Emacs configuration file using straight.el + Helm

Description

Configuration files to customize the aspect of emacs and extend its default capabilities. It consists of two files, init.el and config.org. The former defines some basic customization, most relevantly, it defines the repositories where to fetch the packages and loads config.org where most of the packages are loaded and configured. The configuration files used in the main branch were modified to use the package manager straight.el which installs packages directly from their repository. This allows one to revert a package version in case the current one is broken; or to install packages that are not yet in a repository. The configuration file uses helm for completion, selection, searching and other functions

Third party software

Dependencies

• Pandoc: [*Recommended*] Required for exporting (converting) org files to other formats (e.g. HTML, markdown, etc). See pandoc's official website for installation instructions
• Zoxide: [*Optional*] Provides a better way to navigate directories [homepage]. The emacs package, zoxide.el, allows a similar functionality using dired.
• Mermaid-cli: [*Optional*] Command line interface to the diagramming and charting tool, Mermaid. In the recommended way to install is through node.js package manager, npm: npm install -g @mermaid-js/mermaid-cli. The path to the binaries should be defined accordingly.

Others

• Anaconda:
• R:
• Tex distribution: TeXLive MikTeX

Two packages that help writing code are format-all and flycheck. These, require additional packages to check the format of the code, those used in the configuration are described below

Language	Package	Notes
R	styler	install.packages("styler")
Bash	shfmt	sudo apt install golang-mvdan-sh-dev
	beautysh	pip install beautysh
Python	various	pip3 install black jedi autopep8 flake8 ipython yapf
Html	tidy	sudo apt install tidy
Latex	auctex	Part of TexLive

Language	Package	Notes
R	lintr	install.packages("lintr")
Awk	gawk	sudo apt install gawk
Bash	shellcheck	sudo apt install shellcheck
Html	tidy	sudo apt install tidy
JavaScript	jshint	npm install -g jshint
Python	various	pip3 install pylint flake8
		sudo apt install pylint
Latex	lacheck	Part of TexLive

Loading

The files should be placed in the .emacs.d folder located in the home directory (On windows, C:\Users\username\.emacs.d and on Linux, /home/your-username/.emacs.d). Make sure there is not an .emacs file already which will take precedence over these files (/i.e./they will not be loaded).

Provided an internet connection is available, the configuration file will install and configure most of the packages automatically.

Packages that require the specification of a pathway

The following packages require the user to specify the pathway where specific files or directories are located. For easier maintenance variables that require a path were grouped in the section Custom variables. Modify these accordingly

1. Path to documents

   Since most of the packages are used to create notes, a custom variable to indicate the Documents path was created. It uses an if statement to distinguish two different locations based on the localization of the system but that could be changed

   (defvar docs-dir
       (if (file-directory-p "~/Documents")
           "~/Documents"
         (if (file-directory-p "~/Documentos")
             "~/Documentos"
           "other")))

2. Python (Anaconda)

   It assumes an anaconda or miniconda installation is present (See official installation page). To be able to use the environments, make sure to specify the pathway to the installation folder, as well as, the environments folder is specified

   ;; Path to anaconda installation 
   (defvar conda-dir
     (if (file-directory-p "/media/discs/shared/miniconda3")
         "/media/discs/shared/miniconda3"
       (if (file-directory-p "~/.local/bin/miniconda3")
           "~/.local/bin/miniconda3"
         "other")))
   
   (defvar my/anaconda-home conda-dir)
   (defvar my/anaconda-venv (concat conda-dir "/envs"))

3. org-roam

   Allows the creation and management of interconnected notes using the Zettelkasten method (see its homepage). It requires to specify a directory where to store the notes. The following line creates a custom variable that is latter used in the org-roam configuration section.

   (setq my/org-roam-dir "~/Documents/Org-files/Org-roam")

4. org-noter

   Provides functions to simplify taking notes on documents particularly pdf files (see its GitHub page). Examples include synchronizing the notes at specific points in the document or creating an overview of the document. It also requires to specify a directory where to store the notes.

   (setq my/org-noter-dir "~/Documents/Org-files/Org_noter")

5. org-ref

   Allows inserting references in a org file. References should be in bibtex format (*.bib) and the path to their location, as well as, that of the associated files should be specified. More information can be found on the official org-ref GitHub page

   ;; Bibtex paths and files
   (setq
      bibtex-completion-bibliography (concat docs-dir "/Refs/Bibtex/Working.bib")
      bibtex-completion-library-path (concat docs-dir "/Papers_Books/")
      bibtex-completion-notes-path (concat docs-dir "/Papers_Books/Summaries"))

6. ebib

   Allows the management of references in bibtex format (see its online manual). The following variables are used to store the location where to search for bibtex files and which files should be load when the package is started.

   ;; ebib
     (setq my/ebib-search-dir (concat docs-dir "/Refs/Bibtex/"))
     (setq my/ebib-bibtex-files
         (list
          (concat docs-dir "/Refs/Bibtex/Articles_zotero.bib")
          (concat docs-dir "/Refs/Bibtex/Books_zotero.bib")))

7. org-reveal

   It is a package to export org files to reveal.js format. The path to the cloned directory should be specified

   ;; org-reveal-path
   (defvar reveal-path
     (if (file-directory-p "/media/discs/shared/Cloned/reveal.js")
         "file:///media/discs/shared/Cloned/reveal.js"
       (if (file-directory-p "/media/particiones/Cloned/reveal.js")
           "file:///media/particiones/Cloned/reveal.js"
         "other")))
   (setq org-reveal-root reveal-path)

8. Mermaid-cli

   ;; Define directory where ananconda is installed
   (defvar conda-dir
     (if (file-directory-p "/media/discs/shared/miniconda3")
         "/media/discs/shared/miniconda3"
       (if (file-directory-p "~/.local/bin/miniconda3")
           "~/.local/bin/miniconda3"
         "other")))
   ;; Concatenate the base directory for anaconda and
   ;; that for mermaid-cli
   (defvar my/mmdc-path (concat conda-dir "/bin/mmdc"))

Troubleshooting

• error the first time emacs is loaded: Sometimes an error may appear the first time emacs is started with this configuration but it is usually resolved after re-starting emacs

• missing fonts: Font used are specified in the Custom variables section in the config.org file. Currently, they are set to Courier New and Verdana.

  ;; Fonts
  (defvar my/mono-font "Courier-New")
  (defvar my/sans-font "Verdana")
  (defvar my/default-font "Courier-New")