bug fixing FTP url

[ypriverol]

PR Type

bug_fix, documentation

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Description

• Fixed the FTP URL in the Files class by removing the 'ftp://' prefix.
• Updated the README to use a variable for the version in the installation command.
• Corrected a minor formatting issue in the README note regarding globus URLs.

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Changes walkthrough 📝

	Relevant files
Bug fix	files.py Fix FTP URL in Files class                                                              pridepy/files/files.py Corrected the FTP URL by removing the 'ftp://' prefix. +1/-1
Documentation	README.md Update installation command and fix formatting                      README.md Updated installation command to use a variable for version. Fixed minor formatting issue in a note. +2/-2

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⚡ Recommended focus areas for review Potential Bug The removal of 'ftp://' prefix from PRIDE_ARCHIVE_FTP might cause issues if the variable is used in code that expects a full URL. Documentation Improvement The installation command now uses a placeholder {version}, which might confuse users if not explained.

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PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Score
Enhancement	Provide a concrete way to determine the package version for installation Replace the placeholder {version} with an actual version number or provide instructions on how to determine the correct version number to use. README.md [35] -$ pip install dist/pridepy-{version}.tar.gz +$ pip install dist/pridepy-$(python setup.py --version).tar.gz Apply this suggestion Suggestion importance[1-10]: 8 Why: This suggestion enhances usability by providing a clear method to determine the package version, reducing potential confusion during installation.	8
	✅ Provide more context about the use of HTTPS instead of the Globus protocol Consider adding a brief explanation or link to documentation about the Globus protocol and why HTTPS is used instead. This would provide more context for users who might be unfamiliar with Globus. README.md [58] ->**NOTE**: Currently we use globus urls (when -p globus is used) via https not globus protocol. +>**NOTE**: Currently we use Globus URLs (when `-p globus` is used) via HTTPS, not the Globus protocol. For more information about Globus, see [Globus documentation](https://www.globus.org/data-transfer). [Suggestion has been applied] Suggestion importance[1-10]: 7 Why: Adding context and a link to the Globus documentation helps users understand the choice of protocol, improving the documentation's clarity and usefulness.	7
Maintainability	Use a constant for the FTP protocol to improve maintainability Consider using a constant or configuration variable for the FTP protocol. This allows for easier management if the protocol needs to be changed in the future, and improves code readability. pridepy/files/files.py [55] -PRIDE_ARCHIVE_FTP = "ftp.pride.ebi.ac.uk" +FTP_PROTOCOL = "ftp" +PRIDE_ARCHIVE_FTP = f"{FTP_PROTOCOL}.pride.ebi.ac.uk" Apply this suggestion Suggestion importance[1-10]: 5 Why: The suggestion to use a constant for the FTP protocol improves maintainability and readability, but it is not critical since the protocol is unlikely to change frequently.	5

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