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Bioconductor / BiocStyle

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BiocStyle looks ugly with the latest pandoc #103

Open LTLA opened 1 year ago

LTLA commented 1 year ago

I recently upgraded to pandoc 3 and now BiocStyle looks terrible. Notice the lack of background for the output chunks, as well as the loss of vertical padding around the code chunks.

Screen Shot 2023-02-01 at 9 39 44 AM

Compare this to the vignette built with the BBS, presumably on an earlier pandoc. The top/bottom padding around the blocks is present and the output chunks are well-distinguished from the text with its own background. (Would be even nicer if the text or background color for output chunks was subtly different, so as to better distinguish from code chunks.)

Screen Shot 2023-02-01 at 9 40 43 AM

I suspect that the problem occurs at pandoc < 3, actually. I previously had 2.17 but I was seeing this show up in systems with 2.19.

Session information ``` > sessionInfo() R Under development (unstable) (2022-11-08 r83316) Platform: x86_64-apple-darwin19.6.0 (64-bit) Running under: macOS Catalina 10.15.7 Matrix products: default BLAS: /Users/luna/Software/R/trunk/lib/libRblas.dylib LAPACK: /Users/luna/Software/R/trunk/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 time zone: America/Los_Angeles tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ResidualMatrix_1.9.0 Matrix_1.5-3 BiocStyle_2.27.1 loaded via a namespace (and not attached): [1] cli_3.6.0 knitr_1.42 rsvd_1.0.5 [4] magick_2.7.3 rlang_1.0.6 xfun_0.36 [7] highr_0.10 jsonlite_1.8.4 DelayedArray_0.25.0 [10] BiocSingular_1.15.0 S4Vectors_0.37.3 htmltools_0.5.4 [13] sass_0.4.4 stats4_4.3.0 MatrixGenerics_1.11.0 [16] rmarkdown_2.20 grid_4.3.0 evaluate_0.20 [19] jquerylib_0.1.4 fastmap_1.1.0 IRanges_2.33.0 [22] yaml_2.3.7 bookdown_0.32 BiocManager_1.30.19 [25] compiler_4.3.0 codetools_0.2-18 irlba_2.3.5.1 [28] Rcpp_1.0.10 BiocParallel_1.33.9 lattice_0.20-45 [31] digest_0.6.31 R6_2.5.1 parallel_4.3.0 [34] magrittr_2.0.3 bslib_0.4.2 tools_4.3.0 [37] beachmat_2.15.0 ScaledMatrix_1.7.0 matrixStats_0.63.0 [40] BiocGenerics_0.45.0 cachem_1.0.6 ```
aoles commented 1 year ago

Do you think you could have a look at this @grimbough? Cheers!