v0.3.0

Fixed

• The ttl command-line tool now correctly capitalizes matching positions when the reverse complement is the best alignment. Previously, minus-strand matches were displayed against the forward consensus, so every aligned position appeared as a lower-case mismatch even for a perfect match.
• _run_tomtom exits gracefully with a message when no hits fall at or below the p-value threshold instead of crashing on an empty max(...).
• fimo(..., dim=1) no longer raises a pandas FutureWarning when some sequences have no hits, and returns an empty list when there are no hits at all.
• Corrected the one_hot_encode docstring to document that it accepts a string (not a list of characters).

Changed

• Bumped supported dependency versions (numpy, and others) and refreshed the packaging configuration.

Added

• Greatly expanded the unit test suite across fimo, tomtom, symmetric_tomtom, io, utils, and the CLI, including edge cases, error paths, and regression coverage for the alignment display (substitutions, shifts, and overhangs on both strands).