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Hierarchical: restructuring and add relative to InnerCalculatorCollector #1245

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merged 66 commits into from
Jan 12, 2024
Merged

Hierarchical: restructuring and add relative to InnerCalculatorCollector #1245

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e441a33
Hier. par. plotting for fides
Doresic Aug 7, 2023
207dd72
hierarchical 'hess' bug
Doresic Aug 9, 2023
69559ec
Fix storing of inner parameters in result
Doresic Aug 10, 2023
e4e3a24
adjusted documentation of hierarichal opt.
LeaSeep Aug 10, 2023
22e39e2
Fix some type issues
Doresic Aug 10, 2023
6a67c9a
Small fix
Doresic Aug 10, 2023
270de79
Merge branch 'develop' into fides_hier_par
Doresic Dec 11, 2023
576f680
Save only values, not names
Doresic Dec 11, 2023
ab7bfa8
Extend to all optimizers
Doresic Dec 11, 2023
72d9d53
Remove redundant
Doresic Dec 11, 2023
3e939b2
Small update
Doresic Dec 11, 2023
1089aaf
Merge branch 'develop' into fides_hier_par
Doresic Dec 12, 2023
7db0c3a
Update parameters.py
Doresic Dec 12, 2023
7e2c8f2
Small typo
Doresic Dec 12, 2023
fcd0c50
Fix some bugs, use lists for saving instead
Doresic Dec 12, 2023
ff8d296
Fix tests
Doresic Dec 12, 2023
b2b9527
Update hierarchical parameter plot test
Doresic Dec 12, 2023
af0e415
Largescale renaming and restructuring
Doresic Dec 12, 2023
7e00e28
Update base_problem.py
Doresic Dec 12, 2023
179ffee
Fix Docstrings
Doresic Dec 12, 2023
c53407e
Daniel&Dilan review changes
Doresic Dec 13, 2023
f0e2a16
Small change
Doresic Dec 13, 2023
40663b5
More Dilan Review changes
Doresic Dec 13, 2023
2905429
Fix testing
Doresic Dec 13, 2023
e90df6b
Fix base test
Doresic Dec 13, 2023
a2c7b1f
Rename notebooks (again)
Doresic Dec 13, 2023
be551a2
Move inner pars to decorator
Doresic Dec 14, 2023
b06bdff
Collect decorators for minimize
Doresic Dec 14, 2023
16e7313
Maren review changes
Doresic Dec 14, 2023
f6c2323
Rename & fix notebooks
Doresic Dec 14, 2023
e7fa4ec
Merge branch 'fides_hier_par' into collect_hierarchical_calculators
Doresic Dec 14, 2023
757de46
Include notebook changes
Doresic Dec 14, 2023
6720bc3
FIx tests
Doresic Dec 14, 2023
476efe2
Add output
Doresic Dec 14, 2023
bc50e40
Include relative into Collector
Doresic Dec 18, 2023
460ba4d
Small documentation update
Doresic Jan 3, 2024
1ea7134
Documentation update
Doresic Jan 3, 2024
d66a8a5
Update the notebooks
Doresic Jan 3, 2024
a8931cc
Update spline_approximation.py
Doresic Jan 3, 2024
9024ebf
Change data_types from list to set
Doresic Jan 4, 2024
87ffcb3
Use add_sim_grad_to_opt_grad
Doresic Jan 4, 2024
4b4e6d4
Rename to semiquantitative in example
Doresic Jan 4, 2024
298c899
mode RES with only RELATIVE data
Doresic Jan 4, 2024
bdf81b2
Add petab data type validation
Doresic Jan 5, 2024
0c13a53
DO TODOs
Doresic Jan 5, 2024
20b93e2
Small TODO
Doresic Jan 5, 2024
29288ea
Merge branch 'develop' into collect_hierarchical_calculators
Doresic Jan 8, 2024
d7249d3
FIx api.rst module name changes
Doresic Jan 8, 2024
d343e31
Update CODEOWNERS module name changes
Doresic Jan 8, 2024
335260a
Fix underline too short & api.rst
Doresic Jan 8, 2024
5dadc96
Fix plotting routines
Doresic Jan 8, 2024
732caec
Inline literal error
Doresic Jan 8, 2024
b06c7c4
Testing error
Doresic Jan 8, 2024
b7b90d2
Testing error 2
Doresic Jan 8, 2024
4192650
Test literal error
Doresic Jan 8, 2024
cd6ac64
Fix missing indentation
Doresic Jan 8, 2024
138ae49
Fix inline
Doresic Jan 8, 2024
e93d9a8
Daniel, Fabian & Stephan review changes
Doresic Jan 9, 2024
6fef45b
Notebook changes
Doresic Jan 9, 2024
d3a8d01
Merge branch 'develop' into collect_hierarchical_calculators
Doresic Jan 9, 2024
9d6f64a
Dilan & Daniel review changes
Doresic Jan 10, 2024
f618e38
Merge branch 'develop' into collect_hierarchical_calculators
Doresic Jan 10, 2024
db6d8d2
Change title of relative_data.ipynb
Doresic Jan 10, 2024
7000d28
Remove observableParameter from solvers
Doresic Jan 10, 2024
909aae7
Notebook changes from #1246
Doresic Jan 11, 2024
407dece
Fabian review change
Doresic Jan 11, 2024
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5 changes: 3 additions & 2 deletions .github/CODEOWNERS
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Validating CODEOWNERS rules …
Original file line number Diff line number Diff line change
Expand Up @@ -20,8 +20,9 @@
/pypesto/engine/mpi_pool.py @PaulJonasJost
/pypesto/ensemble/ @dilpath @PaulJonasJost
/pypesto/hierarchical/ @dweindl @Doresic
/pypesto/hierarchical/optimal_scaling_approach/ @Doresic
/pypesto/hierarchical/spline_approximation/ @Doresic
/pypesto/hierarchical/ordinal/ @Doresic
/pypesto/hierarchical/relative/ @dweindl @Doresic
/pypesto/hierarchical/semiquantitative/ @Doresic
/pypesto/history/ @PaulJonasJost
/pypesto/objective/ @PaulJonasJost
/pypesto/objective/amici/ @dweindl @FFroehlich
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5 changes: 3 additions & 2 deletions doc/api.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,9 @@ API reference
pypesto.engine
pypesto.ensemble
pypesto.hierarchical
pypesto.hierarchical.optimal_scaling
pypesto.hierarchical.spline_approximation
pypesto.hierarchical.ordinal
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pypesto.hierarchical.relative
pypesto.hierarchical.semiquantitative
pypesto.history
pypesto.logging
pypesto.objective
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8 changes: 4 additions & 4 deletions doc/example.rst
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Expand Up @@ -51,10 +51,10 @@ Algorithms and features
example/store.ipynb
example/model_selection.ipynb
example/julia.ipynb
example/hierarchical.ipynb
example/ordinal.ipynb
example/censored.ipynb
example/nonlinear_monotone.ipynb
example/relative_data.ipynb
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example/ordinal_data.ipynb
example/censored_data.ipynb
example/semiquantitative_data.ipynb

Application examples
--------------------
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