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[DOC] Remove ..figure directive in examples #2944

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merged 8 commits into from
Nov 2, 2023

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@skoudoro skoudoro commented Oct 19, 2023

Sphinx gallery generate its own figure directive. So, currently our ..figure directive are not processed and shows unfound files in our tutorials which is confusing.

Furthermore, I added .. rst-class:: centered small fst-italic fw-semibold directive to simulate and not lose some captions.

@skoudoro skoudoro linked an issue Oct 19, 2023 that may be closed by this pull request
* print issue, internal link,
* follow sphx-glr syntax convention,
* moving import at the top of the file
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codecov bot commented Oct 20, 2023

Codecov Report

Merging #2944 (b1d2d74) into master (3ad9ec1) will decrease coverage by 0.06%.
Report is 157 commits behind head on master.
The diff coverage is 80.00%.

❗ Current head b1d2d74 differs from pull request most recent head fbc1d04. Consider uploading reports for the commit fbc1d04 to get more accurate results

Additional details and impacted files

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@@            Coverage Diff             @@
##           master    #2944      +/-   ##
==========================================
- Coverage   81.77%   81.71%   -0.06%     
==========================================
  Files         146      147       +1     
  Lines       20401    20484      +83     
  Branches     3238     3277      +39     
==========================================
+ Hits        16682    16739      +57     
- Misses       2901     2913      +12     
- Partials      818      832      +14     
Files Coverage Δ
dipy/data/fetcher.py 40.25% <ø> (ø)
dipy/info.py 100.00% <100.00%> (ø)
dipy/io/stateful_tractogram.py 76.96% <100.00%> (ø)
dipy/reconst/dti.py 92.57% <0.00%> (ø)
dipy/tracking/local_tracking.py 94.44% <96.29%> (ø)
dipy/io/utils.py 88.83% <90.00%> (ø)
dipy/io/streamline.py 84.92% <75.00%> (ø)
dipy/align/imwarp.py 95.60% <37.50%> (ø)

... and 13 files with indirect coverage changes

- fix streamlines bad rendering
- convert some tutorial to new standard
- small others fix for failing tutorial
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skoudoro commented Nov 2, 2023

Ok, this PR is ready to go.

is there any comments/suggestions ? I will go ahead and merge this tomorrow at noon if no comments.

This cleaning was needed and more to come after the release.

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Looks good to me! I spotted a couple of typos along the way, but that doesn't mean there aren't any other ones :-)

doc/examples/bundlewarp_registration.py Outdated Show resolved Hide resolved
doc/examples/denoise_mppca.py Outdated Show resolved Hide resolved
doc/examples/denoise_mppca.py Outdated Show resolved Hide resolved
doc/examples/denoise_mppca.py Outdated Show resolved Hide resolved
doc/examples/denoise_mppca.py Outdated Show resolved Hide resolved
doc/examples/denoise_mppca.py Outdated Show resolved Hide resolved
doc/examples/denoise_patch2self.py Outdated Show resolved Hide resolved
Co-authored-by: Ariel Rokem <arokem@gmail.com>
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skoudoro commented Nov 2, 2023

thank you for the review @arokem!

For sure there is other ones, like old functions a simpler way to do stuff in many tutorials. We will continue to update that.during the year.

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skoudoro commented Nov 2, 2023

ps: building the doc in parallel, just waiting the build to finish before merging this PR.

remove n_frame to record
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skoudoro commented Nov 2, 2023

ok, all good, merging

@skoudoro skoudoro merged commit 2bac62a into dipy:master Nov 2, 2023
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@skoudoro skoudoro deleted the update-tutorials branch November 2, 2023 14:20
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Some left-overs from sphinx-gallery conversion
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