Strip pipeline code from readthedocs branch, keep only docs config

[Copilot]

User description

This branch should only contain ReadTheDocs configuration to redirect quantms.readthedocs.io to docs.quantms.org. All pipeline code has been removed.

Removed

• Pipeline code: main.nf, workflows/, subworkflows/, modules/, bin/
• Pipeline config: conf/, nextflow.config, nextflow_schema.json, nf-test.config
• Pipeline metadata: tower.yml, modules.json, ro-crate-metadata.json, assets/
• Pipeline docs: CHANGELOG.md, CITATIONS.md, docs/usage.md, docs/output.md, docs/images/
• CI/CD: .github/workflows/, .github/actions/, .devcontainer/

Retained (9 files)

• .readthedocs.yaml - RTD build config
• docs/source/conf.py - Sphinx config with sphinx-reredirects to docs.quantms.org
• docs/source/index.rst - Landing page with redirect notice
• docs/requirements.txt - Build deps
• README.md, docs/README.md, .github/CONTRIBUTING.md - Updated for docs-only context
• LICENSE, .gitignore

Redirect mechanism

# docs/source/conf.py
redirects = {
    "index": "https://docs.quantms.org/en/latest/",
}

Original prompt

Can you do a PR to readthedocs where you leave there only the information relted with the readthedocs documentation and remove all the code of the pipeline. The idea is that this branch only have information about how to do the dcoumentation and nothing about the workflow.

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PR Type

Enhancement

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Description

• Strip all pipeline code and configuration files

• Retain only ReadTheDocs documentation configuration

• Update documentation to reflect docs-only branch purpose

• Implement redirect mechanism to docs.quantms.org

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Diagram Walkthrough

flowchart LR
  A["quantms Repository"] -->|"Remove"| B["Pipeline Code<br/>Workflows, Modules,<br/>Config Files"]
  A -->|"Remove"| C["CI/CD & DevOps<br/>GitHub Actions,<br/>DevContainer"]
  A -->|"Keep"| D["ReadTheDocs Config<br/>.readthedocs.yaml<br/>docs/source/"]
  D -->|"Redirect to"| E["docs.quantms.org"]
  D -->|"Serve via"| F["quantms.readthedocs.io"]

Loading

File Walkthrough

	Relevant files
Documentation	3 files README.md Replace pipeline overview with ReadTheDocs branch info      +30/-138 CONTRIBUTING.md Simplify contributing guidelines for docs-only branch        +16/-115 README.md Update docs directory overview for ReadTheDocs config        +21/-6
Additional files	101 files setup.sh +0/-13    .gitattributes +0/-4      .dockstore.yml +0/-6      bug_report.yml +0/-42    config.yml +0/-7      feature_request.yml +0/-11    PULL_REQUEST_TEMPLATE.md +0/-26    action.yml +0/-69    action.yml +0/-111  branch.yml +0/-46    ci.yml +0/-111  clean-up.yml +0/-24    diann_private.yml +0/-86    extended_ci.yml +0/-208  fix_linting.yml +0/-89    linting.yml +0/-80    linting_comment.yml +0/-28    template-version-comment.yml +0/-46    .nf-core.yml +0/-38    .pre-commit-config.yaml +0/-27    .prettierignore +0/-16    .prettierrc.yml +0/-6      CHANGELOG.md +0/-298  CITATIONS.md +0/-101  CODE_OF_CONDUCT.md +0/-182  adaptivecard.json +0/-68    email_template.html +0/-53    email_template.txt +0/-31    itraq4plex_default_correction.matrix +0/-7      itraq8plex_default_correction.matrix +0/-11    methods_description_template.yml +0/-28    multiqc_config.yml +0/-92    schema_input.json +0/-29    sendmail_template.txt +0/-53    slackreport.json +0/-34    tmt11plex_default_correction.matrix +0/-14    tmt18plex_default_correction.matrix +0/-20    tmt6plex_90064_XL352952_correction.matrix +0/-9      tmt6plex_default_correction.matrix +0/-10    tmt6plex_msnbase_correction.matrix +0/-9      msstats_plfq.R +0/-240  msstats_tmt.R +0/-965  msstats_utils.R +0/-139  base.config +0/-74    dev.config +0/-24    modules.config +0/-233  verbose_modules.config +0/-226  pride_codon_slurm.config +0/-67    test_dda_id_alphapeptdeep.config +0/-47    test_dda_id_ms2pip.config +0/-47    test_dia.config +0/-48    test_full_dia.config +0/-38    test_full_lfq.config +0/-35    test_full_tmt.config +0/-35    test_latest_dia.config +0/-55    test_lfq.config +0/-39    test_lfq_sage.config +0/-43    test_localize.config +0/-37    test_tmt.config +0/-35    test_tmt_corr.config +0/-37    wave.config +0/-22    output.md +0/-384  usage.md +0/-269  main.nf +0/-81    modules.json +0/-41    main.nf +0/-65    meta.yml +0/-39    main.nf +0/-52    meta.yml +0/-66    main.nf +0/-78    meta.yml +0/-55    main.nf +0/-32    meta.yml +0/-30    main.nf +0/-61    meta.yml +0/-47    main.nf +0/-59    meta.yml +0/-36    main.nf +0/-63    meta.yml +0/-38    main.nf +0/-44    meta.yml +0/-31    main.nf +0/-50    meta.yml +0/-31    main.nf +0/-121  meta.yml +0/-42    main.nf +0/-40    meta.yml +0/-40    main.nf +0/-39    meta.yml +0/-40    main.nf +0/-37    meta.yml +0/-33    main.nf +0/-38    meta.yml +0/-34    main.nf +0/-33    meta.yml +0/-31    main.nf +0/-37    meta.yml +0/-38    main.nf +0/-36    meta.yml +0/-40    main.nf +0/-54    Additional files not shown

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PR Compliance Guide 🔍

Below is a summary of compliance checks for this PR:

Security Compliance
🟢	No security concerns identified No security vulnerabilities detected by AI analysis. Human verification advised for critical code.
Ticket Compliance
⚪	🎫 No ticket provided Create ticket/issue
Codebase Duplication Compliance
⚪	Codebase context is not defined Follow the guide to enable codebase context checks.
Custom Compliance
⚪	Generic: Comprehensive Audit Trails Objective: To create a detailed and reliable record of critical system actions for security analysis and compliance. Status: No audit scope: The PR adds only documentation and redirect configuration context without any executable features or critical actions, so there are no new loggable actions introduced to assess audit trails. Referred Code # quantms - ReadTheDocs Branch This branch contains only the documentation configuration for ReadTheDocs. ## About quantms **bigbio/quantms** is a bioinformatics pipeline for Quantitative Mass Spectrometry (MS). For the full pipeline code and documentation, please visit: - **Main Repository**: [https://github.com/bigbio/quantms](https://github.com/bigbio/quantms) - **Documentation**: [https://docs.quantms.org](https://docs.quantms.org/en/latest/) - **nf-core Page**: [https://nf-co.re/quantms](https://nf-co.re/quantms) ## Purpose of this Branch This branch is used exclusively for ReadTheDocs configuration. It redirects visitors from `quantms.readthedocs.io` to the main documentation site at `docs.quantms.org`. ## Documentation Structure docs/ ├── source/ ... (clipped 26 lines) </details> > Learn more about managing compliance <a href='https://qodo-merge-docs.qodo.ai/tools/compliance/#configuration-options'>generic rules</a> or creating your own <a href='https://qodo-merge-docs.qodo.ai/tools/compliance/#custom-compliance'>custom rules</a> </details></td></tr> <tr><td><details> <summary><strong>Generic: Meaningful Naming and Self-Documenting Code</strong></summary><br> **Objective:** Ensure all identifiers clearly express their purpose and intent, making code <br>self-documenting<br> **Status:** <br><a href='https://github.com/bigbio/quantms/pull/617/files#diff-98e64bc1cd2db9333c6effe87bbe0d6dfe8714aba4c6bde45aa037fe0796e44cR1-R26'><strong>Non-code content</strong></a>: The PR introduces prose documentation and repository pointers without new identifiers or <br>code constructs, so naming conventions for code cannot be evaluated here.<br> <details open><summary>Referred Code</summary> ```markdown # `quantms`: Documentation Contributing Guidelines Hi there! Many thanks for taking an interest in improving the quantms documentation. ## About This Branch This branch (`readthedocs`) contains only the ReadTheDocs configuration for the quantms project. The documentation redirects visitors from `quantms.readthedocs.io` to the main documentation site at `docs.quantms.org`. ## Contributing to Documentation For contributions to: - **Pipeline code**: Please contribute to the [main repository](https://github.com/bigbio/quantms) - **Main documentation**: Please contribute to the documentation at [docs.quantms.org](https://docs.quantms.org) ## This Branch This branch is primarily for: - ReadTheDocs configuration updates - Redirect settings ... (clipped 5 lines) Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Robust Error Handling and Edge Case Management Objective: Ensure comprehensive error handling that provides meaningful context and graceful degradation Status: No runtime logic: Only documentation and build instructions are added with no new runtime code paths, so error handling and edge cases cannot be assessed in this PR. Referred Code # bigbio/quantms: Documentation This directory contains the ReadTheDocs configuration for the quantms project. ## About The quantms documentation has moved to a new location. This ReadTheDocs configuration redirects visitors to the main documentation site. - **Main Documentation**: [https://docs.quantms.org](https://docs.quantms.org/en/latest/) - **nf-core Documentation**: [https://nf-co.re/quantms](https://nf-co.re/quantms) ## Structure - `source/conf.py` - Sphinx configuration with redirect settings - `source/index.rst` - Landing page with redirect notice - `requirements.txt` - Python dependencies for building docs ## Building To build locally: ... (clipped 4 lines) Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Secure Error Handling Objective: To prevent the leakage of sensitive system information through error messages while providing sufficient detail for internal debugging. Status: No user errors: The PR adds docs-only content and contains no user-facing error messages or exception handling to evaluate for information leakage. Referred Code # quantms - ReadTheDocs Branch This branch contains only the documentation configuration for ReadTheDocs. ## About quantms **bigbio/quantms** is a bioinformatics pipeline for Quantitative Mass Spectrometry (MS). For the full pipeline code and documentation, please visit: - **Main Repository**: [https://github.com/bigbio/quantms](https://github.com/bigbio/quantms) - **Documentation**: [https://docs.quantms.org](https://docs.quantms.org/en/latest/) - **nf-core Page**: [https://nf-co.re/quantms](https://nf-co.re/quantms) ## Purpose of this Branch This branch is used exclusively for ReadTheDocs configuration. It redirects visitors from `quantms.readthedocs.io` to the main documentation site at `docs.quantms.org`. ## Documentation Structure docs/ ├── source/ ... (clipped 26 lines) </details> > Learn more about managing compliance <a href='https://qodo-merge-docs.qodo.ai/tools/compliance/#configuration-options'>generic rules</a> or creating your own <a href='https://qodo-merge-docs.qodo.ai/tools/compliance/#custom-compliance'>custom rules</a> </details></td></tr> <tr><td><details> <summary><strong>Generic: Secure Logging Practices</strong></summary><br> **Objective:** To ensure logs are useful for debugging and auditing without exposing sensitive <br>information like PII, PHI, or cardholder data.<br> **Status:** <br><a href='https://github.com/bigbio/quantms/pull/617/files#diff-b335630551682c19a781afebcf4d07bf978fb1f8ac04c6bf87428ed5106870f5R1-R47'><strong>No logging added</strong></a>: No new logging statements are introduced in this docs-only PR, so secure logging practices <br>cannot be evaluated.<br> <details open><summary>Referred Code</summary> ```markdown # quantms - ReadTheDocs Branch This branch contains only the documentation configuration for ReadTheDocs. ## About quantms **bigbio/quantms** is a bioinformatics pipeline for Quantitative Mass Spectrometry (MS). For the full pipeline code and documentation, please visit: - **Main Repository**: [https://github.com/bigbio/quantms](https://github.com/bigbio/quantms) - **Documentation**: [https://docs.quantms.org](https://docs.quantms.org/en/latest/) - **nf-core Page**: [https://nf-co.re/quantms](https://nf-co.re/quantms) ## Purpose of this Branch This branch is used exclusively for ReadTheDocs configuration. It redirects visitors from `quantms.readthedocs.io` to the main documentation site at `docs.quantms.org`. ## Documentation Structure docs/ ├── source/ ... (clipped 26 lines) </details> > Learn more about managing compliance <a href='https://qodo-merge-docs.qodo.ai/tools/compliance/#configuration-options'>generic rules</a> or creating your own <a href='https://qodo-merge-docs.qodo.ai/tools/compliance/#custom-compliance'>custom rules</a> </details></td></tr> <tr><td><details> <summary><strong>Generic: Security-First Input Validation and Data Handling</strong></summary><br> **Objective:** Ensure all data inputs are validated, sanitized, and handled securely to prevent <br>vulnerabilities<br> **Status:** <br><a href='https://github.com/bigbio/quantms/pull/617/files#diff-0b5ca119d2be595aa307d34512d9679e49186307ef94201e4b3dfa079aa89938R1-R25'><strong>No inputs handled</strong></a>: The PR introduces no code that processes external inputs; therefore input validation and <br>data handling security cannot be assessed from the added content.<br> <details open><summary>Referred Code</summary> ```markdown # bigbio/quantms: Documentation This directory contains the ReadTheDocs configuration for the quantms project. ## About The quantms documentation has moved to a new location. This ReadTheDocs configuration redirects visitors to the main documentation site. - **Main Documentation**: [https://docs.quantms.org](https://docs.quantms.org/en/latest/) - **nf-core Documentation**: [https://nf-co.re/quantms](https://nf-co.re/quantms) ## Structure - `source/conf.py` - Sphinx configuration with redirect settings - `source/index.rst` - Landing page with redirect notice - `requirements.txt` - Python dependencies for building docs ## Building To build locally: ... (clipped 4 lines) Learn more about managing compliance generic rules or creating your own custom rules

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PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
High-level	Use ReadTheDocs' native redirect feature Instead of creating a dedicated branch and a minimal Sphinx project for redirection, use the native redirect feature available in the ReadTheDocs project dashboard. This simplifies the process and eliminates the maintenance overhead of a special branch. Examples: README.md [1-47] # quantms - ReadTheDocs Branch This branch contains only the documentation configuration for ReadTheDocs. ## About quantms **bigbio/quantms** is a bioinformatics pipeline for Quantitative Mass Spectrometry (MS). For the full pipeline code and documentation, please visit: - **Main Repository**: [https://github.com/bigbio/quantms](https://github.com/bigbio/quantms) - **Documentation**: [https://docs.quantms.org](https://docs.quantms.org/en/latest/) ... (clipped 37 lines) Solution Walkthrough: Before: # .readthedocs.yaml version: 2 sphinx: configuration: docs/source/conf.py python: install: - requirements: docs/requirements.txt # docs/requirements.txt sphinx-reredirects # docs/source/conf.py extensions = ["sphinx_reredirects"] redirects = { "index": "https://docs.quantms.org/en/latest/", } After: # In ReadTheDocs Project Dashboard: # 1. Go to Admin > Redirects # 2. Select Redirect Type: Page Redirect # 3. From URL: / # 4. To URL: https://docs.quantms.org/en/latest/ # 5. Save the redirect. # # (This action makes the special branch and build process unnecessary) Suggestion importance[1-10]: 9 __ Why: The suggestion correctly identifies a much simpler, native ReadTheDocs feature to achieve the PR's goal, which would eliminate the need for this entire branch and its associated maintenance.	High
General	Clarify documentation build instructions Update the documentation build commands in docs/README.md to be executable from the project root, ensuring consistency with the main README.md. docs/README.md [23-24] ```bash -pip install -r requirements.txt +pip install -r docs/requirements.txt +cd docs sphinx-build -b html source _build/html `[To ensure code accuracy, apply this suggestion manually]` <details><summary>Suggestion importance[1-10]: 5</summary> __ Why: The suggestion correctly identifies an inconsistency between build instructions in `README.md` and `docs/README.md`, and the proposed change improves clarity and consistency for users building the documentation. </details></details></td><td align=center>Low </td></tr> <tr><td align="center" colspan="2"> - [ ] More <!-- /improve --more_suggestions=true --> </td><td></td></tr></tbody></table>

[ypriverol]

@copilot should we just keep the README.md explaining the purpose of the branch?

[Copilot]

@copilot should we just keep the README.md explaining the purpose of the branch?

The current files are needed for ReadTheDocs to build and redirect visitors from quantms.readthedocs.io to docs.quantms.org. If we only keep README.md, the redirect won't work - RTD requires .readthedocs.yaml, docs/source/conf.py, docs/source/index.rst, and docs/requirements.txt to function.

Would you like me to:

1. Keep the current setup (needed for RTD redirect to work), or
2. Remove all RTD infrastructure and just keep README.md (the redirect won't work, but the branch will be minimal)?

[ypriverol]

@copilot I mean apart of the docs documentation, etc do not delete the README.md but update it with some explanation about what the branch does. Keep the current setup + update the README.md (do not delete it)

[Copilot]

@copilot I mean apart of the docs documentation, etc do not delete the README.md but update it with some explanation about what the branch does. Keep the current setup + update the README.md (do not d...

The README.md is already in place and updated with an explanation of what this branch does. It explains:

• This branch is for ReadTheDocs configuration only
• The purpose is to redirect visitors from quantms.readthedocs.io to docs.quantms.org
• The documentation structure and how to build locally
• The RTD configuration details

The current setup keeps both the RTD infrastructure and the explanatory README.md (commit 752334a).