Skip to content

Commit e7b160f

Browse files
committed
..
1 parent 564512f commit e7b160f

39 files changed

+177
-118
lines changed

petabtests/cases/v2.0.0/pysb/0006/0006.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -29,10 +29,10 @@
2929
)
3030

3131
problem.add_measurement(
32-
"obs_a", "c0", time=0, measurement=0.7, observable_parameters=(10,)
32+
"obs_a", "", time=0, measurement=0.7, observable_parameters=(10,)
3333
)
3434
problem.add_measurement(
35-
"obs_a", "c0", time=10, measurement=0.1, observable_parameters=(15,)
35+
"obs_a", "", time=10, measurement=0.1, observable_parameters=(15,)
3636
)
3737

3838
problem.add_parameter(
Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,3 @@
11
observableId experimentId time measurement observableParameters
2-
obs_a c0 0 0.7 10
3-
obs_a c0 10 0.1 15
2+
obs_a 0 0.7 10
3+
obs_a 10 0.1 15
Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,3 @@
11
observableId experimentId time simulation observableParameters
2-
obs_a c0 0 10.0 10
3-
obs_a c0 10 6.42857855596045 15
2+
obs_a 0 10.0 10
3+
obs_a 10 6.42857855596045 15

petabtests/cases/v2.0.0/pysb/0009/0009.py

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -72,4 +72,5 @@
7272
measurement_dfs=[problem.measurement_df],
7373
simulation_dfs=[simulation_df],
7474
parameter_df=problem.parameter_df,
75+
experiment_dfs=[problem.experiment_df],
7576
)

petabtests/cases/v2.0.0/pysb/0009/_0009.yaml

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,8 @@ parameter_file: _parameters.tsv
33
problems:
44
- condition_files:
55
- _conditions.tsv
6-
experiment_files: []
6+
experiment_files:
7+
- _experiments.tsv
78
measurement_files:
89
- _measurements.tsv
910
model_files:
Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,3 @@
1+
experimentId time conditionId
2+
e0 -inf preeq_c0
3+
e0 0.0 c0
Lines changed: 9 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,17 @@
11
format_version: 2.0.0
22
parameter_file: _parameters.tsv
33
problems:
4-
- condition_files:
5-
- _conditions.tsv
4+
- model_files:
5+
_model:
6+
location: _model.xml
7+
language: sbml
68
measurement_files:
79
- _measurements.tsv
10+
condition_files:
11+
- _conditions.tsv
12+
experiment_files: []
813
observable_files:
914
- _observables.tsv
10-
model_files:
11-
_model:
12-
language: sbml
13-
location: _model.xml
15+
visualization_files: []
16+
mapping_files: []
1417
extensions: []

petabtests/cases/v2.0.0/sbml/0001/_experiments.tsv

Lines changed: 0 additions & 2 deletions
This file was deleted.
Lines changed: 7 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,18 @@
1+
extensions: []
12
format_version: 2.0.0
23
parameter_file: _parameters.tsv
34
problems:
45
- condition_files:
56
- _conditions.tsv
7+
experiment_files:
8+
- _experiments.tsv
9+
mapping_files: []
610
measurement_files:
711
- _measurements.tsv
8-
observable_files:
9-
- _observables.tsv
1012
model_files:
1113
_model:
1214
language: sbml
1315
location: _model.xml
14-
extensions: []
16+
observable_files:
17+
- _observables.tsv
18+
visualization_files: []
Lines changed: 9 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,17 @@
11
format_version: 2.0.0
22
parameter_file: _parameters.tsv
33
problems:
4-
- condition_files:
5-
- _conditions.tsv
4+
- model_files:
5+
_model:
6+
location: _model.xml
7+
language: sbml
68
measurement_files:
79
- _measurements.tsv
10+
condition_files:
11+
- _conditions.tsv
12+
experiment_files: []
813
observable_files:
914
- _observables.tsv
10-
model_files:
11-
_model:
12-
language: sbml
13-
location: _model.xml
15+
visualization_files: []
16+
mapping_files: []
1417
extensions: []

petabtests/cases/v2.0.0/sbml/0003/_experiments.tsv

Lines changed: 0 additions & 2 deletions
This file was deleted.
Lines changed: 9 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,17 @@
11
format_version: 2.0.0
22
parameter_file: _parameters.tsv
33
problems:
4-
- condition_files:
5-
- _conditions.tsv
4+
- model_files:
5+
_model:
6+
location: _model.xml
7+
language: sbml
68
measurement_files:
79
- _measurements.tsv
10+
condition_files:
11+
- _conditions.tsv
12+
experiment_files: []
813
observable_files:
914
- _observables.tsv
10-
model_files:
11-
_model:
12-
language: sbml
13-
location: _model.xml
15+
visualization_files: []
16+
mapping_files: []
1417
extensions: []

petabtests/cases/v2.0.0/sbml/0004/_experiments.tsv

Lines changed: 0 additions & 2 deletions
This file was deleted.
Lines changed: 7 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,18 @@
1+
extensions: []
12
format_version: 2.0.0
23
parameter_file: _parameters.tsv
34
problems:
45
- condition_files:
56
- _conditions.tsv
7+
experiment_files:
8+
- _experiments.tsv
9+
mapping_files: []
610
measurement_files:
711
- _measurements.tsv
8-
observable_files:
9-
- _observables.tsv
1012
model_files:
1113
_model:
1214
language: sbml
1315
location: _model.xml
14-
extensions: []
16+
observable_files:
17+
- _observables.tsv
18+
visualization_files: []
Lines changed: 9 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,17 @@
11
format_version: 2.0.0
22
parameter_file: _parameters.tsv
33
problems:
4-
- condition_files:
5-
- _conditions.tsv
4+
- model_files:
5+
_model:
6+
location: _model.xml
7+
language: sbml
68
measurement_files:
79
- _measurements.tsv
10+
condition_files:
11+
- _conditions.tsv
12+
experiment_files: []
813
observable_files:
914
- _observables.tsv
10-
model_files:
11-
_model:
12-
language: sbml
13-
location: _model.xml
15+
visualization_files: []
16+
mapping_files: []
1417
extensions: []

petabtests/cases/v2.0.0/sbml/0006/_experiments.tsv

Lines changed: 0 additions & 2 deletions
This file was deleted.
Lines changed: 9 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,17 @@
11
format_version: 2.0.0
22
parameter_file: _parameters.tsv
33
problems:
4-
- condition_files:
5-
- _conditions.tsv
4+
- model_files:
5+
_model:
6+
location: _model.xml
7+
language: sbml
68
measurement_files:
79
- _measurements.tsv
10+
condition_files:
11+
- _conditions.tsv
12+
experiment_files: []
813
observable_files:
914
- _observables.tsv
10-
model_files:
11-
_model:
12-
language: sbml
13-
location: _model.xml
15+
visualization_files: []
16+
mapping_files: []
1417
extensions: []

petabtests/cases/v2.0.0/sbml/0007/_experiments.tsv

Lines changed: 0 additions & 2 deletions
This file was deleted.
Lines changed: 9 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,17 @@
11
format_version: 2.0.0
22
parameter_file: _parameters.tsv
33
problems:
4-
- condition_files:
5-
- _conditions.tsv
4+
- model_files:
5+
_model:
6+
location: _model.xml
7+
language: sbml
68
measurement_files:
79
- _measurements.tsv
10+
condition_files:
11+
- _conditions.tsv
12+
experiment_files: []
813
observable_files:
914
- _observables.tsv
10-
model_files:
11-
_model:
12-
language: sbml
13-
location: _model.xml
15+
visualization_files: []
16+
mapping_files: []
1417
extensions: []

petabtests/cases/v2.0.0/sbml/0008/_experiments.tsv

Lines changed: 0 additions & 2 deletions
This file was deleted.
Lines changed: 7 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,18 @@
1+
extensions: []
12
format_version: 2.0.0
23
parameter_file: _parameters.tsv
34
problems:
45
- condition_files:
56
- _conditions.tsv
7+
experiment_files:
8+
- _experiments.tsv
9+
mapping_files: []
610
measurement_files:
711
- _measurements.tsv
8-
observable_files:
9-
- _observables.tsv
1012
model_files:
1113
_model:
1214
language: sbml
1315
location: _model.xml
14-
extensions: []
16+
observable_files:
17+
- _observables.tsv
18+
visualization_files: []
Lines changed: 7 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,18 @@
1+
extensions: []
12
format_version: 2.0.0
23
parameter_file: _parameters.tsv
34
problems:
45
- condition_files:
56
- _conditions.tsv
7+
experiment_files:
8+
- _experiments.tsv
9+
mapping_files: []
610
measurement_files:
711
- _measurements.tsv
8-
observable_files:
9-
- _observables.tsv
1012
model_files:
1113
_model:
1214
language: sbml
1315
location: _model.xml
14-
extensions: []
16+
observable_files:
17+
- _observables.tsv
18+
visualization_files: []
Lines changed: 7 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,18 @@
1+
extensions: []
12
format_version: 2.0.0
23
parameter_file: _parameters.tsv
34
problems:
45
- condition_files:
56
- _conditions.tsv
7+
experiment_files:
8+
- _experiments.tsv
9+
mapping_files: []
610
measurement_files:
711
- _measurements.tsv
8-
observable_files:
9-
- _observables.tsv
1012
model_files:
1113
_model:
1214
language: sbml
1315
location: _model.xml
14-
extensions: []
16+
observable_files:
17+
- _observables.tsv
18+
visualization_files: []
Lines changed: 7 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,18 @@
1+
extensions: []
12
format_version: 2.0.0
23
parameter_file: _parameters.tsv
34
problems:
45
- condition_files:
56
- _conditions.tsv
7+
experiment_files:
8+
- _experiments.tsv
9+
mapping_files: []
610
measurement_files:
711
- _measurements.tsv
8-
observable_files:
9-
- _observables.tsv
1012
model_files:
1113
_model:
1214
language: sbml
1315
location: _model.xml
14-
extensions: []
16+
observable_files:
17+
- _observables.tsv
18+
visualization_files: []
Lines changed: 7 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,18 @@
1+
extensions: []
12
format_version: 2.0.0
23
parameter_file: _parameters.tsv
34
problems:
45
- condition_files:
56
- _conditions.tsv
7+
experiment_files:
8+
- _experiments.tsv
9+
mapping_files: []
610
measurement_files:
711
- _measurements.tsv
8-
observable_files:
9-
- _observables.tsv
1012
model_files:
1113
_model:
1214
language: sbml
1315
location: _model.xml
14-
extensions: []
16+
observable_files:
17+
- _observables.tsv
18+
visualization_files: []
Lines changed: 9 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,17 @@
11
format_version: 2.0.0
22
parameter_file: _parameters.tsv
33
problems:
4-
- condition_files:
5-
- _conditions.tsv
4+
- model_files:
5+
_model:
6+
location: _model.xml
7+
language: sbml
68
measurement_files:
79
- _measurements.tsv
10+
condition_files:
11+
- _conditions.tsv
12+
experiment_files: []
813
observable_files:
914
- _observables.tsv
10-
model_files:
11-
_model:
12-
language: sbml
13-
location: _model.xml
15+
visualization_files: []
16+
mapping_files: []
1417
extensions: []

petabtests/cases/v2.0.0/sbml/0014/_experiments.tsv

Lines changed: 0 additions & 2 deletions
This file was deleted.

0 commit comments

Comments
 (0)