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Issues with mistune V3.1.0 #2198

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abbasidaniyal opened this issue Dec 30, 2024 · 2 comments · Fixed by #2199
Closed

Issues with mistune V3.1.0 #2198

abbasidaniyal opened this issue Dec 30, 2024 · 2 comments · Fixed by #2199

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@abbasidaniyal
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In the latest release of mistune (3.1.0), they have renamed all the "axt" typos Link

This has broken nbconvert as in the dependencies, we have "mistune>=2.0.3,<4".

As a quick fix, we should probably cap the upper limit of the version in the dependencies whilst updating the MathBlock class to support the new convention.

For context, I have suggesed the mistune maintainers to add support for the old name convention as it is not a major version release. Refer

I'd be more than happy to take up the required changes based on the approach we want to take.
@fcollonval
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To be more specific, the issue is in the following line:

nbconvert/nbconvert/filters/markdown_mistune.py

Line 95 in 6e5fdb3

"axt_heading": AXT_HEADING_WITHOUT_LEADING_SPACES,

This was referenced Dec 30, 2024
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@doctrino doctrino mentioned this issue Dec 30, 2024
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@ReenigneArcher ReenigneArcher mentioned this issue Dec 30, 2024
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@mfisher87 mfisher87 mentioned this issue Dec 30, 2024
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@lgautier lgautier mentioned this issue Dec 30, 2024
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@sarahmish sarahmish mentioned this issue Dec 30, 2024
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@bollwyvl bollwyvl mentioned this issue Dec 30, 2024
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@avigailmo avigailmo mentioned this issue Dec 31, 2024
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avigailmo added a commit to Ultimagen/ugbio-utils that referenced this issue Dec 31, 2024
@avigailmo
cap mistune to solve jupyter/nbconvert#2198
9e3f022
This was referenced Dec 31, 2024
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@krassowski krassowski mentioned this issue Jan 1, 2025
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inbalzelig-ugi pushed a commit to Ultimagen/ugbio-utils that referenced this issue Jan 1, 2025
@avigailmo
cap mistune version to solve jupyter/nbconvert#2198 (#82)
271fa3d 
* mistune_cap

---------

Co-authored-by: avigailmo <avigailmo@users.noreply.github.com>
@onuralpszr onuralpszr mentioned this issue Jan 2, 2025
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@david-yz-liu david-yz-liu mentioned this issue Jan 2, 2025
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avigailmo added a commit to Ultimagen/ugbio-utils that referenced this issue Jan 2, 2025
@avigailmo
cap mistune to solve jupyter/nbconvert#2198
34cf6e5
avigailmo added a commit to Ultimagen/ugbio-utils that referenced this issue Jan 2, 2025
@avigailmo
add single_sample_qc report resources to core (#81)
073733f 
* add single_sample_qc report resources to core

* add reports optional deps

* cap mistune to solve jupyter/nbconvert#2198

* add test to report

* use iloc to prevent FutureWarning: Series.__getitem__ treating keys.
morotti added a commit to man-group/notebooker that referenced this issue Jan 2, 2025
@morotti
deps: block mistune 3.1.0
3279d36 
mistune had a bad release 3 days ago that renamed functions and nbconvert.

waiting for fixes to be merged
jupyter/nbconvert#2198
@caponetto caponetto mentioned this issue Jan 2, 2025
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@krassowski
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nbconvert v7.16.5 includes the fix. Thank you!

@caponetto caponetto mentioned this issue Jan 2, 2025
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ianpittwood added a commit to ianpittwood/jumpstart_examples that referenced this issue Jan 6, 2025
@ianpittwood
Upgrade nbconvert to 7.16.5 for mistune bugfix
8bcec53 
See jupyter/nbconvert#2198 for fix in [7.16.5 release](https://github.com/jupyter/nbconvert/releases/tag/v7.16.5)
@ianpittwood ianpittwood mentioned this issue Jan 6, 2025
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Add support for mistune 3.1.0 fcollonval/nbconvert
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@krassowski @fcollonval @abbasidaniyal