Some updates for efficiency

[dsfulf]

Updates for streamlining and efficiency.

I've altered some things to reduce the verbosity of the code required to use Daft.

1. Pass through of parameters when using add_node() and add_plate() to automatically define the class so that the use of the two is matched to add_edge(). Maintains compatibility with existing code by checking if first parameter is the class instead of the first parameter passed to the class.
2. Fixed Plate() class kwargs -> plot_params.
3. Added kwarg to set linewidth for Plate() class rectangle object.
4. Set default face color of bbox to 'None' as opposed to matplotlib default of cyan (meaning it nearly always had to be specified because cyan is likely a terrible choice).
5. Added parameter to add_plate() and Plate() class to set fontsize.
6. Added parameter to add_node() and Node() class to set fontsize. This already existed in label_params but was done for consistency with add_plate() and Plate().
7. Wrapped pgm.render() in new function pgm.show() to add a plt.show() call. pgm.figure.savefig() still works after pgm.show().

Both sets of code below still function properly, but the proposed changes simplify things somewhat.

Example #1 before changes:

#105  Instantiate the PGM.
pgm = daft.PGM([2.3, 2.05], origin=[0.3, 0.3])

# Hierarchical parameters.
pgm.add_node(daft.Node("alpha", r"$\alpha$", 0.5, 2, fixed=True))
pgm.add_node(daft.Node("beta", r"$\beta$", 1.5, 2))

# Latent variable.
pgm.add_node(daft.Node("w", r"$w_n$", 1, 1))

# Data.
pgm.add_node(daft.Node("x", r"$x_n$", 2, 1, observed=True))

# Add in the edges.
pgm.add_edge("alpha", "beta")
pgm.add_edge("beta", "w")
pgm.add_edge("w", "x")
pgm.add_edge("beta", "x")

# And a plate.
pgm.add_plate(daft.Plate([0.5, 0.5, 2, 1], label=r"$n = 1, \cdots, N$",
    shift=-0.1))

# Render and save.
pgm.render()

Example #1 after changes:

# Instantiate the PGM.
pgm = daft.PGM([2.3, 2.05], origin=[0.3, 0.3])

# Hierarchical parameters.
pgm.add_node("alpha", r"$\alpha$", 0.5, 2, fixed=True)
pgm.add_node("beta", r"$\beta$", 1.5, 2,)

# Latent variable.
pgm.add_node("w", r"$w_n$", 1, 1,)

# Data.
pgm.add_node("x", r"$x_n$", 2, 1, observed=True)

# Add in the edges.
pgm.add_edge("alpha", "beta")
pgm.add_edge("beta", "w")
pgm.add_edge("w", "x")
pgm.add_edge("beta", "x")

# And a plate.
pgm.add_plate([0.5, 0.5, 2, 1], label=r"$n = 1, \cdots, N$",
    shift=-0.1,)

# Render and save.
pgm.show()

[davidwhogg]

@dfm comments?

[dsfulf]

I've made some additional updates to automatically determine figure origin and shape.

A daft.PGM() class can be created just by:

pgm = daft.PGM()

[dsfulf]

I added some additional options for setting the DPI of the displayed figure, and made a wrapper for plt.savefig() that correct the default margin setting so it does not lop off the top of a figure that has been tightly spaced with the auto-sizing routine.

The DPI does not override the matplotlib backend, and can be set either on the PGM class instantiation, or in pgm.render(), pgm.show(), and the new pgm.savefig().

[davidwhogg]

Did you update the documentation and examples so that they all still run?

[dsfulf]

Yes. There were a couple of corrections to the examples, but nothing related to anything I've changed.

1. Use of float division rather than integer division in Python 3.* in recursive.py
2. A string did not have backslashes escaped in thicklines.py

I have not changed any other examples because it is not necessary. They could be updated to reflect that the shape and origin parameters are not required any longer. I have verified that everything looks exactly the same when these are not provided.

There is a minor detail of the "magic number" used to offset X-coord for the fixed=True parameter in PGM.Node that needs to be adjusted when the figure is auto-sized. I am unable to determine why, and suspect it is internal to matplotlib. I've put in a correction for this case and the examples, specifically yike.py that has 3 fixed nodes, all seem to display identically.

[dsfulf]

@dfm @davidwhogg Any hurdles to pass to merge this?

[dfm]

This looks awesome! Thanks.