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Add sphinx configuration #57

Merged
merged 8 commits into from
Nov 7, 2023
Merged

Add sphinx configuration #57

merged 8 commits into from
Nov 7, 2023

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dweindl
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@dweindl dweindl commented Oct 23, 2023

Add some basic sphinx configuration and make docstrings sphinx-compatible.

cd doc && make html && xdg-open _build/html/index.html

Related to #7

Add some basic sphinx configuration.
WARNING: Cannot resolve forward reference in type annotations of "petab_select.misc.hash_parameter_dict": name 'estimate' is not defined
WARNING: Cannot resolve forward reference in type annotations of "petab_select.misc.hash_parameter_options": name 'estimate' is not defined
WARNING: Cannot resolve forward reference in type annotations of "petab_select.misc.hash_parameter_dict": name 'estimate' is not defined
WARNING: Cannot resolve forward reference in type annotations of "petab_select.misc.hash_parameter_options": name 'estimate' is not defined
WARNING: Cannot resolve forward reference in type annotations of "petab_select.model.Model.get_parameter_values": name 'estimate' is not defined
WARNING: Cannot resolve forward reference in type annotations of "petab_select.model_subspace.ModelSubspace": name 'estimate' is not defined
WARNING: Cannot resolve forward reference in type annotations of "petab_select.model_subspace.ModelSubspace.__init__": name 'estimate' is not defined
WARNING: Cannot resolve forward reference in type annotations of "petab_select.model_subspace.ModelSubspace.get_estimated": name 'estimate' is not defined
WARNING: Cannot resolve forward reference in type annotations of "petab_select.model_subspace.ModelSubspace.indices_to_parameters": name 'estimate' is not defined
WARNING: Cannot resolve forward reference in type annotations of "petab_select.model_subspace.ModelSubspace.parameters_all": name 'estimate' is not defined
WARNING: Cannot resolve forward reference in type annotations of "petab_select.model_subspace.ModelSubspace.parameters_to_indices": name 'estimate' is not defined
WARNING: Cannot resolve forward reference in type annotations of "petab_select.model_subspace.ModelSubspace.parameters_to_model": name 'estimate' is not defined
WARNING: Cannot resolve forward reference in type annotations of "petab_select.model_subspace.decompress_parameter_values": name 'estimate' is not defined
WARNING: Cannot resolve forward reference in type annotations of "petab_select.model_subspace.decompress_parameter_values": name 'estimate' is not defined
WARNING: Cannot resolve forward reference in type annotations of "petab_select.model_subspace.ModelSubspace": name 'estimate' is not defined
petab_select/constants.py Outdated Show resolved Hide resolved
@dweindl dweindl mentioned this pull request Nov 7, 2023
@dweindl dweindl changed the title Sphinx doc Add sphinx configuration Nov 7, 2023
@dweindl dweindl requested a review from dilpath November 7, 2023 08:28
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codecov-commenter commented Nov 7, 2023

Codecov Report

Merging #57 (ab71771) into develop (bb36956) will decrease coverage by 0.05%.
The diff coverage is 62.50%.

@@             Coverage Diff             @@
##           develop      #57      +/-   ##
===========================================
- Coverage    60.52%   60.48%   -0.05%     
===========================================
  Files           14       14              
  Lines         1510     1516       +6     
===========================================
+ Hits           914      917       +3     
- Misses         596      599       +3     
Files Coverage Δ
petab_select/candidate_space.py 51.85% <ø> (ø)
petab_select/constants.py 100.00% <100.00%> (ø)
petab_select/criteria.py 38.09% <100.00%> (+0.99%) ⬆️
petab_select/model_subspace.py 80.62% <100.00%> (+0.06%) ⬆️
petab_select/ui.py 24.69% <ø> (ø)
petab_select/model.py 67.45% <0.00%> (-0.41%) ⬇️
petab_select/model_space.py 65.95% <0.00%> (-0.71%) ⬇️
petab_select/problem.py 26.38% <50.00%> (+0.67%) ⬆️

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dweindl commented Nov 7, 2023

@dilpath : This allows generating basic API documentation. More fixes and readthedocs configuration in #63. You decide whether you want to merge this, or prettify the documentation first. Or whether I should split it into separate PRs for sphinx-config and docstrings.

@dweindl dweindl marked this pull request as ready for review November 7, 2023 08:34
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Nice! Thanks

petab_select/problem.py Outdated Show resolved Hide resolved
Co-authored-by: Dilan Pathirana <[email protected]>
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dilpath commented Nov 7, 2023

@dilpath : This allows generating basic API documentation. More fixes and readthedocs configuration in #63. You decide whether you want to merge this, or prettify the documentation first. Or whether I should split it into separate PRs for sphinx-config and docstrings.

Sounds good 👍 I'll merge this already since it passes the non-RTD tests.

@dweindl dweindl merged commit b15a59c into develop Nov 7, 2023
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@dweindl dweindl deleted the doc_sphinx branch November 7, 2023 13:33
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3 participants