PEtab-dev · sebapersson · Mar 6, 2026 · Feb 26, 2026
diff --git a/assets/inputs/convert.jl b/assets/inputs/convert.jl
diff --git a/assets/inputs/net3_input1.hdf5 b/assets/inputs/net3_input1.hdf5
diff --git a/assets/inputs/net3_input2.hdf5 b/assets/inputs/net3_input2.hdf5
diff --git a/assets/inputs/net6_input1.hdf5 b/assets/inputs/net6_input1.hdf5
diff --git a/assets/inputs/net6_input2.hdf5 b/assets/inputs/net6_input2.hdf5
diff --git a/assets/parameters/edit.jl b/assets/parameters/edit.jl
diff --git a/assets/parameters/net1_OBS1_ps.hdf5 b/assets/parameters/net1_OBS1_ps.hdf5
diff --git a/assets/parameters/net1_UDE1_ps.hdf5 b/assets/parameters/net1_UDE1_ps.hdf5
diff --git a/assets/parameters/net1_pre_ODE1_ps.hdf5 b/assets/parameters/net1_pre_ODE1_ps.hdf5
diff --git a/assets/parameters/net1_pre_ODE2_ps.hdf5 b/assets/parameters/net1_pre_ODE2_ps.hdf5
diff --git a/assets/parameters/net1_pre_ODE3_ps.hdf5 b/assets/parameters/net1_pre_ODE3_ps.hdf5
diff --git a/assets/parameters/net1_pre_ODE5_ps.hdf5 b/assets/parameters/net1_pre_ODE5_ps.hdf5
diff --git a/assets/parameters/net2_OBS1_ps.hdf5 b/assets/parameters/net2_OBS1_ps.hdf5
diff --git a/assets/parameters/net2_UDE1_ps.hdf5 b/assets/parameters/net2_UDE1_ps.hdf5
diff --git a/assets/parameters/net2_pre_ODE1_ps.hdf5 b/assets/parameters/net2_pre_ODE1_ps.hdf5
diff --git a/assets/parameters/net3_pre_ODE1_ps.hdf5 b/assets/parameters/net3_pre_ODE1_ps.hdf5
diff --git a/assets/parameters/net3_pre_ODE2_ps.hdf5 b/assets/parameters/net3_pre_ODE2_ps.hdf5
diff --git a/assets/parameters/net4_COMBO1_ps.hdf5 b/assets/parameters/net4_COMBO1_ps.hdf5
diff --git a/assets/parameters/net4_OBS1_ps.hdf5 b/assets/parameters/net4_OBS1_ps.hdf5
diff --git a/assets/parameters/net4_UDE1_ps.hdf5 b/assets/parameters/net4_UDE1_ps.hdf5
diff --git a/assets/parameters/net4_pre_ODE1_ps.hdf5 b/assets/parameters/net4_pre_ODE1_ps.hdf5
diff --git a/assets/parameters/net5_OBS1_ps.hdf5 b/assets/parameters/net5_OBS1_ps.hdf5
diff --git a/assets/parameters/net5_UDE1_ps.hdf5 b/assets/parameters/net5_UDE1_ps.hdf5
diff --git a/assets/parameters/net5_pre_ODE1_ps.hdf5 b/assets/parameters/net5_pre_ODE1_ps.hdf5
diff --git a/assets/parameters/net6_OBS1_ps.hdf5 b/assets/parameters/net6_OBS1_ps.hdf5
diff --git a/assets/parameters/net6_OBS2_ps.hdf5 b/assets/parameters/net6_OBS2_ps.hdf5
diff --git a/assets/parameters/net6_UDE1_ps.hdf5 b/assets/parameters/net6_UDE1_ps.hdf5
diff --git a/assets/parameters/net6_UDE2_ps.hdf5 b/assets/parameters/net6_UDE2_ps.hdf5
diff --git a/src/helper.jl b/src/helper.jl
@@ -93,7 +93,7 @@ function save_io(
         g_output0["data"] = xsave
     end
     g_metadata = HDF5.create_group(f, "metadata")
-    g_metadata["perm"] = "row"
+    g_metadata["pytorch_format"] = true
     close(f)
     return nothing
 end
@@ -124,7 +124,7 @@ function nn_ps_to_h5(
 
     # In the PEtabSciML standard parameters are Row-Major
     g_metadata = HDF5.create_group(file, "metadata")
-    g_metadata["perm"] = "row"
+    g_metadata["pytorch_format"] = true
     close(file)
     return nothing
 end

diff --git a/test_cases/initialization/001/net1_ref.hdf5 b/test_cases/initialization/001/net1_ref.hdf5
diff --git a/test_cases/initialization/001/petab/net1_ps.hdf5 b/test_cases/initialization/001/petab/net1_ps.hdf5
diff --git a/test_cases/initialization/002/net1_ref.hdf5 b/test_cases/initialization/002/net1_ref.hdf5
diff --git a/test_cases/initialization/002/petab/net1_ps.hdf5 b/test_cases/initialization/002/petab/net1_ps.hdf5
diff --git a/test_cases/initialization/003/net1_ref.hdf5 b/test_cases/initialization/003/net1_ref.hdf5
diff --git a/test_cases/initialization/003/petab/net1_ps.hdf5 b/test_cases/initialization/003/petab/net1_ps.hdf5
diff --git a/test_cases/ml_model_import/001/net_input_1.hdf5 b/test_cases/ml_model_import/001/net_input_1.hdf5
diff --git a/test_cases/ml_model_import/001/net_input_2.hdf5 b/test_cases/ml_model_import/001/net_input_2.hdf5
diff --git a/test_cases/ml_model_import/001/net_input_3.hdf5 b/test_cases/ml_model_import/001/net_input_3.hdf5
diff --git a/test_cases/ml_model_import/001/net_output_1.hdf5 b/test_cases/ml_model_import/001/net_output_1.hdf5
diff --git a/test_cases/ml_model_import/001/net_output_2.hdf5 b/test_cases/ml_model_import/001/net_output_2.hdf5
diff --git a/test_cases/ml_model_import/001/net_output_3.hdf5 b/test_cases/ml_model_import/001/net_output_3.hdf5
diff --git a/test_cases/ml_model_import/001/net_ps_1.hdf5 b/test_cases/ml_model_import/001/net_ps_1.hdf5
diff --git a/test_cases/ml_model_import/001/net_ps_2.hdf5 b/test_cases/ml_model_import/001/net_ps_2.hdf5
diff --git a/test_cases/ml_model_import/001/net_ps_3.hdf5 b/test_cases/ml_model_import/001/net_ps_3.hdf5
diff --git a/test_cases/ml_model_import/002/net_input_1.hdf5 b/test_cases/ml_model_import/002/net_input_1.hdf5
diff --git a/test_cases/ml_model_import/002/net_input_2.hdf5 b/test_cases/ml_model_import/002/net_input_2.hdf5
diff --git a/test_cases/ml_model_import/002/net_input_3.hdf5 b/test_cases/ml_model_import/002/net_input_3.hdf5
diff --git a/test_cases/ml_model_import/002/net_output_1.hdf5 b/test_cases/ml_model_import/002/net_output_1.hdf5
diff --git a/test_cases/ml_model_import/002/net_output_2.hdf5 b/test_cases/ml_model_import/002/net_output_2.hdf5
diff --git a/test_cases/ml_model_import/002/net_output_3.hdf5 b/test_cases/ml_model_import/002/net_output_3.hdf5
diff --git a/test_cases/ml_model_import/002/net_ps_1.hdf5 b/test_cases/ml_model_import/002/net_ps_1.hdf5
diff --git a/test_cases/ml_model_import/002/net_ps_2.hdf5 b/test_cases/ml_model_import/002/net_ps_2.hdf5
diff --git a/test_cases/ml_model_import/002/net_ps_3.hdf5 b/test_cases/ml_model_import/002/net_ps_3.hdf5
diff --git a/test_cases/ml_model_import/003/net_input_1.hdf5 b/test_cases/ml_model_import/003/net_input_1.hdf5
diff --git a/test_cases/ml_model_import/003/net_input_2.hdf5 b/test_cases/ml_model_import/003/net_input_2.hdf5
diff --git a/test_cases/ml_model_import/003/net_input_3.hdf5 b/test_cases/ml_model_import/003/net_input_3.hdf5
diff --git a/test_cases/ml_model_import/003/net_output_1.hdf5 b/test_cases/ml_model_import/003/net_output_1.hdf5
diff --git a/test_cases/ml_model_import/003/net_output_2.hdf5 b/test_cases/ml_model_import/003/net_output_2.hdf5
diff --git a/test_cases/ml_model_import/003/net_output_3.hdf5 b/test_cases/ml_model_import/003/net_output_3.hdf5
diff --git a/test_cases/ml_model_import/003/net_ps_1.hdf5 b/test_cases/ml_model_import/003/net_ps_1.hdf5
diff --git a/test_cases/ml_model_import/003/net_ps_2.hdf5 b/test_cases/ml_model_import/003/net_ps_2.hdf5
diff --git a/test_cases/ml_model_import/003/net_ps_3.hdf5 b/test_cases/ml_model_import/003/net_ps_3.hdf5
diff --git a/test_cases/ml_model_import/004/net_input_1.hdf5 b/test_cases/ml_model_import/004/net_input_1.hdf5
diff --git a/test_cases/ml_model_import/004/net_input_2.hdf5 b/test_cases/ml_model_import/004/net_input_2.hdf5
diff --git a/test_cases/ml_model_import/004/net_input_3.hdf5 b/test_cases/ml_model_import/004/net_input_3.hdf5
diff --git a/test_cases/ml_model_import/004/net_output_1.hdf5 b/test_cases/ml_model_import/004/net_output_1.hdf5
diff --git a/test_cases/ml_model_import/004/net_output_2.hdf5 b/test_cases/ml_model_import/004/net_output_2.hdf5
diff --git a/test_cases/ml_model_import/004/net_output_3.hdf5 b/test_cases/ml_model_import/004/net_output_3.hdf5
diff --git a/test_cases/ml_model_import/004/net_ps_1.hdf5 b/test_cases/ml_model_import/004/net_ps_1.hdf5
diff --git a/test_cases/ml_model_import/004/net_ps_2.hdf5 b/test_cases/ml_model_import/004/net_ps_2.hdf5
diff --git a/test_cases/ml_model_import/004/net_ps_3.hdf5 b/test_cases/ml_model_import/004/net_ps_3.hdf5
diff --git a/test_cases/ml_model_import/005/net_input_1.hdf5 b/test_cases/ml_model_import/005/net_input_1.hdf5
diff --git a/test_cases/ml_model_import/005/net_input_2.hdf5 b/test_cases/ml_model_import/005/net_input_2.hdf5
diff --git a/test_cases/ml_model_import/005/net_input_3.hdf5 b/test_cases/ml_model_import/005/net_input_3.hdf5
diff --git a/test_cases/ml_model_import/005/net_output_1.hdf5 b/test_cases/ml_model_import/005/net_output_1.hdf5
diff --git a/test_cases/ml_model_import/005/net_output_2.hdf5 b/test_cases/ml_model_import/005/net_output_2.hdf5
diff --git a/test_cases/ml_model_import/005/net_output_3.hdf5 b/test_cases/ml_model_import/005/net_output_3.hdf5
diff --git a/test_cases/ml_model_import/005/net_ps_1.hdf5 b/test_cases/ml_model_import/005/net_ps_1.hdf5
diff --git a/test_cases/ml_model_import/005/net_ps_2.hdf5 b/test_cases/ml_model_import/005/net_ps_2.hdf5
diff --git a/test_cases/ml_model_import/005/net_ps_3.hdf5 b/test_cases/ml_model_import/005/net_ps_3.hdf5
diff --git a/test_cases/ml_model_import/006/net_input_1.hdf5 b/test_cases/ml_model_import/006/net_input_1.hdf5
diff --git a/test_cases/ml_model_import/006/net_input_2.hdf5 b/test_cases/ml_model_import/006/net_input_2.hdf5
diff --git a/test_cases/ml_model_import/006/net_input_3.hdf5 b/test_cases/ml_model_import/006/net_input_3.hdf5
diff --git a/test_cases/ml_model_import/006/net_output_1.hdf5 b/test_cases/ml_model_import/006/net_output_1.hdf5
diff --git a/test_cases/ml_model_import/006/net_output_2.hdf5 b/test_cases/ml_model_import/006/net_output_2.hdf5
diff --git a/test_cases/ml_model_import/006/net_output_3.hdf5 b/test_cases/ml_model_import/006/net_output_3.hdf5
diff --git a/test_cases/ml_model_import/006/net_ps_1.hdf5 b/test_cases/ml_model_import/006/net_ps_1.hdf5
diff --git a/test_cases/ml_model_import/006/net_ps_2.hdf5 b/test_cases/ml_model_import/006/net_ps_2.hdf5
diff --git a/test_cases/ml_model_import/006/net_ps_3.hdf5 b/test_cases/ml_model_import/006/net_ps_3.hdf5
diff --git a/test_cases/ml_model_import/007/net_input_1.hdf5 b/test_cases/ml_model_import/007/net_input_1.hdf5
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diff --git a/test_cases/ml_model_import/007/net_input_3.hdf5 b/test_cases/ml_model_import/007/net_input_3.hdf5
diff --git a/test_cases/ml_model_import/007/net_output_1.hdf5 b/test_cases/ml_model_import/007/net_output_1.hdf5
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