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Merged
dweindl merged 12 commits into from
Mar 13, 2025
Merged

v2: Observable/conditions/experiments/... objects #345

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3c4f7ff
observables
dweindl Dec 16, 2024
3d61574
conditions
dweindl Dec 16, 2024
5c5aa5c
getitem
dweindl Dec 19, 2024
70f283e
Measurements
dweindl Dec 19, 2024
e2a98d3
mapping,parameters
dweindl Dec 19, 2024
b1ed794
store ids
dweindl Dec 20, 2024
53e0d8a
..
dweindl Dec 20, 2024
fd2b372
single condition per timepoint
dweindl Mar 12, 2025
10502bd
Add operators
dweindl Mar 12, 2025
35e4098
valueType/operationType
dweindl Mar 12, 2025
ac77767
Apply suggestions from code review
dweindl Mar 12, 2025
7e021ce
..
dweindl Mar 12, 2025
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27 changes: 10 additions & 17 deletions petab/v2/C.py
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Original file line number Diff line number Diff line change
Expand Up @@ -130,30 +130,23 @@
CONDITION_NAME = "conditionName"
#: Column in the condition table with the ID of an entity that is changed
TARGET_ID = "targetId"
#: Column in the condition table with the type of value that is changed
VALUE_TYPE = "valueType"
#: Column in the condition table with the operation type
OPERATION_TYPE = "operationType"
#: Column in the condition table with the new value of the target entity
TARGET_VALUE = "targetValue"
# value types:
VT_CONSTANT = "constant"
VT_INITIAL = "initial"
VT_RATE = "rate"
VT_ASSIGNMENT = "assignment"
VT_RELATIVE_RATE = "relativeRate"
VT_RELATIVE_ASSIGNMENT = "relativeAssignment"
VALUE_TYPES = [
VT_CONSTANT,
VT_INITIAL,
VT_RATE,
VT_ASSIGNMENT,
VT_RELATIVE_RATE,
VT_RELATIVE_ASSIGNMENT,
# operation types:
OT_CUR_VAL = "setCurrentValue"
OT_NO_CHANGE = "noChange"
Comment on lines +138 to +139
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@dilpath dilpath Mar 12, 2025

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Other constants in C.py are not shortened, so could stick to that "convention". To reduce the length, OT/OPERATION_TYPE could be dropped from the start of the name, since I don't think we have that style elsewhere either.

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@dweindl dweindl Mar 12, 2025

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I would prefer introducing prefixes elsewhere than dropping them. I find that this makes it clearer where they belong.

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@dweindl dweindl Mar 12, 2025

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Also fine to completely replace them by enums.

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@dweindl dweindl Mar 13, 2025

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I'll leave it for now, as there is a good chance that "operation types" will be dropped completely


OPERATION_TYPES = [
OT_CUR_VAL,
OT_NO_CHANGE,
]

CONDITION_DF_COLS = [
CONDITION_ID,
TARGET_ID,
VALUE_TYPE,
OPERATION_TYPE,
TARGET_VALUE,
]

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