docs: Clarify the lookup function docstring by peterjc · Pull Request #3091 · snakemake/snakemake

peterjc · 2024-09-18T13:25:35Z

This described the is_nrows argument, and tries to make it clear what applies with a mapping input.

[It does seem this would be cleaner as two functions, one for pandas lookup, one for dpath]

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

Documentation
- Enhanced documentation for the lookup function, clarifying parameter usage and behavior.
- Added details on how to handle different input types and improved error handling guidance, including the introduction of a default fallback value.

This described the is_nrows argument, and tries to make it clear what applies with a mapping input.

coderabbitai · 2024-09-18T13:25:47Z

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Commits

Files that changed from the base of the PR and between 6834814 and c26fb13.

Walkthrough

The changes made to the lookup function in snakemake/ioutils.py focus on enhancing the documentation for better clarity regarding the function's parameters. The updates specify the types of input accepted by the within parameter, detail the behavior of the query, cols, and is_nrows parameters based on the input type, and outline the usage of the dpath parameter when a Python mapping is provided. Additionally, the documentation now includes information about error handling related to the dpath parameter.

Changes

File	Change Summary
snakemake/ioutils.py	Updated documentation for `def lookup()` to clarify the behavior and requirements of parameters: `within`, `query`, `dpath`, `cols`, `is_nrows`, and `default`.

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coderabbitai

Actionable comments posted: 0

Outside diff range and nitpick comments (2)

snakemake/ioutils.py (2)
144-145: Documentation looks good, but please fix the spelling error.

The addition of the documentation for the is_nrows argument is helpful in clarifying its behavior when used with a pandas DataFrame.

However, please fix the spelling error:
-Finally, if the interger argument ``is_nrows`` is used, this returns true
+Finally, if the integer argument ``is_nrows`` is used, this returns true
Tools

GitHub Check: Check for spelling errors

[failure] 144-144:
interger ==> integer

122-122: Please fix the spelling error.
-case use ``query``, and optionaly ``cols`` and ``is_nrows``), or a Python
+case use ``query``, and optionally ``cols`` and ``is_nrows``), or a Python
Tools

GitHub Check: Check for spelling errors

[failure] 122-122:
optionaly ==> optionally

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between e9ce4a3 and 33bcd1f.

Files selected for processing (1)

snakemake/ioutils.py (2 hunks)

Additional context used

Path-based instructions (1)

snakemake/ioutils.py (1)

Pattern **/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

GitHub Check: Check for spelling errors

snakemake/ioutils.py

[failure] 122-122:
optionaly ==> optionally

[failure] 144-144:
interger ==> integer

Additional comments not posted (2)

snakemake/ioutils.py (2)

121-123: LGTM!

The changes to the docstring provide clearer documentation on the expected types for the within argument and the corresponding arguments to use with each type. This improves the understanding of how to use the lookup function correctly.

Tools

GitHub Check: Check for spelling errors

[failure] 122-122:
optionaly ==> optionally

150-154: Great improvement to the documentation!

The changes provide clearer documentation on the behavior when within is a Python mapping. Explicitly stating that query, cols, and is_nrows are ignored in this case helps avoid confusion.

Additionally, documenting the default argument and the LookupError exception improves clarity around error handling.

coderabbitai

Actionable comments posted: 1

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Commits

Files that changed from the base of the PR and between 33bcd1f and 6834814.

Files selected for processing (1)

snakemake/ioutils.py (2 hunks)

Additional context used

Path-based instructions (1)

snakemake/ioutils.py (1)

Pattern **/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of the self argument of methods.
Do not suggest type annotation of the cls argument of classmethods.
Do not suggest return type annotation if a function or method does not contain a return statement.

GitHub Check: Check for spelling errors

snakemake/ioutils.py

[failure] 122-122:
optionaly ==> optionally

Additional comments not posted (1)

snakemake/ioutils.py (1)

Line range hint 121-154: Documentation changes look good!

The updated documentation provides clearer guidance on the function's parameters and their expected behavior:

Explicitly defines the within parameter to accept either a pandas DataFrame, Series, or a Python mapping.

Clarifies that when a Python mapping is used, the dpath parameter is employed, while the query, cols, and is_nrows arguments are disregarded.

Specifies that if the dpath is not found, a LookupError will be raised unless a default fallback value is provided via the default argument.

These enhancements improve the understanding of the function's behavior across different input types and strengthen error handling.

snakemake/ioutils.py

sonarqubecloud · 2024-09-18T13:50:55Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

🤖 I have created a release *beep* *boop* --- ## [8.20.4](v8.20.3...v8.20.4) (2024-09-20) ### Bug Fixes * cache conda envs to fix performance regression introduced in #1300 ([#3093](#3093)) ([66600c4](66600c4)) * Flatten conda pip dependencies for report rule info ([#3085](#3085)) ([56a1f20](56a1f20)) * improve runtime complexity of post-job checkpoint handling ([#3096](#3096)) ([ba30781](ba30781)) ### Documentation * Clarify the lookup function docstring ([#3091](#3091)) ([94177d5](94177d5)) * Update lookup signature ([#3090](#3090)) ([655d6a1](655d6a1)) --- 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>

Clarify the lookup function docstring

33bcd1f

This described the is_nrows argument, and tries to make it clear what applies with a mapping input.

peterjc requested a review from johanneskoester as a code owner September 18, 2024 13:25

coderabbitai bot reviewed Sep 18, 2024

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peterjc added 2 commits September 18, 2024 14:44

Fix spelling

3095e77

Remove trailing whitespace

6834814

coderabbitai bot reviewed Sep 18, 2024

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snakemake/ioutils.py Outdated Show resolved Hide resolved

spelling

c26fb13

johanneskoester approved these changes Sep 19, 2024

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johanneskoester merged commit 94177d5 into snakemake:main Sep 19, 2024

github-actions bot mentioned this pull request Sep 19, 2024

chore(main): release 8.20.4 #3094

Merged

peterjc deleted the patch-3 branch September 19, 2024 14:22

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docs: Clarify the lookup function docstring#3091

docs: Clarify the lookup function docstring#3091
johanneskoester merged 4 commits intosnakemake:mainfrom
peterjc:patch-3

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