Convert skip_if_downloaded_already to a boolean flag

[Copilot]

The -skip option required explicitly passing true or false values, unlike other boolean flags in the CLI (e.g., --checksum_check).

Changes

• Converted -skip/--skip_if_downloaded_already to --skip-if-downloaded-already/--no-skip-if-downloaded-already using Click's is_flag=True
• Applied to all four download commands: download-all-public-raw-files, download-all-public-category-files, download-file-by-name, download-px-raw-files
• Updated README documentation
• Standardized help text across commands

Usage

Before:

pridepy download-all-public-raw-files -a PXD012353 -o /path/ -skip true

After:

# Default: skip existing files
pridepy download-all-public-raw-files -a PXD012353 -o /path/

# Force re-download
pridepy download-all-public-raw-files -a PXD012353 -o /path/ --no-skip-if-downloaded-already

Default behavior unchanged: files are skipped if already downloaded.

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• proteomecentral.proteomexchange.org
  • Triggering command: /usr/bin/python3 python3 (dns block)
• www.ebi.ac.uk
  • Triggering command: /usr/bin/python3 python3 -m pytest pridepy/tests/test_raw_files.py -v (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

Original prompt

On pridepy.py, Can you make this @click.option(
"-skip",
"--skip_if_downloaded_already",
required=False,
default=True,
help="Boolean value to skip the download if the file has already been downloaded.",
) a flag, currelty we have to pass true or false, every time we used it.

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