Standardize CLI flags to use hyphens instead of underscores

[Copilot]

The CLI interface had inconsistent flag naming—some used hyphens (--skip-if-downloaded-already) while others used underscores (--output_folder, --aspera_maximum_bandwidth).

Changes

• CLI flags: Converted all multi-word options to use hyphens consistently:

  • --output_folder → --output-folder
  • --file_name → --file-name
  • --aspera_maximum_bandwidth → --aspera-maximum-bandwidth
  • --checksum_check → --checksum-check
  • --output_file → --output-file
  • --page_size → --page-size
  • --sort_direction → --sort-direction
  • --sort_fields → --sort-fields

• Documentation: Updated README examples to reflect hyphenated flags

Example

# Before
pridepy download-all-public-raw-files -a PXD012353 -o /path/ --aspera_maximum_bandwidth 100M

# After
pridepy download-all-public-raw-files -a PXD012353 -o /path/ --aspera-maximum-bandwidth 100M

Note: Python function parameters remain unchanged (underscored) as Click automatically converts hyphens to underscores for internal use.

---

💬 We'd love your input! Share your thoughts on Copilot coding agent in our 2 minute survey.

[coderabbitai]

Important

Review skipped

Bot user detected.

To trigger a single review, invoke the @coderabbitai review command.

You can disable this status message by setting the reviews.review_status to false in the CodeRabbit configuration file.

---

_{Comment @coderabbitai help to get the list of available commands and usage tips.}

[qodo-code-review]

PR Code Suggestions ✨

No code suggestions found for the PR.