Upload the files explaining the algorithm and the benchmark results#15
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Note Other AI code review bot(s) detectedCodeRabbit has detected other AI code review bot(s) in this pull request and will avoid duplicating their findings in the review comments. This may lead to a less comprehensive review. WalkthroughAdds new and updated documentation: a new Changes
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docs/README.md (1)
1-22: Strong introduction and feature overview.The project description and key features are clear, well-organized, and effectively communicate the package's value proposition.
docs/benchmark.md (2)
1-28: Well-documented benchmark methodology.The overview and methodology sections clearly explain the data processing pipeline, filtering criteria for each tool, and uncertainty classification approach. The setup ensures fair comparison across tools.
87-108: Strong conclusions with clear tool recommendations.The analysis clearly articulates each tool's strengths and provides evidence-based recommendations. The trade-off analysis between precision and sensitivity is particularly helpful for users choosing between tools.
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🧹 Nitpick comments (1)
README.md (1)
309-316: Citation format is simplified; consider adding more metadata.The citation section (lines 309-316) provides a simple text-based citation format. While acceptable, consider expanding it to include: authors, publication year, DOI or GitHub URL, and optionally a BibTeX entry for users who need structured citation formats. This would improve usability for academic citations.
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README.md (7)
1-43: Documentation introduction and feature overview are clear and well-structured.The opening sections effectively communicate the package purpose, key features, and algorithm overview with proper academic citations. Structure is logical and helps new users quickly understand onsite's capabilities.
45-156: Installation and usage documentation is comprehensive and well-presented.Clear step-by-step instructions for multiple installation methods (Poetry, pip, development) and comprehensive CLI examples showing both basic and advanced usage patterns with custom parameters. The distinction between unified CLI and individual tool invocation is helpful for users.
158-209: Command-line options tables are well-structured and internally consistent.The tables clearly document parameter defaults and descriptions for all three algorithms. Parameter names match the CLI usage examples, and defaults appear sensible (e.g., conservative mass tolerances, single-threaded by default). The increased complexity of LucXor (14 options vs 8 for others) appropriately reflects its two-stage workflow.
229-242: Verify PhosphoRS parameter documentation matches CLI interface.Lines 234-237 document "Window size: 100.0" and "Max depth: 8" as key parameters for PhosphoRS, but these parameters do not appear in the PhosphoRS command-line options table (lines 173-184). This discrepancy suggests either: (1) these are internal defaults not exposed via CLI, or (2) the documentation is outdated/inconsistent. Please clarify whether these parameters should be included in the CLI options table or if the algorithm details section should be updated to reflect only the exposed CLI parameters.
278-280: Verify example result file paths are correct.Lines 278-280 reference example files with paths like
../data/1_ascore_result.idXML. If this README is in the repository root (standard practice), the relative paths should usedata/...without the../prefix. The../suggests the README may be in a subdirectory (e.g.,docs/), but the PR description indicates updates to the root README. Please verify these paths match the actual file locations.
282-289: Documentation links may reference non-existent files.Lines 286-289 link to algorithm documentation and citations files (
algorithms/ascore.md,algorithms/phosphors.md,algorithms/lucxor.md,citations.md) that are not mentioned in the PR description. The PR addsdocs/README.mdanddocs/benchmark.md, but no algorithm-specific documentation files under analgorithms/directory. Please verify these files exist or update the links to point to the correct documentation locations (e.g.,docs/README.mdor files indocs/).
305-307: Verify LICENSE file path.Line 307 references the LICENSE file with path
../LICENSE. If this README is in the repository root, the path should beLICENSEwithout the../prefix. This is consistent with the earlier path inconsistency noted in the example results section. Please verify the relative path is correct for the actual location of the README file.
Removed detailed project description and installation instructions from README.md.
Updated references and citations for algorithms in the onsite package, including corrections to author names, publication years, and DOIs.
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Pull Request Overview
This PR adds comprehensive documentation for the onsite package, including algorithm descriptions, installation instructions, usage examples, and benchmark results comparing phosphorylation site localization tools.
Key Changes
- Added detailed package documentation covering AScore, PhosphoRS, and LucXor algorithms with installation and CLI usage instructions
- Included benchmark analysis of four phosphorylation site localization tools on the PXD000138 dataset with methodology and comparative results
- Updated root README.md with streamlined content and added example result file references
Reviewed Changes
Copilot reviewed 4 out of 7 changed files in this pull request and generated 9 comments.
| File | Description |
|---|---|
| docs/README.md | Comprehensive package documentation with algorithm details, installation, CLI usage, and command-line options for all three algorithms |
| docs/benchmark.md | Benchmark methodology and comparative results for LuciPHOr, Ascore, pyLucXor, and PhosphoRS tools on PXD000138 dataset |
| README.md | Streamlined root README with key features, algorithm summaries, and references to detailed documentation |
| data/*.idXML | Example result files demonstrating output format for each algorithm |
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| - [AScore Algorithm Documentation](algorithms/ascore.md) | ||
| - [PhosphoRS Algorithm Documentation](algorithms/phosphors.md) | ||
| - [LucXor Algorithm Documentation](algorithms/lucxor.md) | ||
| - [Citations and References](citations.md) |
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Broken relative links: The documentation links point to files that don't exist in this PR (algorithms/ascore.md, algorithms/phosphors.md, algorithms/lucxor.md, citations.md). Either these files should be included in this PR, or the links should be removed/updated to point to existing documentation.
| - [AScore Algorithm Documentation](algorithms/ascore.md) | |
| - [PhosphoRS Algorithm Documentation](algorithms/phosphors.md) | |
| - [LucXor Algorithm Documentation](algorithms/lucxor.md) | |
| - [Citations and References](citations.md) | |
| <!-- Documentation links removed due to missing files. --> |
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README.md (3)
1-7: Branding updates are consistent and well-applied.The root README successfully rebrand from "OnSite" to "onsite" with updated badge URLs and consistent lowercase usage throughout. The structure and formatting are clear and professional.
242-250: All example result files verified.The verification confirms that all three example result files referenced in lines 242–250 exist in the
data/directory:
data/1_ascore_result.idXML✓data/1_phosphors_result.idXML✓data/1_lucxor_result.idXML✓The relative paths in the README are correct and resolve properly.
102-111: Documentation verified as accurate.All three CLI commands (
ascore,phosphors,lucxor) are properly registered as entry points inpyproject.tomland added as subcommands inonsite/onsitec.py. The documented parameter names (-in,-id,-out) match the actual CLI implementation, and the example invocations are executable as shown in the README.
| - **onsite Documentation**: https://github.com/bigbio/onsite/docs | ||
| - **PyOpenMS Documentation**: https://pyopenms.readthedocs.io/ | ||
| - **OpenMS Documentation**: https://openms.readthedocs.io/ | ||
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| ### Tutorials and Examples | ||
| - **OnSite Tutorials**: https://github.com/bigbio/onsite/docs/tutorials | ||
| - **onsite Tutorials**: https://github.com/bigbio/onsite/docs/tutorials | ||
| - **Algorithm Comparisons**: https://github.com/bigbio/onsite/docs/benchmarks | ||
| - **API Reference**: https://github.com/bigbio/onsite/docs/api |
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Fix malformed GitHub documentation URLs.
Lines 195–202 contain GitHub URLs that don't follow standard GitHub path conventions. These links will not resolve correctly.
Correct the URLs to use proper GitHub tree or blob paths:
### Online Documentation
-
- **onsite Documentation**: https://github.com/bigbio/onsite/docs
- **PyOpenMS Documentation**: https://pyopenms.readthedocs.io/
- **OpenMS Documentation**: https://openms.readthedocs.io/
### Tutorials and Examples
-
- **onsite Tutorials**: https://github.com/bigbio/onsite/docs/tutorials
- **Algorithm Comparisons**: https://github.com/bigbio/onsite/docs/benchmarks
- **API Reference**: https://github.com/bigbio/onsite/docs/api
+
+- **onsite Documentation**: https://github.com/bigbio/onsite/tree/main/docs
+- **PyOpenMS Documentation**: https://pyopenms.readthedocs.io/
+- **OpenMS Documentation**: https://openms.readthedocs.io/
+
+### Tutorials and Examples
+
+- **onsite Tutorials**: https://github.com/bigbio/onsite/tree/main/docs
+- **Algorithm Comparisons**: https://github.com/bigbio/onsite/blob/main/docs/benchmark.md
+- **API Reference**: https://github.com/bigbio/onsite/tree/main/docsAlternatively, if you plan to publish documentation on ReadTheDocs or GitHub Pages, update these URLs to point to the proper documentation host.
Committable suggestion skipped: line range outside the PR's diff.
🤖 Prompt for AI Agents
In docs/citations.md around lines 195 to 202, the GitHub documentation URLs are
malformed and won't resolve; update them to point to the correct repository
paths (e.g. use tree/blob with branch like /tree/main/docs,
/tree/main/docs/tutorials, /tree/main/docs/benchmarks, /tree/main/docs/api) or
replace them with the proper ReadTheDocs/GitHub Pages URLs if docs are hosted
elsewhere; ensure each link uses the full correct path including branch (main or
current default) and verify each URL resolves.
Updated README to include project title, badges, and improved algorithm descriptions.
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Removed key parameters and two-stage workflow details for AScore, PhosphoRS, and LucXor algorithms from the README.
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
PR Type
Documentation
Description
Add comprehensive README documentation for onsite package
Document three PTM localization algorithms: AScore, PhosphoRS, LucXor
Include installation instructions, CLI usage, and command-line options
Add benchmark results comparing four phosphorylation site localization tools
Provide example result files and algorithm parameter documentation
Diagram Walkthrough
File Walkthrough
README.md
Main package documentation and user guidedocs/README.md
capabilities
options
LucXor implementations
tool
benchmark.md
Benchmark results and tool comparison analysisdocs/benchmark.md
on PXD000138 dataset
criteria
and overall quality metrics
distribution
requirements
1_ascore_result.idXML
AScore algorithm example resultsdata/1_ascore_result.idXML
1_lucxor_result.idXML
LucXor algorithm example resultsdata/1_lucxor_result.idXML
1_phosphors_result.idXML
PhosphoRS algorithm example resultsdata/1_phosphors_result.idXML
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