Add test cases for PEtab v2.0.0 (#53)

including test cases for multilanguage proposal  PEtab-dev/PEtab#538

.ci_pip_reqs.txt

@@ -1,3 +1,3 @@
 pytest
 flake8
-https://github.com/petab-dev/libpetab-python/archive/develop.zip
+https://github.com/petab-dev/libpetab-python/archive/model_pysb.zip

.github/workflows/ci_tests.yml

@@ -31,5 +31,7 @@ jobs:
         pip install -e .
     - name: Run tests
       run: |
-        python -m flake8 --exclude=build,doc,tmp,petabtests/cases/pysb/*/_model.py,petabtests/cases/pysb/*/conversion_modified_pysb.py,petabtests/conversion_pysb.py --extend-ignore=F403,F405
+        python -m flake8 \
+          --exclude=build,doc,tmp,_model.py,conversion_modified_pysb.py,conversion_pysb.py \
+          --extend-ignore=F403,F405
         pytest test

petabtests/C.py

@@ -6,8 +6,6 @@
 BASE_DIR = Path(__file__).parent
 
 CASES_DIR = BASE_DIR / 'cases'
-SBML_DIR = CASES_DIR / 'sbml'
-PYSB_DIR = CASES_DIR / 'pysb'
 
 DEFAULT_SBML_FILE = BASE_DIR / 'conversion.xml'
 DEFAULT_PYSB_FILE = BASE_DIR / 'conversion_pysb.py'

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

@@ -1,11 +1,13 @@
-format_version: 1
+format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  model_files:
+    model_0:
+      language: pysb
+      location: _model.py
   observable_files:
   - _observables.tsv
-  sbml_files:
-  - _model.py

petabtests/cases/pysb/0002/_0002.yaml → petabtests/cases/v2.0.0/pysb/0002/_0002.yaml

@@ -1,11 +1,13 @@
-format_version: 1
+format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  model_files:
+    model_0:
+      language: pysb
+      location: _model.py
   observable_files:
   - _observables.tsv
-  sbml_files:
-  - _model.py

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

@@ -1,11 +1,13 @@
-format_version: 1
+format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  model_files:
+    model_0:
+      language: pysb
+      location: _model.py
   observable_files:
   - _observables.tsv
-  sbml_files:
-  - _model.py

petabtests/cases/pysb/0004/_0004.yaml → petabtests/cases/v2.0.0/pysb/0004/_0004.yaml

@@ -1,11 +1,13 @@
-format_version: 1
+format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  model_files:
+    model_0:
+      language: pysb
+      location: _model.py
   observable_files:
   - _observables.tsv
-  sbml_files:
-  - _model.py

petabtests/cases/pysb/0005/_0005.yaml → petabtests/cases/v2.0.0/pysb/0005/_0005.yaml

@@ -1,11 +1,13 @@
-format_version: 1
+format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  model_files:
+    model_0:
+      language: pysb
+      location: _model.py
   observable_files:
   - _observables.tsv
-  sbml_files:
-  - _model.py

petabtests/cases/pysb/0006/_0006.yaml → petabtests/cases/v2.0.0/pysb/0006/_0006.yaml

@@ -1,11 +1,13 @@
-format_version: 1
+format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  model_files:
+    model_0:
+      language: pysb
+      location: _model.py
   observable_files:
   - _observables.tsv
-  sbml_files:
-  - _model.py

petabtests/cases/pysb/0007/_0007.yaml → petabtests/cases/v2.0.0/pysb/0007/_0007.yaml

@@ -1,11 +1,13 @@
-format_version: 1
+format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  model_files:
+    model_0:
+      language: pysb
+      location: _model.py
   observable_files:
   - _observables.tsv
-  sbml_files:
-  - _model.py

petabtests/cases/pysb/0008/_0008.yaml → petabtests/cases/v2.0.0/pysb/0008/_0008.yaml

@@ -1,11 +1,13 @@
-format_version: 1
+format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  model_files:
+    model_0:
+      language: pysb
+      location: _model.py
   observable_files:
   - _observables.tsv
-  sbml_files:
-  - _model.py

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

@@ -1,11 +1,13 @@
-format_version: 1
+format_version: 2.0.0
 parameter_file: _parameters.tsv
 problems:
 - condition_files:
   - _conditions.tsv
   measurement_files:
   - _measurements.tsv
+  model_files:
+    model_0:
+      language: pysb
+      location: _model.py
   observable_files:
   - _observables.tsv
-  sbml_files:
-  - _model.py

petabtests/cases/v2.0.0/pysb/0010/0010.py

@@ -0,0 +1,83 @@
+from inspect import cleandoc
+
+import pandas as pd
+from petab.C import *
+
+from petabtests import DEFAULT_PYSB_FILE, PetabTestCase, analytical_a
+
+DESCRIPTION = cleandoc("""
+## Objective
+
+This case tests support for partial preequilibration.
+
+The model is to be simulated for a preequilibration condition and a
+simulation condition.
+Species `B` is to be reinitialized after preequilibration.
+For `A` the preequilibration result is to be used.
+
+## Model
+
+A simple conversion reaction `A <=> B` in a single compartment, following
+mass action kinetics.
+""")
+
+# problem --------------------------------------------------------------------
+
+condition_df = pd.DataFrame(data={
+    CONDITION_ID: ['preeq_c0', 'c0'],
+    'k1': [0.3, 0.8],
+    'B': [0, 1],
+}).set_index([CONDITION_ID])
+
+measurement_df = pd.DataFrame(data={
+    OBSERVABLE_ID: ['obs_a', 'obs_a'],
+    PREEQUILIBRATION_CONDITION_ID: ['preeq_c0', 'preeq_c0'],
+    SIMULATION_CONDITION_ID: ['c0', 'c0'],
+    TIME: [1, 10],
+    MEASUREMENT: [0.7, 0.1]
+})
+
+observable_df = pd.DataFrame(data={
+    OBSERVABLE_ID: ['obs_a'],
+    OBSERVABLE_FORMULA: ['A'],
+    NOISE_FORMULA: [0.5]
+}).set_index([OBSERVABLE_ID])
+
+parameter_df = pd.DataFrame(data={
+    PARAMETER_ID: ['k2'],
+    PARAMETER_SCALE: [LIN],
+    LOWER_BOUND: [0],
+    UPPER_BOUND: [10],
+    NOMINAL_VALUE: [0.6],
+    ESTIMATE: [1],
+}).set_index(PARAMETER_ID)
+
+mapping_df = pd.DataFrame(data={
+    PETAB_ENTITY_ID: ['A', 'B'],
+    MODEL_ENTITY_ID: ['A_() ** compartment', 'B_() ** compartment'],
+}).set_index(PETAB_ENTITY_ID)
+
+# solutions ------------------------------------------------------------------
+
+simulation_df = measurement_df.copy(deep=True).rename(
+    columns={MEASUREMENT: SIMULATION})
+# simulate for far time point as steady state
+steady_state_a = analytical_a(1000, 1, 0, 0.3, 0.6)
+# use steady state as initial state
+simulation_df[SIMULATION] = [
+    analytical_a(t, steady_state_a, 1, 0.8, 0.6)
+    for t in simulation_df[TIME]]
+
+case = PetabTestCase(
+    id=10,
+    brief="Simulation. Preequilibration. One species reinitialized, one not. "
+          "InitialAssignment to species overridden.",
+    description=DESCRIPTION,
+    model=DEFAULT_PYSB_FILE,
+    condition_dfs=[condition_df],
+    observable_dfs=[observable_df],
+    measurement_dfs=[measurement_df],
+    simulation_dfs=[simulation_df],
+    parameter_df=parameter_df,
+    mapping_df=mapping_df,
+)

petabtests/cases/v2.0.0/pysb/0010/_0010.yaml

@@ -0,0 +1,14 @@
+format_version: 2.0.0
+parameter_file: _parameters.tsv
+problems:
+- condition_files:
+  - _conditions.tsv
+  mapping_file: _mapping.tsv
+  measurement_files:
+  - _measurements.tsv
+  model_files:
+    model_0:
+      language: pysb
+      location: _model.py
+  observable_files:
+  - _observables.tsv

petabtests/cases/v2.0.0/pysb/0010/_mapping.tsv

@@ -0,0 +1,3 @@
+petabEntityId	modelEntityId
+A	A_() ** compartment
+B	B_() ** compartment

petabtests/cases/v2.0.0/pysb/0011/0011.py

@@ -0,0 +1,73 @@
+from inspect import cleandoc
+
+import pandas as pd
+from petab.C import *
+
+from petabtests import PetabTestCase, analytical_a
+
+DESCRIPTION = cleandoc("""
+## Objective
+
+This case tests initial concentrations in the condition table.
+For species `B`, the initial concentration is specified in the condition
+table, while for `A` it is given via an assignment rule in the SBML model.
+
+## Model
+
+A simple conversion reaction `A <=> B` in a single compartment, following
+mass action kinetics.
+""")
+
+# problem --------------------------------------------------------------------
+
+condition_df = pd.DataFrame(data={
+    CONDITION_ID: ['c0'],
+    'B': [2]
+}).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_df = pd.DataFrame(data={
+    OBSERVABLE_ID: ['obs_a'],
+    OBSERVABLE_FORMULA: ['A'],
+    NOISE_FORMULA: [0.5]
+}).set_index([OBSERVABLE_ID])
+
+parameter_df = pd.DataFrame(data={
+    PARAMETER_ID: ['k1', 'k2'],
+    PARAMETER_SCALE: [LIN] * 2,
+    LOWER_BOUND: [0] * 2,
+    UPPER_BOUND: [10] * 2,
+    NOMINAL_VALUE: [0.8, 0.6],
+    ESTIMATE: [1] * 2,
+}).set_index(PARAMETER_ID)
+
+mapping_df = pd.DataFrame(data={
+    PETAB_ENTITY_ID: ['A', 'B'],
+    MODEL_ENTITY_ID: ['A_() ** compartment', 'B_() ** compartment'],
+}).set_index(PETAB_ENTITY_ID)
+
+# solutions ------------------------------------------------------------------
+
+simulation_df = measurement_df.copy(deep=True).rename(
+    columns={MEASUREMENT: SIMULATION})
+simulation_df[SIMULATION] = [analytical_a(t, 1, 2, 0.8, 0.6)
+                             for t in simulation_df[TIME]]
+
+case = PetabTestCase(
+    id=11,
+    brief="Simulation. InitialAssignment to species overridden.",
+    description=DESCRIPTION,
+    model='conversion_modified_pysb.py',
+    condition_dfs=[condition_df],
+    observable_dfs=[observable_df],
+    measurement_dfs=[measurement_df],
+    simulation_dfs=[simulation_df],
+    parameter_df=parameter_df,
+    mapping_df=mapping_df,
+)

petabtests/cases/v2.0.0/pysb/0011/_0011.yaml

@@ -0,0 +1,14 @@
+format_version: 2.0.0
+parameter_file: _parameters.tsv
+problems:
+- condition_files:
+  - _conditions.tsv
+  mapping_file: _mapping.tsv
+  measurement_files:
+  - _measurements.tsv
+  model_files:
+    model_0:
+      language: pysb
+      location: _model.py
+  observable_files:
+  - _observables.tsv

petabtests/cases/v2.0.0/pysb/0011/_mapping.tsv

@@ -0,0 +1,3 @@
+petabEntityId	modelEntityId
+A	A_() ** compartment
+B	B_() ** compartment