{"id":22901407,"url":"https://github.com/mooerslab/diary2023inlatex","last_synced_at":"2025-05-08T01:46:30.334Z","repository":{"id":65359832,"uuid":"532432511","full_name":"MooersLab/diary2023inLaTeX","owner":"MooersLab","description":"LaTeX template for diary, log book, or lab notebook for 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MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)\n\n# Diary for 2023 in LaTeX\n\nGo to this [site](https://github.com/MooersLab/diary2024inLaTeX) for the 2024 version of this diary.\n\n## What is this?\n\nThis repo contains a template book with 365 blank tex files, one for each day of the year.\nThese tex files are collated and rendered into a PDF with latex and bibtex compilers.\nIt is set up for 2023.\nIt is configured to generate the following automatically:\n\n- Chapter headings and section headings (add subsections and lower in your daily writing).\n- Chapters and sections are automatically numbered.\n- Table of Contents, hyperlinked\n- References Cited, hyperlinked\n- Index, hyperlinked\n- Lists of code listings, hyperlinked\n- List of Figures, hyperlinked\n- List of Tables, hyperlinked\n- An appendix that uses chapters that are arranged in alphabetical order by letters instead of numbers.\n- Page numbers\n- Epigraphs for Chapter header pages\n- URLs in footnotes to prevent them from running into the right margin.\n- Syntax highlighting of code via the minted package\n- Supports the use of equations with captions (i.e., makes it possible to generate lists of equations).\n\n\nThe document is based on the Springer book format, but it has a 7 by 9-inch area for writing and conservative margins to save paper.\n\n\n## What is this good for?\n\nThis can be used for the following purposes:\n\n- diary\n- laboratory notebook\n- log book\n- managing todo lists and plans\n- provide material for an autobiography, biography, or to stimulate nonfiction and fiction books.\n- to document one's life to inspire one's descendants\n- storage site for daily writing on sites like 750words.com\n\nThis document's design was stimulated by the last use.\nI wanted an independent place to store my daily writing on [750words.com](https://750words.com), where it is stored in plain text files that are hard to search.\nI wanted that writing to be indexable and searchable in a single PDF for a calendar year rather than 365 files.\nThis document has been very useful for finding information, including data wrangling protocols and computer code, that I used in the past.\nIt can gather information for annual reports if used as a \"Captian's log\" of one's personal Enterprise.\nFor example, lists of accomplishments can be stored in the Appendices.\n\n## Prior Experience\n\nI have been using something like this since 2012, and this document has been in its current format since 2015.\nEach year's document has run about 1000-1200 pages in length.\nIt is part of my daily routine to paste the day's writing into this document before retiring for the day or first thing in the following morning.\n\n## Limitations\n\nWriting in LaTeX has some limitations:\n\n- The document is limited by computer RAM to one year. \n- The document is limited by RAM regarding the number of lists and indices that can be generated simultaneously.\n- Debugging can sometimes involve commenting out chapters in the 0AAAContent document to isolate the error. \n\nNot to worry! The debugger on Overleaf will locate the bug by document name and line number. \nA click on an arrow will take you to the bug in the correct file.\n\nI generally fall behind on my debugging and will comment out earlier chapters to prevent their errors from stopping compiling.\nI debug the old writing occasionally during the year when I am too tired to do anything else and during winter break before the start of the new year.\n\n## Compiling\n\nThe *main.tex* document is fed to the compiler.\n\nCompile with lualatex and the `-escape-shell` key (for the minted package).\nThe `compile.sh` script runs at the top level of the folder `2023diary`, which you can rename.\nThe document is easy to compile with the click of a button using the Overleaf website.\nThe empty shell document takes several seconds to compile.\nA 1000-page document will be compiled in about 60 seconds.\n\nThis long compile time is another advantage of the modular approach as opposed to having everything in one tex file.\nI comment out the inactive months in the *0AAAContents.tex* file to shorten the compile time to a few seconds.\n\n## Role of the 0AAAContents.tex file.\n\nThe *0AAAContents.tex* file is the central nervous system of the document.\nIt is trival to comment out entire chapters via a single percent sign.\nIt is also trivial in Emacs to shuffle the order of the chapters by moving lines up or down.\nYou can add prose to the *0AAAContents.tex* file, but I find it adds clutter to this file.\n\n## Configuration\n\n- Edit the title and author at the top of the A000Contents.tex file in the Content subfolder.\n- Change the cover figure to suit by loading a new image into the ./Content/Figures subfolder and by editing the path to the image to specify this new figure. Some image file formats like tiff are not supported. Png  and PDF are reliable.\n- Comment out the lists you do not intend to use in 0AAAContent. For example, if you do not save computer code, the list of listings will not be used.\n- Add new appendices like your annual plan as a text file.\n\n## Daily use\n\nThe documents to be edited are in chapter subfolders in the Content subfolders.\nEach day's entry is in a separate tex file.\nNavigate to the file corresponding to the current date and write on line two.\nThe code on the first line must remain in place for the document to compile.\n\nEach file forms a section of a chapter.\nThis book has one chapter per month.\nAll sections for a month are in a chapter subfolder in the Content folder.\n\n## On-line editor\n\nI recommend using the online editor Overleaf for the smoothest operation.\nI have been editing this document on Overleaf for six years.\nYou do NOT have to run each of the steps of compiling separately.\nYou just click a button, and the latex and bibtex compilers are run seamlessly.\nI store the URL for this project on my private home page for rapid access.\n\nYou can compile the entire document with any document open in the text area because the main document is set in the menu panel on the left.\nThis menu is also where you configure the compiler, key bindings, color theme, etc.\n\n## Local editors\n\nIn terms of local editing, there are many (\u003e20) freely available text editors that are highly supported for editing documents in LaTeX.\nThe following are perhaps the most popular general-purpose editors that have great support for LaTeX:\n\n- TextMate for the Mac (very easy to compile with `cmd-R`)\n- Sublime Text\n- VSC\n- Vim\n- Emacs\n\nTextMate for the Mac does not get enough love these days.\nIt starts lightning fast.\nI open the editor most frequently, although I am trying to migrate to Emacs.\n\nThanks to elisp and a dedicated developer community, Emacs is the most configurable editor.\n\n### Emacs\n\nMust be configured to use laulatex and -escape-shell. \nIt might be easiest to call the shell with `M-!` and enter `compile.sh, main.tex` to compile and open in your default PDF viewer.\nOr just run the compile.sh script externally to Emacs.\n\nSee the `latex-emacs` repo for a sample configuration.\nIf you have citations, you will have to run bibtex on main.tex.\n\n## Best of both worlds: use local editor to edit today's entry on Overleaf\n\nThe Google Chrome extension [GhostText](https://ghosttext.fregante.com/) supports using several kinds of local editors to edit text areas in web browsers.\nThe opened *toadayDate.tex* file is a text area in Overleaf.\nYou can bring your favorite LaTeX snippets to bear on Overleaf, which does not support snippets directly.\n\nFor example, I start the day by opening Emacs, logging into 750words, and clicking on the GhostText icon to open the connection to Emacs.\nIn Emacs in the **Write your words** buffer, I enter `start` and hit `TAB` or `C-o`. \nThis action inserts the following boilerplate from the `start` snippet file, which is available above.\nI have [configured](https://github.com/MooersLab/latex-emacs) the Emacs package [atomic-chrome](https://github.com/alpha22jp/atomic-chrome) to open `Write your words` in the latex-mode so that I can have access to my latex-mode snippets, which are available [here](https://github.com/MooersLab/snippet-latex-mode).\n\n```latex\n\\subsection{Last night}\nchange me\n\n\n\\subsection{This morning}\nchange me\n\n\n\\subsection{To Be Done Today}\n\\index{To Be Done!2022-09-04}\n\\begin{itemize}\n\\item change me\n\\item change me\n\\item change me\n\\item change me\n\\item change me\n\\item change me\n\\item change me\n\\item change me\n\\item change me\n\\item change me\n\\end{itemize}\n\n```\n\nThe cursor advances to `change me` under *Last night*.\nI write some notes about what I did.\nThen I hit tab to advance to the next `change me` to write notes about the morning.\nI hit tab again to advance to the first item in my TODO list for the day.\nWhen I reach the bottom of the list, I enter `C-c C-j` to enter the next **\\item** properly aligned and with the cursor in the right position.\n\nA call to a macro inside the yasnippet snippet called *start* inserts the correct date in the index key.\nI create an index key without lifting a finger.\n**See, Life can be Good in Emacs!**\n\nSee the end of this [slideshow](https://github.com/MooersLab/BerlinEmacsAugust2022) for the application of GhostText to LaTeX editing with Emacs.\nFor Jupyter users, you can likewise use GhostText to edit code and markdown cells with your favorite editor.\nSee [slideshow](https://github.com/MooersLab/DSW22ghosttext) about this exciting topic.\nSee the corresponding [video](https://mediasite.ouhsc.edu/Mediasite/Channel/python/watch/4da0872f028c4255ae12935655e911321d).\n\n## Related projects of possible interest\n\n- [LaTeX manuscript template](https://github.com/MooersLab/manuscriptInLaTeX/edit/main/README.md)\n- [Writing log template in LaTeX](https://github.com/MooersLab/writingLogTemplate)\n- [Slideshow template in LaTeX](https://github.com/MooersLab/slideshowTemplateLaTeX)\n- [Annotated bibliography Template in LaTeX](https://github.com/MooersLab/annotatedBibliography)\n- [Diary for 2022 in LaTeX](https://github.com/MooersLab/diary2022inLaTeX)\n- [Diary for 2023 in LaTeX](https://github.com/MooersLab/diary2023inLaTeX)\n- [latex-emacs profile](https://github.com/MooersLab/latex-emacs)\n- [snippets for latex-mode in Emacs](https://github.com/MooersLab/snippet-latex-mode)\n- [Quizzes about Emacs to improve recall of keybindings](https://github.com/MooersLab/qemacs)\n- [Slides from talk about GhostText, Data Science Workshop, July 2022](https://github.com/MooersLab/DSW22ghosttext)\n- [Video link to talk about GhostText, Data Science Workshop, July 2022](https://mediasite.ouhsc.edu/Mediasite/Channel/python/watch/4da0872f028c4255ae12935655e911321d)\n- [The writer's law](https://github.com/MooersLab/thewriterslaw)\n\n## Update history\n\n|Version      | Changes                                                                                                                                    | Date                 |\n|:-----------:|:------------------------------------------------------------------------------------------------------------------------------------------:|:--------------------:|\n| Version 0.2 |   Added badges, funding, and update table.                                                                                                 | 2024 May 23          |\n\n\n## Sources of funding\n\n- NIH: R01 CA242845\n- NIH: R01 AI088011\n- NIH: P30 CA225520 (PI: R. Mannel)\n- NIH: P20 GM103640 and P30 GM145423 (PI: A. West)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmooerslab%2Fdiary2023inlatex","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmooerslab%2Fdiary2023inlatex","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmooerslab%2Fdiary2023inlatex/lists"}