Release 3.8

[lldelisle]

Potential release text:

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 Support for mcool files with hic_matrix_square #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.

[LeilyR]

@lldelisle thanks!

[lldelisle]

Maybe it is better to wait for open2c/cooler#303 before rerunning the CI and releasing...

[lldelisle]

There is a new build for cooler but the CI does not use it... I will wait for Monday.

[lldelisle]

It seems that mamba does not want to use the last build except if we specify numpy >=1.16, <1.24... Do you think we should write it into the dependencies?

[lldelisle]

I need to update HiCMatrix before we merge it.