Export notebook to latex with citations fail

[danielcoral]

Hi,

Extremely useful extension, thanks for the hard work. I have an issue with numeric styles (e.g. Vancouver). It all looks fine within JupyterLab, but when I tried exporting the notebook to latex then the first citation is exported correctly, while the rest are not:

In JupyterLab:

Mbatchou J, Barnard L, Backman J, Marcketta A, Kosmicki JA, Ziyatdinov A, et al. Computationally efficient whole-genome regression for quantitative and binary traits. Nat Genet [Internet]. 2021 Jul [cited 2021 Nov 24];53(7):1097–103. Available from: https://www.nature.com/articles/s41588-021-00870-7
2.
Galinsky KJ, Bhatia G, Loh P-R, Georgiev S, Mukherjee S, Patterson NJ, et al. Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia. The American Journal of Human Genetics [Internet]. 2016 Mar 3 [cited 2021 Nov 24];98(3):456–72. Available from: https://www.sciencedirect.com/science/article/pii/S0002929716000033
3.
Yengo L, Sidorenko J, Kemper KE, Zheng Z, Wood AR, Weedon MN, et al. Meta-analysis of genome-wide association studies for height and body mass index in ∼700000 individuals of European ancestry. Human Molecular Genetics [Internet]. 2018 Oct 15 [cited 2021 Nov 24];27(20):3641–9. Available from: https://doi.org/10.1093/hmg/ddy271

In the latex file:

    \begin{enumerate}
\def\labelenumi{\arabic{enumi}.}
\item
  Mbatchou J, Barnard L, Backman J, Marcketta A, Kosmicki JA, Ziyatdinov
  A, et al. Computationally efficient whole-genome regression for
  quantitative and binary traits. Nat Genet {[}Internet{]}. 2021 Jul
  {[}cited 2021 Nov 24{]};53(7):1097--103. Available from:
  https://www.nature.com/articles/s41588-021-00870-7
\end{enumerate}

\begin{verbatim}
<div class="csl-left-margin">2. </div><div class="csl-right-inline">Galinsky KJ, Bhatia G, Loh P-R, Georgiev S, Mukherjee S, Patterson NJ, et al. Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia. The American Journal of Human Genetics [Internet]. 2016 Mar 3 [cited 2021 Nov 24];98(3):456–72. Available from: https://www.sciencedirect.com/science/article/pii/S0002929716000033</div>
\end{verbatim}

\begin{verbatim}
<div class="csl-left-margin">3. </div><div class="csl-right-inline">Yengo L, Sidorenko J, Kemper KE, Zheng Z, Wood AR, Weedon MN, et al. Meta-analysis of genome-wide association studies for height and body mass index in ∼700000 individuals of European ancestry. Human Molecular Genetics [Internet]. 2018 Oct 15 [cited 2021 Nov 24];27(20):3641–9. Available from: https://doi.org/10.1093/hmg/ddy271</div>
\end{verbatim}

[krassowski]

Thanks for highlighting it! It might be a simple as adding some spacing for consistency - I will look into this. I will also try to fix the latex mode output (which can be enabled in settings but it appears it has some issues).

[krassowski]

Hi @danielcoral thank again for engaging here! I now added proper LaTeX support in #42 which was included in newly released version 0.2.0. It can be enabled by following the steps described in README.md: Exporting to LaTeX. Please let me know if this works for you - I'm curious to see how it fares in real world workflows.

[danielcoral]

I've had just the time to test it. The final PDF includes two numberings, like this:

[1] 1. Bulik-Sullivan BK, Loh P-R, Finucane HK, Ripke S, Yang J, Patterson N, et al. LD
Score regression distinguishes confounding from polygenicity in genome-wide association
studies. Nat Genet [Internet]. 2015 Mar [cited 2021 Dec 7];47(3):291–5. Available from:
https://www.nature.com/articles/ng.3211
[2] 2. Ning Z, Pawitan Y, Shen X. High-definition likelihood inference of genetic correlations across
human complex traits. Nat Genet [Internet]. 2020 Aug [cited 2021 Dec 7];52(8):859–64. Available
from: https://www.nature.com/articles/s41588-020-0653-y
[3] 3. Elsworth B, Lyon M, Alexander T, Liu Y, Matthews P, Hallett J, et al. The MRC IEU OpenGWAS data infrastructure [Internet]. 2020 Aug [cited 2021 Dec 7] p. 2020.08.10.244293. Available
from: https://www.biorxiv.org/content/10.1101/2020.08.10.244293v1

I guess this can be easily fixed manually. Really thanks a lot for the work!