Macbook-setup
Setting up a new Macbook
MacBook Pro (13-inch, 2019, Four Thunderbolt 3 ports)
2.4 GHz Intel Core i5
16 GB 2133 MHz LPDDR3
500 GB
Chrome
Download Chrome, launch it and set as default browser.
Git and SSH keys
Launch the Terminal.
Set up git config:
git config --global user.name "John Doe"
If they aren't already installed you'll be prompted now to install Command Line Tools.
git config --global user.email johndoe@example.com
Confirm:
git config --list
Create SSH key:
ls -al ~/.ssh
# Lists the files in your .ssh directory, if they exist
If none exist:
ssh-keygen -t rsa -b 4096 -C "your_email@example.com"
Show contents of public SSH key to copy to add to web git service:
cat ~/.ssh/id_rsa.pub
Add SSH key to webservice and then clone repo using SSH in the area you want it on your computer (for example create a Version Controlled folder in your home directory):
e.g. with Gitlab
git clone git@gitlab.com:YOURGITUSERNAME/YOURREPO.git
Add public key to any servers you need to access:
ssh-copy-id -i ~/.ssh/id_rsa.pub YOUR_USER_NAME@IP_ADDRESS_OF_THE_SERVER
Homebrew
Install homebrew as a package manager:
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
bash
Default is version 3.2.57(1)-release over 10 years old, update with:
brew install bash
Verify installation (should see install in /usr/local/bin/bash):
which -a bash
Whitelist new shell:
sudo vim /etc/shells and add /usr/local/bin/bash to the file
Set as default shell:
chsh -s /usr/local/bin/bash
Change for root user:
sudo chsh -s /usr/local/bin/bash
Add some aliases to short cut commands, e.g.:
vim .bash_profile
and add:
alias work='ssh YOURUSERNAME@SERVERIPADDRESS'
Vim
Default Vim is version 8.1.1312, update with:
brew install vim
Add alias to ~/.bashrc file so homebrew version loads instead of system version:
alias vim=/usr/local/bin/vim
Then let's install VimPlug:
curl -fLo ~/.vim/autoload/plug.vim --create-dirs \
https://raw.githubusercontent.com/junegunn/vim-plug/master/plug.vim
Then copy .vimrc which I store in a git repository to home folder:
e.g. navigate to folder and then
cp .vimrc ~/
And then install the plug ins from within the .vimrc file in Vim by typing:
:PlugInstall
LaTeX
MacTex 2020 comes with ghostscript 9.5 so this will be fine. Notes below left for posterity but I've since given up on this approach as it was difficult to update individual packages if a new version of LaTeX was released, so instead head to:
https://www.tug.org/mactex/mactex-download.html
and download and install MacTeX.
Using homebrew for the install as otherwise the MacTex installation of ghostscript can conflict with other homebrew packages. (Ghostscript is useful to shrink pdf files.)
brew cask install basictex
Note this is Basic Tex. Then add path to bashrc:
PATH=/usr/local/texlive/2019basic/bin/x86_64-darwin:"${PATH}"
Update tlmgr:
sudo tlmgr update --self
Then add specific LaTeX packages as required with tlmgr, e.g.:
sudo tlmgr install subfiles isodate substr enumitem datatool xfor fp pdfpages csquotes microtype hyphenat xcolor fancyhdr lastpage fira mweights fontaxes wrapfig capt-of mdframed needspace tcolorbox pgf environ trimspaces titlesec titlecaps ifnextok floatrow placeins adjustbox collectbox lcg relsize lineno pgfplots xltxtra float tabulary lipsum marginnote import l3backend l3kernel pagecolor titling footmisc rotating
Ghostscript
This is not needed now as it comes with MacTeX.
I use Ghostscript to shrink PDF files:
brew install ghostscript
Poppler
For PDF tools such as pdftotext:
brew install poppler
Pandoc
To convert document formats:
brew install pandoc
OCRmyPDF
To OCR PDFs example: ocrmypdf -l eng input.pdf output.pdf
brew install ocrmypdf
LaTeX diff
To show diffs in LaTeX:
brew install latexdiff
Rename
For flexible tools to rename file in bash:
brew install rename
Parallel
To use muliple cores in bash:
brew install parallel
XQuartz
Replace X11 with Xquartz to resolve some issues that I ran into with the installation of some R packages.
brew cask install xquartz
Mosh
For more persistent remote terminal access.
brew install mosh
Git Large File Storage
To use git with large files (see https://git-lfs.github.com/)
brew install git-lfs
R and R Studio
Download and install R:
Enter R via the terminal as superuser:
sudo R
Let's install the packages we need in one command:
install.packages(c("ggplot2","tidyverse","knitr","ggthemes","scales","ggmap","plotly","ggfortify","leaflet","leaflet.extras","rgdal","forecast","treemapify","dbscan","survival","googleVis","rmarkdown","flexdashboard","highcharter","devtools","maptools","mapview","treemap","networkD3","visNetwork","DiagrammeR","DT","ggcorrplot","Hmisc","anomalize", "fpp2", "h2o", "sweep", "timetk", "xgboost", "prophet", "survminer","ggwordcloud", "ggsn", "formattable", "IMD", "car", "RSelenium", "netstat", "fuzzyjoin", "this.path"))
This will take a while.
After it complete to enable mapshot to work:
webshot::install_phantomjs()
q() to exit R
Download and install R Studio:
https://rstudio.com/products/rstudio/download/
Google API key for ggmap
register_google(key = "[your key]", write = TRUE)
Python 3 packages
Python 3 will have been installed as a dependancy at some point. Add additional packages using pip3 install
pip3 install pandas numpy matplotlib sklearn quandl xlsx2csv boto3
(xlsx2csv is a useful tool to convert excel files into csv files with for example xlsx2csv -s 0 in.xlsx output)
Now think it is better to install python through brew as ended up with two versions of Python 3 - one 3.7 and one 3.9.
Ended up making sure that python and pip call most up to date versions by:
export PATH=/usr/local/opt/python/libexec/bin:$PATH
See: https://stackoverflow.com/questions/51885394/brew-install-doesnt-link-python3
and installing again:
pip install six
and
pip install openpyxl
and fixing ghostscript by:
sudo chown -R `whoami` /usr/local/share/doc/ghostscript
brew link --overwrite ghostscript
See: https://stackoverflow.com/questions/25695934/ghostscript-not-writable
Java
Necessary for some utilities.
Download and install the runtime environment:
https://www.java.com/en/download/mac_download.jsp
And also the development kit:
https://www.oracle.com/technetwork/java/javase/downloads/jdk13-downloads-5672538.html
datatooltk
Speeds up the handling of data in LaTeX.
Download from:
https://ctan.org/pkg/datatooltk
Install with:
sudo java -jar datatooltk-installer.jar
EPS2PGF
Download from:
https://sourceforge.net/projects/eps2pgf/files/latest/download
Acorn
Nice graphics editor:
Sublime Text
Keynote
Download from App Store.
Microsoft Office
https://account.microsoft.com/services/office/install
Additional Fonts
Fira Sans - download and batch install by unpacking, and selecting all files with Finder and dragging into Font Book:
https://fonts.google.com/specimen/Fira+Sans?selection.family=Fira+Sans
Tex Gyre Heroes - download and batch install by unpacking, and selecting all files with Finder and dragging into Font Book: