1.4.6

Fixed the nlmpy error I had created by moving the 'module not avail' error inside the only function that uses nlmpy but forgetting to move the import statement there too.

1.4.5

Fixes a bug in species._plot_movement_or_dispersal that accidentally set movement_distr_param2 to the value of movement_distr_param1

1.4.4

Added plot_movement() and plot_dispersal() methods to the Model object, to help with visual design and debugging of sims.

1.4.3

Fixes some minor bugs and better handles when Species._remove_individuals() does and does not print out information.

1.4.2

Debugged so that gnx can now row models with rectangular landscapes (checked by plotting genetic PCA for randomly generated landscape, plotting genetic PCA for a raster-loaded landscape with an msprime-initiated population, and plotting phenotypes for raster-loaded landscape with selection). Also debugged burn-in for msprime-initiated species, which were still needlessly running one burn-in timestep before dumping and replacing individuals. Also made some other minor tweaks along the way (see commits).

1.4.1

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).

1.4.0

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').)

1.3.14

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

1.3.13

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

1.3.12

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