gk-nodes script mode

[manauref]

This commit improves the storage of data and plot handles so that when gk-nodes is used from a python script one has greater control over the plot, allowing the python script to manipulate the data or the plot.

For example, here's an example where we extract the nodes data and separately resize the figure

  #[ Create a click context (needed to call pgkyl command).
  ctx = click.core.Context(cli)
  ctx.obj = {}
  ctx.obj["data"] = pg.commands.DataSpace()
  ctx.obj["verbose"] = False

  ctx.invoke(pg.commands.gk_nodes, name=sim_name, path=data_dir, wall_file=wall_coords,
    psi_file=psi_pol, contour=psi_contour, cnlevels=psi_contour_num_levels, no_show=True)

  #[ Nodes data.
  nodes = ctx.obj["data"].get_dataset(tag="nodes",idx=0)
  nodes_majorR = nodes.get_grid()
  nodes_vertZ = nodes.get_values()

  #[ Resize figure:
  plot_h = ctx.obj["plot_handles"]
  fig_h = plot_h["figure"]
  fig_width, fig_height = fig_h.get_size_inches() #[ In inches.
  fig_h.set_size_inches(fig_width*0.85, fig_height*0.9)

We also fixed:

• the y label from R (z) to Z (m).
• an error in collect due to the way we checked for the key period in the context. Also made that change elsewhere.