Differences

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--- developers_notes [2024/08/18 23:42] – mike
+++ developers_notes [2024/09/01 22:27] (current) – [Style guide] mike
@@ Line 1: / Line 1: @@
-Note that the LaTeX syntax using the JaxMath plugin does NOT work in footnotes. (2024-08-18)
+===== Style guide =====
+Center all tables and images. Image centering is built-in functionality when inserting; tables use the %%<columns>%% tag as part of the Columns plugin.
+Genes and gene symbols should use $\LaTeX$ formatting: e.g., $URA3$ or $unc\text{-117}$. In retrospect this was not a great idea because autolink 4 does not recognize $\LaTeX$ formatted text. It does make genes stand out, so there is that.
+Chapter numbers should use two-digit format (e.g., Chapter 01).
+The Captions plugin does not support equation numbering, so genetic crosses and other equation-like objects should be labeled as %%<figure>%%
+===== Technical notes =====
+Note that the LaTeX syntax using the MathJax plugin does NOT work in footnotes. (2024-08-18) It does, however, work in headers, which is weird because headers are not supposed to support any kind of formatting.
+Use %%<columns 100% *100%*></columns>%% to center tables - <div centeralign> works for images but not tables. Function of the Columns plugin.
+JaxMath understands %%\text{}%% syntax from the amsmath package for LaTeX.
+The [[https://www.dokuwiki.org/plugin:commentsyntax|Comment Syntax plugin]] allows for comments using the %%\* this is a comment *\%% format.
+using the nowiki tag or % delimiters does NOT work for the MathJax plugin. Instead, use %%/$%%
+%%{{anchor:anchor_name}}%% is used to generate anchor links. Use %%[[page_name#anchor_name|text]]%% to link to it.
+%%~~NOTOC~~%% suppresses display of table of contents for each page.
+Using autotooltips and autolink 4 plugins for glossary. basically: glossary entries go into the "glossary:" name space. Simply use %%[[glossary:page_name_goes_here|link text goes here]]%% to generate the glossary entry page. The first line of the glossary entry should be a one line summary for the tooltip, can add other content below if needed. IN the autolink plugin config page, need to add an entry, see examples therein.
+===== To-do list =====
+see if can host MathJax locally instead of relying on remote service. Note: tried this on 08/25/2024 - it does not look easy. sticking with the remote call for now.
+More of a wishlist item: add a section on human/medically relevant pop-gen. OCW has a decent set of notes for this, should not be too hard to expand. (Part 4: Population genetics?)
+Also a wishlist item: a chapter on epigenetics. Not part of OCW notes. (Part 5: Weird stuff we don't fully understand yet?)
+Add appendix B: basically the lab manual.
-Use %%<columns 100% *100%*></columns>%% to center tables - <div centeralign> works for images but not tables. Function of the Columns plugin.