dotfiles

This is a public copy of my dotfiles, recently updated

Original README follows.

Better command-line tools

• tldr instead of man
• fd to find files
• ag to search file contents

(Install instructions below)

Setting up coding environment on new Mac

NOTE: This guide is a work in progress.

On macOS Terminal, new shell runs dotfiles in this order, per current setup:

.zprofile (manually loads .profile
.profile (manually loads .profile_local)
.profile_local
.zshrc

Start here

Install brew: https://brew.sh

Install git with brew

brew

See apps in brew_leaves.txt

Install with xargs brew install < brew_leaves.txt

Generate via brew leaves > brew_leaves.txt.

Additional:

brew tap homebrew/cask-fonts                  # you only have to do this once!
brew install font-inconsolata
brew install --cask qlstephen
brew install --cask stats

Utils:

brew leaves
brew list --pinned

brew's git

I am using brew's git (which -a git) which seems to have trouble with autocomplete (it hangs on git add ..., eg)

Not sure how to resolve.

Tmux

First, install plug in manager: https://github.com/tmux-plugins/tpm

Then install tmux resurrect, etc

Python

Manage python with Brew

brew pin [email protected] to prevent automatic upgrades. See pins with brew list --pinned

To upgrade to 3.8.x, use brew reinstall [email protected]. Otherwise, brew upgrade will update python to latest version (eg, 3.9). Also see pin above.

Use Python 2 kernel in Jupyter: http://ipython.readthedocs.io/en/stable/install/kernel_install.html

Current usage:

• use python3 and pip or pip3 command
• without virtualenv, do NOT need (????) --local in pip. It installs locally, probably after the following:
• I got pip command after python3 -m pip install --upgrade pip
• Previously, there was only pip3 and no pip command

Check with

brew info python or brew info [email protected]

Virtual envs

Use either:

• For global/shared envs, use virtualenvwrapper such as mkvirtualenv. Pass python version with -p
• To store at project root, use python3 -m venv env

Jupyter:

• In Terminal, activate virtual env, then install ipykernel and register it (search online)
• See: https://ipython.readthedocs.io/en/stable/install/kernel_install.html#kernels-for-different-environments

References

• PROJECT_HOME, virtualenv projects: https://stackoverflow.com/a/9425560/3217870

Conda

Conda is not used by default. Activate only as needed:

source ~/miniforge3/bin/activate

This was installed into ~/miniforge3 with:

You have chosen to not have conda modify your shell scripts at all.
To activate conda's base environment in your current shell session:

eval "$(/Users/paul/miniforge3/bin/conda shell.YOUR_SHELL_NAME hook)" 

... per https://developer.apple.com/metal/tensorflow-plugin

Tensorflow

Install(ed) per https://developer.apple.com/metal/tensorflow-plugin/

R

R installation should install it for Terminal at /usr/local/bin/R

Emacs

Update: macOS Big Sur seems to fix the following issue

macOS Catalina Problems: spotlight switching and desktop file access. Resolve:

1. Install from https://emacsformacosx.com
2. Then OPEN emacs for the first time, to overcome the "unsigned package" dialog and so that next steps work. Otherwise you may get a "Emacs package is corrupted" or similar error..
3. Carefully rename some files inside the package contents

• mv the *_10 not the *_14 binary (on my setup)
• See this link

1. Now, you can try opening desktop files. Maybe it will prompt for access. If not, go into macOS security and privacy settings per above link and add disk access for Emacs

Also, maybe related: https://docs.brew.sh/FAQ#my-mac-apps-dont-find-usrlocalbin-utilities

Start with .emacs (from .emacs.lite) then install packages from .emacs.d/.emacs.local as needed.

M-x package-install RET my_package_name

Packages to install

• exec-path-from-shell
• flycheck
• magit
• more in .emacs

Reference for package management: https://dotfilehub.com/knoebber/emacs

Run R from SSH session

Elpy

Set up Emacs and Elpy to use homebrew python:

• Do not chagne paths. Instead,
• Change the location of python for both Emacs and elpy. See .emacs

ESS for Emacs

Now using MELPA source, via:

M-x package-install ess

Notes:

[ESS] Failure to parse long R functions when ess-eval-visibly nil

• In iESS buffer, this error print lots of "^G" like "^G^G^G^G" etc
• Solution 1: Temporarily toggle ess-eval-visibly to t (use Menu)
• Solution 2: "A workaround for this is to load the file with C-c C-l. That is, keep all you functions in a remote file and load it whenever needed."
• https://stat.ethz.ch/pipermail/ess-help/2015-October/010775.html

Remote python

May be tricky to set up, but you can open local or remote python files, and use a remote python session, interactively.

See helpers in .emacs that set up and load python shell interpreter.

Tramp

Working with tramp with remote files could be very slow due to the backups on the server side. The following setting makes it much faster:

(setq tramp-auto-save-directory "~/.backups/tramp/")

Clean up tramp connection

**M-x tramp-cleanup-all-buffers**		 It closes also all remote buffers, which might be in the way.
M-x tramp-cleanup-this-connection
M-x tramp-cleanup-connection
M-x tramp-cleanup-all-connections

Lintr in Emacs-ESS

Emacs 26+ has built-in flymake which is used by ESS to lint R code (on by default).

Disable lintr with: (setq ess-use-flymake t)

Set linter config in project-specific file .lintr. Its location is buffer-specific, set in ess-r--lintr-file, which seems not able to be made global.

Example contents of .lintr file:

linters: with_defaults(line_length_linter(120), infix_spaces_linter=NULL)

May need to disable cache, which is on by default. Disable with (setq ess-r-flymake-lintr-cache nil)

References

• Search "lintr" in ESS Docs

Ruby

Manage with brew, like for python. Pin version to prevent updates: brew pin ruby

Installed Homebrew per mac.install.guide/ruby/index.html especially ruby/13.

Utils

Clean up files with cli and other utils: freespace.tdhopper.com

Improving touchbar

Note: recently disabled, didn't find it too useful.

Requires Better Touch Tool.

My custom configuration is saved in touchbar-preset.json (can import to BTT), and is based on:

1. Great instructions here: vas3k.com/blog/touchbar/
2. Fn key customizations from "You can still access the control strip" at alexw.me/2017/01/what-if-you-could-customize-your-new-touch-bar/

Misc

Change Emacs dock icon. Use Emacs.icns and follow the rest of these instructions.

Add file types to Quick Look via custom plist file:

• Check diff, then rename file from/to:
• qlstephen_qlgenerator_contents_info.plist
• ~/Library/QuickLook/QLStephen.qlgenerator/Contents/Info.plist
• Reference: whomwah/qlstephen/issues/87#issuecomment-831399689

Safari - Vimtastic https://github.com/guyht/vimari

References

https://github.com/whomwah/qlstephen

https://github.com/toland/qlmarkdown