..

petabtests/cases/v2.0.0/pysb/0001/0001.py

@@ -1,9 +1,8 @@
 from inspect import cleandoc
 
-import pandas as pd
-from petab.v1.C import *
-
 from petabtests import DEFAULT_PYSB_FILE, PetabTestCase, analytical_a
+from petab.v2 import Problem
+from petab.v2.C import *
 
 DESCRIPTION = cleandoc("""
 ## Objective
@@ -19,43 +18,21 @@
 
 # problem --------------------------------------------------------------------
 
-condition_df = pd.DataFrame(
-    data={
-        CONDITION_ID: ["c0"],
-    }
-).set_index([CONDITION_ID])
+problem = Problem()
 
-measurement_df = pd.DataFrame(
-    data={
-        OBSERVABLE_ID: ["obs_a", "obs_a"],
-        SIMULATION_CONDITION_ID: ["c0", "c0"],
-        TIME: [0, 10],
-        MEASUREMENT: [0.7, 0.1],
-    }
-)
+problem.add_observable("obs_a", "A", noise_formula=0.5)
 
-observable_df = pd.DataFrame(
-    data={
-        OBSERVABLE_ID: ["obs_a"],
-        OBSERVABLE_FORMULA: ["A"],
-        NOISE_FORMULA: [0.5],
-    }
-).set_index([OBSERVABLE_ID])
+problem.add_measurement("obs_a", "", time=0, measurement=0.7)
+problem.add_measurement("obs_a", "", time=10, measurement=0.1)
 
-parameter_df = pd.DataFrame(
-    data={
-        PARAMETER_ID: ["a0", "b0", "k1", "k2"],
-        PARAMETER_SCALE: [LIN] * 4,
-        LOWER_BOUND: [0] * 4,
-        UPPER_BOUND: [10] * 4,
-        NOMINAL_VALUE: [1, 0, 0.8, 0.6],
-        ESTIMATE: [1] * 4,
-    }
-).set_index(PARAMETER_ID)
+problem.add_parameter("a0", lb=0, ub=10, nominal_value=1, scale=LIN)
+problem.add_parameter("b0", lb=0, ub=10, nominal_value=0, scale=LIN)
+problem.add_parameter("k1", lb=0, ub=10, nominal_value=0.8, scale=LIN)
+problem.add_parameter("k2", lb=0, ub=10, nominal_value=0.6, scale=LIN)
 
 # solutions ------------------------------------------------------------------
 
-simulation_df = measurement_df.copy(deep=True).rename(
+simulation_df = problem.measurement_df.copy(deep=True).rename(
     columns={MEASUREMENT: SIMULATION}
 )
 simulation_df[SIMULATION] = [
@@ -68,9 +45,9 @@
     brief="Simulation. Nothing special.",
     description=DESCRIPTION,
     model=DEFAULT_PYSB_FILE,
-    condition_dfs=[condition_df],
-    observable_dfs=[observable_df],
-    measurement_dfs=[measurement_df],
+    condition_dfs=[problem.condition_df],
+    observable_dfs=[problem.observable_df],
+    measurement_dfs=[problem.measurement_df],
     simulation_dfs=[simulation_df],
-    parameter_df=parameter_df,
+    parameter_df=problem.parameter_df,
 )

petabtests/cases/v2.0.0/pysb/0001/_0001.yaml

@@ -1,8 +1,8 @@
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
-- condition_files:
-  - _conditions.tsv
+- condition_files: []
+  experiment_files: []
   measurement_files:
   - _measurements.tsv
   model_files:

petabtests/cases/v2.0.0/pysb/0001/_measurements.tsv

@@ -1,3 +1,3 @@
-observableId	simulationConditionId	time	measurement
-obs_a	c0	0	0.7
-obs_a	c0	10	0.1
+observableId	experimentId	time	measurement
+obs_a		0	0.7
+obs_a		10	0.1

petabtests/cases/v2.0.0/pysb/0001/_parameters.tsv

@@ -1,5 +1,5 @@
-parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-a0	lin	0	10	1.0	1
-b0	lin	0	10	0.0	1
-k1	lin	0	10	0.8	1
-k2	lin	0	10	0.6	1
+parameterId	estimate	nominalValue	parameterScale	lowerBound	upperBound
+a0	1	1.0	lin	0	10
+b0	1	0.0	lin	0	10
+k1	1	0.8	lin	0	10
+k2	1	0.6	lin	0	10

petabtests/cases/v2.0.0/pysb/0001/_simulations.tsv

@@ -1,3 +1,3 @@
-observableId	simulationConditionId	time	simulation
-obs_a	c0	0	1.0
-obs_a	c0	10	0.42857190373069665
+observableId	experimentId	time	simulation
+obs_a		0	1.0
+obs_a		10	0.42857190373069665

petabtests/cases/v2.0.0/pysb/0003/0003.py

@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
-import pandas as pd
-from petab.v1.C import *
+from petab.v2 import Problem
+from petab.v2.C import *
 
 from petabtests import DEFAULT_PYSB_FILE, PetabTestCase, analytical_a
 
@@ -24,47 +24,29 @@
 """)
 
 # problem --------------------------------------------------------------------
+problem = Problem()
 
-condition_df = pd.DataFrame(
-    data={
-        CONDITION_ID: ["c0"],
-    }
-).set_index([CONDITION_ID])
-
-measurement_df = pd.DataFrame(
-    data={
-        OBSERVABLE_ID: ["obs_a", "obs_a"],
-        SIMULATION_CONDITION_ID: ["c0", "c0"],
-        TIME: [0, 10],
-        MEASUREMENT: [0.7, 0.1],
-        OBSERVABLE_PARAMETERS: ["0.5;2", "0.5;2"],
-    }
+problem.add_observable(
+    "obs_a",
+    "observableParameter1_obs_a * A + observableParameter2_obs_a",
+    noise_formula=0.5,
 )
 
-observable_df = pd.DataFrame(
-    data={
-        OBSERVABLE_ID: ["obs_a"],
-        OBSERVABLE_FORMULA: [
-            "observableParameter1_obs_a * A + " "observableParameter2_obs_a"
-        ],
-        NOISE_FORMULA: [0.5],
-    }
-).set_index([OBSERVABLE_ID])
+problem.add_measurement(
+    "obs_a", "", time=0, measurement=0.7, observable_parameters=(0.5, 2)
+)
+problem.add_measurement(
+    "obs_a", "", time=10, measurement=0.1, observable_parameters=(0.5, 2)
+)
 
-parameter_df = pd.DataFrame(
-    data={
-        PARAMETER_ID: ["a0", "b0", "k1", "k2"],
-        PARAMETER_SCALE: [LIN] * 4,
-        LOWER_BOUND: [0] * 4,
-        UPPER_BOUND: [10] * 4,
-        NOMINAL_VALUE: [1, 0, 0.8, 0.6],
-        ESTIMATE: [1] * 4,
-    }
-).set_index(PARAMETER_ID)
+problem.add_parameter("a0", lb=0, ub=10, nominal_value=1, scale=LIN)
+problem.add_parameter("b0", lb=0, ub=10, nominal_value=0, scale=LIN)
+problem.add_parameter("k1", lb=0, ub=10, nominal_value=0.8, scale=LIN)
+problem.add_parameter("k2", lb=0, ub=10, nominal_value=0.6, scale=LIN)
 
 # solutions ------------------------------------------------------------------
 
-simulation_df = measurement_df.copy(deep=True).rename(
+simulation_df = problem.measurement_df.copy(deep=True).rename(
     columns={MEASUREMENT: SIMULATION}
 )
 simulation_df[SIMULATION] = [
@@ -77,9 +59,9 @@
     "table.",
     description=DESCRIPTION,
     model=DEFAULT_PYSB_FILE,
-    condition_dfs=[condition_df],
-    observable_dfs=[observable_df],
-    measurement_dfs=[measurement_df],
+    condition_dfs=[problem.condition_df],
+    observable_dfs=[problem.observable_df],
+    measurement_dfs=[problem.measurement_df],
     simulation_dfs=[simulation_df],
-    parameter_df=parameter_df,
+    parameter_df=problem.parameter_df,
 )

petabtests/cases/v2.0.0/pysb/0003/_0003.yaml

@@ -1,8 +1,8 @@
 format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
-- condition_files:
-  - _conditions.tsv
+- condition_files: []
+  experiment_files: []
   measurement_files:
   - _measurements.tsv
   model_files:

petabtests/cases/v2.0.0/pysb/0003/_measurements.tsv

@@ -1,3 +1,3 @@
-observableId	simulationConditionId	time	measurement	observableParameters
-obs_a	c0	0	0.7	0.5;2
-obs_a	c0	10	0.1	0.5;2
+observableId	experimentId	time	measurement	observableParameters
+obs_a		0	0.7	0.5;2
+obs_a		10	0.1	0.5;2

petabtests/cases/v2.0.0/pysb/0003/_parameters.tsv

@@ -1,5 +1,5 @@
-parameterId	parameterScale	lowerBound	upperBound	nominalValue	estimate
-a0	lin	0	10	1.0	1
-b0	lin	0	10	0.0	1
-k1	lin	0	10	0.8	1
-k2	lin	0	10	0.6	1
+parameterId	estimate	nominalValue	parameterScale	lowerBound	upperBound
+a0	1	1.0	lin	0	10
+b0	1	0.0	lin	0	10
+k1	1	0.8	lin	0	10
+k2	1	0.6	lin	0	10

petabtests/cases/v2.0.0/pysb/0003/_simulations.tsv

@@ -1,3 +1,3 @@
-observableId	simulationConditionId	time	simulation	observableParameters
-obs_a	c0	0	2.5	0.5;2
-obs_a	c0	10	2.214285951865348	0.5;2
+observableId	experimentId	time	simulation	observableParameters
+obs_a		0	2.5	0.5;2
+obs_a		10	2.214285951865348	0.5;2

petabtests/cases/v2.0.0/sbml/0019/_0019.yaml

@@ -2,6 +2,7 @@ format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files: []
+  experiment_files: []
   mapping_files:
   - _mapping.tsv
   measurement_files:

petabtests/cases/v2.0.0/sbml/0019/_simulations.tsv

@@ -1,3 +1,3 @@
-observableId	simulationConditionId	time	simulation
+observableId	experimentId	time	simulation
 obs_a	c0	0	1.0
 obs_a	c0	10	0.42857190373069665

petabtests/cases/v2.0.0/sbml/0020/_experiments.tsv

@@ -0,0 +1,2 @@
+experimentId	conditionId	time
+experiment_c0	c0	0

petabtests/cases/v2.0.0/sbml/0020/_measurements.tsv

@@ -1,3 +1,3 @@
-observableId	simulationConditionId	time	measurement
-obs_a	c0	0	0.7
-obs_a	c0	10	0.1
+experimentId	observableId	time	measurement
+experiment_c0	obs_a	0	0.7
+experiment_c0	obs_a	10	0.1

petabtests/core.py

@@ -54,7 +54,9 @@ def create():
             case_dir = get_case_dir(
                 format_=format_, version=version, id_=case_id
             )
-            logger.info("# ", format_, version, case_id, case_dir)
+            logger.info(
+                f"Processing {version}/{format_} #{case_id} at {case_dir}"
+            )
 
             # load test case module
             #  directory needs to be removed from path again and the module
@@ -76,6 +78,7 @@ def create():
                 test_id=case.id,
                 parameter_df=case.parameter_df,
                 condition_dfs=case.condition_dfs,
+                experiment_dfs=case.experiment_dfs,
                 observable_dfs=case.observable_dfs,
                 measurement_dfs=case.measurement_dfs,
                 model_files=case.model,
@@ -125,3 +128,10 @@ def clear():
             for file_ in os.scandir(case_dir):
                 if file_.name.startswith("_") and not file_.is_dir():
                     os.remove(file_.path)
+
+
+def _cli_create():
+    """`petabtests_create` entry point."""
+    # initialize logging
+    logging.basicConfig(level=logging.INFO)
+    create()

petabtests/file.py

@@ -11,6 +11,12 @@
 import yaml
 from petab.v1.C import *  # noqa: F403
 from .C import *  # noqa: F403
+from pprint import pprint
+import logging
+from petab.v2.C import EXPERIMENT_FILES
+
+logger = logging.getLogger("petab_test_suite")
+
 
 __all__ = [
     "get_case_dir",
@@ -39,6 +45,7 @@ class PetabTestCase:
     simulation_dfs: list[pd.DataFrame]
     parameter_df: pd.DataFrame
     mapping_df: pd.DataFrame = None
+    experiment_dfs: list[pd.DataFrame] = None
 
 
 def get_case_dir(id_: int | str, format_: str, version: str) -> Path:
@@ -76,6 +83,7 @@ def write_problem(
     test_id: int,
     parameter_df: pd.DataFrame,
     condition_dfs: list[pd.DataFrame] | pd.DataFrame,
+    experiment_dfs: list[pd.DataFrame] | pd.DataFrame,
     observable_dfs: list[pd.DataFrame] | pd.DataFrame,
     measurement_dfs: list[pd.DataFrame] | pd.DataFrame,
     model_files: list[Path] | Path,
@@ -90,6 +98,7 @@ def write_problem(
     test_id: Identifier of the test.
     parameter_df: PEtab parameter table.
     condition_dfs: PEtab condition tables.
+    experiment_dfs: PEtab experiment tables.
     observable_dfs: PEtab observable tables.
     measurement_dfs: PEtab measurement tables.
     model_files: PEtab SBML/PySB files.
@@ -163,6 +172,7 @@ def write_problem(
     else:
         petab = v2
         config[PROBLEMS][0][MODEL_FILES] = {}
+        config[PROBLEMS][0][EXPERIMENT_FILES] = []
         for model_idx, model_file in enumerate(copied_model_files):
             config[PROBLEMS][0][MODEL_FILES][f"model_{model_idx}"] = {
                 MODEL_LANGUAGE: format_,
@@ -201,6 +211,16 @@ def write_problem(
         config[PROBLEMS][0][MEASUREMENT_FILES],
     )
 
+    # write experiments
+    if experiment_dfs is not None:
+        _write_dfs_to_files(
+            dir_,
+            "experiments",
+            v2.write_experiment_df,
+            experiment_dfs,
+            config[PROBLEMS][0][EXPERIMENT_FILES],
+        )
+
     if format_version != 1 and mapping_df is not None:
         # write mapping table
         mappings_file = "_mapping.tsv"
@@ -225,7 +245,15 @@ def write_problem(
     ):
         from petab.v2.petab1to2 import petab1to2
 
+        # delete previously auto-generated experiments.tsv
+        exp_file = Path(dir_, "_experiments.tsv")
+        if exp_file.exists():
+            exp_file.unlink()
         petab1to2(yaml_path, dir_)
+        # rename auto-generated experiments.tsv
+        tmp_exp_file = Path(dir_, "experiments.tsv")
+        if tmp_exp_file.exists():
+            tmp_exp_file.rename(exp_file)
         format_version = 2
 
     # FIXME Until a first libpetab with petab.v1 subpackage is released
@@ -244,9 +272,11 @@ def write_problem(
                 )
         else:
             # v2
-            validation_result = lint_problem_v2(yaml_path)
-            if validation_result:
-                print(validation_result)
+            validation_results = lint_problem_v2(yaml_path)
+            if validation_results:
+                logger.error(f"Validation failed for {dir_}:")
+                for issue in validation_results:
+                    pprint(issue)
                 raise RuntimeError(
                     "Invalid PEtab problem, see messages above."
                 )
@@ -322,6 +352,7 @@ def _write_dfs_to_files(
     config_list: list[str] = None,
 ):
     """Write data frames to files and add them to config."""
+    dfs = [df for df in dfs if df is not None]
     for idx, df in enumerate(dfs):
         if len(dfs) == 1:
             idx = ""