= foo-dogsquared's wiki
:toc: true

:art-file-prefix: fds-illustration


Keep taking notes and stop worrying about file organization!

Muh wiki.
This documents the "infrastructure" of my notes because I like documenting and I always forget things.
It primarily uses the link:https://zk.zettel.page/[Zettelkasten note-taking method] which means all of my notes are scattered in just one location.
Fun.

[NOTE]
====
On another note, this supersedes my link:https://github.com/foo-dogsquared/personal-notes[personal notes].
I'm not going to import them because I want to start on a clean slate.

Also, not everything on this Git repo is here (at least yet).
Some of them are private files and so I want them to not appear anywhere else.
Fortunately for me, most of the private files are connected with each other (a separate org-roam instance would be better in this case).
====




== Getting started

Interested in copying my setup?
Here's my IKEA-esque manual for you.


=== Prerequisites

It needs the following list of software.
All of them are required unless noted otherwise.

* link:https://www.gnu.org/software/emacs/[GNU Emacs] because link:https://orgmode.org/[org-mode].

** Uses link:https://github.com/hlissner/doom-emacs/[Doom Emacs] as the preferred Emacs distro with the `org` module enabled.
This is optional and you can use your own Emacs config.

** link:https://github.com/org-roam/org-roam[org-roam], the star of the show, is installed.

* link:https://nixos.org/[Nix package manager] because link:https://orgmode.org/manual/Working-with-Source-Code.html[org-babel].
You can fully replicate the environment without Nix by looking at the dependencies at link:./shell.nix[`./shell.nix`] and install them with your package manager (or anything else, you do you) but I recommend to do so because I say so.

* link:https://direnv.net/i[direnv] (optional, by the way) because automatic shell environment.
footnote:[You can enable the direnv module from the Doom Emacs config.]


=== Setting up

Now with the pieces complete and assuming you've already have my wiki in your folder, fire up Emacs, open the wiki folder, and do your thing.
This project has a link:./.dir-locals.el[local Emacs config] (see link:https://www.gnu.org/software/emacs/manual/html_node/emacs/Directory-Variables.html[related section]).
If you've set `enable-local-variables` to `:safe` or any value that makes Emacs to ignore them, you may want to configure related variables for it to work.

If you have direnv installed, you can also enable automatic shell environments by allowing `.entry` to set it up for you.
Just run `direnv allow`!

If you have link:https://github.com/target/lorri[lorri] installed, you're better to go with the faster startup for the environment.




== Conventions

* There are certain times to use custom link:https://orgmode.org/manual/Blocks.html[Org mode blocks] inspired from Asciidoctor.

** Abstract — e.g., `#+begin_abstract`.
** Appendix — e.g., `#+begin_appendix`.
** link:https://docs.asciidoctor.org/asciidoc/latest/blocks/admonitions/[Admonition blocks] — e.g., `\#+begin_important`, `#+begin_tip`, `#+begin_warning`.

* Mainly uses https://zk.zettel.page/types-of-notes[the convention of note categories found in zk.zettel.page].
That said, not all notes are going to be self-contained.
footnote:[Also, not all notes have the same structure so that makes it complicated.]

** Fleeting notes are in link:./daily/[`./daily/`].
The fleeting notes are ignored since they're meant to processed on the daily so having them in the worktree will make a messy history.

** Literature notes are in link:./literature/[`./literature/`].
The literature notes may be a combination of Org roam notes and other notes from previous set of notes.
Practically, this is your 2D system of notes — the hierarchical notebook.

** The permanent and index notes are in the root folder.

** Additional types of notes can be put in a separate folder (e.g., cards, microposts).
There is not set hierarchy but be sure to create a new type only if the change is major.

* The above structure makes it easier for retrieval.
If you want to search all of the fleeting notes, just search in `daily/`, etc.

** For searching tools, prefer desktop search tools such as link:https://www.lesbonscomptes.com/recoll/[Recoll] or link:https://sourceforge.net/projects/docfetcher/[DocFetcher].
** Quick search tools such as grep or link:https://github.com/BurntSushi/ripgrep[ripgrep] are also nice.

* Uses timestamp (at localtime) as the filename, it is unique enough (for personal purposes) and doesn't need to change.
footnote:[If you use the title as the basis, that'll depend if you have tolerance for the misaligning relation between the filename and the title.]
The format for the filename is equivalent to `$(date +%F-%H-%M-%S).org`.

* Uses link:https://orgmode.org/guide/Tags.html[plain org-mode tags] for consistency.
It also happens to be the only supported tag format starting from link:https://org-roam.discourse.group/t/org-roam-major-redesign/1198[org-roam v2] so hoorah for me. :)

* A list of references are stored at link:./references.bib[`./references.bib`] for link:https://github.com/jkitchin/org-ref[org-ref-styled workflows].
It is managed with link:https://www.zotero.org/[Zotero] with the link:https://github.com/retorquere/zotero-better-bibtex[better-bibtex Zotero extension] but you can replace however you manage and generate the Bibtex file.

* A creation datetime and a modification datetime is a cruicial part of my notes.
It lets me know how up-to-date my notes are without relying on the filesystem metadata because I copy them carelessly, not to mention how various tools deal with them differently.
The modification datetime is handled with link:https://www.gnu.org/software/emacs/manual/html_node/emacs/Time-Stamps.html[timestamps] automatically.
Here's an example Doom Emacs configuration for that:
+
[source, elisp]
----
(after! org
  (setq
   time-stamp-start "date_modified:[ 	]+\\\\?[\"<]+"
   time-stamp-format "%Y-%02m-%02d %02H:%02M:%02S %:z"))

; Automate updating timestamps on save.
(add-hook 'before-save-hook 'time-stamp)
----
+
Just see my link:https://github.com/foo-dogsquared/dotfiles/tree/4e8f036b73a71d02f5909f4f28898a79c2311147/emacs[Doom Emacs config] in my dotfiles.

* The related assets are stored in the link:./assets/[`./assets/`].
The asset folder names should be the same as the filename of the org-mode document — e.g., `2021-04-06-15-04-11.org` should have an asset folder in `./assets/2021-04-06-15-04-11/`.

** I sometimes draw a visual aid just to strengthen my learning as well as an excuse to use my graphics tablet and I want to store them in a reasonable location without dumping it like in a landfill.
Unfortunately, this means having to scour the assets folder like a clueless babboon holding a hammer because all of it is named after a timestamp but I can deal with it.

** link:https://orgmode.org/worg/org-contrib/babel/intro.html[org-mode can also generate files including text and graphics].
I'm lazy and I fear conflicting asset filenames so I'll just put them in separate folders instead alongside opening a can of worms.
footnote:[This includes trying to name an asset that doesn't exist already to not overwrite the file that one note needed. It's also a lot more subtle when trying to build it altogether or if the notes get any bigger.]

** For my hand-drawn visual aids, I usually name with a prefix (e.g., `{art-file-prefix}-${WHAT_THE_GRAPHICS_IS_ABOUT}.webp`).
As a side effect, this mitigates against overwriting of generated assets from org-mode if I remember to not name it `{art-file-prefix}-*`.




== Future tasks

This also means expect the following changes if you're watching this repo for some reason.
Keep in mind all of the details are still under consideration.

* Create a static site for my wiki.
org-roam doesn't have a built-in export option yet but there are solutions.
For now, I'm not worrying to much on this one.

** I could make a custom publication script.
I did create a publication script back then for a small org-mode-based for testing purposes but it is messy and life happened so I wasn't able to get back on it immediately.
Here's a link:https://git.sr.ht/~brettgilio/website/[very good example of a org-mode-and-Emacs-powered site] complete with features and without JavaScript!
footnote:[link:https://brettgilio.com/[Brett Gilio] is kind enough to answer my noob org-mode related questions back then so big thanks to him for the guidance. :)]
The advantage is complete control and the disadvantage is starting from scratch.
Still, you can start from already existing solutions.

** Convert the org documents to commonly-supported text formats like Markdown and use static site generators.
Most of them supports Markdown and there is an "export to Markdown" option for org-mode.
I could whip up an Elisp script and export it by batch then move them over to an SSG setup like Hugo.
This is also how link:https://github.com/jethrokuan/braindump[Jethro Kuan's org-roam notes] are setup.

** Use a parser outside of Emacs.
link:https://github.com/rasendubi/uniorg/tree/master/examples/org-braindump[uniorg] has a good example with Next.js as the site generator.
It requires an external JavaScript-based setup but it can also be an advantage.

* Migrate the notes for link:https://org-roam.discourse.group/t/org-roam-major-redesign/1198[org-roam v2].
Though I consider v1 to be feature-complete, I do like v2's reimagining of the plugin with the node (instead of files) as the new atomic unit.
It is closer to its original inspiration (Roam Research).
It also brings a few simplified options along the way such as choosing to only support `tags` property as well as replacing IDs for linking instead of file links.
Aaaand the primary maintainer said more performance so yay for me.

** Expect to change the links since it doesn't accept file links anymore.

** Expect to generate IDs for each node/file.
The community is ready to help for it since my Elisp-fu sucks.

* Try out link:https://github.com/srid/neuron/[Neuron].
I've used it on and off and even tried to support both org-roam and Neuron because I like the static site generated and also because org-roam doesn't have a killer HTML exporter yet (in my opinion).
It is simple and nice but I can deviate from that with link:https://orgmode.org/manual/Publishing.html[org-publish] or any supported static site generators like link:https://gohugo.io/[Hugo].
Once link:https://github.com/srid/neuron/issues/557[org-mode is reimplemented in Neuron v2], it's a 100% addition to my workflow.

* Add/replace Nix with link:https://guix.gnu.org/[Guix].
Maybe add a file intended for setting up a Guix environment.
I like both Nix and Guix, all right.

