fix: Flatten conda pip dependencies for report rule info by votti · Pull Request #3085 · snakemake/snakemake

votti · 2024-09-11T16:06:40Z

Currently pip dependencies specified in conda environments break the rule_info of the snakemake html report as reported in #3084

This works around this issue by flattening the pip secion as:
pip: <dependency 1>
pip: <dependency 2>

before displaying which fixes this issue.

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).

Additional considerations

I am not a React/Javascript expert at all, so it is very well possible my fix is not very ideomatic - I am mainly interested in getting the report.html working, so any alternative/better solution would be very welcome as well
Only manual testing was done as I dont know how to test javascript rendering
Aesthetics: currently I am simply flattening the entries of the pip section of the conda envrionment:

dependencies:
- python
- pip
- pip:
   - dependencya
   - dependencyb

will be rendered as:

python
pip
pip: dependencya
pip: dependencyb

Potentially one could do this nicer with indenting.

Example rendering:

Summary by CodeRabbit

New Features
- Improved rendering of software dependencies in the RuleInfo component, allowing for better handling of complex nested data structures.
Bug Fixes
- Enhanced processing of input lists containing objects and arrays, ensuring accurate representation of dependencies.

Currenlty pip dependencies specified in conda environments break the rule_info of the snakemake report. This flattens the pip secion as: pip: <dependency 1> pip: <dependency 2> before displaying which fixes this issue. Fixes: Issue snakemake#3084

coderabbitai · 2024-09-11T16:06:52Z

Walkthrough

The pull request introduces a new function, flattenList, in the rule_info.js file, which processes input lists containing objects and arrays. This function flattens nested structures into a single list format. It is then integrated into the renderSoftware method of the RuleInfo class, replacing the previous method of handling dependencies. This change enhances the representation of software dependencies, particularly for complex nested data structures.

Changes

File Path	Change Summary
`snakemake/report/html_reporter/template/components/rule_info.js`	Added `function flattenList(inputList)` and updated `renderSoftware` to utilize `flattenList` for processing dependencies.

Possibly related issues

Report rendering of rule fails if conda environment contains pip dependency #3084: The changes address the issue of rendering failures when a conda environment contains nested pip dependencies, which aligns with the reported problem of the renderItems expecting a flat list.

Recent review details

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Commits

Files that changed from the base of the PR and between c426207 and d32de6d.

Files selected for processing (1)

snakemake/report/html_reporter/template/components/rule_info.js (2 hunks)

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

snakemake/report/html_reporter/template/components/rule_info.js

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coderabbitai

Actionable comments posted: 1

Outside diff range and nitpick comments (1)

snakemake/report/html_reporter/template/components/rule_info.js (1)
54-54: Improve consistency of the renderSoftware method.

The renderSoftware method returns an empty array if the rule has no conda environment, which is not consistent with the other render methods.

Apply this diff to improve the method:
-        } else {
-            return [];
+        } else {
+            return null;
         }

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between e9ce4a3 and c426207.

Files selected for processing (1)

snakemake/report/html_reporter/template/components/rule_info.js (2 hunks)

snakemake/report/html_reporter/template/components/rule_info.js

I manually testest that this still work and but have to trust the AI that it is really better Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

sonarqubecloud · 2024-09-11T16:16:51Z

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>

votti requested a review from johanneskoester as a code owner September 11, 2024 16:06

coderabbitai bot reviewed Sep 11, 2024

View reviewed changes

snakemake/report/html_reporter/template/components/rule_info.js Show resolved Hide resolved

Update flattenList with codderrabittai suggestion

d32de6d

I manually testest that this still work and but have to trust the AI that it is really better Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

johanneskoester approved these changes Sep 19, 2024

View reviewed changes

johanneskoester merged commit 56a1f20 into snakemake:main Sep 19, 2024

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

chore(main): release 8.20.4 #3094

Merged

votti deleted the bugfix/reportpip branch September 20, 2024 08:19

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fix: Flatten conda pip dependencies for report rule info#3085

fix: Flatten conda pip dependencies for report rule info#3085
johanneskoester merged 2 commits intosnakemake:mainfrom
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