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Cleanup pypesto.profile #1225

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merged 11 commits into from
Nov 30, 2023
Merged

Cleanup pypesto.profile #1225

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ec854bb
Cleanup pypesto.profile
dweindl Nov 29, 2023
256ea22
..
dweindl Nov 30, 2023
f292c3c
doc
dweindl Nov 30, 2023
2b1865c
..
dweindl Nov 30, 2023
5b19cc3
..
dweindl Nov 30, 2023
8add454
..
dweindl Nov 30, 2023
4db3654
doc
dweindl Nov 30, 2023
7d6d0f2
..
dweindl Nov 30, 2023
5697fec
..
dweindl Nov 30, 2023
f197b8c
Update pypesto/profile/validation_intervals.py
dweindl Nov 30, 2023
66e7b28
Merge branch 'develop' into cleanup_profile
dweindl Nov 30, 2023
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2 changes: 2 additions & 0 deletions doc/conf.py
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Expand Up @@ -73,6 +73,8 @@
autodoc_mock_imports = ["amici"]
autodoc_class_signature = "separated"

# napoleon options
napoleon_use_rtype = False

# links for intersphinx
intersphinx_mapping = {
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3 changes: 1 addition & 2 deletions pypesto/profile/approximate.py
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Expand Up @@ -50,8 +50,7 @@ def approximate_parameter_profile(

Returns
-------
result:
The profile results are filled into `result.profile_result`.
The profile results are filled into `result.profile_result`.
"""
# Handling defaults
# profiling indices
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9 changes: 5 additions & 4 deletions pypesto/profile/profile.py
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Expand Up @@ -30,7 +30,7 @@ def parameter_profile(
overwrite: bool = False,
) -> Result:
"""
Call to do parameter profiling.
Compute parameter profiles.

Parameters
----------
Expand All @@ -45,6 +45,7 @@ def parameter_profile(
The optimizer to be used along each profile.
engine:
The engine to be used.
Defaults to :class:`pypesto.engine.SingleCoreEngine`.
profile_index:
List with the parameter indices to be profiled
(by default all free indices).
Expand All @@ -61,12 +62,13 @@ def parameter_profile(
:func:`pypesto.profile.profile_next_guess.next_guess`.
profile_options:
Various options applied to the profile optimization.
See :class:`pypesto.profile.options.ProfileOptions`.
progress_bar:
Whether to display a progress bar.
filename:
Name of the hdf5 file, where the result will be saved. Default is
None, which deactivates automatic saving. If set to
"Auto" it will automatically generate a file named
``Auto`` it will automatically generate a file named
``year_month_day_profiling_result.hdf5``.
Optionally a method, see docs for :func:`pypesto.store.auto.autosave`.
overwrite:
Expand All @@ -75,8 +77,7 @@ def parameter_profile(

Returns
-------
result:
The profile results are filled into `result.profile_result`.
The profile results are filled into `result.profile_result`.
"""
# Copy the problem to avoid side effects
problem = copy.deepcopy(problem)
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