[JAlvarezJarreta]

Additional changes:

• Moved the requirements.txt file to the root of the repository as this is the most standard approach in Python repositories
• REdat (mipsREdat_9.3p) is no longer downloadable, so have removed it from the Makefile with a message
• Upgraded repeats scripts to work with Python 3.12 and SQLAlchemy 2.0.52+
  • Note: These changes have been provided by Claude and reviewed and tested by me
• Added .gitignore file to avoid adding software or test files by mistake
• Updated g++ to v16 as v10 is getting old and was causing trouble for the CI pipeline
  • Tested v16 to compile Red and minimap2 and worked without issues

[eead-csic-compbio]

Will have a look next week @JAlvarezJarreta

[eead-csic-compbio]

We might have to think about warning potential users that some parts of this code depend on the archived old Ensembl site