Happy New Year 2023 Release

3.8

Enhancement:

• A new type was introduced in 3.7 (announcement has been forgotten): a vhighlight to be able to hightlight a whole region across all tracks.
• Much more parameters for vhighlight and vlines
  • 'zorder' to set it on top or behind.
  • 'line_width', 'color', 'alpha', 'border_color' for vhighlight and 'line_style' for vlines
• You can now set multiple vlines
• For gtf, the output of make_tracks_file set prefered_name to gene_name instead of transcript_name.

Bugfix:

• Support mcool files for hic_matrix_square. This solves #404
• Works with gffutils version 0.11.0 where ValueError became gffutils.exceptions.EmptyInputError for empty gtf.
• The installation instructions have been updated
• Fixed a small bug in links track with "use_middle" enabled, where midpoints could have different ordering than start points (Thanks to @Jeff1995 ).
• Fix a bug when plotting gtf in the middle of a large intron.
• Fix plot genes with orientation = inverted
• Support Numpy 1.24, drop support below 1.20

Relax version control on matplotlib:

• Any version of matplotlib from 3.1.1 to 3.6.2 is now accepted.