Geonomics

Corrected and clarified documentation for 'rand_genarch' parameter, and added assert statement to make sure that the number of rows in a custom genomic architecture file matches the genome length stipulated in the parameters file. Clarified documentation for 'msprime' parameters block in Species 'init' parameters. Fixed implementation of 'msprime' init parameters so that burn-in is now short-circuited (since the burnt-in population would be entirely replaced by the msprime-derived individuals anyhow).

Added new functionality to the package to remove any number of Individuals from a Species (`Model.remove_individuals`), and to add any number of Individuals to a Species (`Model.add_individuals`) by either pulling them from another Species object or simulating them with msprime (`gnx.sim_msprime_individuals`). Along with this, also added a new, optional section to the species 'init' section of the parameters file (keyed to 'msprime') which provides parameters for simulating any number of Individuals from any number of msprime populations and placing them at specified coordinates on the Landscape (replacing the gnx-simulated starting population). (Also added a convenience method, `Model.burn`, to burn in a Model, because I was getting annoyed having to type something like `Model.walk(10000, 'burn')`.)

fixed the plot_allele_frequency plot to show a basic line plot again (so that it can better depict linkage blocks)

fixed error in mod.plot_allele_frequencies stemming from integration of tskit; also tried to delete dual_mode_debug_helper_fns.py from package build

add an `n_pcs` arg to `Model.plot_genetic_PCA()`, allowing for colorblind-friendly visualizations of the top 1 and 2 PCs

Fixed bug that made recorded population size and population-data filesize differ for a given time step.