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Improve handling of notebooks in documentation #425

Merged
merged 28 commits into from
Feb 7, 2023
Merged

Improve handling of notebooks in documentation #425

merged 28 commits into from
Feb 7, 2023

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baharcos
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@baharcos baharcos commented Jan 17, 2023 •
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This PR changes the handling of notebooks in documentation from nbsphinx to myst-nb.

  • up-to-date/maintained better
  • option to force the execution of notebooks without needing to delete the outputs
  • option to exclude some notebooks from the forced execution
  • adjustable maximum cell execution time

Current caveats:

  • the download feature of the notebooks is lost but potentially can be reintroduced
  • it has to be manually checked whether the notebook cells run without errors

Jax is used as the example case:
developer notes
readthedocs.yml
configuration
requirements

@baharcos baharcos self-assigned this Jan 17, 2023
@baharcos baharcos linked an issue Jan 17, 2023 that may be closed by this pull request
Improve handling of notebooks in documentation #422
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@baharcos baharcos changed the title Improve handling of notebooks in documentation (closes #422) Improve handling of notebooks in documentation Jan 17, 2023
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codecov bot commented Jan 17, 2023 •
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Codecov Report

Merging #425 (78ae2f0) into main (66ac796) will increase coverage by 0.02%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##             main     #425      +/-   ##
==========================================
+ Coverage   92.84%   92.87%   +0.02%     
==========================================
  Files         231      231              
  Lines       17590    17590              
==========================================
+ Hits        16332    16337       +5     
+ Misses       1258     1253       -5
Impacted Files Coverage Δ
src/estimagic/optimization/subsolvers/bntr.py 86.77% <0.00%> (+0.38%) ⬆️
src/estimagic/optimization/subsolvers/_trsbox.py 85.77% <0.00%> (+0.81%) ⬆️
src/estimagic/__init__.py 100.00% <0.00%> (+8.33%) ⬆️

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@baharcos baharcos removed their assignment Jan 17, 2023
baharcos and others added 19 commits January 18, 2023 12:15
@baharcos
Exclude notebook with patsy.
e6e6ee9
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
d61dd14 
for more information, see https://pre-commit.ci
@baharcos
Fix configuration?
8ad464a
@baharcos
Add myst-nb to conf.
d167947
@baharcos
Fix bug
dbe3b81
@baharcos
Re-adjust the environment.
70e2104
@baharcos
Add .ipynb for excluded notebooks to source suffix.
f243a8e
@baharcos
ipynb before md
1fefbd3
@baharcos
Remove myst-parser
f78487b
@baharcos
Fix?
3b6bf29
@baharcos
Fix cell errors?
f83cde3
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
9391d9c 
for more information, see https://pre-commit.ci
@baharcos
pip install three packages
0fc1214
@baharcos
Merge branch 'nb-docs' of https://github.com/OpenSourceEconomics/esti…
78378c1 
…magic into nb-docs
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
dc88b0e 
for more information, see https://pre-commit.ci
@baharcos
add ipython to rtd_environment
e9f9a17
@baharcos
Merge branch 'nb-docs' of https://github.com/OpenSourceEconomics/esti…
9c25f94 
…magic into nb-docs
@baharcos
Execute all notebooks.
fda3d69
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
4695127 
for more information, see https://pre-commit.ci
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baharcos commented Jan 24, 2023 •
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The latex rendering is not working properly in this notebook even when it's not executed while building and I couldn't fix.
@janosg Do you know how to have
from IPython.core.display import HTML, Latex
from IPython.display import IFrame
in the rtd_environment (ipython is already in the rtd_environment)?

@baharcos baharcos requested a review from janosg January 24, 2023 16:41
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janosg
janosg approved these changes Feb 7, 2023
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Thanks!

@janosg janosg merged commit 74c292b into main Feb 7, 2023
@janosg janosg deleted the nb-docs branch February 7, 2023 10:47
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Improve handling of notebooks in documentation
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