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Merged
TaranRallings merged 72 commits into from
Dec 4, 2024
Merged

Animal - Feature/multi grid no community #538

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9b88fe0
Basic outline of an Animal Territories class.
TaranRallings Jul 10, 2024
b963654
Added methods for initialize territory, territory size, updating terr…
TaranRallings Jul 10, 2024
e988161
Revised initialize_territory to use breadth-first search.
TaranRallings Jul 11, 2024
4b64df3
Merge branch 'develop' into feature/multi_grid_occupancy
TaranRallings Jul 11, 2024
11a8326
Added a Territory protocol to avoid circular reference.
TaranRallings Jul 11, 2024
0286b62
Added calls to initialize_territory to birth, migration, and metamorp…
TaranRallings Jul 11, 2024
0e3d2a3
Changed initialize_territory to use dynamic importing.
TaranRallings Jul 11, 2024
58a32a5
Added testing for AnimalTerritory.
TaranRallings Jul 11, 2024
67e0997
Refactored initialize_territory so that bfs_territory is a stand alon…
TaranRallings Jul 12, 2024
195417b
Added test for bfs_territory.
TaranRallings Jul 12, 2024
0aa128f
Added test for initialize_territory.
TaranRallings Jul 12, 2024
49ae8bb
Merge branch 'develop' into feature/multi_grid_occupancy
TaranRallings Jul 15, 2024
54639cb
Fixed test_calculate_potential_consumed_mass.
TaranRallings Jul 15, 2024
4c7fe4c
Reworking of types and protocols.
TaranRallings Jul 16, 2024
1766d88
Updated defecate for all pools in territory.
TaranRallings Jul 16, 2024
24f0c47
Merge branch 'develop' into feature/multi_grid_occupancy
TaranRallings Jul 17, 2024
aaa75e5
Many small changes to get typing to work between files/classes. This …
TaranRallings Jul 18, 2024
4ceba3c
die_individual now calls update_carcass_pools.
TaranRallings Jul 18, 2024
bb70dfb
Updated excrete for multi-grid.
TaranRallings Jul 18, 2024
1e93fc4
Added a community.occupancy attribute to track cohorts partially in a…
TaranRallings Jul 19, 2024
a896d0f
Added abandon_communities method to animal territory.
TaranRallings Jul 19, 2024
56ee5d0
Added a reinitialize_territory method and modified migrate.
TaranRallings Jul 19, 2024
d6313bf
Updated test_animal_territories.
TaranRallings Jul 22, 2024
6798997
Updated tests for animal_cohorts.
TaranRallings Jul 23, 2024
1eba4f2
Added all_occupying_cohorts method and revised test_forage_community.
TaranRallings Jul 24, 2024
1f85190
Revised test_inflict_non_predation_mortality.
TaranRallings Jul 25, 2024
af6bb16
Fully revised test_animal_communities for multi-grid.
TaranRallings Jul 25, 2024
c68a9e7
Updated animal model tests.
TaranRallings Jul 25, 2024
81cd1f4
Finished revising all animal tests for multi grid occupancy.
TaranRallings Jul 25, 2024
5b5708d
Merge branch 'develop' into feature/multi_grid_occupancy
TaranRallings Jul 26, 2024
4dbb2d8
Added temporary solution to problem with plant data and ve_run testing.
TaranRallings Jul 26, 2024
4efee34
Added test for reinitialize territory.
TaranRallings Jul 26, 2024
a777fc2
Small docstring fix in animal communities.
TaranRallings Jul 29, 2024
fbae47b
Added a mass check on forage_cohort.
TaranRallings Jul 30, 2024
dddfa6b
Adjusted defecate docstring to fix doc build errors.
TaranRallings Jul 30, 2024
1908f0a
Modified test_generate_animal_model to deal with stochastic warnings.
TaranRallings Jul 30, 2024
8c68c14
Fixed defecate docstring bug.
TaranRallings Jul 30, 2024
b979702
Merge branch 'develop' into feature/multi_grid_occupancy
TaranRallings Aug 2, 2024
eb5064c
Small todo update in animalcohorts.
TaranRallings Aug 6, 2024
08f8559
Refactor of code such that the AnimalCommunity class is removed.
TaranRallings Aug 15, 2024
4808ec7
Removed the now-defunct AnimalCommunity class.
TaranRallings Aug 28, 2024
83cb851
Replaced set with list for tracking pools and cohorts.
TaranRallings Aug 29, 2024
ae06802
Merge branch 'develop' into feature/multi_grid_no_community
TaranRallings Aug 29, 2024
1be4309
Merge branch 'develop' into feature/multi_grid_no_community
TaranRallings Sep 10, 2024
867536f
Small updates to conftest and territories.
TaranRallings Sep 17, 2024
4af4eb6
Removed animalterritories and protocols, moved functionality into ani…
TaranRallings Sep 18, 2024
4804a01
Turns out I needed those protocols.
TaranRallings Sep 18, 2024
5f9e8e2
Fixed existing animalcohort tests.
TaranRallings Sep 19, 2024
351990f
Fixed pre-existing animal model tests.
TaranRallings Sep 27, 2024
feed6ed
New tests for migrate and migrate_community.
TaranRallings Sep 27, 2024
62ec1c2
Revised birth and birth testing.
TaranRallings Sep 27, 2024
2fc6a1d
Small modification to forage_community, tests for birth community and…
TaranRallings Sep 30, 2024
6ee1a7b
Testing for metamorphose.
TaranRallings Sep 30, 2024
d4df50f
Updated a number of animal data fixtures for currently abiotic struct…
TaranRallings Oct 3, 2024
a1af08a
Worked recent decay pool updates into refactor with no community.
TaranRallings Oct 4, 2024
8e5227f
Updated animal tests for new decay functionality.
TaranRallings Oct 4, 2024
ff0f939
Further integration of decay module updates into multi-grid format.
TaranRallings Oct 11, 2024
4c9c76e
Integrated new decay methods to animal model and cleaned up related t…
TaranRallings Oct 24, 2024
7c12452
Updated cohort herbivory methods for new herbivorywaste pools.
TaranRallings Oct 25, 2024
cc1e8ad
Finished revising AnimalCohort tests.
TaranRallings Oct 28, 2024
c071d86
Fixed plant resource test.
TaranRallings Oct 28, 2024
af5357d
Merge of develop and multi-grid refactor.
TaranRallings Oct 30, 2024
7539d4b
Merge branch 'refactor-merge' into feature/multi_grid_no_community
TaranRallings Oct 30, 2024
b472681
Updating docs for no community.
TaranRallings Oct 30, 2024
a20df22
Updating docs for no community p2.
TaranRallings Oct 30, 2024
4b337ae
Docstring fixes - bad indentation in Args sections
davidorme Oct 30, 2024
d343841
Fixing sphinx issues. Odd ones: uuid.UUID not being resolved, AnimalM…
davidorme Oct 30, 2024
5c0c3e5
Merge branch 'develop' into feature/multi_grid_no_community
TaranRallings Dec 3, 2024
d9f598b
Removed input_partition.py as it was no longer in use.
TaranRallings Dec 3, 2024
1bed87b
Added helper functions to reset the decomposed components of the carc…
jacobcook1995 Dec 3, 2024
509f7d7
Removed vestigal damuths law in AnimalCohort.
TaranRallings Dec 3, 2024
f46162a
Merge branch 'feature/multi_grid_no_community' of https://github.com/…
TaranRallings Dec 3, 2024
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2 changes: 0 additions & 2 deletions docs/source/_toc.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -147,8 +147,6 @@ subtrees:
entries:
- file: api/models/animal/animal_cohorts
title: The animal_cohorts submodule
- file: api/models/animal/animal_communities
title: The animal_communities submodule
- file: api/models/animal/animal_model
title: The animal_model submodule
- file: api/models/animal/animal_traits
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33 changes: 0 additions & 33 deletions docs/source/api/models/animal/animal_communities.md
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2 changes: 1 addition & 1 deletion docs/source/api/models/animal/animal_model.md
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Expand Up @@ -30,5 +30,5 @@ language_info:
.. automodule:: virtual_ecosystem.models.animal.animal_model
:autosummary:
:members:
:exclude-members: model_name
:exclude-members: model_name, random
```
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