Update README with corrected CLI commands and formatting

[ypriverol]

User description

Summary

Updated the README documentation to reflect the current CLI command names and improve formatting consistency throughout the guide.

Key Changes

• Command list reorganization: Removed deprecated/renamed commands and updated the commands section with current command names:

  • Renamed download-files-by-category → download-all-public-category-files
  • Renamed get-files-by-filter → removed (no longer listed)
  • Renamed get-files-by-project-accession → removed (no longer listed)
  • Renamed get-private-files → list-private-files
  • Renamed get-projects → removed (no longer listed)
  • Renamed get-projects-by-accession → removed (no longer listed)
  • Added new command: download-px-raw-files

• Command usage examples: Updated code examples to use correct command names:

  • Updated download by category example to use download-all-public-category-files
  • Fixed command invocation from python -m pridepy.pridepy to pridepy for consistency

• Formatting improvements:

  • Aligned command descriptions in the commands list for better readability
  • Removed trailing whitespace
  • Standardized command invocation format throughout examples

Notes

These changes ensure the documentation accurately reflects the current CLI interface and provides users with correct command names and usage patterns.

https://claude.ai/code/session_017TpGVPTK44DCWtaSpVHaVj

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PR Type

Documentation

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Description

• Updated CLI command list to match actual implementation

• Removed non-existent commands from help output

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

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

• Improved command list formatting with consistent alignment

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Diagram Walkthrough

flowchart LR
  A["README.md"] -->|Remove outdated commands| B["Cleaned command list"]
  A -->|Add missing commands| C["Updated command list"]
  A -->|Fix command names| D["Corrected examples"]
  A -->|Standardize invocation| E["Consistent CLI format"]
  B --> F["Accurate documentation"]
  C --> F
  D --> F
  E --> F

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File Walkthrough

Relevant files

Documentation

README.md Corrected CLI commands and formatting in README                    README.md Removed 6 non-existent commands from the help output section (get-files-by-filter, get-files-by-project-accession, get-private-files, get-projects, get-projects-by-accession) Added 3 missing commands: download-all-public-category-files, download-px-raw-files, list-private-files Updated command example from download-files-by-category to download-all-public-category-files Changed command invocation from python -m pridepy.pridepy to pridepy in two examples Improved command list formatting with consistent spacing and alignment +10/-13

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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 claude/verify-readme-cli-examples-msrYJ

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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.
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🟢	Generic: Comprehensive Audit Trails Objective: To create a detailed and reliable record of critical system actions for security analysis and compliance. Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	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
	Generic: Robust Error Handling and Edge Case Management Objective: Ensure comprehensive error handling that provides meaningful context and graceful degradation Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
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[qodo-code-review]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
General	Improve command description for clarity Update the description for the download-all-public-category-files command to clarify that it downloads files by project accession for better consistency and user understanding. README.md [52-53] + download-all-public-raw-files Download all public raw files... -+ download-all-public-category-files Download all public files of specific category... ++ download-all-public-category-files Download all public files of a specific category by project accession... [To ensure code accuracy, apply this suggestion manually] Suggestion importance[1-10]: 4 __ Why: The suggestion correctly points out that adding 'by project accession' to the command description improves clarity and consistency, as confirmed by the command's example usage in the file.	Low
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