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Add PySB testcases #27

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merged 16 commits into from
Nov 17, 2020
Merged

Add PySB testcases #27

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8cff68f
add pysb tests
FFroehlich Jul 29, 2020
3efba58
fixups
FFroehlich Jul 30, 2020
38d52bd
Fix list of test cases
dweindl Jul 30, 2020
697b4e3
Add observables
dweindl Jul 30, 2020
991ec98
Change species names to have A,B for pysb-observable IDs
dweindl Jul 31, 2020
e18428a
Merge branch 'master' into pysb
dweindl Nov 9, 2020
d10d55d
trigger ci
dweindl Nov 9, 2020
05cb575
Revert "trigger ci"
dweindl Nov 9, 2020
e9b3cc7
Flake8 should ignore pysb models
dweindl Nov 9, 2020
0dbb927
Revert changes to SBML models
dweindl Nov 9, 2020
39e0731
Remove empty file
dweindl Nov 9, 2020
705fd20
Recreate
dweindl Nov 9, 2020
6c56081
Fixup: Revert to use conversion_modified.xml for 5, 11, 13
dweindl Nov 9, 2020
eb1a3d1
Add cases/pysb/00{05,11,13}/conversion_modified_pysb.py
dweindl Nov 10, 2020
75bda27
flake exclude
dweindl Nov 10, 2020
2aea3ae
flake exclude
dweindl Nov 10, 2020
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2 changes: 1 addition & 1 deletion .github/workflows/ci_tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -31,5 +31,5 @@ jobs:
pip install -e .
- name: Run tests
run: |
python -m flake8 --exclude=build,doc,tmp --extend-ignore=F403,F405
python -m flake8 --exclude=build,doc,tmp,cases/pysb/*/_model.py,cases/pysb/*/conversion_modified_pysb.py,petabtests/conversion_pysb.py --extend-ignore=F403,F405
pytest test
17 changes: 1 addition & 16 deletions cases/0001/0001.py
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Expand Up @@ -9,7 +9,7 @@

# problem --------------------------------------------------------------------

model = DEFAULT_MODEL_FILE
model = DEFAULT_SBML_FILE

condition_df = pd.DataFrame(data={
CONDITION_ID: ['c0'],
Expand Down Expand Up @@ -37,15 +37,6 @@
ESTIMATE: [1] * 4,
}).set_index(PARAMETER_ID)


# write files

write_problem(test_id=test_id,
parameter_df=parameter_df,
condition_dfs=[condition_df],
observable_dfs=[observable_df],
measurement_dfs=[measurement_df])

# solutions ------------------------------------------------------------------

simulation_df = measurement_df.copy(deep=True).rename(
Expand All @@ -59,9 +50,3 @@
llh = petab.calculate_llh(
measurement_df, simulation_df, observable_df, parameter_df)
print(llh)
# write files

write_solution(test_id=test_id,
chi2=chi2,
llh=llh,
simulation_dfs=[simulation_df])
17 changes: 1 addition & 16 deletions cases/0002/0002.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@

# problem --------------------------------------------------------------------

model = DEFAULT_MODEL_FILE
model = DEFAULT_SBML_FILE
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Unused everywhere... really needs some cleanup 😬 (elsewhere)


condition_df = pd.DataFrame(data={
CONDITION_ID: ['c0', 'c1'],
Expand Down Expand Up @@ -38,15 +38,6 @@
ESTIMATE: [1] * 3,
}).set_index(PARAMETER_ID)


# write files

write_problem(test_id=test_id,
parameter_df=parameter_df,
condition_dfs=[condition_df],
observable_dfs=[observable_df],
measurement_dfs=[measurement_df])

# solutions ------------------------------------------------------------------

simulation_df = measurement_df.copy(deep=True).rename(
Expand All @@ -62,9 +53,3 @@
llh = petab.calculate_llh(
measurement_df, simulation_df, observable_df, parameter_df)
print(llh)
# write files

write_solution(test_id=test_id,
chi2=chi2,
llh=llh,
simulation_dfs=[simulation_df])
17 changes: 1 addition & 16 deletions cases/0003/0003.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@

# problem --------------------------------------------------------------------

model = DEFAULT_MODEL_FILE
model = DEFAULT_SBML_FILE

condition_df = pd.DataFrame(data={
CONDITION_ID: ['c0'],
Expand Down Expand Up @@ -39,15 +39,6 @@
ESTIMATE: [1] * 4,
}).set_index(PARAMETER_ID)


# write files

write_problem(test_id=test_id,
parameter_df=parameter_df,
condition_dfs=[condition_df],
observable_dfs=[observable_df],
measurement_dfs=[measurement_df])

# solutions ------------------------------------------------------------------

simulation_df = measurement_df.copy(deep=True).rename(
Expand All @@ -61,9 +52,3 @@
llh = petab.calculate_llh(
measurement_df, simulation_df, observable_df, parameter_df)
print(llh)
# write files

write_solution(test_id=test_id,
chi2=chi2,
llh=llh,
simulation_dfs=[simulation_df])
16 changes: 1 addition & 15 deletions cases/0004/0004.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@

# problem --------------------------------------------------------------------

model = DEFAULT_MODEL_FILE
model = DEFAULT_SBML_FILE

condition_df = pd.DataFrame(data={
CONDITION_ID: ['c0'],
Expand Down Expand Up @@ -38,14 +38,6 @@
}).set_index(PARAMETER_ID)


# write files

write_problem(test_id=test_id,
parameter_df=parameter_df,
condition_dfs=[condition_df],
observable_dfs=[observable_df],
measurement_dfs=[measurement_df])

# solutions ------------------------------------------------------------------

simulation_df = measurement_df.copy(deep=True).rename(
Expand All @@ -59,9 +51,3 @@
llh = petab.calculate_llh(
measurement_df, simulation_df, observable_df, parameter_df)
print(llh)
# write files

write_solution(test_id=test_id,
chi2=chi2,
llh=llh,
simulation_dfs=[simulation_df])
17 changes: 1 addition & 16 deletions cases/0005/0005.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@

# problem --------------------------------------------------------------------

model = DEFAULT_MODEL_FILE
model = 'conversion_modified.xml'

condition_df = pd.DataFrame(data={
CONDITION_ID: ['c0', 'c1'],
Expand Down Expand Up @@ -39,15 +39,6 @@
}).set_index(PARAMETER_ID)


# write files

write_problem(test_id=test_id,
parameter_df=parameter_df,
condition_dfs=[condition_df],
observable_dfs=[observable_df],
measurement_dfs=[measurement_df],
sbml_files=['conversion_modified.xml'])

# solutions ------------------------------------------------------------------

simulation_df = measurement_df.copy(deep=True).rename(
Expand All @@ -61,9 +52,3 @@
llh = petab.calculate_llh(
measurement_df, simulation_df, observable_df, parameter_df)
print(llh)
# write files

write_solution(test_id=test_id,
chi2=chi2,
llh=llh,
simulation_dfs=[simulation_df])
16 changes: 1 addition & 15 deletions cases/0006/0006.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@

# problem --------------------------------------------------------------------

model = DEFAULT_MODEL_FILE
model = DEFAULT_SBML_FILE

condition_df = pd.DataFrame(data={
CONDITION_ID: ['c0'],
Expand Down Expand Up @@ -39,14 +39,6 @@
}).set_index(PARAMETER_ID)


# write files

write_problem(test_id=test_id,
parameter_df=parameter_df,
condition_dfs=[condition_df],
observable_dfs=[observable_df],
measurement_dfs=[measurement_df])

# solutions ------------------------------------------------------------------

simulation_df = measurement_df.copy(deep=True).rename(
Expand All @@ -60,9 +52,3 @@
llh = petab.calculate_llh(
measurement_df, simulation_df, observable_df, parameter_df)
print(llh)
# write files

write_solution(test_id=test_id,
chi2=chi2,
llh=llh,
simulation_dfs=[simulation_df])
16 changes: 1 addition & 15 deletions cases/0007/0007.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@

# problem --------------------------------------------------------------------

model = DEFAULT_MODEL_FILE
model = DEFAULT_SBML_FILE

condition_df = pd.DataFrame(data={
CONDITION_ID: ['c0'],
Expand Down Expand Up @@ -39,14 +39,6 @@
}).set_index(PARAMETER_ID)


# write files

write_problem(test_id=test_id,
parameter_df=parameter_df,
condition_dfs=[condition_df],
observable_dfs=[observable_df],
measurement_dfs=[measurement_df])

# solutions ------------------------------------------------------------------

simulation_df = measurement_df.copy(deep=True).rename(
Expand All @@ -62,9 +54,3 @@
llh = petab.calculate_llh(
measurement_df, simulation_df, observable_df, parameter_df)
print(llh)
# write files

write_solution(test_id=test_id,
chi2=chi2,
llh=llh,
simulation_dfs=[simulation_df])
16 changes: 1 addition & 15 deletions cases/0008/0008.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@

# problem --------------------------------------------------------------------

model = DEFAULT_MODEL_FILE
model = DEFAULT_SBML_FILE

condition_df = pd.DataFrame(data={
CONDITION_ID: ['c0'],
Expand Down Expand Up @@ -38,14 +38,6 @@
}).set_index(PARAMETER_ID)


# write files

write_problem(test_id=test_id,
parameter_df=parameter_df,
condition_dfs=[condition_df],
observable_dfs=[observable_df],
measurement_dfs=[measurement_df])

# solutions ------------------------------------------------------------------

simulation_df = measurement_df.copy(deep=True).rename(
Expand All @@ -59,9 +51,3 @@
llh = petab.calculate_llh(
measurement_df, simulation_df, observable_df, parameter_df)
print(llh)
# write files

write_solution(test_id=test_id,
chi2=chi2,
llh=llh,
simulation_dfs=[simulation_df])
16 changes: 1 addition & 15 deletions cases/0009/0009.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@

# problem --------------------------------------------------------------------

model = DEFAULT_MODEL_FILE
model = DEFAULT_SBML_FILE

condition_df = pd.DataFrame(data={
CONDITION_ID: ['preeq_c0', 'c0'],
Expand Down Expand Up @@ -40,14 +40,6 @@
}).set_index(PARAMETER_ID)


# write files

write_problem(test_id=test_id,
parameter_df=parameter_df,
condition_dfs=[condition_df],
observable_dfs=[observable_df],
measurement_dfs=[measurement_df])

# solutions ------------------------------------------------------------------

simulation_df = measurement_df.copy(deep=True).rename(
Expand All @@ -66,9 +58,3 @@
llh = petab.calculate_llh(
measurement_df, simulation_df, observable_df, parameter_df)
print(llh)
# write files

write_solution(test_id=test_id,
chi2=chi2,
llh=llh,
simulation_dfs=[simulation_df])
17 changes: 1 addition & 16 deletions cases/0010/0010.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@

# problem --------------------------------------------------------------------

model = DEFAULT_MODEL_FILE
model = DEFAULT_SBML_FILE

condition_df = pd.DataFrame(data={
CONDITION_ID: ['preeq_c0', 'c0'],
Expand Down Expand Up @@ -41,15 +41,6 @@
}).set_index(PARAMETER_ID)


# write files

write_problem(test_id=test_id,
parameter_df=parameter_df,
condition_dfs=[condition_df],
observable_dfs=[observable_df],
measurement_dfs=[measurement_df],
sbml_files=['conversion_modified.xml'])

# solutions ------------------------------------------------------------------

simulation_df = measurement_df.copy(deep=True).rename(
Expand All @@ -67,9 +58,3 @@
llh = petab.calculate_llh(
measurement_df, simulation_df, observable_df, parameter_df)
print(llh)
# write files

write_solution(test_id=test_id,
chi2=chi2,
llh=llh,
simulation_dfs=[simulation_df])
7 changes: 7 additions & 0 deletions cases/0010/_model.xml
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Expand Up @@ -28,6 +28,8 @@
</listOfSpecies>

<listOfParameters>
<parameter id="a0" name="a0" value="1" constant="true">
</parameter>
<parameter id="b0" name="b0" value="1" constant="true">
</parameter>
<parameter id="k1" name="k1" value="0" constant="true">
Expand All @@ -37,6 +39,11 @@
</listOfParameters>

<listOfInitialAssignments>
<initialAssignment symbol="A">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> a0 </ci>
</math>
</initialAssignment>
<initialAssignment symbol="B">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> b0 </ci>
Expand Down
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