Skip to content

Remove amici.pandas.* #3064

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
dweindl merged 1 commit into from
Nov 20, 2025
Merged

Remove amici.pandas.* #3064

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
75 changes: 0 additions & 75 deletions doc/examples/getting_started_extended/GettingStartedExtended.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,11 +36,6 @@
" ParameterScaling,\n",
" SensitivityMethod,\n",
" SensitivityOrder,\n",
" get_data_observables_as_data_frame,\n",
" get_edata_from_data_frame,\n",
" get_residuals_as_data_frame,\n",
" get_simulation_observables_as_data_frame,\n",
" get_simulation_states_as_data_frame,\n",
" run_simulation,\n",
")"
]
Expand Down Expand Up @@ -1349,76 +1344,6 @@
"source": [
"plot_sensitivities(\"y\", eps)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Export as DataFrame\n",
"\n",
"Experimental data and simulation results can both be exported as pandas Dataframe to allow for an easier inspection of numeric values"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# run the simulation\n",
"rdata = run_simulation(model, solver, edata)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# look at the ExpData as DataFrame\n",
"df = get_data_observables_as_data_frame(model, [edata])\n",
"df"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# from the exported dataframe, we can actually reconstruct a copy of the ExpData instance\n",
"reconstructed_edata = get_edata_from_data_frame(model, df)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# look at the States in rdata as DataFrame\n",
"get_residuals_as_data_frame(model, [edata], [rdata])"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# look at the Observables in rdata as DataFrame\n",
"get_simulation_observables_as_data_frame(model, [edata], [rdata])"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# look at the States in rdata as DataFrame\n",
"get_simulation_states_as_data_frame(model, [edata], [rdata])"
]
}
],
"metadata": {
Expand Down
67 changes: 0 additions & 67 deletions python/tests/test_pandas.py
View file
Open in desktop

This file was deleted.

83 changes: 0 additions & 83 deletions python/tests/test_sbml_import.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,19 +25,12 @@
AMICI_SUCCESS,
Constraint,
ExpData,
ExpDataView,
ModelModule,
ParameterScaling,
ReturnDataView,
SensitivityMethod,
SensitivityOrder,
SteadyStateSensitivityMode,
get_data_observables_as_data_frame,
get_edata_from_data_frame,
get_expressions_as_dataframe,
get_residuals_as_data_frame,
get_simulation_observables_as_data_frame,
get_simulation_states_as_data_frame,
parameter_scaling_from_int_vector,
run_simulation,
run_simulations,
Expand Down Expand Up @@ -466,63 +459,6 @@ def test_steadystate_simulation(model_steadystate_module):
assert rdata[0].status == AMICI_SUCCESS
assert rdata[0].id == edata[0].id

# check roundtripping of DataFrame conversion
df_edata = get_data_observables_as_data_frame(model, edata)
edata_reconstructed = get_edata_from_data_frame(model, df_edata)

assert_allclose(
ExpDataView(edata[0])["observed_data"],
ExpDataView(edata_reconstructed[0])["observed_data"],
rtol=1.0e-5,
atol=1.0e-8,
)

assert_allclose(
ExpDataView(edata[0])["observed_data_std_dev"],
ExpDataView(edata_reconstructed[0])["observed_data_std_dev"],
rtol=1.0e-5,
atol=1.0e-8,
)

if len(edata[0].fixed_parameters):
assert list(edata[0].fixed_parameters) == list(
edata_reconstructed[0].fixed_parameters
)

else:
assert list(model.get_fixed_parameters()) == list(
edata_reconstructed[0].fixed_parameters
)

assert list(edata[0].fixed_parameters_pre_equilibration) == list(
edata_reconstructed[0].fixed_parameters_pre_equilibration
)

df_state = get_simulation_states_as_data_frame(model, edata, rdata)
assert_allclose(
rdata[0]["x"],
df_state[list(model.get_state_ids())].values,
rtol=1.0e-5,
atol=1.0e-8,
)

df_obs = get_simulation_observables_as_data_frame(model, edata, rdata)
assert_allclose(
rdata[0]["y"],
df_obs[list(model.get_observable_ids())].values,
rtol=1.0e-5,
atol=1.0e-8,
)
get_residuals_as_data_frame(model, edata, rdata)

df_expr = get_expressions_as_dataframe(model, edata, rdata)
assert_allclose(
rdata[0]["w"],
df_expr[list(model.get_expression_ids())].values,
rtol=1.0e-5,
atol=1.0e-8,
)

solver.set_relative_tolerance(1e-12)
solver.set_absolute_tolerance(1e-12)
check_derivatives(
Expand Down Expand Up @@ -630,25 +566,6 @@ def test_likelihoods(model_test_likelihoods):
assert np.all(np.isfinite(rdata["sllh"]))
assert np.any(rdata["sllh"])

rdata_df = get_simulation_observables_as_data_frame(
model, edata, rdata, by_id=True
)
edata_df = get_data_observables_as_data_frame(model, edata, by_id=True)

# check correct likelihood value
llh_exp = -sum(
[
normal_nllh(edata_df["o1"], rdata_df["o1"], sigmas[0]),
log_normal_nllh(edata_df["o2"], rdata_df["o2"], sigmas[1]),
log10_normal_nllh(edata_df["o3"], rdata_df["o3"], sigmas[2]),
laplace_nllh(edata_df["o4"], rdata_df["o4"], sigmas[3]),
log_laplace_nllh(edata_df["o5"], rdata_df["o5"], sigmas[4]),
log10_laplace_nllh(edata_df["o6"], rdata_df["o6"], sigmas[5]),
custom_nllh(edata_df["o7"], rdata_df["o7"], sigmas[6]),
]
)
assert np.isclose(rdata["llh"], llh_exp)

# check gradient
for sensi_method in [
SensitivityMethod.forward,
Expand Down
Loading