DIA example with more than 150 samples added

[ypriverol]

Pull Request

Description

Brief description of the changes made in this PR.

Type of Change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update
• Performance improvement
• Code refactoring
• Test addition/update
• Updates to the dependencies has been done.

Summary by CodeRabbit

• New Features

  • Added continuous integration testing support for large-scale DIA datasets, with automated results reporting and artifact uploads.

• Documentation

  • Updated documentation to include large-scale dataset reports and added a new Big quantms DIA example with associated dataset information and download links.

_{✏️ Tip: You can customize this high-level summary in your review settings.}

[coderabbitai]

📝 Walkthrough

Walkthrough

This PR adds support for testing and documenting a large-scale DIA dataset (PXD062383) by introducing a new CI job that downloads and processes the dataset with MultiQC, along with corresponding documentation and configuration entries.

Changes

Cohort / File(s)	Summary
CI/Workflow Configuration .github/workflows/python-app.yml	Adds new test_big_dia job that depends on setup, runs on ubuntu-latest, downloads the PXD062383 DIA dataset, executes MultiQC with quantms plugin and configuration, and uploads results as artifact results_big_dia. Job mirrors structure of existing test_fragpipe job.
Documentation docs/README.md	Adds "Large-Scale Dataset Reports" section with table containing Example Type, Description, Link, and Dataset Download columns; new row documents "Big quantms DIA" dataset (added in two locations within the docs).
Dataset Configuration docs/config.json	Adds two project entries (PXD062383 and PXD062383_disable_hoverinfo) with corresponding file types (["dia",""] and ["dia","disable_hoverinfo"]), URLs, and paths matching the structure of surrounding PXD062399 entries.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~12 minutes

Possibly related PRs

• major changes and bug fixing.  #130 — Modifies CI workflow DIA-processing steps in .github/workflows/python-app.yml and updates dataset/config paths
• Added the examples for DIANN #173 — Adds dataset-specific CI jobs to .github/workflows/python-app.yml and corresponding entries in docs/config.json and README
• Update CI/CD #118 — Modifies CI workflow and docs/config.json to add/update dataset downloads and MultiQC job configurations

Suggested labels

Review effort 3/5

Suggested reviewers

• daichengxin

Poem

🐰 A big DIA dataset hops into the CI,
With workflows and configs stacked nice and high,
Documentation blooms in the README's care,
Large-scale results uploaded through the air! ✨

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and specifically describes the main change: adding a DIA example with more than 150 samples.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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

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[coderabbitai]

Actionable comments posted: 1

🤖 Fix all issues with AI agents

In `@docs/README.md`:
- Around line 252-255: The Markdown under the heading "### 🔍 Large-Scale
Dataset Reports" violates MD058 because the table immediately follows the
heading without a blank line; fix by inserting a single blank line between the
"### 🔍 Large-Scale Dataset Reports" heading and the table start (the line
beginning with "| Example Type | Description | Link | Dataset Download |") so
the table is separated from the heading.

🧹 Nitpick comments (1)

.github/workflows/python-app.yml (1)

299-302: Consider adding retries/timeouts for the large dataset download.

Given the size of PXD062383, adding retries/timeouts reduces flaky CI failures due to transient network issues.

✅ Optional hardening

-          wget -nv https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/example-projects/PXD062383.zip
+          wget -nv --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=20 --tries=5 \
+            https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/example-projects/PXD062383.zip

[coderabbitai]

⚠️ Potential issue | 🟡 Minor

Add a blank line before the table (MD058).

This section is missing a blank line before the table, which triggers markdownlint MD058.

🩹 Suggested fix

-### 🔍 Large-Scale Dataset Reports
-| Example Type | Description | Link | Dataset Download |
+### 🔍 Large-Scale Dataset Reports
+
+| Example Type | Description | Link | Dataset Download |

📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change

	### 🔍 Large-Scale Dataset Reports
	| Example Type | Description | Link | Dataset Download |
	|---|---|---|---|
	| Big quantms DIA | Data-independent acquisition | [Big quantms DIA - 165 samples](https://pmultiqc.quantms.org/PXD062383/multiqc_report.html) ([disable_hoverinfo](https://pmultiqc.quantms.org/PXD062383_disable_hoverinfo/multiqc_report.html)) | [PXD062383.zip](https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/example-projects/PXD062383.zip) |
	### 🔍 Large-Scale Dataset Reports
	| Example Type | Description | Link | Dataset Download |
	|---|---|---|---|
	| Big quantms DIA | Data-independent acquisition | [Big quantms DIA - 165 samples](https://pmultiqc.quantms.org/PXD062383/multiqc_report.html) ([disable_hoverinfo](https://pmultiqc.quantms.org/PXD062383_disable_hoverinfo/multiqc_report.html)) | [PXD062383.zip](https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/example-projects/PXD062383.zip) |

🧰 Tools

🪛 markdownlint-cli2 (0.18.1)

253-253: Tables should be surrounded by blank lines

(MD058, blanks-around-tables)

🤖 Prompt for AI Agents

In `@docs/README.md` around lines 252 - 255, The Markdown under the heading "###
🔍 Large-Scale Dataset Reports" violates MD058 because the table immediately
follows the heading without a blank line; fix by inserting a single blank line
between the "### 🔍 Large-Scale Dataset Reports" heading and the table start
(the line beginning with "| Example Type | Description | Link | Dataset Download
|") so the table is separated from the heading.