Update TOC in markdown files

actions-user · actions-user · commit d5f7ca6f858b · 2025-06-17T15:47:52.000Z
diff --git a/group-syllabus/challenges.md b/group-syllabus/challenges.md
@@ -1,3 +1,11 @@
+<!-- START doctoc generated TOC please keep comment here to allow auto update -->
+<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+## Table of Contents
+
+- [Challenges and Mental Health](#challenges-and-mental-health)
+
+<!-- END doctoc generated TOC please keep comment here to allow auto update -->
+
 ## Challenges and Mental Health
 
 The research or Ph.D. experience can be very challenging, sometimes in unexpected ways.
diff --git a/group-syllabus/computers.md b/group-syllabus/computers.md
@@ -1,16 +1,11 @@
 ## Computers
 
-<!-- toc -->
-- [GT PACE Phoenix](#gt-pace-phoenix)
-- [GT ICE](#gt-ice)
-- [GT Rogues Gallery](#gt-rogues-gallery)
-- [GT Wingtip-gpu3](#gt-wingtip-gpu3)
-- [ACCESS-CI computers](#access-ci-computers)
-- [Oak Ridge National Lab OLCF](#oak-ridge-national-lab-olcf-frontierwombatandesetc)
-- [Sandia National Lab (SNL)](#sandia-national-lab-snl)
-- [LLNL Livermore Computing](#llnl-livermore-computing-lassen-tioga-etc)
-- [Department of Defense](#department-of-defense)
-<!-- tocstop -->
+<!-- START doctoc generated TOC please keep comment here to allow auto update -->
+<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+
+
+
+<!-- END doctoc generated TOC please keep comment here to allow auto update -->
 
 * GT PACE Phoenix
     * User guide [here](https://docs.pace.gatech.edu/phoenix_cluster/gettingstarted_phnx/)
diff --git a/group-syllabus/doing-research.md b/group-syllabus/doing-research.md
@@ -5,15 +5,18 @@ It may seem obvious, but it's easy to lose track of the importance of your resea
 Some of these will be fun; many will feel more important at the time than making progress on your research.
 However, I would like you to prioritize your research and triage everything else after this.
 
-<!-- toc -->
+<!-- START doctoc generated TOC please keep comment here to allow auto update -->
+<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+## Table of Contents
+
 - [Selecting problems](#selecting-problems)
 - [Expected Output](#expected-output)
 - [Staying organized](#staying-organized)
 - [Research Ideas and Directions](#research-ideas-and-directions)
 - [Where to find ideas](#where-to-find-ideas)
 - [Deciding what Ideas to Pursue](#deciding-what-ideas-to-pursue)
 
-<!-- tocstop -->
+<!-- END doctoc generated TOC please keep comment here to allow auto update -->
 
 ### Selecting problems
 
diff --git a/group-syllabus/figures.md b/group-syllabus/figures.md
@@ -2,7 +2,10 @@
 
 **Companion documents: [Formatting your work](formatting.md)**
 
-<!-- toc -->
+<!-- START doctoc generated TOC please keep comment here to allow auto update -->
+<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+## Table of Contents
+
 - [This seems like a lot of work. Why am I doing this?](#this-seems-like-a-lot-of-work-why-am-i-doing-this)
 - [What tool should you use to make figures?](#what-tool-should-you-use-to-make-figures)
 - [Standalone compilation](#standalone-compilation)
@@ -13,14 +16,15 @@
 - [White space](#white-space)
 - [Shared plots and legends](#shared-plots-and-legends)
 - [Color bars](#color-bars)
-- [Coordinate direction arrow triad](#coordinate-direction-arrow-triad)
+- [Coordinate direction arrow triad.](#coordinate-direction-arrow-triad)
 - [Axis bounds and ticks](#axis-bounds-and-ticks)
 - [Axis labels](#axis-labels)
 - [Information quantity](#information-quantity)
 - [Consistency](#consistency)
 - [Useful references](#useful-references)
 - [Additional Resources](#additional-resources)
-<!-- tocstop -->
+
+<!-- END doctoc generated TOC please keep comment here to allow auto update -->
 
 See [here](../templates/paper/figures) for examples.
 
diff --git a/group-syllabus/formatting.md b/group-syllabus/formatting.md
@@ -2,7 +2,10 @@
 
 **Companion documents: [Improving your writing](improving-your-writing.md), [Making a figure](figures.md)**
 
-<!-- toc -->
+<!-- START doctoc generated TOC please keep comment here to allow auto update -->
+<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+## Table of Contents
+
 - [Why should I read this?](#why-should-i-read-this)
 - [Consistency](#consistency)
 - [Compiling and other boilerplate](#compiling-and-other-boilerplate)
@@ -15,8 +18,11 @@
 - [Creating your bibliography](#creating-your-bibliography)
 - [Colors](#colors)
 - [Referencing equations, figures, tables, and sections](#referencing-equations-figures-tables-and-sections)
+  - [Figures, tables, sections](#figures-tables-sections)
+  - [Equations](#equations)
 - ["Dashes"](#dashes)
-<!-- tocstop -->
+
+<!-- END doctoc generated TOC please keep comment here to allow auto update -->
 
 ### Why should I read this?
 
diff --git a/group-syllabus/funding.md b/group-syllabus/funding.md
@@ -1,3 +1,14 @@
+<!-- START doctoc generated TOC please keep comment here to allow auto update -->
+<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+## Table of Contents
+
+- [Funding](#funding)
+  - [Research and Teaching Assistantship](#research-and-teaching-assistantship)
+  - [Fellowships](#fellowships)
+  - [Stipend](#stipend)
+
+<!-- END doctoc generated TOC please keep comment here to allow auto update -->
+
 ## Funding
 
 If you are an undergraduate, [click here](undergraduate-specifics.md).
diff --git a/group-syllabus/giving-talks.md b/group-syllabus/giving-talks.md
@@ -3,14 +3,18 @@
 Talks are important: They show your command of your research and your ability to stitch together a story worth listening to.
 Most professors will agree that the new faculty hired into the school are judged primarily on their job talk.
 
-<!-- toc -->
+<!-- START doctoc generated TOC please keep comment here to allow auto update -->
+<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+## Table of Contents
+
 - [What are you trying to achieve?](#what-are-you-trying-to-achieve)
 - [How to](#how-to)
 - [Feedback](#feedback)
 - [Q&A](#qa)
   - [If you are answering the questions (you're the speaker)](#if-you-are-answering-the-questions-youre-the-speaker)
   - [If you are asking the questions (you're in the audience)](#if-you-are-asking-the-questions-youre-in-the-audience)
-<!-- tocstop -->
+
+<!-- END doctoc generated TOC please keep comment here to allow auto update -->
 
 ### What are you trying to achieve?
 Giving a talk is presumably associated with some goals, otherwise, why give it?
diff --git a/group-syllabus/going-to-conferences.md b/group-syllabus/going-to-conferences.md
@@ -1,3 +1,17 @@
+<!-- START doctoc generated TOC please keep comment here to allow auto update -->
+<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+## Table of Contents
+
+- [Submitting and going to conferences](#submitting-and-going-to-conferences)
+  - [What's the point, anyway?](#whats-the-point-anyway)
+  - [Am I going?!](#am-i-going)
+  - [Can I go to observe? (without a paper or abstract)](#can-i-go-to-observe-without-a-paper-or-abstract)
+  - [Registration, flights, and hotels](#registration-flights-and-hotels)
+  - [Spend authorization](#spend-authorization)
+  - [Actually going to the conference](#actually-going-to-the-conference)
+
+<!-- END doctoc generated TOC please keep comment here to allow auto update -->
+
 ## Submitting and going to conferences
 
 __Related documents: [Giving talks](giving-talks.md)__
diff --git a/group-syllabus/hardware.md b/group-syllabus/hardware.md
@@ -1,3 +1,11 @@
+<!-- START doctoc generated TOC please keep comment here to allow auto update -->
+<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+## Table of Contents
+
+- [Whose hardware is this, anyway?](#whose-hardware-is-this-anyway)
+
+<!-- END doctoc generated TOC please keep comment here to allow auto update -->
+
 ## Whose hardware is this, anyway?
 
 During your Ph.D. or, sometimes, undergraduate work, you will acquire hardware that appears to be "from me" to assist with your research.
diff --git a/group-syllabus/improving-your-writing.md b/group-syllabus/improving-your-writing.md
@@ -2,21 +2,25 @@
 
 **Companion documents: [Formatting your work](formatting.md), [Improving your writing](improving-your-writing.md), [Making a figure](figures.md), [Responding to reviewers](responding-to-reviewers.md)**
 
-<!-- toc -->
-- [Why should I read this?](#why-should-i-read-this)
-- [Automatic grammar, spelling, and syntax checkers](#automatic-grammar-spelling-and-syntax-checkers)
-- [Consistency](#consistency)
-- [Nomenclature](#nomenclature)
-- [Variable Naming](#variable-naming)
-- [Concise writing](#concise-writing)
-- [What goes where](#what-goes-where)
-- [Guidelines, tips, and more!](#guidelines-tips-and-more)
-  - [Things to avoid](#things-to-avoid-from-the-angry-reviewer)
-  - [From some tips for scientific writing](#from-some-tips-for-scientific-writing)
-  - [From Koen Hufkens](#from-koen-hufkens)
-- [Required watching](#required-watching)
-- [Other links](#other-links)
-<!-- tocstop -->
+<!-- START doctoc generated TOC please keep comment here to allow auto update -->
+<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+## Table of Contents
+
+- [Why should I read this?](#why-should-i-read-this)
+- [Automatic grammar, spelling, and syntax checkers](#automatic-grammar-spelling-and-syntax-checkers)
+- [Consistency](#consistency)
+- [Nomenclature](#nomenclature)
+- [Variable Naming](#variable-naming)
+- [Concise writing](#concise-writing)
+- [What goes where](#what-goes-where)
+- [Guidelines, tips, and more!](#guidelines-tips-and-more)
+  - [Things to avoid; from the Angry Reviewer](#things-to-avoid-from-the-angry-reviewer)
+  - [From some tips for scientific writing](#from-some-tips-for-scientific-writing)
+  - [From Koen Hufkens](#from-koen-hufkens)
+- [Required watching](#required-watching)
+- [Other links](#other-links)
+
+<!-- END doctoc generated TOC please keep comment here to allow auto update -->
 
 ### Why should I read this?
 
diff --git a/group-syllabus/intro-to-group.md b/group-syllabus/intro-to-group.md
@@ -1,3 +1,19 @@
+<!-- START doctoc generated TOC please keep comment here to allow auto update -->
+<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+## Table of Contents
+
+- [Welcome to the Computational Physics @ GT CSE research group!](#welcome-to-the-computational-physics--gt-cse-research-group)
+  - [Getting started](#getting-started)
+    - [CODA](#coda)
+    - [Websites, software, course numbers, and such](#websites-software-course-numbers-and-such)
+    - [Computers](#computers)
+  - [Research meetings](#research-meetings)
+  - [Group GitHub Page](#group-github-page)
+  - [Collaboration](#collaboration)
+  - [Social activities](#social-activities)
+
+<!-- END doctoc generated TOC please keep comment here to allow auto update -->
+
 # Welcome to the Computational Physics @ GT CSE research group!
 
 The most important thing about this document is that I/we are _very glad_ to have you.
diff --git a/group-syllabus/publishing.md b/group-syllabus/publishing.md
@@ -1,3 +1,15 @@
+<!-- START doctoc generated TOC please keep comment here to allow auto update -->
+<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+## Table of Contents
+
+- [Publishing](#publishing)
+  - [Important: The "-X days" internal revision process and deadlines](#important-the--x-days-internal-revision-process-and-deadlines)
+  - [Process: writing alone, better together](#process-writing-alone-better-together)
+  - [Co-authorship](#co-authorship)
+  - [Conference and Other Presentations](#conference-and-other-presentations)
+
+<!-- END doctoc generated TOC please keep comment here to allow auto update -->
+
 ## Publishing
 
 **Companion documents: [Formatting your work](formatting.md), [Improving your writing](improving-your-writing.md), [Making a figure](figures.md), [Responding to reviewers](responding-to-reviewers.md)**
diff --git a/group-syllabus/responding-to-reviewers.md b/group-syllabus/responding-to-reviewers.md
@@ -1,3 +1,15 @@
+<!-- START doctoc generated TOC please keep comment here to allow auto update -->
+<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+## Table of Contents
+
+- [Responding to reviewers](#responding-to-reviewers)
+  - [Principle of charity](#principle-of-charity)
+  - [Knowing what to and not to do](#knowing-what-to-and-not-to-do)
+  - [The details of a response document](#the-details-of-a-response-document)
+  - [Examples](#examples)
+
+<!-- END doctoc generated TOC please keep comment here to allow auto update -->
+
 ## Responding to reviewers
 
 When you submit a paper, you will likely get reviews that request changes to your work.
diff --git a/group-syllabus/undergraduate-specifics.md b/group-syllabus/undergraduate-specifics.md
@@ -4,7 +4,10 @@ Much of this 'syllabus' applies to undergraduates and graduate students.
 But, there are a few things specific to undergraduate researchers.
 Below is my attempt to explain them.
 
-<!-- toc -->
+<!-- START doctoc generated TOC please keep comment here to allow auto update -->
+<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+## Table of Contents
+
 - [Meetings](#meetings)
 - [Remote work](#remote-work)
 - [Money](#money)
@@ -15,7 +18,8 @@ Below is my attempt to explain them.
 - [Office space](#office-space)
 - [Working with people](#working-with-people)
 - [Going to conferences](#going-to-conferences)
-<!-- tocstop -->
+
+<!-- END doctoc generated TOC please keep comment here to allow auto update -->
 
 ### Meetings
 
diff --git a/group-syllabus/when-where-working.md b/group-syllabus/when-where-working.md
@@ -1,3 +1,14 @@
+<!-- START doctoc generated TOC please keep comment here to allow auto update -->
+<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+## Table of Contents
+
+- [The Where and When of Working](#the-where-and-when-of-working)
+  - [Are you working enough? Or too much?](#are-you-working-enough-or-too-much)
+  - [Can I take a vacation?](#can-i-take-a-vacation)
+  - [Work location](#work-location)
+
+<!-- END doctoc generated TOC please keep comment here to allow auto update -->
+
 ## The Where and When of Working
 
 One of the biggest challenges for student researchers is time management.
diff --git a/group-syllabus/why-phd.md b/group-syllabus/why-phd.md
@@ -1,3 +1,12 @@
+<!-- START doctoc generated TOC please keep comment here to allow auto update -->
+<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+## Table of Contents
+
+- [The What and Why of a Ph.D.](#the-what-and-why-of-a-phd)
+  - [How long is a Ph.D.?](#how-long-is-a-phd)
+
+<!-- END doctoc generated TOC please keep comment here to allow auto update -->
+
 ## The What and Why of a Ph.D.
 
 Advising and working with Ph.D. students is the *best part of my job*.
diff --git a/group-syllabus/working-with-me.md b/group-syllabus/working-with-me.md
@@ -1,3 +1,18 @@
+<!-- START doctoc generated TOC please keep comment here to allow auto update -->
+<!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
+## Table of Contents
+
+- [Working with Me](#working-with-me)
+  - [Advising "style"](#advising-style)
+    - [Spencer's quirks](#spencers-quirks)
+  - [Power Structures](#power-structures)
+  - [Co-advising](#co-advising)
+  - [Time with me and Others](#time-with-me-and-others)
+  - [How to get a hold of me](#how-to-get-a-hold-of-me)
+  - [Useful links](#useful-links)
+
+<!-- END doctoc generated TOC please keep comment here to allow auto update -->
+
 ## Working with Me
 
 The advisor-advisee relationship represents a significant responsibility and commitment on both our parts.
