`annotate` needs a `num_chromosomes` argument

[petrelharp]

As pointed out on SLiM-discuss, right now using annotate for a multichromosome set-up with more than 8 chromosomes fails when reading into SLiM with the error

ERROR (Species::__TabulateSubpopulationsFromTreeSequence): unexpected node metadata length; this file cannot be read.

The reason is that the node metadata length increases with every 8 chromosomes, because of how vacancy is recorded.

The problem is that annotate_tables calls set_metadata_schema, which accepts the num_chromosomes arguments... but annotate_tables itself does not.

Here is a workaround, that demonstrates setting the top-level metadata
and node table metadata appropriately for a multichromosome simulation
(warning: this is NOT tested beyond verifying it runs!):

import msprime, pyslim, tskit

num_chroms = 10

big_ts = msprime.sim_ancestry(1, sequence_length=num_chroms)

tslist = [big_ts.keep_intervals([[k, k+1]]).trim() for k in range(num_chroms)]

top_md = pyslim.default_slim_metadata('tree_sequence')['SLiM']
chrom_md = top_md['this_chromosome']
chrom_md_list = []
for k in range(num_chroms):
    chrom_md.update({'id': k+1, 'index': k})
    chrom_md_list.append(chrom_md)

for k in range(num_chroms):
    ts = tslist[k]
    t = tslist[0].dump_tables()
    pyslim.annotate_tables(t, model_type='nonWF', tick=1)

    md = t.metadata
    md['SLiM']['chromosomes'] = chrom_md_list
    md['SLiM']['this_chromosome'] = chrom_md_list[k]
    t.metadata = md

    t.nodes.clear()
    t.nodes.metadata_schema = pyslim.slim_node_metadata_schema(num_chroms)
    for n in ts.nodes():
        md = pyslim.default_slim_metadata('node', num_chromosomes=num_chroms)
        t.nodes.append(n.replace(metadata=md))

    tslist[k] = t.tree_sequence()

# next, write out the tree sequences

This was actually kinda intentional: we have thus far provided no support for writing out multichromosome trees archives from pyslim, but the lack of the argument to annotate makes it extra hard.

Note: The "metadata" page's description for nodes in the docs needs to be updated as well.