landlab / landlab / 6515 / 3
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component to model species evolution (#1065)

* First commit

* species tracked by identifiers

* Added plot_trees function for phylogenetics

* renamed seamless folder and file, incorporated species class

* componentized seamless

* tree troubleshotting print statements added

* species range is now tracked in species class

* species handles updating range

* added plot_species_range

* get_species_by_identifier fixed to set input as uuid

* update imported modules

* added stream_species as a subclass of species

* modified area captured calculation

* implemented habitat patches

* begun patches in run_one_step

* Habitat processing added to BiotaEvolver run_one_step

* habitat patches now tracked by vector objects

* improvements to tree plot

* parent species added at Species attribute

* species ids change to tuples from uuids

* tree plots by new clade ids

* biota_evolver record subclassed to dict

* habitat patch adds capture count to be record

* function to calc E/MSY

* function to get species array count

* data stored in pandas dataframes

* corrected error in get_surviving_species function

* update record code in E/MSY function

* update species array func for pandas

* species object outputs dictionary

* species DataFrame record extinction time

* fixed issues leading to SettingWithCopyWarnings

* removed old tree plots

* removed remaining habitat files

* remove erroneous zone additions

* new record append function

* species evolved by subtype

* species_with_identifier dynamically infers identifier element type

* BiotaEvolver renamed as SpeciesEvolver

* species and zone at time return data frames

* introducing species automatically determines intro time

* macroevolution renamed to evolution

* zone threshold set by input

* dataframe set as property of record

* main record collection functions added

* added docstring examples to get... (continued)

15854 of 18836 relevant lines covered (84.17%)

0.84 hits per line

Source Files on job 6515.3 (CONDA_ENV=3.7)