next steps

[marco-mariotti]

Small edits

• all imports in docs should look like: import pyrangeyes as pe and fitting with this (e.g. pe.plot(...))
• height_col, depth_col, shape_col: move to last args shown in docstring of plot()
• pe.adapters alone should return a nice string derived from pe.adapters.describe(), plus some message (e.g. see print_options('mRNA') ... )
• remove thick_cds arg (adapter mRNA works!)
• text as possible key of colormap

Big objectives

• add reverse=.. argument to reverse (coords: from big to small) all plots [True], or none [False], or some ['chr1', 'chr2'] ..also accepted: {'chr1':True, 'chr2':True}, or only those chromosome/regions wherein all intervals are on the negative strand ['auto'] -> default.
• controllable height and width, compatible with rendering in jupyter or floating window. briefly: must have a way to have a nice UX, sometimes size goes out of control
• density/bigwig like visualization

Debug

• packed mode is still buggy. it may be a more difficult problem than anticipated. The function must know more than it does?
• .browse()

Human

• test + update tutorial, add images

[ginitheclaw]

Solved items from this checklist:

• Docs/import examples now use import pyrangeyes as pe and pe.plot(...) style.
• height_col, depth_col, and shape_col were moved to the end of the plot() docstring argument list.
• pe.adapters now renders a friendly summary derived from pe.adapters.describe(), with guidance toward adapter options such as pe.print_options('mRNA').
• The public thick_cds plot argument was removed; adapter='mRNA' is the intended path.
• text is now supported as a colormap channel, alongside text_color_col / fixed text_color behavior.

These landed in v0.3.7 via #34 and v0.3.8 via #37:

• chore: remove thick_cds and polish adapter docs #34
• Simplify text labels and map text colors #37

[ginitheclaw]

Reminder from current showcase review: tooltips are hard to showcase because they only appear on mouse hover. We should keep this in mind for a later docs/demo pass, possibly by adding a static/screenshot workaround (e.g. programmatic hover capture, annotated screenshot, or an explicit tooltip example cell) rather than trying to show them in the normal static gallery.