Reduce doc size

Former-commit-id: 6f92f375e9cf92159e769ce562071bb56a871819
2025-06-29 16:20:46 +00:00 · 2024-01-04 14:17:44 +01:00
parent 74854fa65c
commit 5b57139450
56 changed files with 6392 additions and 31860 deletions
--- a/doc/book/OBITools-V4.tex
+++ b/doc/book/OBITools-V4.tex
@ -213,7 +213,7 @@

 \begin{document}
 \maketitle
-\ifdefined\Shaded\renewenvironment{Shaded}{\begin{tcolorbox}[breakable, interior hidden, enhanced, boxrule=0pt, borderline west={3pt}{0pt}{shadecolor}, sharp corners, frame hidden]}{\end{tcolorbox}}\fi
+\ifdefined\Shaded\renewenvironment{Shaded}{\begin{tcolorbox}[boxrule=0pt, breakable, enhanced, borderline west={3pt}{0pt}{shadecolor}, frame hidden, interior hidden, sharp corners]}{\end{tcolorbox}}\fi

 \renewcommand*\contentsname{Table of contents}
 {
--- a/doc/book/_freeze/formats/execute-results/html.json
+++ b/doc/book/_freeze/formats/execute-results/html.json
--- a/doc/book/_quarto.yml
+++ b/doc/book/_quarto.yml
@ -41,7 +41,7 @@ execute:
 format:
  html:
    theme: zephyr
-    embed-resources: true
+    html-math-method: mathml
  pdf:
    documentclass: scrreprt
    keep-tex: true
--- a/doc/book/comm_computation_files/figure-html/unnamed-chunk-1-1.png
+++ b/doc/book/comm_computation_files/figure-html/unnamed-chunk-1-1.png
--- a/doc/book/comm_computation_files/figure-pdf/unnamed-chunk-1-1.pdf
+++ b/doc/book/comm_computation_files/figure-pdf/unnamed-chunk-1-1.pdf
--- a/doc/book/comm_metabarcode_design.html.REMOVED.git-id
+++ b/doc/book/comm_metabarcode_design.html.REMOVED.git-id
@ -1 +0,0 @@
-c9abc6ef1d9b10058625347639c0a133059bfe90
--- a/doc/book/comm_reformat.html
+++ b/doc/book/comm_reformat.html
--- a/doc/book/commands.html.REMOVED.git-id
+++ b/doc/book/commands.html.REMOVED.git-id
@ -1 +0,0 @@
-9be990e7b56476a941dcdd1d074f31e666ec8dc8
--- a/doc/book/common_options.html.REMOVED.git-id
+++ b/doc/book/common_options.html.REMOVED.git-id
@ -1 +0,0 @@
-4e6501bd48200758a94734704f075dcadd97a712
--- a/doc/book/expressions.html.REMOVED.git-id
+++ b/doc/book/expressions.html.REMOVED.git-id
@ -1 +0,0 @@
-fcbb404e0aba238ccfab3f5e1ca388985be78115
--- a/doc/book/formats.html.REMOVED.git-id
+++ b/doc/book/formats.html.REMOVED.git-id
@ -1 +0,0 @@
-3c08c12ad322472ca9f3f1137e6dcc9fc9c504b1
--- a/doc/book/index.html
+++ b/doc/book/index.html
--- a/doc/book/installation.html.REMOVED.git-id
+++ b/doc/book/installation.html.REMOVED.git-id
@ -1 +0,0 @@
-66c05db68b31d840135dabdb2bfa4ddee8fd3957
--- a/doc/book/intro.html.REMOVED.git-id
+++ b/doc/book/intro.html.REMOVED.git-id
@ -1 +0,0 @@
-396888557eb60df9c0c43140545cb945f94dba19
--- a/doc/book/inupt.html.REMOVED.git-id
+++ b/doc/book/inupt.html.REMOVED.git-id
@ -1 +0,0 @@
-6190e7e7d926a7ed289145ae9808076d3a5e5e18
--- a/doc/book/output.html.REMOVED.git-id
+++ b/doc/book/output.html.REMOVED.git-id
@ -1 +0,0 @@
-aaa1261fd473ee852e6462abb4cefae7eb36a486
--- a/doc/book/tutorial.html.REMOVED.git-id
+++ b/doc/book/tutorial.html.REMOVED.git-id
@ -1 +0,0 @@
-568390348c10625dee9c6f3d6d1a3ba54a08aee3
--- a/doc/book/tutorial_files/figure-epub/unnamed-chunk-10-1.png
+++ b/doc/book/tutorial_files/figure-epub/unnamed-chunk-10-1.png
--- a/doc/book/tutorial_files/figure-epub/unnamed-chunk-9-1.png
+++ b/doc/book/tutorial_files/figure-epub/unnamed-chunk-9-1.png
--- a/doc/book/tutorial_files/figure-pdf/unnamed-chunk-10-1.pdf
+++ b/doc/book/tutorial_files/figure-pdf/unnamed-chunk-10-1.pdf
--- a/doc/book/tutorial_files/figure-pdf/unnamed-chunk-9-1.pdf
+++ b/doc/book/tutorial_files/figure-pdf/unnamed-chunk-9-1.pdf