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CARCADE refactor into v3 #101

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CARCADE refactor into v3 #101

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@allison-li-1016 allison-li-1016 commented Nov 15, 2024 •
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allison-li-1016 and others added 30 commits October 23, 2023 14:13
@allison-li-1016
adding new cell states to enum + add tests for enum interface
5476c24
@allison-li-1016
move step() down to TissueCell
7ddfb2c
@allison-li-1016
move state fractions down from PatchCell to TissueCell
925ab28
@allison-li-1016
IN PROGRESS adding CART cell class
fac3611
@allison-li-1016
making patchCARTCell an abstract class
bbe57e0
@allison-li-1016
implementing CART class, CARTCD4 class, added antigen binding to enum…
773175b 
…s and enum tests
@allison-li-1016
implemented bindTarget function
b588f78
@allison-li-1016
adding PatchCellCARTCD8 subclass
6d1dd0a
@allison-li-1016
adding comments
ba7c3bf
@allison-li-1016
added some comments
bf6e61a
@allison-li-1016
Merge branch 'develop' into allison/carcade-refactor
b37a7d8 
alskdlskjdlajd
@allison-li-1016
adding new tests
6724768
@allison-li-1016
temp add of inflammation module, in help of casting issues
6e7c491
@allison-li-1016
added kill process
6576ea8
Merge remote-tracking branch 'origin/develop' into allison/carcade-re…
dc5b8e7 
…factor

include newest patch updates into refactor
initial CART agent refactoring file push
ec2cdae
initial Inflammation module refactorization file push
06ffa1f
including CART agent tags for default CART agent and module parameter…
0552a45 
… values
adding IL2 layers into env
3b7a882
adding in treat action from CARCADE helper options
450f66b
adding treat module
566a23a
adding CART cell killing and reseting rule edits
4aba068
changing kill scheduling functionality
12cd23c
changing reset action scheduling functionalities
eda1b22
editing CART metabolism stepping rules
85ee85b
changing inflammation rules
5db7439
adding antigen and target parameters in patch cells
fd177cc
adding CAR-T specific parameters to parameter file
b6b76cb
post merge with develop branch
1200b20
debugging CART metabolism
691a540
@allison-li-1016
adding CART cell tests
1a9e7ed
@allison-li-1016
adding cell
6a3f6be
@allison-li-1016
Merge branch 'allison/carcade-refactor' of https://github.com/bagheri…
98e081f 
…lab/ARCADE into allison/carcade-refactor
@allison-li-1016
applying linting
a86a860
@allison-li-1016
testing git access
2fea3ea
@allison-li-1016
testing git again
47bb54a
@allison-li-1016
I am once again, testing git
82c4e37
@allison-li-1016
editing test for edge case
485cdb3
@allison-li-1016
writing java documentation for T cell agents
dcac9d0
@allison-li-1016
fixing documentation for these classes
b76be6a
@allison-li-1016
adding testing specific methods to access field values
b0b31d3
@allison-li-1016
adding metabolism tests for CART cells
edd42cb
@allison-li-1016
adding cd8 inflammation module tests
36a9c65
@allison-li-1016
update array size in inflammation cd8 tests
6d27509
@allison-li-1016
adding update process tests to CART metabolism
f599061
@allison-li-1016
adding additional accessor method for testing purposes
b240171
@allison-li-1016
adding cd4 inflammation tests
7bf29da
@allison-li-1016
adding tests for inflammation, treat, kill
e64eeff
@allison-li-1016
updating inflammation documentation, adding unit tests for inflammati…
4cb5faa 
…on class
@allison-li-1016
updating documentation for reset action, adding unit tests for reset …
8d6428f 
…action:
@allison-li-1016
updating documentation for kill action, adding unit tests for kill ac…
08527d8 
…tion:
@allison-li-1016
updating documentation, swapping out comparisons for object safe equa…
68e1e91 
…lity methods
@allison-li-1016
merge new changes from main
7b1d638
@allison-li-1016
adding in cell age death to T cells
4b090e3
@allison-li-1016
adding new parameters: cell death age and max confluency
93d3303
@allison-li-1016
changing T cell tests to accomodate for cell death due to age
0413b6c
@allison-li-1016
updating treat documentation, adding unit tests for treat class
7a0f2df
@allison-li-1016
had to change the subclass because of step() refactoring from PatchCell
3fde90e
@allison-li-1016
edit confluency limit
e741e78
@allison-li-1016
changing test structure after editing confluency limitation in treat …
c1bbf59 
…class
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Integrate CARCADE into v3
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