fix: Added documentation for scale variable #40

mrburke00 · 2025-03-06T22:18:49Z

Added documentation relevant to PR #38

Summary by CodeRabbit

New Features
- Introduced an optional configuration parameter to toggle between explicit resource limits and automatic scaling for resources such as GPUs, threads, and memory.
Documentation
- Updated guidance on resource scaling with detailed instructions.
- Added a debugging tip to help resolve issues with large job scheduling.
- Improved formatting for enhanced clarity.

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

coderabbitai · 2025-03-06T22:18:59Z

📝 Walkthrough

Walkthrough

The documentation for the Snakemake Kubernetes executor plugin has been updated. A new optional parameter scale (defaulting to 0) has been added in the resource definition section. When set to 1, explicit resource limits for GPUs, threads, and memory are omitted, allowing the pods to scale automatically. Additionally, a debugging tip for large job scheduling has been included, and the resource definition formatting has been adjusted to include a comma after machine_type.

Changes

File	Change Summary
docs/further.md	Added new optional `scale` parameter (default `0`) to conditionally include/omit explicit resource limits; added a debugging tip for scheduling large jobs; adjusted formatting with a comma after `machine_type`.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant ExecutorDoc
    User->>ExecutorDoc: Set resource definition parameters (including scale)
    ExecutorDoc-->>User: Evaluate `scale` parameter
    alt scale == 1
        ExecutorDoc-->>User: Omit explicit resource limits
    else scale == 0
        ExecutorDoc-->>User: Apply explicit resource limits for GPUs, threads, memory, etc.
    end

Possibly related PRs

fix: Adding additional logic to handle resource limit requirements #38: Introduces logic based on a scale_value variable to conditionally set resource limits in code.
feat: Added GPU node pool support for GKE, better logging, error and exception handling #31: Enhances GPU resource management and modifies resource definitions with a new manufacturer field.

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johanneskoester

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coderabbitai

Actionable comments posted: 2

🧹 Nitpick comments (1)

docs/further.md (1)

54-56: Enhance Debugging Tip Clarity for Large Job Scheduling
In the debugging tips section, the description on line 56 could benefit from minor rephrasing for clarity. There appears to be a missing comma, and the phrase “scaling to very large jobs” might be reworded (e.g., “when scaling large jobs”) to sound less subjective. Please consider adjusting the sentence for improved readability and consistency with the rest of the document.

🧰 Tools

🪛 LanguageTool

[uncategorized] ~56-~56: Possible missing comma found.
Context: ...y default configurations for Kubernetes clusters there is a limit range or some other ad...

(AI_HYDRA_LEO_MISSING_COMMA)

[style] ~56-~56: As an alternative to the over-used intensifier ‘very’, consider replacing this phrase.
Context: ...sts and resource limits when scaling to very large jobs. Try setting scale=0 and ensurin...

(EN_WEAK_ADJECTIVE)

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between f9d2c7a and 1142b44.

📒 Files selected for processing (1)

docs/further.md (2 hunks)

🧰 Additional context used

🪛 LanguageTool

docs/further.md

[uncategorized] ~38-~38: Loose punctuation mark.
Context: ... # Optional (default=1) ``` - gpu: the number of GPUs to be requested ...

(UNLIKELY_OPENING_PUNCTUATION)

[uncategorized] ~40-~40: Loose punctuation mark.
Context: ...le nodes with GPUs. - gpu_manufacturer: Specifies the GPU vendor. Use "nvidia" ...

(UNLIKELY_OPENING_PUNCTUATION)

[uncategorized] ~41-~41: Loose punctuation mark.
Context: ... or "amd" for AMD GPUs. - machine_type: machine type for the GPU enabled node. ...

(UNLIKELY_OPENING_PUNCTUATION)

[style] ~43-~43: In American English, abbreviations like “etc.” require a period.
Context: ...include resource (GPU, threads, memory, etc) limits - those limits being equal to t...

(ETC_PERIOD)

[uncategorized] ~44-~44: The determiner “the” seems more likely in this context.
Context: ...qual to the resource requests. - If scale=1(the default), we omit the limits entirely. ...

(AI_EN_LECTOR_REPLACEMENT_DETERMINER)

[uncategorized] ~56-~56: Possible missing comma found.
Context: ...y default configurations for Kubernetes clusters there is a limit range or some other ad...

(AI_HYDRA_LEO_MISSING_COMMA)

[style] ~56-~56: As an alternative to the over-used intensifier ‘very’, consider replacing this phrase.
Context: ...sts and resource limits when scaling to very large jobs. Try setting scale=0 and ensurin...

(EN_WEAK_ADJECTIVE)

🪛 markdownlint-cli2 (0.17.2)

docs/further.md

39-39: Unordered list indentation
Expected: 2; Actual: 4

(MD007, ul-indent)

42-42: Unordered list indentation
Expected: 2; Actual: 4

(MD007, ul-indent)

42-42: Bare URL used
null

(MD034, no-bare-urls)

44-44: Unordered list indentation
Expected: 2; Actual: 4

(MD007, ul-indent)

45-45: Unordered list indentation
Expected: 2; Actual: 4

(MD007, ul-indent)

⏰ Context from checks skipped due to timeout of 90000ms (1)

GitHub Check: testing

coderabbitai · 2025-03-06T22:21:48Z

docs/further.md

+    machine_type="n1-standard-16", 
+    scale=0                     # Optional (default=1)


⚠️ Potential issue

Inconsistent Default Value for scale Parameter
The resource definition block on lines 35–36 shows scale=0 while the inline comment indicates “(default=1)”. This conflicts with both the PR summary and the subsequent bullet explanations. Please clarify and update the default value consistently throughout the documentation.

coderabbitai · 2025-03-06T22:21:48Z

docs/further.md

+-  `scale`: variable allows us to conditionally include resource (GPU, threads, memory, etc) limits - those limits being equal to the resource requests.
+    - If `scale=1`(the default), we omit the limits entirely. This is how the plugin currently operates and will allow the pods to scale up as needed.
+    - If `scale=0` we explicitly set the resource limits for each requested resource type.


⚠️ Potential issue

Clarify the scale Parameter Explanation and Fix Punctuation
The bullet points describing the scale parameter introduce an inconsistency: line 44 states “If scale=1 (the default)” but the resource declaration (and PR summary) imply that the default is 0. Additionally, the abbreviation “etc” on line 43 should end with a period (“etc.”). Please revise these statements to reflect the correct default value and improve punctuation.

🧰 Tools

🪛 LanguageTool

[style] ~43-~43: In American English, abbreviations like “etc.” require a period.
Context: ...include resource (GPU, threads, memory, etc) limits - those limits being equal to t...

(ETC_PERIOD)

[uncategorized] ~44-~44: The determiner “the” seems more likely in this context.
Context: ...qual to the resource requests. - If scale=1(the default), we omit the limits entirely. ...

(AI_EN_LECTOR_REPLACEMENT_DETERMINER)

🪛 markdownlint-cli2 (0.17.2)

44-44: Unordered list indentation
Expected: 2; Actual: 4

(MD007, ul-indent)

45-45: Unordered list indentation
Expected: 2; Actual: 4

(MD007, ul-indent)

johanneskoester · 2025-03-14T21:53:39Z

Or maybe have a look whether coderabbit is correct with its comments @mrburke00.

mrburke00 · 2025-03-14T22:00:06Z

coderabbit may have gotten confused. Everything looks alright to me.

Default = 1 -> allow plugin to maintain status quo and scale
Setting scale = 0 -> turn on the limits and thus turn off the scaling, not the default

🤖 I have created a release *beep* *boop* --- ## [0.4.0](v0.3.2...v0.4.0) (2025-04-04) ### Features * use k8s job API and improve status check robustness in case of injected containers ([#43](#43)) ([1ff6927](1ff6927)) ### Bug Fixes * Added documentation for scale variable ([#40](#40)) ([1b668c1](1b668c1)) * properly catch and report ApiExceptions ([#42](#42)) ([92375e6](92375e6)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

mrburke00 and others added 12 commits March 5, 2025 16:07

Update __init__.py

535ecb2

Update __init__.py

160421e

Update snakemake_executor_plugin_kubernetes/__init__.py

2bf4c15

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

Update snakemake_executor_plugin_kubernetes/__init__.py

1f11816

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

Update __init__.py

0cfcca6

poetry

6429830

eof

b764bbf

Update __init__.py

03556e5

Update __init__.py

6e3b5ac

Update __init__.py

0b7cae6

Merge branch 'snakemake:main' into main

e8a58b4

Update further.md

1142b44

mrburke00 requested a review from johanneskoester March 6, 2025 22:18

coderabbitai bot reviewed Mar 6, 2025

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johanneskoester approved these changes Mar 14, 2025

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mrburke00 merged commit 1b668c1 into snakemake:main Mar 14, 2025
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github-actions bot mentioned this pull request Mar 14, 2025

chore(main): release 0.4.0 #41

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		machine_type="n1-standard-16",
		scale=0 # Optional (default=1)

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