Dev

[ypriverol]

PR Type

Documentation

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Description

• Update README CLI commands to match actual implementation

• Remove non-existent commands from help output

• Add missing commands: download-all-public-category-files, download-px-raw-files, list-private-files

• Fix command name: download-files-by-category to download-all-public-category-files

• Standardize command invocation to use pridepy instead of python -m pridepy.pridepy

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Diagram Walkthrough

flowchart LR
  A["README.md<br/>CLI Documentation"] -->|Remove incorrect commands| B["Deleted commands:<br/>get-files-by-filter<br/>get-files-by-project-accession<br/>get-private-files<br/>get-projects<br/>get-projects-by-accession"]
  A -->|Add missing commands| C["Added commands:<br/>download-all-public-category-files<br/>download-px-raw-files<br/>list-private-files"]
  A -->|Fix command names| D["download-files-by-category<br/>→<br/>download-all-public-category-files"]
  A -->|Standardize invocation| E["python -m pridepy.pridepy<br/>→<br/>pridepy"]

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File Walkthrough

Relevant files

Documentation

README.md Correct CLI commands and standardize documentation              README.md Removed 5 non-existent CLI commands from help output section Added 3 missing CLI commands: download-all-public-category-files, download-px-raw-files, list-private-files Corrected command name from download-files-by-category to download-all-public-category-files in usage example Standardized command invocation from python -m pridepy.pridepy to pridepy in example Improved formatting and alignment of command descriptions in help output +10/-13

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Summary by CodeRabbit

• Documentation
  • Updated CLI commands documentation with new and renamed command options.
  • Refreshed usage examples to reflect the current command structure.
  • Made minor formatting adjustments to improve readability of command lists.

[qodo-code-review]

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.
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Custom Compliance
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	Generic: Meaningful Naming and Self-Documenting Code Objective: Ensure all identifiers clearly express their purpose and intent, making code self-documenting Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
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	Generic: Secure Error Handling Objective: To prevent the leakage of sensitive system information through error messages while providing sufficient detail for internal debugging. Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Secure Logging Practices Objective: To ensure logs are useful for debugging and auditing without exposing sensitive information like PII, PHI, or cardholder data. Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Security-First Input Validation and Data Handling Objective: Ensure all data inputs are validated, sanitized, and handled securely to prevent vulnerabilities Status: Passed Learn more about managing compliance generic rules or creating your own custom rules

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🟡 - Partial Compliant
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⚪ - Requires Further Human Verification
🏷️ - Compliance label

[coderabbitai]

📝 Walkthrough

Walkthrough

This PR updates the README.md documentation to reflect changes in CLI command names and usage. Legacy commands are removed, new and renamed commands are added, and usage examples are updated to match the new command names. Minor formatting adjustments are included.

Changes

Cohort / File(s)	Summary
Documentation Update README.md	Updated CLI command references (removed legacy commands, added new/renamed commands like download-all-public-category-files, download-px-raw-files, list-private-files, search-projects-by-keywords-and-filters), and adjusted usage examples to reflect new command names and invocation syntax.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~5 minutes

Possibly related PRs

• add to README #68 — Both PRs add/describe the ProteomeXchange raw-files download command (download-px-raw-files) in README documentation.
• major refactoring #59 — Both PRs modify CLI commands and update README references including new/renamed commands like download-all-public-category-files.
• move to poetry #61 — README command name changes in this PR directly correspond to CLI commands implemented and documented in that PR.

Suggested labels

Review effort 1/5

Suggested reviewers

• selvaebi

Poem

🐰 Commands hop and commands change,
CLI listings rearrange,
Old commands fade to memory's field,
New names shine, their purpose revealed,
Documentation fresh and bright! ✨

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 inconclusive)

Check name	Status	Explanation	Resolution
Title check	❓ Inconclusive	The title 'Dev' is vague and generic, providing no meaningful information about the changeset's primary purpose or content.	Use a descriptive title that reflects the main changes, such as 'Update CLI commands and usage examples in README' or 'Refactor README with updated CLI command references'.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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✨ Finishing touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch dev

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[qodo-code-review]

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