conditionally install curl when remote environment files are fetched and perform cleanup of package lists to reduce image size.
Tests
- Added test coverage validating Apptainer containerization behavior for wrapper-rule scenarios, including dependency installation and cleanup steps.

Fix snakemake#4114 `--containerize apptainer` option from snakemake#4030, is used to create apptainer definition file from workflow. When the workflow has rule with `wrapper` the image doesn't build, it's missing `curl`. Add check for a wrapper rule in workflow and add `curl`. Add image size optimization if wrapper rule in workflow. Add test for containerize with wrapper.

coderabbitai · 2026-03-17T22:14:28Z

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: a6eef6e4-fe43-48b7-9d7b-cd3c3bc6c21e

📥 Commits

Reviewing files that changed from the base of the PR and between 6af8e5b and 33dab2f.

📒 Files selected for processing (1)

src/snakemake/deployment/containerize.py

🚧 Files skipped from review as they are similar to previous changes (1)

src/snakemake/deployment/containerize.py

📝 Walkthrough

Walkthrough

Adds conditional installation of curl and a guarded apt-list cleanup into the Apptainer containerization output when remote environment files are fetched; also adds a test validating generated apptainer.def contains the curl installation and environment source reference.

Changes

Cohort / File(s)	Summary
Container curl & cleanup logic `src/snakemake/deployment/containerize.py`	Adds detection of remote env fetch need and injects `apt-get update` + `apt-get install -y curl` before fetching remote environment files, and appends `rm -rf /var/lib/apt/lists/*` cleanup guarded by the same condition.
Apptainer wrapper test `tests/tests_using_conda.py`	Adds `test_containerize_wrapper_apptainer` to exercise `--containerize apptainer`, asserting `apptainer.def` includes the wrapper environment source and the apt-get/curl steps.

Sequence Diagram(s)

sequenceDiagram
    participant Snakemake
    participant Containerizer
    participant BaseImage
    participant RemoteRepo

    Snakemake->>Containerizer: request containerize (apptainer) for rule with wrapper env
    Containerizer->>BaseImage: emit %post commands
    alt needs_curl == true
        Containerizer->>BaseImage: add "apt-get update" / "apt-get install -y curl"
        BaseImage->>RemoteRepo: curl -L fetch environment.yaml
        RemoteRepo-->>BaseImage: environment.yaml
        Containerizer->>BaseImage: add "rm -rf /var/lib/apt/lists/*"
    else
        BaseImage->>RemoteRepo: (no remote fetch)
    end
    Containerizer-->>Snakemake: write apptainer.def

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 25.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title accurately describes the main change: adding curl when containerizing with wrapper rules for Apptainer.
Description check	✅ Passed	The description is comprehensive, includes all required QC checklist items (marked as completed), explains the issue clearly, references the related issue `#4114`, and includes AI-assistance disclosure.
Linked Issues check	✅ Passed	The PR addresses all coding requirements from issue `#4114`: detects wrapper rules, installs curl when needed, optimizes image size, and includes test coverage for the functionality.
Out of Scope Changes check	✅ Passed	All changes are directly related to fixing issue `#4114`: modifications to containerize.py handle curl installation for wrapper rules, and the new test validates the containerization with wrappers.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

🧪 Generate unit tests (beta)

Create PR with unit tests

📝 Coding Plan

Generate coding plan for human review comments

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

_{Comment @coderabbitai help to get the list of available commands and usage tips.}

Tip

You can disable the changed files summary in the walkthrough.

Disable the reviews.changed_files_summary setting to disable the changed files summary in the walkthrough.

coderabbitai

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@src/snakemake/deployment/containerize.py`:
- Around line 238-240: The guard using has_wrapper_rule (computed from
workflow.rules) is incorrect; change the condition so curl is installed only
when building an Apptainer image or when any remote environment file requires
curl (e.g. replace has_wrapper_rule with a boolean like needs_curl =
is_apptainer_build() or any(env.is_remote for env in workflow.environments)),
then call formatter.run_command("apt-get update") and
formatter.run_command("apt-get install -y --no-install-recommends curl") only
when needs_curl is true; update the two places referencing has_wrapper_rule to
use this new needs_curl check so Docker builds won’t get apt commands and
Apptainer/remote-env cases are covered.

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 5de541ed-8f41-424c-86a7-2bc696ef86c1

📥 Commits

Reviewing files that changed from the base of the PR and between 4bba4a9 and 6af8e5b.

📒 Files selected for processing (2)

src/snakemake/deployment/containerize.py
tests/tests_using_conda.py

src/snakemake/deployment/containerize.py

🤖 I have created a release *beep* *boop* --- ## [9.17.3](v9.17.2...v9.17.3) (2026-03-24) ### Bug Fixes * add curl when containerize with wrapper ([#4115](#4115)) ([44979e4](44979e4)) * ensure proper wrapper prefix is passed to CWL and shown in wrapper error messages ([#4121](#4121)) ([11b6f29](11b6f29)) * ensure that strings that purely contain integers or floats (e.g. "42") remain strings when parsing profiles ([#4119](#4119)) ([3ca08e1](3ca08e1)) * incorrect highlighting in HTML report ([#4120](#4120)) ([1ef224d](1ef224d)) ### Documentation * document an accidental (sorry) recent breaking change in type checking compatibility of Python scripts, in favor of a clean and robust new syntax ([#4116](#4116)) ([013bc43](013bc43)) * Rework tutorial ([#4068](#4068)) ([4bba4a9](4bba4a9)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please).  ## Summary by CodeRabbit * **Chores** * Released version 9.17.3

GaspardR requested a review from johanneskoester as a code owner March 17, 2026 22:14

GaspardR requested a review from ManarRashad March 17, 2026 22:14

coderabbitai bot reviewed Mar 17, 2026

View reviewed changes

src/snakemake/deployment/containerize.py Outdated Show resolved Hide resolved

fix: add guard for remove env

33dab2f

johanneskoester approved these changes Mar 19, 2026

View reviewed changes

johanneskoester merged commit 44979e4 into snakemake:main Mar 19, 2026
60 checks passed

snakemake-bot mentioned this pull request Mar 19, 2026

chore(main): release 9.17.3 #4112

Merged

GaspardR deleted the fix-#4114 branch March 19, 2026 13:43

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

fix: add curl when containerize with wrapper#4115

fix: add curl when containerize with wrapper#4115
johanneskoester merged 2 commits intosnakemake:mainfrom
GaspardR:fix-#4114

GaspardR commented Mar 17, 2026 •

edited by coderabbitai bot

Loading

Uh oh!

coderabbitai bot commented Mar 17, 2026 •

edited

Loading

Walkthrough

Changes

Sequence Diagram(s)

Estimated code review effort

❌ Failed checks (1 warning)

Uh oh!

coderabbitai bot left a comment

Uh oh!

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

Conversation

GaspardR commented Mar 17, 2026 • edited by coderabbitai bot Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

QC

AI-assistance disclosure

Summary by CodeRabbit

Uh oh!

coderabbitai bot commented Mar 17, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Walkthrough

Changes

Sequence Diagram(s)

Estimated code review effort

❌ Failed checks (1 warning)

Uh oh!

coderabbitai bot left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

GaspardR commented Mar 17, 2026 •

edited by coderabbitai bot

Loading

coderabbitai bot commented Mar 17, 2026 •

edited

Loading