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PaulJonasJostPaulJonasJost
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Amibguous imprt in C.py of constants
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‎src/petab_gui/C.py‎

Lines changed: 134 additions & 92 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
"""Constants for the PEtab edit GUI."""
22

33
import numpy as np
4-
import petab.v1.C as C
4+
import petab.v1.C as PETAB_C
55

66
#: Application name
77
APP_NAME = "PEtab-GUI"
@@ -12,79 +12,94 @@
1212

1313
COLUMNS = {
1414
"measurement": {
15-
C.OBSERVABLE_ID: {"type": np.object_, "optional": False},
16-
C.PREEQUILIBRATION_CONDITION_ID: {
15+
PETAB_C.OBSERVABLE_ID: {"type": np.object_, "optional": False},
16+
PETAB_C.PREEQUILIBRATION_CONDITION_ID: {
1717
"type": np.object_,
1818
"optional": True,
1919
},
20-
C.SIMULATION_CONDITION_ID: {"type": np.object_, "optional": False},
21-
C.TIME: {"type": np.float64, "optional": False},
22-
C.MEASUREMENT: {"type": np.float64, "optional": False},
23-
C.OBSERVABLE_PARAMETERS: {"type": np.object_, "optional": True},
24-
C.NOISE_PARAMETERS: {"type": np.object_, "optional": True},
25-
C.DATASET_ID: {"type": np.object_, "optional": True},
26-
C.REPLICATE_ID: {"type": np.object_, "optional": True},
20+
PETAB_C.SIMULATION_CONDITION_ID: {
21+
"type": np.object_,
22+
"optional": False,
23+
},
24+
PETAB_C.TIME: {"type": np.float64, "optional": False},
25+
PETAB_C.MEASUREMENT: {"type": np.float64, "optional": False},
26+
PETAB_C.OBSERVABLE_PARAMETERS: {"type": np.object_, "optional": True},
27+
PETAB_C.NOISE_PARAMETERS: {"type": np.object_, "optional": True},
28+
PETAB_C.DATASET_ID: {"type": np.object_, "optional": True},
29+
PETAB_C.REPLICATE_ID: {"type": np.object_, "optional": True},
2730
},
2831
"simulation": {
29-
C.OBSERVABLE_ID: {"type": np.object_, "optional": False},
30-
C.PREEQUILIBRATION_CONDITION_ID: {
32+
PETAB_C.OBSERVABLE_ID: {"type": np.object_, "optional": False},
33+
PETAB_C.PREEQUILIBRATION_CONDITION_ID: {
3134
"type": np.object_,
3235
"optional": True,
3336
},
34-
C.SIMULATION_CONDITION_ID: {"type": np.object_, "optional": False},
35-
C.TIME: {"type": np.float64, "optional": False},
36-
C.SIMULATION: {"type": np.float64, "optional": False},
37-
C.OBSERVABLE_PARAMETERS: {"type": np.object_, "optional": True},
38-
C.NOISE_PARAMETERS: {"type": np.object_, "optional": True},
39-
C.DATASET_ID: {"type": np.object_, "optional": True},
40-
C.REPLICATE_ID: {"type": np.object_, "optional": True},
37+
PETAB_C.SIMULATION_CONDITION_ID: {
38+
"type": np.object_,
39+
"optional": False,
40+
},
41+
PETAB_C.TIME: {"type": np.float64, "optional": False},
42+
PETAB_C.SIMULATION: {"type": np.float64, "optional": False},
43+
PETAB_C.OBSERVABLE_PARAMETERS: {"type": np.object_, "optional": True},
44+
PETAB_C.NOISE_PARAMETERS: {"type": np.object_, "optional": True},
45+
PETAB_C.DATASET_ID: {"type": np.object_, "optional": True},
46+
PETAB_C.REPLICATE_ID: {"type": np.object_, "optional": True},
4147
},
4248
"observable": {
43-
C.OBSERVABLE_ID: {"type": np.object_, "optional": False},
44-
C.OBSERVABLE_NAME: {"type": np.object_, "optional": True},
45-
C.OBSERVABLE_FORMULA: {"type": np.object_, "optional": False},
46-
C.OBSERVABLE_TRANSFORMATION: {"type": np.object_, "optional": True},
47-
C.NOISE_FORMULA: {"type": np.object_, "optional": False},
48-
C.NOISE_DISTRIBUTION: {"type": np.object_, "optional": True},
49+
PETAB_C.OBSERVABLE_ID: {"type": np.object_, "optional": False},
50+
PETAB_C.OBSERVABLE_NAME: {"type": np.object_, "optional": True},
51+
PETAB_C.OBSERVABLE_FORMULA: {"type": np.object_, "optional": False},
52+
PETAB_C.OBSERVABLE_TRANSFORMATION: {
53+
"type": np.object_,
54+
"optional": True,
55+
},
56+
PETAB_C.NOISE_FORMULA: {"type": np.object_, "optional": False},
57+
PETAB_C.NOISE_DISTRIBUTION: {"type": np.object_, "optional": True},
4958
},
5059
"parameter": {
51-
C.PARAMETER_ID: {"type": np.object_, "optional": False},
52-
C.PARAMETER_NAME: {"type": np.object_, "optional": True},
53-
C.PARAMETER_SCALE: {"type": np.object_, "optional": False},
54-
C.LOWER_BOUND: {"type": np.float64, "optional": False},
55-
C.UPPER_BOUND: {"type": np.float64, "optional": False},
56-
C.NOMINAL_VALUE: {"type": np.float64, "optional": False},
57-
C.ESTIMATE: {"type": np.object_, "optional": False},
58-
C.INITIALIZATION_PRIOR_TYPE: {"type": np.object_, "optional": True},
59-
C.INITIALIZATION_PRIOR_PARAMETERS: {
60+
PETAB_C.PARAMETER_ID: {"type": np.object_, "optional": False},
61+
PETAB_C.PARAMETER_NAME: {"type": np.object_, "optional": True},
62+
PETAB_C.PARAMETER_SCALE: {"type": np.object_, "optional": False},
63+
PETAB_C.LOWER_BOUND: {"type": np.float64, "optional": False},
64+
PETAB_C.UPPER_BOUND: {"type": np.float64, "optional": False},
65+
PETAB_C.NOMINAL_VALUE: {"type": np.float64, "optional": False},
66+
PETAB_C.ESTIMATE: {"type": np.object_, "optional": False},
67+
PETAB_C.INITIALIZATION_PRIOR_TYPE: {
68+
"type": np.object_,
69+
"optional": True,
70+
},
71+
PETAB_C.INITIALIZATION_PRIOR_PARAMETERS: {
72+
"type": np.object_,
73+
"optional": True,
74+
},
75+
PETAB_C.OBJECTIVE_PRIOR_TYPE: {"type": np.object_, "optional": True},
76+
PETAB_C.OBJECTIVE_PRIOR_PARAMETERS: {
6077
"type": np.object_,
6178
"optional": True,
6279
},
63-
C.OBJECTIVE_PRIOR_TYPE: {"type": np.object_, "optional": True},
64-
C.OBJECTIVE_PRIOR_PARAMETERS: {"type": np.object_, "optional": True},
6580
},
6681
"condition": {
67-
C.CONDITION_ID: {"type": np.object_, "optional": False},
68-
C.CONDITION_NAME: {"type": np.object_, "optional": False},
82+
PETAB_C.CONDITION_ID: {"type": np.object_, "optional": False},
83+
PETAB_C.CONDITION_NAME: {"type": np.object_, "optional": False},
6984
},
7085
"visualization": {
71-
C.PLOT_ID: {"type": np.object_, "optional": False},
72-
C.PLOT_NAME: {"type": np.object_, "optional": True},
73-
C.PLOT_TYPE_SIMULATION: {
86+
PETAB_C.PLOT_ID: {"type": np.object_, "optional": False},
87+
PETAB_C.PLOT_NAME: {"type": np.object_, "optional": True},
88+
PETAB_C.PLOT_TYPE_SIMULATION: {
7489
"type": np.object_,
7590
"optional": True,
7691
},
77-
C.PLOT_TYPE_DATA: {"type": np.object_, "optional": True},
78-
C.DATASET_ID: {"type": np.object_, "optional": True},
79-
C.X_VALUES: {"type": np.object_, "optional": True},
80-
C.X_OFFSET: {"type": np.float64, "optional": True},
81-
C.X_LABEL: {"type": np.object_, "optional": True},
82-
C.X_SCALE: {"type": np.object_, "optional": True},
83-
C.Y_VALUES: {"type": np.object_, "optional": True},
84-
C.Y_OFFSET: {"type": np.float64, "optional": True},
85-
C.Y_LABEL: {"type": np.object_, "optional": True},
86-
C.Y_SCALE: {"type": np.object_, "optional": True},
87-
C.LEGEND_ENTRY: {"type": np.object_, "optional": True},
92+
PETAB_C.PLOT_TYPE_DATA: {"type": np.object_, "optional": True},
93+
PETAB_C.DATASET_ID: {"type": np.object_, "optional": True},
94+
PETAB_C.X_VALUES: {"type": np.object_, "optional": True},
95+
PETAB_C.X_OFFSET: {"type": np.float64, "optional": True},
96+
PETAB_C.X_LABEL: {"type": np.object_, "optional": True},
97+
PETAB_C.X_SCALE: {"type": np.object_, "optional": True},
98+
PETAB_C.Y_VALUES: {"type": np.object_, "optional": True},
99+
PETAB_C.Y_OFFSET: {"type": np.float64, "optional": True},
100+
PETAB_C.Y_LABEL: {"type": np.object_, "optional": True},
101+
PETAB_C.Y_SCALE: {"type": np.object_, "optional": True},
102+
PETAB_C.LEGEND_ENTRY: {"type": np.object_, "optional": True},
88103
},
89104
}
90105

@@ -133,36 +148,48 @@
133148

134149
# Default Configurations of Default Values
135150
ALLOWED_STRATEGIES_OBS = {
136-
C.OBSERVABLE_ID: STRATEGIES_DEFAULT,
137-
C.OBSERVABLE_NAME: STRATEGIES_DEFAULT,
138-
C.OBSERVABLE_FORMULA: STRATEGIES_DEFAULT,
139-
C.OBSERVABLE_TRANSFORMATION: [USE_DEFAULT, NO_DEFAULT, MODE],
140-
C.NOISE_FORMULA: [COPY_FROM, USE_DEFAULT, NO_DEFAULT, MODE],
141-
C.NOISE_DISTRIBUTION: [USE_DEFAULT, NO_DEFAULT, MODE],
151+
PETAB_C.OBSERVABLE_ID: STRATEGIES_DEFAULT,
152+
PETAB_C.OBSERVABLE_NAME: STRATEGIES_DEFAULT,
153+
PETAB_C.OBSERVABLE_FORMULA: STRATEGIES_DEFAULT,
154+
PETAB_C.OBSERVABLE_TRANSFORMATION: [USE_DEFAULT, NO_DEFAULT, MODE],
155+
PETAB_C.NOISE_FORMULA: [COPY_FROM, USE_DEFAULT, NO_DEFAULT, MODE],
156+
PETAB_C.NOISE_DISTRIBUTION: [USE_DEFAULT, NO_DEFAULT, MODE],
142157
}
143158
ALLOWED_STRATEGIES_PAR = {
144-
C.PARAMETER_ID: STRATEGIES_DEFAULT,
145-
C.PARAMETER_NAME: STRATEGIES_DEFAULT,
146-
C.PARAMETER_SCALE: [USE_DEFAULT, NO_DEFAULT, MODE],
147-
C.LOWER_BOUND: [MIN_COLUMN, MAX_COLUMN, USE_DEFAULT, NO_DEFAULT, MODE],
148-
C.UPPER_BOUND: [MAX_COLUMN, MAX_COLUMN, USE_DEFAULT, NO_DEFAULT, MODE],
149-
C.NOMINAL_VALUE: [USE_DEFAULT, NO_DEFAULT, SBML_LOOK],
150-
C.ESTIMATE: [USE_DEFAULT, NO_DEFAULT, MODE],
159+
PETAB_C.PARAMETER_ID: STRATEGIES_DEFAULT,
160+
PETAB_C.PARAMETER_NAME: STRATEGIES_DEFAULT,
161+
PETAB_C.PARAMETER_SCALE: [USE_DEFAULT, NO_DEFAULT, MODE],
162+
PETAB_C.LOWER_BOUND: [
163+
MIN_COLUMN,
164+
MAX_COLUMN,
165+
USE_DEFAULT,
166+
NO_DEFAULT,
167+
MODE,
168+
],
169+
PETAB_C.UPPER_BOUND: [
170+
MAX_COLUMN,
171+
MAX_COLUMN,
172+
USE_DEFAULT,
173+
NO_DEFAULT,
174+
MODE,
175+
],
176+
PETAB_C.NOMINAL_VALUE: [USE_DEFAULT, NO_DEFAULT, SBML_LOOK],
177+
PETAB_C.ESTIMATE: [USE_DEFAULT, NO_DEFAULT, MODE],
151178
}
152179
ALLOWED_STRATEGIES_COND = {
153-
C.CONDITION_ID: STRATEGIES_DEFAULT,
154-
C.CONDITION_NAME: STRATEGIES_DEFAULT,
180+
PETAB_C.CONDITION_ID: STRATEGIES_DEFAULT,
181+
PETAB_C.CONDITION_NAME: STRATEGIES_DEFAULT,
155182
}
156183
ALLOWED_STRATEGIES_MEAS = {
157-
C.OBSERVABLE_ID: STRATEGIES_DEFAULT,
158-
C.PREEQUILIBRATION_CONDITION_ID: STRATEGIES_DEFAULT_EXT,
159-
C.SIMULATION_CONDITION_ID: STRATEGIES_DEFAULT_EXT,
160-
C.TIME: [NO_DEFAULT, USE_DEFAULT, MODE],
161-
C.MEASUREMENT: [NO_DEFAULT, USE_DEFAULT, MODE],
162-
C.OBSERVABLE_PARAMETERS: STRATEGIES_DEFAULT_EXT,
163-
C.NOISE_PARAMETERS: STRATEGIES_DEFAULT_EXT,
164-
C.DATASET_ID: [COPY_FROM, USE_DEFAULT, NO_DEFAULT, MODE],
165-
C.REPLICATE_ID: [COPY_FROM, USE_DEFAULT, NO_DEFAULT, MODE],
184+
PETAB_C.OBSERVABLE_ID: STRATEGIES_DEFAULT,
185+
PETAB_C.PREEQUILIBRATION_CONDITION_ID: STRATEGIES_DEFAULT_EXT,
186+
PETAB_C.SIMULATION_CONDITION_ID: STRATEGIES_DEFAULT_EXT,
187+
PETAB_C.TIME: [NO_DEFAULT, USE_DEFAULT, MODE],
188+
PETAB_C.MEASUREMENT: [NO_DEFAULT, USE_DEFAULT, MODE],
189+
PETAB_C.OBSERVABLE_PARAMETERS: STRATEGIES_DEFAULT_EXT,
190+
PETAB_C.NOISE_PARAMETERS: STRATEGIES_DEFAULT_EXT,
191+
PETAB_C.DATASET_ID: [COPY_FROM, USE_DEFAULT, NO_DEFAULT, MODE],
192+
PETAB_C.REPLICATE_ID: [COPY_FROM, USE_DEFAULT, NO_DEFAULT, MODE],
166193
}
167194
ALLOWED_STRATEGIES = {
168195
"observable": ALLOWED_STRATEGIES_OBS,
@@ -171,34 +198,49 @@
171198
"measurement": ALLOWED_STRATEGIES_MEAS,
172199
}
173200
DEFAULT_OBS_CONFIG = {
174-
C.OBSERVABLE_ID: {
201+
PETAB_C.OBSERVABLE_ID: {
175202
"strategy": COPY_FROM,
176-
SOURCE_COLUMN: C.OBSERVABLE_FORMULA,
203+
SOURCE_COLUMN: PETAB_C.OBSERVABLE_FORMULA,
177204
DEFAULT_VALUE: "new_observable",
178205
},
179-
C.OBSERVABLE_NAME: {"strategy": COPY_FROM, SOURCE_COLUMN: C.OBSERVABLE_ID},
180-
C.NOISE_FORMULA: {"strategy": USE_DEFAULT, DEFAULT_VALUE: 1},
181-
C.OBSERVABLE_TRANSFORMATION: {
206+
PETAB_C.OBSERVABLE_NAME: {
207+
"strategy": COPY_FROM,
208+
SOURCE_COLUMN: PETAB_C.OBSERVABLE_ID,
209+
},
210+
PETAB_C.NOISE_FORMULA: {"strategy": USE_DEFAULT, DEFAULT_VALUE: 1},
211+
PETAB_C.OBSERVABLE_TRANSFORMATION: {
182212
"strategy": USE_DEFAULT,
183-
DEFAULT_VALUE: C.LIN,
213+
DEFAULT_VALUE: PETAB_C.LIN,
214+
},
215+
PETAB_C.NOISE_DISTRIBUTION: {
216+
"strategy": USE_DEFAULT,
217+
DEFAULT_VALUE: PETAB_C.NORMAL,
184218
},
185-
C.NOISE_DISTRIBUTION: {"strategy": USE_DEFAULT, DEFAULT_VALUE: C.NORMAL},
186219
}
187220
DEFAULT_PAR_CONFIG = {
188-
C.PARAMETER_NAME: {
221+
PETAB_C.PARAMETER_NAME: {
189222
"strategy": COPY_FROM,
190-
SOURCE_COLUMN: C.PARAMETER_ID,
223+
SOURCE_COLUMN: PETAB_C.PARAMETER_ID,
191224
DEFAULT_VALUE: "new_parameter",
192225
},
193-
C.PARAMETER_SCALE: {"strategy": USE_DEFAULT, DEFAULT_VALUE: C.LOG10},
194-
C.LOWER_BOUND: {"strategy": MIN_COLUMN},
195-
C.UPPER_BOUND: {"strategy": MAX_COLUMN},
196-
C.ESTIMATE: {"strategy": USE_DEFAULT, DEFAULT_VALUE: 1},
197-
C.NOMINAL_VALUE: {"strategy": SBML_LOOK},
226+
PETAB_C.PARAMETER_SCALE: {
227+
"strategy": USE_DEFAULT,
228+
DEFAULT_VALUE: PETAB_C.LOG10,
229+
},
230+
PETAB_C.LOWER_BOUND: {"strategy": MIN_COLUMN},
231+
PETAB_C.UPPER_BOUND: {"strategy": MAX_COLUMN},
232+
PETAB_C.ESTIMATE: {"strategy": USE_DEFAULT, DEFAULT_VALUE: 1},
233+
PETAB_C.NOMINAL_VALUE: {"strategy": SBML_LOOK},
198234
}
199235
DEFAULT_COND_CONFIG = {
200-
C.CONDITION_ID: {"strategy": USE_DEFAULT, DEFAULT_VALUE: "new_condition"},
201-
C.CONDITION_NAME: {"strategy": COPY_FROM, SOURCE_COLUMN: C.CONDITION_ID},
236+
PETAB_C.CONDITION_ID: {
237+
"strategy": USE_DEFAULT,
238+
DEFAULT_VALUE: "new_condition",
239+
},
240+
PETAB_C.CONDITION_NAME: {
241+
"strategy": COPY_FROM,
242+
SOURCE_COLUMN: PETAB_C.CONDITION_ID,
243+
},
202244
}
203245
DEFAULT_MEAS_CONFIG = {}
204246
DEFAULT_CONFIGS = {

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