From bea6768bd6cee47c8c88e180bbae566e0498e953 Mon Sep 17 00:00:00 2001 From: Branwen Snelling Date: Thu, 12 Mar 2026 09:46:49 +0000 Subject: [PATCH] update estimate format - add required version number to yamls --- src/petab/parameters.jl | 2 +- src/petab/yaml.jl | 6 +- test_cases/initialization/001/net1_ref.hdf5 | Bin 9896 -> 9896 bytes .../initialization/001/petab/parameters.tsv | 10 +-- .../initialization/001/petab/problem.yaml | 4 +- test_cases/initialization/002/net1_ref.hdf5 | Bin 9896 -> 9896 bytes .../initialization/002/petab/parameters.tsv | 10 +-- .../initialization/002/petab/problem.yaml | 4 +- test_cases/initialization/003/net1_ref.hdf5 | Bin 9896 -> 9896 bytes .../initialization/003/petab/parameters.tsv | 10 +-- .../initialization/003/petab/problem.yaml | 4 +- .../sciml_problem_import/001/grad_mech.tsv | 2 +- .../sciml_problem_import/001/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../001/petab/parameters.tsv | 8 +- .../001/petab/problem.yaml | 4 +- .../sciml_problem_import/002/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../002/petab/parameters.tsv | 12 +-- .../002/petab/problem.yaml | 4 +- .../sciml_problem_import/003/grad_mech.tsv | 4 +- .../sciml_problem_import/003/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../003/petab/parameters.tsv | 12 +-- .../003/petab/problem.yaml | 4 +- .../sciml_problem_import/004/grad_mech.tsv | 2 +- .../sciml_problem_import/004/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../004/petab/parameters.tsv | 10 +-- .../004/petab/problem.yaml | 4 +- .../sciml_problem_import/005/grad_mech.tsv | 4 +- .../sciml_problem_import/005/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../005/petab/parameters.tsv | 10 +-- .../005/petab/problem.yaml | 4 +- .../sciml_problem_import/006/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../006/petab/parameters.tsv | 12 +-- .../006/petab/problem.yaml | 4 +- .../sciml_problem_import/007/grad_mech.tsv | 2 +- .../sciml_problem_import/007/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../007/petab/parameters.tsv | 14 ++-- .../007/petab/problem.yaml | 4 +- .../sciml_problem_import/007/simulations.tsv | 4 +- .../sciml_problem_import/008/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../sciml_problem_import/008/grad_net2.hdf5 | Bin 9896 -> 9896 bytes .../008/petab/parameters.tsv | 16 ++-- .../008/petab/problem.yaml | 4 +- .../sciml_problem_import/009/grad_mech.tsv | 2 +- .../sciml_problem_import/009/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../sciml_problem_import/009/grad_net2.hdf5 | Bin 9896 -> 9896 bytes .../009/petab/parameters.tsv | 12 +-- .../009/petab/problem.yaml | 4 +- .../sciml_problem_import/010/grad_mech.tsv | 2 +- .../sciml_problem_import/010/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../sciml_problem_import/010/grad_net2.hdf5 | Bin 9896 -> 9896 bytes .../010/petab/parameters.tsv | 8 +- .../010/petab/problem.yaml | 4 +- .../sciml_problem_import/011/grad_mech.tsv | 2 +- .../sciml_problem_import/011/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../sciml_problem_import/011/grad_net2.hdf5 | Bin 9896 -> 9896 bytes .../011/petab/parameters.tsv | 12 +-- .../011/petab/problem.yaml | 4 +- .../sciml_problem_import/012/grad_mech.tsv | 2 +- .../sciml_problem_import/012/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../sciml_problem_import/012/grad_net2.hdf5 | Bin 9896 -> 9896 bytes .../012/petab/parameters.tsv | 10 +-- .../012/petab/problem.yaml | 4 +- .../sciml_problem_import/013/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../sciml_problem_import/013/grad_net2.hdf5 | Bin 9896 -> 9896 bytes .../013/petab/parameters.tsv | 14 ++-- .../013/petab/problem.yaml | 4 +- .../sciml_problem_import/014/grad_mech.tsv | 6 +- .../sciml_problem_import/014/grad_net3.hdf5 | Bin 8448 -> 8448 bytes .../014/petab/parameters.tsv | 8 +- .../014/petab/problem.yaml | 4 +- .../sciml_problem_import/014/simulations.tsv | 40 ++++----- .../sciml_problem_import/014/solutions.yaml | 2 +- .../sciml_problem_import/015/grad_mech.tsv | 6 +- .../sciml_problem_import/015/grad_net3.hdf5 | Bin 8448 -> 8448 bytes .../015/petab/parameters.tsv | 8 +- .../015/petab/problem.yaml | 4 +- .../sciml_problem_import/015/simulations.tsv | 78 +++++++++--------- .../sciml_problem_import/015/solutions.yaml | 2 +- .../sciml_problem_import/016/grad_mech.tsv | 2 +- .../016/petab/parameters.tsv | 8 +- .../016/petab/problem.yaml | 4 +- .../017/petab/parameters.tsv | 12 +-- .../017/petab/problem.yaml | 4 +- .../sciml_problem_import/018/grad_mech.tsv | 2 +- .../018/petab/parameters.tsv | 10 +-- .../018/petab/problem.yaml | 4 +- .../sciml_problem_import/019/grad_mech.tsv | 2 +- .../sciml_problem_import/019/grad_net4.hdf5 | Bin 9896 -> 9896 bytes .../019/petab/parameters.tsv | 6 +- .../019/petab/problem.yaml | 4 +- .../sciml_problem_import/019/simulations.tsv | 2 +- .../sciml_problem_import/020/grad_mech.tsv | 2 +- .../sciml_problem_import/020/grad_net4.hdf5 | Bin 9896 -> 9896 bytes .../020/petab/parameters.tsv | 10 +-- .../020/petab/problem.yaml | 4 +- .../sciml_problem_import/021/grad_mech.tsv | 4 +- .../sciml_problem_import/021/grad_net4.hdf5 | Bin 9896 -> 9896 bytes .../021/petab/parameters.tsv | 10 +-- .../021/petab/problem.yaml | 4 +- .../sciml_problem_import/021/simulations.tsv | 2 +- .../sciml_problem_import/022/grad_mech.tsv | 2 +- .../sciml_problem_import/022/grad_net4.hdf5 | Bin 9896 -> 9896 bytes .../022/petab/parameters.tsv | 8 +- .../022/petab/problem.yaml | 4 +- .../sciml_problem_import/023/grad_mech.tsv | 2 +- .../sciml_problem_import/023/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../023/petab/parameters.tsv | 10 +-- .../023/petab/problem.yaml | 4 +- .../sciml_problem_import/024/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../024/petab/parameters.tsv | 14 ++-- .../024/petab/problem.yaml | 4 +- .../sciml_problem_import/025/grad_mech.tsv | 2 +- .../sciml_problem_import/025/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../025/petab/parameters.tsv | 12 +-- .../025/petab/problem.yaml | 4 +- .../sciml_problem_import/026/grad_mech.tsv | 2 +- .../sciml_problem_import/026/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../026/petab/parameters.tsv | 10 +-- .../026/petab/problem.yaml | 4 +- .../sciml_problem_import/027/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../027/petab/parameters.tsv | 14 ++-- .../027/petab/problem.yaml | 4 +- .../sciml_problem_import/028/grad_mech.tsv | 2 +- .../sciml_problem_import/028/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../028/petab/parameters.tsv | 12 +-- .../028/petab/problem.yaml | 4 +- .../sciml_problem_import/029/grad_mech.tsv | 2 +- .../sciml_problem_import/029/grad_net5.hdf5 | Bin 9896 -> 9896 bytes .../029/petab/parameters.tsv | 8 +- .../029/petab/problem.yaml | 4 +- .../sciml_problem_import/030/grad_net5.hdf5 | Bin 9896 -> 9896 bytes .../030/petab/parameters.tsv | 12 +-- .../030/petab/problem.yaml | 4 +- .../sciml_problem_import/031/grad_mech.tsv | 2 +- .../sciml_problem_import/031/grad_net5.hdf5 | Bin 9896 -> 9896 bytes .../031/petab/parameters.tsv | 10 +-- .../031/petab/problem.yaml | 4 +- .../sciml_problem_import/032/grad_mech.tsv | 6 +- .../sciml_problem_import/032/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../032/petab/parameters.tsv | 12 +-- .../032/petab/problem.yaml | 4 +- .../sciml_problem_import/032/solutions.yaml | 2 +- .../sciml_problem_import/033/grad_mech.tsv | 6 +- .../sciml_problem_import/033/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../033/petab/parameters.tsv | 14 ++-- .../033/petab/problem.yaml | 4 +- .../sciml_problem_import/033/solutions.yaml | 2 +- .../sciml_problem_import/034/grad_mech.tsv | 6 +- .../sciml_problem_import/034/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../034/petab/parameters.tsv | 14 ++-- .../034/petab/problem.yaml | 4 +- .../sciml_problem_import/034/solutions.yaml | 2 +- .../sciml_problem_import/035/grad_net1.hdf5 | Bin 9896 -> 9896 bytes .../035/petab/parameters.tsv | 8 +- .../035/petab/problem.yaml | 4 +- .../sciml_problem_import/036/grad_mech.tsv | 4 +- .../sciml_problem_import/036/grad_net6.hdf5 | Bin 9896 -> 9896 bytes .../036/petab/parameters.tsv | 8 +- .../036/petab/problem.yaml | 4 +- .../sciml_problem_import/037/grad_mech.tsv | 6 +- .../sciml_problem_import/037/grad_net6.hdf5 | Bin 9896 -> 9896 bytes .../037/petab/parameters.tsv | 10 +-- .../037/petab/problem.yaml | 4 +- .../sciml_problem_import/038/grad_mech.tsv | 2 +- .../sciml_problem_import/038/grad_net6.hdf5 | Bin 9896 -> 9896 bytes .../038/petab/parameters.tsv | 8 +- .../038/petab/problem.yaml | 4 +- .../sciml_problem_import/039/grad_mech.tsv | 6 +- .../sciml_problem_import/039/grad_net6.hdf5 | Bin 9896 -> 9896 bytes .../039/petab/parameters.tsv | 10 +-- .../039/petab/problem.yaml | 4 +- 171 files changed, 470 insertions(+), 384 deletions(-) diff --git a/src/petab/parameters.jl b/src/petab/parameters.jl index 8fdf6c5..4330572 100644 --- a/src/petab/parameters.jl +++ b/src/petab/parameters.jl @@ -141,7 +141,7 @@ function save_parameters_table( net_ids = @. string(_net_ids) * "_ps" df_nn = DataFrame( parameterId = net_ids, parameterScale = :lin, lowerBound = "-inf", - upperBound = "inf", nominalValue = "array", estimate = Int(estimate_net_parameters) + upperBound = "inf", nominalValue = "array", estimate = string(estimate_net_parameters) ) df_save = vcat(df_mech, df_nn, cols = :union) diff --git a/src/petab/yaml.jl b/src/petab/yaml.jl index 0956483..9afb1c3 100644 --- a/src/petab/yaml.jl +++ b/src/petab/yaml.jl @@ -3,7 +3,7 @@ function save_petab_yaml( condition_table_id::Symbol ) yaml_dict = Dict( - :format_version => 2, + :format_version => "2.0.0", :measurement_files => ["measurements.tsv"], :experiment_files => ["experiments.tsv"], :observable_files => ["observables.tsv"], @@ -24,7 +24,9 @@ function save_petab_yaml( ext = Dict( :hybridization_files => ["hybridization.tsv"], :neural_nets => Dict(), - :array_files => String[] + :array_files => String[], + :version => "0.1.0", + :required => true ) for (net_id, net_info) in nets_info ext[:neural_nets][net_id] = Dict( diff --git a/test_cases/initialization/001/net1_ref.hdf5 b/test_cases/initialization/001/net1_ref.hdf5 index 4e75b37445de7b556f0ca304c335c097ca8db973..bb7c50a4c85151e6ffecaa7d7ffbbf38e14536a9 100644 GIT binary patch delta 91 zcmZ4CyTW(F6CP%nj!l#MrB-g9z`KM4%(*W;dGjf;L(Cw~=6)$(Mlj>PbSMiPbSMiPbSMi delta 91 zcmZ4CyTW(F6CP%NsRfh!rB-g9z`KM4%(*W;dGjf;L(Cw~=6)$(Mlj>PbSMiPbSMi delta 91 zcmZ4CyTW(F6CP%NsRfh!rB-g9z`KM4%(*W;dGjf;L(Cw~=6)$(Mlj>PbSMioMcBtFCuW;6! zXonN`&R@TJ*4W5FW=da|eBYkyuyloA#Ubsi0|Cazg=!pY92T29rdQla zJHTb*$yKpx>jA;ZC;7|`tqiZPJy}}pu=9dmj{fnj4yO0Kl%`H-bKu&>I?p3&%7KMF z=?86GryXEnO6(9bh_kt0%9jz$xGx>b0uP@D3QOQh XrIcndvjdf8GB8Y-xNz#^0JR7J0KuAm delta 335 zcmZ4CyTW(F6CUP$k_#sHORbzdf!BdatYq>fUbp(`PSP_Ber$0Fo#=gZZtcbc3y&nP zT5xf-!}|{}e|oQ3aiC}^_p=7x4GwP)GI!sdx#Yk#S9`hL6Ivb8eRzZC88jYnDy+D` zIJM59?Ld_9v31P{V$&m7s<|s2Uaebb^Ek%$0PoFslb5Eh2bQ+|t)8Oj>@elnzQS2^ zq8;R4p1*$etg(@U%!Ib*KTcI0aBlZkeBYkyuyloA#Ubsi0|Cazg=!pY9GH6B(kkwx 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0.0 15.0 1.3 1 -delta lin 0.0 15.0 1.8 1 -beta lin 0.0 15.0 0.9 1 -net1_input_pre1 lin -inf inf 1.0 0 -net1_ps lin -inf inf array 1 +alpha lin 0.0 15.0 1.3 true +delta lin 0.0 15.0 1.8 true +beta lin 0.0 15.0 0.9 true +net1_input_pre1 lin -inf inf 1.0 false +net1_ps lin -inf inf array true diff --git a/test_cases/sciml_problem_import/005/petab/problem.yaml b/test_cases/sciml_problem_import/005/petab/problem.yaml index 8fd38b4..fc2aac9 100644 --- a/test_cases/sciml_problem_import/005/petab/problem.yaml +++ b/test_cases/sciml_problem_import/005/petab/problem.yaml @@ -6,7 +6,7 @@ measurement_files: - "measurements.tsv" observable_files: - "observables.tsv" -format_version: 2 +format_version: "2.0.0" experiment_files: - "experiments.tsv" parameter_files: @@ -17,8 +17,10 @@ extensions: sciml: array_files: - "net1_ps.hdf5" + version: "0.1.0" hybridization_files: - "hybridization.tsv" + required: true neural_nets: net1: location: "net1.yaml" diff --git 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b/test_cases/sciml_problem_import/010/petab/parameters.tsv index 3f0c3ac..844e7b0 100644 --- a/test_cases/sciml_problem_import/010/petab/parameters.tsv +++ b/test_cases/sciml_problem_import/010/petab/parameters.tsv @@ -1,5 +1,5 @@ parameterId parameterScale lowerBound upperBound nominalValue estimate -delta lin 0.0 15.0 1.8 1 -beta lin 0.0 15.0 0.9 1 -net2_ps lin -inf inf array 1 -net1_ps lin -inf inf array 1 +delta lin 0.0 15.0 1.8 true +beta lin 0.0 15.0 0.9 true +net2_ps lin -inf inf array true +net1_ps lin -inf inf array true diff --git a/test_cases/sciml_problem_import/010/petab/problem.yaml b/test_cases/sciml_problem_import/010/petab/problem.yaml index 57a520f..34a4de4 100644 --- a/test_cases/sciml_problem_import/010/petab/problem.yaml +++ b/test_cases/sciml_problem_import/010/petab/problem.yaml @@ -6,7 +6,7 @@ measurement_files: - "measurements.tsv" observable_files: - "observables.tsv" -format_version: 2 +format_version: "2.0.0" experiment_files: - "experiments.tsv" parameter_files: @@ -18,8 +18,10 @@ extensions: array_files: - "net2_ps.hdf5" - "net1_ps.hdf5" + version: "0.1.0" hybridization_files: - "hybridization.tsv" + required: true neural_nets: net2: location: "net2.yaml" diff --git a/test_cases/sciml_problem_import/011/grad_mech.tsv b/test_cases/sciml_problem_import/011/grad_mech.tsv index 92c8f3d..0212be1 100644 --- a/test_cases/sciml_problem_import/011/grad_mech.tsv +++ b/test_cases/sciml_problem_import/011/grad_mech.tsv @@ -1,3 +1,3 @@ parameterId value -alpha 2538.780077320352 +alpha 2538.7800773211884 delta 573.6670521169216 diff --git a/test_cases/sciml_problem_import/011/grad_net1.hdf5 b/test_cases/sciml_problem_import/011/grad_net1.hdf5 index a947c3371961a101753576393d9dd23e44ab6208..8fb0ca8f3e1ace37b689a2c24d597510cb3379d1 100644 GIT binary patch delta 335 zcmZ4CyTW(F6CUR9u1%BsrB+U!!0W&?yJGSsUbp&eAL$teKejl8PV_!Hw|3)!gGZBB zEx5Sa;r)k~KfTwiI8d~d`&k3;28Wu1%-wfqE;(?)#$ImsgjNSoMcBtFCuW;6! 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array true diff --git a/test_cases/sciml_problem_import/014/petab/problem.yaml b/test_cases/sciml_problem_import/014/petab/problem.yaml index f73ed2f..901a34c 100644 --- a/test_cases/sciml_problem_import/014/petab/problem.yaml +++ b/test_cases/sciml_problem_import/014/petab/problem.yaml @@ -6,7 +6,7 @@ measurement_files: - "measurements.tsv" observable_files: - "observables.tsv" -format_version: 2 +format_version: "2.0.0" experiment_files: - "experiments.tsv" parameter_files: @@ -18,8 +18,10 @@ extensions: array_files: - "net3_ps.hdf5" - "net3_input1.hdf5" + version: "0.1.0" hybridization_files: - "hybridization.tsv" + required: true neural_nets: net3: location: "net3.yaml" diff --git a/test_cases/sciml_problem_import/014/simulations.tsv b/test_cases/sciml_problem_import/014/simulations.tsv index 6b2d713..a4e435f 100644 --- a/test_cases/sciml_problem_import/014/simulations.tsv +++ b/test_cases/sciml_problem_import/014/simulations.tsv @@ -1,21 +1,21 @@ observableId experimentId simulation time -prey_o e1 0.1996432344128231 1.0 -prey_o e1 0.4842534621198982 2.0 -prey_o e1 1.6063512056977 3.0 -prey_o e1 5.494139655954648 4.0 -prey_o e1 3.078213487078415 5.0 -prey_o e1 0.19515376127176481 6.0 -prey_o e1 0.29649755227373153 7.0 -prey_o e1 0.9041408036540782 8.0 -prey_o e1 3.10913199149817 9.0 -prey_o e1 8.851586911027294 10.0 -predator_o e1 0.9224424008593197 1.0 -predator_o e1 0.19470291525642644 2.0 -predator_o e1 0.06760604257225629 3.0 -predator_o e1 0.1418700352798924 4.0 -predator_o e1 6.698671429685438 5.0 -predator_o e1 1.9955511106531993 6.0 -predator_o e1 0.3922752142581838 7.0 -predator_o e1 0.09942290206371006 8.0 -predator_o e1 0.06834921504989715 9.0 -predator_o e1 1.2238133862048879 10.0 +prey_o e1 0.19964323441282023 1.0 +prey_o e1 0.4842534621198607 2.0 +prey_o e1 1.6063512056973333 3.0 +prey_o e1 5.494139655954669 4.0 +prey_o e1 3.0782134870784272 5.0 +prey_o e1 0.19515376127175768 6.0 +prey_o e1 0.2964975522737117 7.0 +prey_o e1 0.9041408036540876 8.0 +prey_o e1 3.1091319914980744 9.0 +prey_o e1 8.851586911027413 10.0 +predator_o e1 0.9224424008593343 1.0 +predator_o e1 0.19470291525644529 2.0 +predator_o e1 0.06760604257226344 3.0 +predator_o e1 0.14187003527988604 4.0 +predator_o e1 6.698671429685512 5.0 +predator_o e1 1.9955511106531847 6.0 +predator_o e1 0.3922752142581998 7.0 +predator_o e1 0.0994229020637052 8.0 +predator_o e1 0.06834921504989125 9.0 +predator_o e1 1.2238133862046814 10.0 diff --git a/test_cases/sciml_problem_import/014/solutions.yaml b/test_cases/sciml_problem_import/014/solutions.yaml index 11467b4..0f809d2 100644 --- a/test_cases/sciml_problem_import/014/solutions.yaml +++ b/test_cases/sciml_problem_import/014/solutions.yaml @@ -4,6 +4,6 @@ tol_grad: 0.1 grad_files: mech: "grad_mech.tsv" net3: "grad_net3.hdf5" -llh: 33.306381502951396 +llh: 33.3063815029473 tol_simulations: 0.001 tol_llh: 0.001 diff --git a/test_cases/sciml_problem_import/015/grad_mech.tsv b/test_cases/sciml_problem_import/015/grad_mech.tsv index f20cea9..f37760d 100644 --- a/test_cases/sciml_problem_import/015/grad_mech.tsv +++ b/test_cases/sciml_problem_import/015/grad_mech.tsv @@ -1,4 +1,4 @@ parameterId value -alpha 1484.35600690352 -delta 304.7728387882481 -beta -984.4987605162647 +alpha 1484.356007051502 +delta 304.7728389355431 +beta -984.4987606926684 diff --git a/test_cases/sciml_problem_import/015/grad_net3.hdf5 b/test_cases/sciml_problem_import/015/grad_net3.hdf5 index 66391c41b69dd02b736ac14d8a7f2754aef96e24..98ec69d1e6e4ffb6ef324ff0c5e92bf9fee42aa4 100644 GIT binary patch delta 977 zcmW-gdoY{_6vauhUR#q^TJb7Utr6QuD3Y?lm>^cg2Gc=DTBdnurDb-%*S@|_BI6ZH zP=+Fnq-j%0v$`!!(H^#udJL9in4O@QA|*;!>y<>e`S0F2Gv{~inYmmz7p~c1YnfX3 zU51(2(Mwli%YWw`DlfHlU^PB1|1>(2cv7<^jCz^E8Y>>v)sgVD?(uqTq%i->;p}vV zf?y)iWp#!^N&k4TbU%%-F>gVn9f^K^q%S#0B0Z*hDBK{!WZjW~OC1Ds%heXbWGS32 zQn`r&0$<(@u``Nj-1d5W?F64jkYPZVRUlz;XC*WzdV#{Bikf22e;It}tB?*fn2bMG z(+3Fx>PFwp8$uF-$*SCF1oL0<=ZHZ9k@nSYTT?Wm%T`<6JY=XTHNKxe zE(39@DC4Jl41!-=uPHvs;Bfee%~=hF;HsH94;}@}@-5@d2A08wDDPyclt$pEo!K#; z(fH)xgNmyOB(ff)zAoyfV5JYJ?RA%-p}r$^>|r)~gHMS+_h+!!a;IyLCjr5cxvxW; z2!x4ZulzbIfzZXiJDo3udx}+_&UCqPXi47vHiMBzvGXCxBz9Hi->>9LV3bG9nz1F> za45)5Qaed8yV+GQCQU$}jHT99IYJV(xq~lID156oy?uqm#@@dNbzTJO3$4d|=VeH< zdKP0AO5*-BFF|~ZK@BTk?0(e{vl%L%1&yxJ6yZP}JnnTO*c-+XK7 znuAWWB1{W7ZuIzxhZ5WFNzva7*Gc2TQhKPQZyyt(C8Ls}*oa>HOY}mSfQ=lXePa(bLKL?tVVTZ)@HGAw|T0#p6|w?#9plx nykyPWZhF!33FmTckA3I%{}*kEQ>^*(VZwRej_2}D_vQZp`YHg{ delta 977 zcmW+#YfzL000iWuxTrZE77u|!jYKmXsXT9h!2yd9Zg8~2@+^!5f&%Wo*B#vV9f2YQ zC?JEx+j27W4m@B&Ko<|=IdUS5#_(1iiVu(z1R*2;?auz$-Pz^*IKL`$D~nnCvM3Xi z&rX%^%^l%=ntRgf9o8|u>{+EF3BlF-qCK`0zHf-Xqc0{g+BNL{XpX{+*e5=mp|GPt z>a;LHA;I_dF8MYZUn+b&0<1~cy(BzI1BqJ&Y>!{R0(sc&b*h=bNQri>C`^tcRUzE) z2?FGPiS=9{4W@eRHz}V+W8XjexDzrKwb~%{=MO35x|L*ZnrA>-B+I)iNZc@-ravJF zJl!RYIWHpNl#q~;u}ET@bIwZE3mG14wwodh1Rm`Vba^>OL#Ul@aB*8T;JbV{ZAgLZ zv5Kh6tqg2$FBfJ;FlhdB(lWM+LizLgDK{R44d?jA3l%H_Nqus}NjZ(Tg$?mvoTd>S z+nRTF9|;Nn@P@#43S-8|qE1%@Jeb}?g9Gu%7w-}Ox`TmZ!Og$l-9$j$VS3)DntsB3uNdJ-1)IkbA9S{WSgi7RSw9~<6 zGKfe;#z7tl-I4LeAZrFqQBEODD2rZV0%%!nL7VC#{a6-SU9VZ zBT(Y52M7L{*?zrN1^zsbU6vU+)DNvSwen@LzVP04`w12{`Oo~DLpW@Vqd8GBi}nt| z+Nw$xPZp&9ri2>2j-ySX)hx=oSN?dI!J#88%S+58LgT-)(YuMm(nht#mdr#%JN3k@ z_vIj!uLP$@awr|T^PpA2Vdj#J>n}PL*4eOIE&2%+`f55^ z+2$SHu0p-iv#V#dx%=N_cU}xlg5JHN@UgE7=7!0bqBs@;%K-XZnhS>yDid@bg4cO# iRxg@6?3k diff --git a/test_cases/sciml_problem_import/015/petab/parameters.tsv b/test_cases/sciml_problem_import/015/petab/parameters.tsv index 88ead60..66c4ee4 100644 --- a/test_cases/sciml_problem_import/015/petab/parameters.tsv +++ b/test_cases/sciml_problem_import/015/petab/parameters.tsv @@ -1,5 +1,5 @@ parameterId parameterScale lowerBound upperBound nominalValue estimate -alpha lin 0.0 15.0 1.3 1 -delta lin 0.0 15.0 1.8 1 -beta lin 0.0 15.0 0.9 1 -net3_ps lin -inf inf array 1 +alpha lin 0.0 15.0 1.3 true +delta lin 0.0 15.0 1.8 true +beta lin 0.0 15.0 0.9 true +net3_ps lin -inf inf array true diff --git a/test_cases/sciml_problem_import/015/petab/problem.yaml b/test_cases/sciml_problem_import/015/petab/problem.yaml index 7f5cf4b..74b20ca 100644 --- a/test_cases/sciml_problem_import/015/petab/problem.yaml +++ b/test_cases/sciml_problem_import/015/petab/problem.yaml @@ -6,7 +6,7 @@ measurement_files: - "measurements.tsv" observable_files: - "observables.tsv" -format_version: 2 +format_version: "2.0.0" experiment_files: - "experiments.tsv" parameter_files: @@ -18,8 +18,10 @@ extensions: array_files: - "net3_ps.hdf5" - "net3_input2.hdf5" + version: "0.1.0" hybridization_files: - "hybridization.tsv" + required: true neural_nets: net3: location: "net3.yaml" diff --git a/test_cases/sciml_problem_import/015/simulations.tsv b/test_cases/sciml_problem_import/015/simulations.tsv index 9941bc2..869536a 100644 --- a/test_cases/sciml_problem_import/015/simulations.tsv +++ b/test_cases/sciml_problem_import/015/simulations.tsv @@ -1,41 +1,41 @@ observableId experimentId simulation time -prey_o e1 0.1996432213599251 1.0 -prey_o e1 0.4842534122931591 2.0 -prey_o e1 1.606351007036983 3.0 -prey_o e1 5.494138728583467 4.0 -prey_o e1 3.0782089229068963 5.0 -prey_o e1 0.1951537276033331 6.0 -prey_o e1 0.29649760449871376 7.0 -prey_o e1 0.9041410068561255 8.0 -prey_o e1 3.109132642131885 9.0 -prey_o e1 8.851583477989651 10.0 -predator_o e1 0.9224424633341638 1.0 -predator_o e1 0.19470294266203902 2.0 -predator_o e1 0.06760606576802042 3.0 -predator_o e1 0.14187017213641684 4.0 -predator_o e1 6.698671661725177 5.0 -predator_o e1 1.9955502786844945 6.0 -predator_o e1 0.39227508144331347 7.0 -predator_o e1 0.0994228939653806 8.0 -predator_o e1 0.06834926869480501 9.0 -predator_o e1 1.223816858674027 10.0 +prey_o e1 0.1996432213599237 1.0 +prey_o e1 0.48425341229315494 2.0 +prey_o e1 1.6063510070368017 3.0 +prey_o e1 5.494138728583478 4.0 +prey_o e1 3.078208922906972 5.0 +prey_o e1 0.19515372760332517 6.0 +prey_o e1 0.29649760449869456 7.0 +prey_o e1 0.9041410068561169 8.0 +prey_o e1 3.109132642131626 9.0 +prey_o e1 8.851583477989726 10.0 +predator_o e1 0.9224424633341811 1.0 +predator_o e1 0.19470294266203983 2.0 +predator_o e1 0.06760606576802435 3.0 +predator_o e1 0.14187017213641487 4.0 +predator_o e1 6.698671661725244 5.0 +predator_o e1 1.9955502786844843 6.0 +predator_o e1 0.392275081443328 7.0 +predator_o e1 0.09942289396537778 8.0 +predator_o e1 0.06834926869479717 9.0 +predator_o e1 1.2238168586737321 10.0 prey_o e2 0.19136749240335596 1.0 -prey_o e2 0.45308487158172284 2.0 -prey_o e2 1.4827794389191593 3.0 -prey_o e2 4.908416225540576 4.0 -prey_o e2 1.4092350639279347 5.0 -prey_o e2 0.18130167962774593 6.0 -prey_o e2 0.3253179190549205 7.0 -prey_o e2 1.0131210339737602 8.0 -prey_o e2 3.4292206201803155 9.0 -prey_o e2 4.863230857407191 10.0 -predator_o e2 0.9628324437183196 1.0 -predator_o e2 0.2123555154084897 2.0 -predator_o e2 0.08303065274093115 3.0 -predator_o e2 0.24730200729200888 4.0 -predator_o e2 6.320932815298152 5.0 -predator_o e2 1.5953488983625213 6.0 -predator_o e2 0.3304382377783172 7.0 -predator_o e2 0.09913253198176014 8.0 -predator_o e2 0.11917759593869119 9.0 -predator_o e2 4.455220054220248 10.0 +prey_o e2 0.45308487158172256 2.0 +prey_o e2 1.482779438919158 3.0 +prey_o e2 4.908416225540572 4.0 +prey_o e2 1.4092350639280227 5.0 +prey_o e2 0.18130167962774174 6.0 +prey_o e2 0.32531791905494656 7.0 +prey_o e2 1.0131210339736951 8.0 +prey_o e2 3.4292206201802005 9.0 +prey_o e2 4.8632308574076095 10.0 +predator_o e2 0.9628324437183179 1.0 +predator_o e2 0.21235551540848976 2.0 +predator_o e2 0.0830306527409313 3.0 +predator_o e2 0.2473020072920063 4.0 +predator_o e2 6.320932815298211 5.0 +predator_o e2 1.5953488983625406 6.0 +predator_o e2 0.33043823777827247 7.0 +predator_o e2 0.09913253198176049 8.0 +predator_o e2 0.11917759593869 9.0 +predator_o e2 4.455220054219919 10.0 diff --git a/test_cases/sciml_problem_import/015/solutions.yaml b/test_cases/sciml_problem_import/015/solutions.yaml index f911ded..9b8d0ff 100644 --- a/test_cases/sciml_problem_import/015/solutions.yaml +++ b/test_cases/sciml_problem_import/015/solutions.yaml @@ -4,6 +4,6 @@ tol_grad: 0.1 grad_files: mech: "grad_mech.tsv" net3: "grad_net3.hdf5" -llh: 68.96501052725615 +llh: 68.96501052725134 tol_simulations: 0.001 tol_llh: 0.001 diff --git a/test_cases/sciml_problem_import/016/grad_mech.tsv b/test_cases/sciml_problem_import/016/grad_mech.tsv index 8dd5bd5..e6059b2 100644 --- a/test_cases/sciml_problem_import/016/grad_mech.tsv +++ b/test_cases/sciml_problem_import/016/grad_mech.tsv @@ -1,4 +1,4 @@ parameterId value -alpha 2538.780077320352 +alpha 2538.7800773211884 delta 573.6670521169216 beta -2188.7753333246887 diff --git a/test_cases/sciml_problem_import/016/petab/parameters.tsv b/test_cases/sciml_problem_import/016/petab/parameters.tsv index 35e6b6d..4551ac7 100644 --- a/test_cases/sciml_problem_import/016/petab/parameters.tsv +++ b/test_cases/sciml_problem_import/016/petab/parameters.tsv @@ -1,5 +1,5 @@ parameterId parameterScale lowerBound upperBound nominalValue estimate -alpha lin 0.0 15.0 1.3 1 -delta lin 0.0 15.0 1.8 1 -beta lin 0.0 15.0 0.9 1 -net1_ps lin -inf inf array 0 +alpha lin 0.0 15.0 1.3 true +delta lin 0.0 15.0 1.8 true +beta lin 0.0 15.0 0.9 true +net1_ps lin -inf inf array false diff --git a/test_cases/sciml_problem_import/016/petab/problem.yaml b/test_cases/sciml_problem_import/016/petab/problem.yaml index 4377bf4..4e2b5ab 100644 --- a/test_cases/sciml_problem_import/016/petab/problem.yaml +++ b/test_cases/sciml_problem_import/016/petab/problem.yaml @@ -6,7 +6,7 @@ measurement_files: - "measurements.tsv" observable_files: - "observables.tsv" -format_version: 2 +format_version: "2.0.0" experiment_files: - "experiments.tsv" parameter_files: @@ -17,8 +17,10 @@ extensions: sciml: array_files: - "net1_ps.hdf5" + version: "0.1.0" hybridization_files: - "hybridization.tsv" + required: true neural_nets: net1: location: "net1.yaml" diff --git a/test_cases/sciml_problem_import/017/petab/parameters.tsv b/test_cases/sciml_problem_import/017/petab/parameters.tsv index 4e1c9b7..d934a33 100644 --- a/test_cases/sciml_problem_import/017/petab/parameters.tsv +++ b/test_cases/sciml_problem_import/017/petab/parameters.tsv @@ -1,7 +1,7 @@ parameterId parameterScale lowerBound upperBound nominalValue estimate -alpha lin 0.0 15.0 1.3 1 -delta lin 0.0 15.0 1.8 1 -beta lin 0.0 15.0 0.9 1 -net1_input_pre1 lin -inf inf 1.0 0 -net1_input_pre2 lin -inf inf 1.0 0 -net1_ps lin -inf inf array 0 +alpha lin 0.0 15.0 1.3 true +delta lin 0.0 15.0 1.8 true +beta lin 0.0 15.0 0.9 true +net1_input_pre1 lin -inf inf 1.0 false +net1_input_pre2 lin -inf inf 1.0 false +net1_ps lin -inf inf array false diff --git a/test_cases/sciml_problem_import/017/petab/problem.yaml b/test_cases/sciml_problem_import/017/petab/problem.yaml index 8fd38b4..fc2aac9 100644 --- a/test_cases/sciml_problem_import/017/petab/problem.yaml +++ b/test_cases/sciml_problem_import/017/petab/problem.yaml @@ -6,7 +6,7 @@ measurement_files: - "measurements.tsv" observable_files: - "observables.tsv" -format_version: 2 +format_version: "2.0.0" experiment_files: - "experiments.tsv" parameter_files: @@ -17,8 +17,10 @@ extensions: sciml: array_files: - "net1_ps.hdf5" + version: "0.1.0" hybridization_files: - "hybridization.tsv" + required: true neural_nets: net1: location: "net1.yaml" diff --git a/test_cases/sciml_problem_import/018/grad_mech.tsv b/test_cases/sciml_problem_import/018/grad_mech.tsv index 8fe693e..475d0a6 100644 --- a/test_cases/sciml_problem_import/018/grad_mech.tsv +++ b/test_cases/sciml_problem_import/018/grad_mech.tsv @@ -1,5 +1,5 @@ parameterId value alpha 1348.3832160092732 -delta 398.79444240316656 +delta 398.79444240445616 beta -839.2207939522068 gamma 431.5736554673321 diff --git a/test_cases/sciml_problem_import/018/petab/parameters.tsv b/test_cases/sciml_problem_import/018/petab/parameters.tsv index 6c6db2b..8304e59 100644 --- a/test_cases/sciml_problem_import/018/petab/parameters.tsv +++ b/test_cases/sciml_problem_import/018/petab/parameters.tsv @@ -1,6 +1,6 @@ parameterId parameterScale lowerBound upperBound nominalValue estimate -alpha lin 0.0 15.0 1.3 1 -delta lin 0.0 15.0 1.8 1 -beta lin 0.0 15.0 0.9 1 -gamma lin 0.0 15.0 0.8 1 -net1_ps lin -inf inf array 0 +alpha lin 0.0 15.0 1.3 true +delta lin 0.0 15.0 1.8 true +beta lin 0.0 15.0 0.9 true +gamma lin 0.0 15.0 0.8 true +net1_ps lin -inf inf array false diff --git a/test_cases/sciml_problem_import/018/petab/problem.yaml b/test_cases/sciml_problem_import/018/petab/problem.yaml index 4377bf4..4e2b5ab 100644 --- a/test_cases/sciml_problem_import/018/petab/problem.yaml +++ b/test_cases/sciml_problem_import/018/petab/problem.yaml @@ -6,7 +6,7 @@ measurement_files: - "measurements.tsv" observable_files: - "observables.tsv" -format_version: 2 +format_version: "2.0.0" experiment_files: - "experiments.tsv" parameter_files: @@ -17,8 +17,10 @@ extensions: sciml: array_files: - "net1_ps.hdf5" + version: "0.1.0" hybridization_files: - "hybridization.tsv" + required: true neural_nets: net1: location: "net1.yaml" diff --git a/test_cases/sciml_problem_import/019/grad_mech.tsv b/test_cases/sciml_problem_import/019/grad_mech.tsv index f86a7e8..813ea11 100644 --- a/test_cases/sciml_problem_import/019/grad_mech.tsv +++ b/test_cases/sciml_problem_import/019/grad_mech.tsv @@ -1,3 +1,3 @@ parameterId value delta 432.80892943594046 -beta -1062.1699857385913 +beta -1062.1699857385877 diff --git a/test_cases/sciml_problem_import/019/grad_net4.hdf5 b/test_cases/sciml_problem_import/019/grad_net4.hdf5 index 48e0c224cfdf58f77159c3180537803c0ec1cfb0..18a6f61fa173f256704a9d36a70c5dee0ebc7648 100644 GIT binary patch delta 390 zcmZ4CyTW(F6CUQIu1%BsrB+U!z-y88;Lf#|pVGPx{M3kAursRfKuOX>o+76?4)IfJ z9~Iu|a#6}K3m*d3_>-a7Au!+}Ch3M~$N++w!sTTaS> zOv@{ue4kc2Buvy@P}JGyuy3Ku`Z)2v16c`eC-wF>AIO+|kWXBy(qW#+=D8aWa4avM z=@7i`z{kg#>#A<-a_C((`4gX+QHrB`|FM&C2Xy`3Go@C|J#g%8<6Ma{_XC@?DQzf{i}?o2qa%z1MZ|1CCfxZRhYy!n*aA!ZO~bH9`?BbaetI+O(- dtPd2Hz?DiV&0=N;D$QhIm@skS)X4#A5dispyTAYd delta 390 zcmZ4CyTW(F6CUQDk_#sHORbzdf!88Q?#8v3pVGPxv>8V&*csJ#fIE94Pm$9chxjSA zj|%T}Iatrq65pUQ*TLD`vZ3e3>I07ZgdTYBICmgZM>6Vq+tven&d=?8UzUHM@SCW0 zeR8hD+{Q&}F25EW@SXgsLA864gZskCT6}t$hif_fT#gqztmC)b!zxmI;EvwbX&E7< z2YBveEN-1)?eO1!=7|VV)dQ)X|94CmcXn8Ho|QL+$@akAwm<)u6j~hkxW#PMx15v% zD}1he@_kzAkT6kqK~ZO)!@h+s>*K`x4rC>?oz&akeBjIEgM8vrRSxq+HqYI7fMa?2 zOo!lg2aY_+Tvv5tm&1o;lRxp98CjdV_a8eMcR<(gJyUAc+ymw>8|O-txgXe+6)my* zaNB`TM&;MPyy!Y0^Go%t;m(8u64sle_;0a+!|lHGPbSMiah-rC+gGcdZHX!J6s~Ndt(j+N6kAG@IKn1^V~t1 ztxv-b^zg`quFOhsc*ZAov5Y(70LwNOM&>(_4mK%buP^#U)*sMPmE+mGB-EjF`IWfd zJ+TKiKV;|=?T>d@p??0}wjHq!pR!L|zxj}KKuofF4o_(6flGg99QzrV?68-k-e}8& zi4J1Z&k8)aKGA{a)bGC*(i0DGnw`>5FYi5I{qyYR-ebKEx%w45lkb-~%x!&oK)|Nl zVcomE4w-Ic2Y&8awjfx4au~l5vl`pO&Ds1X*}#!=UwZQ9Q(}jhL7dI~Qof8}#(n8f g7I@q}P*?(2Dy1}wnH{J!lYwEv#D!BQ2dG5=0QtY^xDa8yZBaxAAr&B3PoLS{ze{vnS-tmrf%MSW5M{v!3X9X*GWDh7wW+8|19L{ z%8<$Ce2VqH$|~%)OM?#_4Ci`$ZfSr+!<2bf3+{&F=NBp$Ba4B~H^(k9CkfR-aba6Xh_KT_z&CH|9Wa)Vxyx@1q^8Qx3^& zeHwmXb`N*x%B%#3XMAE8%eW&BEIq}-$b2W#Av=}n^+lh^`U4X=<#;wP33Vu4ekHDV zPwWAyJcd5e{&)w?>*w!n+Y#%~weGa_n-56`Vwu|J@Pwuwxb%0%v7dp-4tqK3jkZjf z=x})2S%C-FCprl1{{7cNdg6g4Ca3h%%X<%Kzd5_P_gJsP-|OW&lkb-~oQ-~SK)|Nl zq4~>RhfKG!13z~yTM(>2IgDS3ndkq5&Ds1X*}#!=UwZQ9Q(}jhL7dI~Qof8}#(n8f g7I@q}P*?(2Dy1}wnH{J!lYwEv#D!BQ2dG5=06@Iv?EnA( diff --git a/test_cases/sciml_problem_import/021/petab/parameters.tsv b/test_cases/sciml_problem_import/021/petab/parameters.tsv index 9812b5a..8eab181 100644 --- a/test_cases/sciml_problem_import/021/petab/parameters.tsv +++ b/test_cases/sciml_problem_import/021/petab/parameters.tsv @@ -1,6 +1,6 @@ parameterId parameterScale lowerBound upperBound nominalValue estimate -delta lin 0.0 15.0 1.8 1 -beta lin 0.0 15.0 0.9 1 -net1_input_pre1 lin -inf inf 1.0 0 -net1_input_pre2 lin -inf inf 1.0 0 -net4_ps lin -inf inf array 1 +delta lin 0.0 15.0 1.8 true +beta lin 0.0 15.0 0.9 true +net1_input_pre1 lin -inf inf 1.0 false +net1_input_pre2 lin -inf inf 1.0 false +net4_ps lin -inf inf array true diff --git a/test_cases/sciml_problem_import/021/petab/problem.yaml b/test_cases/sciml_problem_import/021/petab/problem.yaml index 5254f49..fb5d46c 100644 --- a/test_cases/sciml_problem_import/021/petab/problem.yaml +++ b/test_cases/sciml_problem_import/021/petab/problem.yaml @@ -6,7 +6,7 @@ measurement_files: - "measurements.tsv" observable_files: - "observables.tsv" -format_version: 2 +format_version: "2.0.0" experiment_files: - "experiments.tsv" parameter_files: @@ -17,8 +17,10 @@ extensions: sciml: array_files: - "net4_ps.hdf5" + version: "0.1.0" hybridization_files: - "hybridization.tsv" + required: true neural_nets: net4: location: "net4.yaml" diff --git a/test_cases/sciml_problem_import/021/simulations.tsv b/test_cases/sciml_problem_import/021/simulations.tsv index 7af45f0..fca4463 100644 --- a/test_cases/sciml_problem_import/021/simulations.tsv +++ b/test_cases/sciml_problem_import/021/simulations.tsv @@ -14,7 +14,7 @@ predator_o e1 0.19470291525643446 2.0 predator_o e1 0.06760604257225866 3.0 predator_o e1 0.14187003527989137 4.0 predator_o e1 6.698671429685424 5.0 -predator_o e1 1.9955511106532229 6.0 +predator_o e1 1.995551110653223 6.0 predator_o e1 0.3922752142581829 7.0 predator_o e1 0.09942290206371376 8.0 predator_o e1 0.06834921504989673 9.0 diff --git a/test_cases/sciml_problem_import/022/grad_mech.tsv b/test_cases/sciml_problem_import/022/grad_mech.tsv index bcf9695..072bc24 100644 --- a/test_cases/sciml_problem_import/022/grad_mech.tsv +++ b/test_cases/sciml_problem_import/022/grad_mech.tsv @@ -1,4 +1,4 @@ parameterId value alpha 1188.5489404986652 delta 457.0027110699171 -beta -410.066612249925 +beta -410.06661224986 diff --git a/test_cases/sciml_problem_import/022/grad_net4.hdf5 b/test_cases/sciml_problem_import/022/grad_net4.hdf5 index 0e605e12f9a606fdbfd7793628a76389efc582fd..a22396e4cd40198a465614c2871393058e7d2d40 100644 GIT binary patch delta 248 zcmZ4CyTW(F6CUP_u1%BsrB+U!z$?MTaA5K(UOC~*f!0^JToyZQzP&yA)ZI>puJ(_U zZ}ZAV-MzQ1-d}C1L*#9lCq-dJ4q^O3zMet82h_{&t(x?-=s=(3YTgjx#Ru|*PQF+k z;CA5qJHzfjR&yMBn4VvjRhe^OLQ}wccqlu3nf52;zyqPlL40b= z^8Yy}SM!;&OnkqUWAYY0A5Ny9Vsb{$9URVX=H%CA2fOsX^yJN_#11ioIGg*Wd>O%v j`_iE-aF0AtSOQlnr8J9~9jG*ufnmbLg;OU7s6_w(ayo3X delta 248 zcmZ4CyTW(F6CP$(sRfh!rB+U!z$?Mzvvcw)UO8dKFzYK^E{h#D-`*a5>TajQ^|toO zw|Qlw_Fmmq@2@u1VftQ~Cq-dJ4q^O3zMet82h_{&t(x?-=s=(3YTgjx#Rs}wc{M@zq^Rz!H2Rwx*2l1&f zd+>8juI4jk`5()`Ie81859j>bA7qW5J2>3m%*n6K4tD8%>B*ZTQnMaE_& diff --git a/test_cases/sciml_problem_import/022/petab/parameters.tsv b/test_cases/sciml_problem_import/022/petab/parameters.tsv index 129c8d5..d75e440 100644 --- a/test_cases/sciml_problem_import/022/petab/parameters.tsv +++ b/test_cases/sciml_problem_import/022/petab/parameters.tsv @@ -1,5 +1,5 @@ parameterId parameterScale lowerBound upperBound nominalValue estimate -alpha lin 0.0 15.0 1.3 1 -delta lin 0.0 15.0 1.8 1 -beta lin 0.0 15.0 0.9 1 -net4_ps lin -inf inf array 1 +alpha lin 0.0 15.0 1.3 true +delta lin 0.0 15.0 1.8 true +beta lin 0.0 15.0 0.9 true +net4_ps lin -inf inf array true diff --git a/test_cases/sciml_problem_import/022/petab/problem.yaml b/test_cases/sciml_problem_import/022/petab/problem.yaml index c7941fb..700cfe7 100644 --- a/test_cases/sciml_problem_import/022/petab/problem.yaml +++ b/test_cases/sciml_problem_import/022/petab/problem.yaml @@ -6,7 +6,7 @@ measurement_files: - "measurements.tsv" observable_files: - "observables.tsv" -format_version: 2 +format_version: "2.0.0" experiment_files: - "experiments.tsv" parameter_files: @@ -17,8 +17,10 @@ extensions: sciml: array_files: - "net4_ps.hdf5" + version: "0.1.0" hybridization_files: - "hybridization.tsv" + required: true neural_nets: net4: location: "net4.yaml" diff --git a/test_cases/sciml_problem_import/023/grad_mech.tsv b/test_cases/sciml_problem_import/023/grad_mech.tsv index 8dd5bd5..e6059b2 100644 --- a/test_cases/sciml_problem_import/023/grad_mech.tsv +++ b/test_cases/sciml_problem_import/023/grad_mech.tsv @@ -1,4 +1,4 @@ parameterId value -alpha 2538.780077320352 +alpha 2538.7800773211884 delta 573.6670521169216 beta -2188.7753333246887 diff --git a/test_cases/sciml_problem_import/023/grad_net1.hdf5 b/test_cases/sciml_problem_import/023/grad_net1.hdf5 index 5e32abab28b1f9b59acb94da15ea0f7bf350f2a6..567ff3775d0fb72d5ec587d8d49e62bf40467e61 100644 GIT binary patch delta 315 zcmZ4CyTW(F6&~j7u1%BgOE*q_z-lph0`C$ifAZ#2e2199oPME`^#_k8uUc?%wZr=l zFMoQkS#h9fDfhDm-VF{l2bsI?&RlZff{nf0?g_09&OW@s^9&jfI2Bf0V4Pa#u<$^X z@UeBx2c*&?SgN@z9jYfUw0Rukd*JQEc$1f=t_PO3{jHv&=H{X{IWr2Ek<>Utnh;Wcnn#IfxRFTQRFk#}tsgncLA^_@O BlnVd= delta 315 zcmZ4CyTW(F6&_|TsRfhoOE*q_z-lph0`C$ifAZ#2e2199oPME`^$U+AuUc?%wZr=l zFMoQkS#h9fDfhDm-VF|K4>EV(ow?+|HCKDN-4j|J(tUV?=NU8}a4M|0z&N$eq3uAF z@UeBx2V&DBSgN@z9bTe%Xs3MbrVZy|PQzr+gMF0Q| CtB*PW diff --git a/test_cases/sciml_problem_import/023/petab/parameters.tsv b/test_cases/sciml_problem_import/023/petab/parameters.tsv index ebb1471..a537ee2 100644 --- a/test_cases/sciml_problem_import/023/petab/parameters.tsv +++ b/test_cases/sciml_problem_import/023/petab/parameters.tsv @@ -1,6 +1,6 @@ parameterId parameterScale lowerBound upperBound nominalValue estimate -alpha lin 0.0 15.0 1.3 1 -delta lin 0.0 15.0 1.8 1 -beta lin 0.0 15.0 0.9 1 -net1_layer1 lin -inf inf array 0 -net1_ps lin -inf inf array 1 +alpha lin 0.0 15.0 1.3 true +delta lin 0.0 15.0 1.8 true +beta lin 0.0 15.0 0.9 true +net1_layer1 lin -inf inf array false +net1_ps lin -inf inf array true diff --git a/test_cases/sciml_problem_import/023/petab/problem.yaml b/test_cases/sciml_problem_import/023/petab/problem.yaml index 4377bf4..4e2b5ab 100644 --- a/test_cases/sciml_problem_import/023/petab/problem.yaml +++ b/test_cases/sciml_problem_import/023/petab/problem.yaml @@ -6,7 +6,7 @@ measurement_files: - "measurements.tsv" observable_files: - "observables.tsv" -format_version: 2 +format_version: "2.0.0" experiment_files: - "experiments.tsv" parameter_files: @@ -17,8 +17,10 @@ extensions: sciml: array_files: - "net1_ps.hdf5" + version: "0.1.0" hybridization_files: - "hybridization.tsv" + required: true neural_nets: net1: location: "net1.yaml" diff --git a/test_cases/sciml_problem_import/024/grad_net1.hdf5 b/test_cases/sciml_problem_import/024/grad_net1.hdf5 index 16ce55165f3b40d3f60a5e3502348b6f633f308a..73a9874ea4f8cfa6c94bbb24bf446ae155ed25be 100644 GIT binary patch delta 375 zcmZ4CyTW(F6&~j7u1%BgOE*q_z-lph0`C$ifAZ#2e2199oPME`^|{&qE=8=cb*PZL zbdagT;edtF|2t3u<*;x33q(@ZCmf~&PhOL&Nhbw`~R;zaXwDiVdkEfUmAV%9m15~+MIQE zIKUw`L#2Vi!QrIA$Eu6h91k3?&|h+Gjflg2e*f*VTMQg(|M{$Tc->wN5fcjz_zGG*esZMnfLP+@ERiC1PzY_lFCEGP4XTxsA1ENgP)cbQGdoa4CIiES Mi3_Jr4p55#0PLErm;e9( delta 375 zcmZ4CyTW(F6&_|TsRfhoOE*q_z-lph0`C$ifAZ#2e2199oPME`^;JeME=8=cb?}&T z^&nG+!vPDU|98%62s^|pMBKCes^<{r-p}py%Ff|sq`GNXmfeAUSF9aWzBo8^THg^> zSSEZxc2(QfJ^S?!+>Y=XtftAt{iPQFa9JsYUb^V5<;saqetf?E>^BweUy5F#;i4-_I zhf`{m2msC*D7XLs delta 94 zcmZ4CyTW(F6&_}8sRfhoOE*q_z-lph0`C$ifAZ#2e217poX!10zMNpjed$mZuynuB d%E=ED5K5(#W-+q^m1Z(9OqjTE>f`{m2mqxFB8mV2 diff --git a/test_cases/sciml_problem_import/025/petab/parameters.tsv b/test_cases/sciml_problem_import/025/petab/parameters.tsv index 4f93bd7..320fdfd 100644 --- a/test_cases/sciml_problem_import/025/petab/parameters.tsv +++ b/test_cases/sciml_problem_import/025/petab/parameters.tsv @@ -1,7 +1,7 @@ parameterId parameterScale lowerBound upperBound nominalValue estimate -alpha lin 0.0 15.0 1.3 1 -delta lin 0.0 15.0 1.8 1 -beta lin 0.0 15.0 0.9 1 -gamma lin 0.0 15.0 0.8 1 -net1_layer1 lin -inf inf array 0 -net1_ps lin -inf inf array 1 +alpha lin 0.0 15.0 1.3 true +delta lin 0.0 15.0 1.8 true +beta lin 0.0 15.0 0.9 true +gamma lin 0.0 15.0 0.8 true +net1_layer1 lin -inf inf array false +net1_ps lin -inf inf array true diff --git a/test_cases/sciml_problem_import/025/petab/problem.yaml b/test_cases/sciml_problem_import/025/petab/problem.yaml index 4377bf4..4e2b5ab 100644 --- a/test_cases/sciml_problem_import/025/petab/problem.yaml +++ b/test_cases/sciml_problem_import/025/petab/problem.yaml @@ -6,7 +6,7 @@ measurement_files: - "measurements.tsv" observable_files: - "observables.tsv" -format_version: 2 +format_version: "2.0.0" experiment_files: - "experiments.tsv" parameter_files: @@ -17,8 +17,10 @@ extensions: sciml: array_files: - "net1_ps.hdf5" + version: "0.1.0" hybridization_files: - "hybridization.tsv" + required: true neural_nets: net1: location: "net1.yaml" diff --git a/test_cases/sciml_problem_import/026/grad_mech.tsv b/test_cases/sciml_problem_import/026/grad_mech.tsv index 8dd5bd5..e6059b2 100644 --- a/test_cases/sciml_problem_import/026/grad_mech.tsv +++ b/test_cases/sciml_problem_import/026/grad_mech.tsv @@ -1,4 +1,4 @@ parameterId value -alpha 2538.780077320352 +alpha 2538.7800773211884 delta 573.6670521169216 beta -2188.7753333246887 diff --git a/test_cases/sciml_problem_import/026/grad_net1.hdf5 b/test_cases/sciml_problem_import/026/grad_net1.hdf5 index 51b67d9836f10bae8dd502a870fa3d672c6c1c68..e0da0fe73bf8d740cd07c935251be70caed6601b 100644 GIT binary patch delta 331 zcmZ4CyTW(F6&~iCu1%BgOE*q_z-lph0`C$ifAZv0d~WsGKGHJ`er$0Fo#=gZZtcbc z2ahJNT5xf-!}|{}e|oQ3aiC}^_p=7x4GuL2nY-`KTyo%ojlJCN39Sy!KD@#63>ptO z6;@neoLc9w@IaLCv31P{q|zf;s<|s2swXeBc^u<=;O)bBlb5Eh2bQ+|t)8Oj>`=FN zU*W7d(GDl>oxgtdtg(@U%!Ib*KTcI0*eOz__`W^YVd)CLibL922Lg|{`6k6;y}?-?q?0W8ywyqWbVE@bIE~guJ&@fC$u`G`|t+OGiW^E zR9JC=acZ4I+kq(IW9ym^#HL5ERC8B4yjr)==5dVg0p6SOCNE804=io_TRlb5*w$@r5AvHE{?fm`_GD?X!_EtOIr_)9I+)(`QkpuU&Eeh#)_ERL zQw}WbNk3@gI_&@pD|d2Z(9{FYn>7WJxj;VO+%M(J2xi=u4rKv{MZeU_$qy9Z;j&pu WX%;g(P-!Lu!-RI!1G(A%E=8=cb*PZLbdagT;edtF z|2tt8;=d;@3t=oa{o9}|no829%{ntHTal*x6eY~aBLtXa+E2Sk8r|tDP@N`4!`VC3N z2To4?n6i;QU&&!zLf;$qv;v2(^Dl}rZ7&ki#tY@3J zfn)Oru{q43z}(y~<;w_W+?Nhz0S9lt)XK>Z6yQO>)OrOshXWQy z|L>gD5O#=Hh`49_RnH;Ly`S6Zm7T-ONOjY&EV~2yu2?&$d~tB-w7w&%uuS-X?5eh{ zd-m%excB6r$gyB+9*1?`o*muv$m&4LyOzn-{Ic~O;sPC?e%m@s%K4x@XPd(TrYna| zoR1TBu;%Cb+UTS25T^Xr=B%^BfznN@R2mo@98Ma1th#v3@xY>kiA%1n5plTB@4sDk zi-Ci!Qr2pRw{8bcu3-!@Z+3T(cH8)T#R(UO_3@Tg4|UxStdy2WoVM5Fz^(PE>o+77 z9|*HyP2I?zujHU_)BT1$t-#?y>}%18i3JCI1+5-GIZ}AQOZ=@?1ZTAa<7P*J^=uP2 zaBTh{HisD$n49~hd>O%v`_iE-;Nb0-S~>ZF0z9ZUODWA_W(O+GWMG&uapBa-0csHd DFSoP& diff --git a/test_cases/sciml_problem_import/027/petab/parameters.tsv b/test_cases/sciml_problem_import/027/petab/parameters.tsv index 626e11b..f0ccc15 100644 --- a/test_cases/sciml_problem_import/027/petab/parameters.tsv +++ b/test_cases/sciml_problem_import/027/petab/parameters.tsv @@ -1,8 +1,8 @@ parameterId parameterScale lowerBound upperBound nominalValue estimate -alpha lin 0.0 15.0 1.3 1 -delta lin 0.0 15.0 1.8 1 -beta lin 0.0 15.0 0.9 1 -net1_input_pre1 lin -inf inf 1.0 0 -net1_input_pre2 lin -inf inf 1.0 0 -net1_layer1_weight lin -inf inf array 0 -net1_ps lin -inf inf array 1 +alpha lin 0.0 15.0 1.3 true +delta lin 0.0 15.0 1.8 true +beta lin 0.0 15.0 0.9 true +net1_input_pre1 lin -inf inf 1.0 false +net1_input_pre2 lin -inf inf 1.0 false +net1_layer1_weight lin -inf inf array false +net1_ps lin -inf inf array true diff --git a/test_cases/sciml_problem_import/027/petab/problem.yaml b/test_cases/sciml_problem_import/027/petab/problem.yaml index 8fd38b4..fc2aac9 100644 --- a/test_cases/sciml_problem_import/027/petab/problem.yaml +++ b/test_cases/sciml_problem_import/027/petab/problem.yaml @@ -6,7 +6,7 @@ measurement_files: - "measurements.tsv" observable_files: - "observables.tsv" -format_version: 2 +format_version: "2.0.0" experiment_files: - "experiments.tsv" parameter_files: @@ -17,8 +17,10 @@ extensions: sciml: array_files: - "net1_ps.hdf5" + version: "0.1.0" hybridization_files: - "hybridization.tsv" + required: true neural_nets: net1: location: "net1.yaml" diff --git a/test_cases/sciml_problem_import/028/grad_mech.tsv b/test_cases/sciml_problem_import/028/grad_mech.tsv index 8fe693e..475d0a6 100644 --- a/test_cases/sciml_problem_import/028/grad_mech.tsv +++ b/test_cases/sciml_problem_import/028/grad_mech.tsv @@ -1,5 +1,5 @@ parameterId value alpha 1348.3832160092732 -delta 398.79444240316656 +delta 398.79444240445616 beta -839.2207939522068 gamma 431.5736554673321 diff --git a/test_cases/sciml_problem_import/028/grad_net1.hdf5 b/test_cases/sciml_problem_import/028/grad_net1.hdf5 index 42f5a8d55571d52af6f652d779c563d50f539a72..ca06cab2b06dfc6c3821810a1a4655a728407fbd 100644 GIT binary patch delta 94 zcmZ4CyTW(F6&~iCu1%BgOE*q_z-lph0`C$ifAZ#2e22I}oX!1GzKmeTed$mZuynuF d%E=ED5K5(#W-+q^m1Z(9OqjTE>f`{m2msP%D9-=@ delta 94 zcmZ4CyTW(F6&_|DsRfhoOE*q_z-lph0`C$ifAZ#2e22I}oX!1GzKmeTed$mZuynuF d%E=ED5K5(#W-+q^m1Z(9OqjTE>f`{m2mq;BBB1~P diff --git a/test_cases/sciml_problem_import/028/petab/parameters.tsv b/test_cases/sciml_problem_import/028/petab/parameters.tsv index 5460bd9..5efe002 100644 --- a/test_cases/sciml_problem_import/028/petab/parameters.tsv +++ b/test_cases/sciml_problem_import/028/petab/parameters.tsv @@ -1,7 +1,7 @@ parameterId parameterScale lowerBound upperBound nominalValue estimate -alpha lin 0.0 15.0 1.3 1 -delta lin 0.0 15.0 1.8 1 -beta lin 0.0 15.0 0.9 1 -gamma lin 0.0 15.0 0.8 1 -net1_layer1_weight lin -inf inf array 0 -net1_ps lin -inf inf array 1 +alpha lin 0.0 15.0 1.3 true +delta lin 0.0 15.0 1.8 true +beta lin 0.0 15.0 0.9 true +gamma lin 0.0 15.0 0.8 true +net1_layer1_weight lin -inf inf array false +net1_ps lin -inf inf array true diff --git a/test_cases/sciml_problem_import/028/petab/problem.yaml b/test_cases/sciml_problem_import/028/petab/problem.yaml index 4377bf4..4e2b5ab 100644 --- a/test_cases/sciml_problem_import/028/petab/problem.yaml +++ b/test_cases/sciml_problem_import/028/petab/problem.yaml @@ -6,7 +6,7 @@ measurement_files: - "measurements.tsv" observable_files: - "observables.tsv" -format_version: 2 +format_version: "2.0.0" experiment_files: - "experiments.tsv" parameter_files: @@ -17,8 +17,10 @@ extensions: sciml: array_files: - "net1_ps.hdf5" + version: "0.1.0" hybridization_files: - "hybridization.tsv" + required: true neural_nets: net1: location: "net1.yaml" diff --git a/test_cases/sciml_problem_import/029/grad_mech.tsv b/test_cases/sciml_problem_import/029/grad_mech.tsv index 8dd5bd5..e6059b2 100644 --- a/test_cases/sciml_problem_import/029/grad_mech.tsv +++ b/test_cases/sciml_problem_import/029/grad_mech.tsv @@ -1,4 +1,4 @@ parameterId value -alpha 2538.780077320352 +alpha 2538.7800773211884 delta 573.6670521169216 beta -2188.7753333246887 diff --git a/test_cases/sciml_problem_import/029/grad_net5.hdf5 b/test_cases/sciml_problem_import/029/grad_net5.hdf5 index 3fb3e07317a98fa05136b9cc296102a076456dfe..89b9e341b6887d7414e0c65e4dfc6b88df14dd0e 100644 GIT binary patch delta 335 zcmZ4CyTW(F6CURLu1%BsrB+U!!0W&?yJGSsUbp&eAL$teKejl8PV_!Hw|3)!gGZBB zEx5Sa;r)k~KfTwiI8d~d`&k3;28Wu1%-wfqE;(?)#$ImsgjNSoMcBtFCuW;6! zXonN`&R@TJ*4W5FW=da|eBYkyuyloA#Ubsi0|Cazg=!pY92T29rdQla 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-beta lin 0.0 15.0 0.9 1 -gamma lin 0.0 15.0 0.8 1 -net5_ps lin -inf inf array 1 +alpha lin 0.0 15.0 1.3 true +delta lin 0.0 15.0 1.8 true +beta lin 0.0 15.0 0.9 true +gamma lin 0.0 15.0 0.8 true +net5_ps lin -inf inf array true diff --git a/test_cases/sciml_problem_import/031/petab/problem.yaml b/test_cases/sciml_problem_import/031/petab/problem.yaml index cd08d41..dfec799 100644 --- a/test_cases/sciml_problem_import/031/petab/problem.yaml +++ b/test_cases/sciml_problem_import/031/petab/problem.yaml @@ -6,7 +6,7 @@ measurement_files: - "measurements.tsv" observable_files: - "observables.tsv" -format_version: 2 +format_version: "2.0.0" experiment_files: - "experiments.tsv" parameter_files: @@ -17,8 +17,10 @@ extensions: sciml: array_files: - "net5_ps.hdf5" + version: "0.1.0" hybridization_files: - "hybridization.tsv" + required: true neural_nets: net5: location: "net5.yaml" diff --git a/test_cases/sciml_problem_import/032/grad_mech.tsv b/test_cases/sciml_problem_import/032/grad_mech.tsv index e33c83f..7afefb9 100644 --- a/test_cases/sciml_problem_import/032/grad_mech.tsv +++ b/test_cases/sciml_problem_import/032/grad_mech.tsv @@ -1,4 +1,4 @@ parameterId value -alpha 1328.8285975198448 -delta 390.6311104472732 -beta -827.8898417171047 +alpha 1328.8285975198899 +delta 390.63111044731846 +beta -827.8898417171947 diff --git a/test_cases/sciml_problem_import/032/grad_net1.hdf5 b/test_cases/sciml_problem_import/032/grad_net1.hdf5 index fce3144ec6203642c9db670ed96b7c7991086f4c..189d15bdd831f2accacd443fdffe4f67e0155f80 100644 GIT binary patch delta 502 zcmZ4CyTW(F6CUQGu1%BsrB+U!z$;PDpDSo+=V#}zWIvm2fU=##B_9Tj3k-G#^0o;+ zKljk~fYXZk(K{M!9BeF=IhVHEIQ%l@d-`Oj)`8;qy;J91(K_&?^i*ZJxy6B^?Y}Pn zP_;O4y|;QohmW0uurX)skw>-%Hmv&neC{F}he>zO$eXfiAGrDD(h)-!ivzc%Y}8#} z*w!DI)WzA=7i{a$(c%}fCCcGIulpJ!=Wjv|Je)I^Nzc@CIASZQ^L~$=!``hP|9s8u z4k(ADwyeMA;BZ#HC0B2%@PWls*sVWo)j#0GW*B8AW9<-Av};!J466e-Zk=@t+Gp!v 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priorDistribution priorParameters -alpha lin 0.0 15.0 1.3 1 uniform 0.0;15.0 -delta lin 0.0 15.0 1.8 1 uniform 0.0;15.0 -beta lin 0.0 15.0 0.9 1 uniform 0.0;15.0 -net1_input_pre1 lin -Inf Inf 1.0 0 -net1_input_pre2 lin -Inf Inf 1.0 0 -net1_ps lin -Inf Inf array 1 normal 0.0;1.0 +alpha lin 0.0 15.0 1.3 true uniform 0.0;15.0 +delta lin 0.0 15.0 1.8 true uniform 0.0;15.0 +beta lin 0.0 15.0 0.9 true uniform 0.0;15.0 +net1_input_pre1 lin -Inf Inf 1.0 false +net1_input_pre2 lin -Inf Inf 1.0 false +net1_ps lin -Inf Inf array true normal 0.0;1.0 diff --git a/test_cases/sciml_problem_import/032/petab/problem.yaml b/test_cases/sciml_problem_import/032/petab/problem.yaml index 8fd38b4..fc2aac9 100644 --- a/test_cases/sciml_problem_import/032/petab/problem.yaml +++ b/test_cases/sciml_problem_import/032/petab/problem.yaml @@ -6,7 +6,7 @@ measurement_files: - "measurements.tsv" observable_files: - "observables.tsv" -format_version: 2 +format_version: "2.0.0" experiment_files: - "experiments.tsv" parameter_files: @@ -17,8 +17,10 @@ extensions: sciml: array_files: - "net1_ps.hdf5" + version: "0.1.0" hybridization_files: - "hybridization.tsv" + required: true neural_nets: net1: location: "net1.yaml" diff --git a/test_cases/sciml_problem_import/032/solutions.yaml b/test_cases/sciml_problem_import/032/solutions.yaml index 6231d07..18ea186 100644 --- a/test_cases/sciml_problem_import/032/solutions.yaml +++ b/test_cases/sciml_problem_import/032/solutions.yaml @@ -5,5 +5,5 @@ grad_files: mech: "grad_mech.tsv" net1: "grad_net1.hdf5" tol_simulations: 0.001 -log_posterior: -22.83360800261655 +log_posterior: -22.833608002616536 tol_log_posterior: 0.001 diff --git a/test_cases/sciml_problem_import/033/grad_mech.tsv b/test_cases/sciml_problem_import/033/grad_mech.tsv index 7beb0fa..3476268 100644 --- a/test_cases/sciml_problem_import/033/grad_mech.tsv +++ b/test_cases/sciml_problem_import/033/grad_mech.tsv @@ -1,4 +1,4 @@ parameterId value -alpha 1328.8285975198223 -delta 390.6311104472362 -beta -827.8898417172687 +alpha 1328.8285975197307 +delta 390.6311104474263 +beta -827.889841717137 diff --git a/test_cases/sciml_problem_import/033/grad_net1.hdf5 b/test_cases/sciml_problem_import/033/grad_net1.hdf5 index 5ff738d633d2bcfbbf6efd3c40b0519782be277e..5b4debbef6fde201dd94cd22bdd9e56338e8a89c 100644 GIT binary patch delta 502 zcmZ4CyTW(F6CUQ`u1%BsrB+U!z$;OoJR|={d#RlRyPZSznJhbp<$SM}Tu`z*@Y%FD zL_pf^fJ8@Ux%yEXhxD>*iyj@baqzZ$bp6r;tpk7G{dR7Au61Ch>6A~0d@K&kDwg+5 z_OLi`Mula96wth~D8o&@K>c0ZHMbU=wQ)$DTk&k!XRQM%A=_F%`db`uUo4^S`ogyU zz@?b=oqfT!4sl{(AzPvx4xGKR)5!Uoki*Ay3ztdH)N_c964H6U$Ic=2o!LKMbGrkt zE`_(OzvkeeTE>v4H&yt6=s|hw4_oyQyqq5yWhP_oa4Yxdtl}9~2RQG&bqm^O>(I|D zB=qfrzyZ6PR+ZN{bq*}5wG^3TV|T#lp2_UO^Yyk4+yztBjTbr`n5*r4?E76Ihkfb$ zh2Eahb9jEnvvj$f!-0>>KHT4Q+uq^2iRX^5YaI{#Sbjce%`y>(tRREi&!!kSXf7_= zm2k=JKwMP`lUJ&{!zQD<-xxNyI51T%FFtTItYuCk zQ@(>`^ih|YV#x&#zAKOG&Fm{U(7+QTwdP>q0VgZJ&DQ)s*}(C1UwZQ9Q(}jhL7dI~ oQof8}#(n8f7I-v1P*?(2Dy1}wnH{J!lYwEv#D!BQ2dG5=0Jy*C$N&HU delta 502 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+net1_input_pre1 lin -Inf Inf 1.0 false +net1_input_pre2 lin -Inf Inf 1.0 false +net1_layer1_weight_prior lin -Inf Inf array true normal 0.0;2.0 +net1_ps lin -Inf Inf array true normal 0.0;1.0 diff --git a/test_cases/sciml_problem_import/034/petab/problem.yaml b/test_cases/sciml_problem_import/034/petab/problem.yaml index 8fd38b4..fc2aac9 100644 --- a/test_cases/sciml_problem_import/034/petab/problem.yaml +++ b/test_cases/sciml_problem_import/034/petab/problem.yaml @@ -6,7 +6,7 @@ measurement_files: - "measurements.tsv" observable_files: - "observables.tsv" -format_version: 2 +format_version: "2.0.0" experiment_files: - "experiments.tsv" parameter_files: @@ -17,8 +17,10 @@ extensions: sciml: array_files: - "net1_ps.hdf5" + version: "0.1.0" hybridization_files: - "hybridization.tsv" + required: true neural_nets: net1: location: "net1.yaml" diff --git a/test_cases/sciml_problem_import/034/solutions.yaml b/test_cases/sciml_problem_import/034/solutions.yaml index 0fa9901..6004a0c 100644 --- a/test_cases/sciml_problem_import/034/solutions.yaml +++ b/test_cases/sciml_problem_import/034/solutions.yaml @@ -5,5 +5,5 @@ grad_files: mech: "grad_mech.tsv" net1: "grad_net1.hdf5" tol_simulations: 0.001 -log_posterior: -29.54253953842064 +log_posterior: -29.542539538420627 tol_log_posterior: 0.001 diff --git a/test_cases/sciml_problem_import/035/grad_net1.hdf5 b/test_cases/sciml_problem_import/035/grad_net1.hdf5 index d93b93d665d26757f5e0f5643acc838242ab7bbc..e5c07fda76634fb8cb1d3fefbcbcd0a0b9262ec3 100644 GIT binary patch delta 335 zcmZ4CyTW(F6CUQ$u1%BsrB+U!!0W&?yJGSsUbp&eAL$teKejl8PV_!Hw|3)!gGZBB zEx5Sa;r)k~KfTwiI8d~d`&k3;28Wu1%-wfqE;(?)#$ImsgjNSoMcBtFCuW;6! zXonN`&R@TJ*4W5FW=da|eBYkyuyloA#Ubsi0|Cazg=!pY92T29rdQla zJHTb*$yKpx>jA;ZC;7|`tqiZPJy}}pu=9dmj{fnj4yO0Kl%`H-bKu&>I?p3&%7KMF z=?86GryXEnO6(9bh_kt0%9jz$xGx>b0uP@D3QOQh XrIcndvjdf8GB8Y-xNz#^0JR7JbhDe| delta 335 zcmZ4CyTW(F6CP%HsRfh!rB+U!!0W&yRxptO6;@ne zoLcA5b|6al*t+HevFQ;k)!da1uhuQJc^u<=fcIv+$xBn$154ZfR!>oMc9?Q(U*W7d 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a/test_cases/sciml_problem_import/038/petab/parameters.tsv +++ b/test_cases/sciml_problem_import/038/petab/parameters.tsv @@ -1,5 +1,5 @@ parameterId parameterScale lowerBound upperBound nominalValue estimate -alpha lin 0.0 15.0 1.3 1 -delta lin 0.0 15.0 1.8 1 -beta lin 0.0 15.0 0.9 1 -net6_ps lin -inf inf array 1 +alpha lin 0.0 15.0 1.3 true +delta lin 0.0 15.0 1.8 true +beta lin 0.0 15.0 0.9 true +net6_ps lin -inf inf array true diff --git a/test_cases/sciml_problem_import/038/petab/problem.yaml b/test_cases/sciml_problem_import/038/petab/problem.yaml index 3dc6f65..9498a53 100644 --- a/test_cases/sciml_problem_import/038/petab/problem.yaml +++ b/test_cases/sciml_problem_import/038/petab/problem.yaml @@ -6,7 +6,7 @@ measurement_files: - "measurements.tsv" observable_files: - "observables.tsv" -format_version: 2 +format_version: "2.0.0" experiment_files: - "experiments.tsv" parameter_files: @@ -18,8 +18,10 @@ extensions: array_files: - "net6_ps.hdf5" - "net6_input2.hdf5" + version: "0.1.0" hybridization_files: - "hybridization.tsv" + required: true neural_nets: net6: location: "net6.yaml" diff --git a/test_cases/sciml_problem_import/039/grad_mech.tsv b/test_cases/sciml_problem_import/039/grad_mech.tsv index d49a697..b3e0ada 100644 --- a/test_cases/sciml_problem_import/039/grad_mech.tsv +++ b/test_cases/sciml_problem_import/039/grad_mech.tsv @@ -1,5 +1,5 @@ parameterId value -alpha 384.67420907758566 -delta -77.22463242359656 +alpha 384.67420907589553 +delta -77.22463242359517 beta -398.4233563340724 -gamma 546.9861905045999 +gamma 546.9861905024623 diff --git a/test_cases/sciml_problem_import/039/grad_net6.hdf5 b/test_cases/sciml_problem_import/039/grad_net6.hdf5 index 368d2fc332a3c01bc89ab41d3f7fef29c036d9b0..923c167927b335c17877b82ce25f44d7b2d8bbe2 100644 GIT binary patch delta 91 zcmZ4CyTW(F6CUP{u1%BsrB-g9z`KM4%(*W;dGjf;L(Cw~=6)$(Mlj>PbSMiPbSMi