New Computer Fan Data-Science Set-up Python (Anaconda), R

New Computer Fan Data-Science Set-up

Python (Anaconda), R (Rstudio), Matlab and Latex (Texlive)

Atom, VScode, Pycharm

Go back to fan’s Tex4Econ and Miscellaneous Repository.

1 Objective

Install various compilers and IDE:

1. Python (Anaconda, Pycharm + VSCode + Atom)

2. R (VSCode + Atom)

3. Matlab

4. Latex and PDF (texlive, Okular, VSCode + Atom + Texstudio)

Test at the end:

1. Do sample py ﬁles work?

• work from command line

• work from atom (hydrogen), Pycharm, VSCode

2. Do sample rmd ﬁles work?

• work from r-studio

• work from atom (hydrogen), VSCode

3. Do tex templates compile?

• tikz ﬁles, template ﬁles with bib

• work from texstudio, VSCode live compile, Atom

Installation Plan outline:

1. Conda install (python)

2. Install Atom along with Hydrogen and other packages.

2 Python and Anaconda Installation

Use conda across platforms, so that locally on windows and ubuntu and remotely on aws, can have the same

software setup environment.

• Search for Anaconda Prompt, right click, choose run as administrator.

• Check software versions.

conda list anaconda

python -V

2.1 First Time Conda Install

Download Anaconda Python 3 and install for all users. Afterwards, Anaconda does not automatically get

added to Windows Path. Need to use Anaconda Prompt to access programs. To access Anaconda packages

from windows prompt, from git bash, from R, etc, need to Add Anaconda to Windows Path.

To install conda in Linux/Debian, follow these instructions. Overall, installations are very similar.

In command/anaconda prompt:

# To remove conda Fully

rm -rf ~/anaconda3

where anaconda

# C:/ProgramData/Anaconda3/Scripts/anaconda.exe

where python

# C:/ProgramData/Anaconda3/python.exe

where jupyter

# C:/ProgramData/Anaconda3/Scripts/jupyter.exe

where jupyter-kernelspec

# if R installed already

where r

###############################

# Add these to Windows PATH:

###############################

# C:\ProgramData\Anaconda3\Scripts

# C:\ProgramData\Anaconda3

To Add Anaconda to Path, In Windows 1. Search for: Environment Variables 2. Edit Environment Variables

3. Add new to Path (lower half): - C:/ProgramData/Anaconda3/Scripts/ - C:/ProgramData/Anaconda3/ 4.

Now open up regular windows command Prompt, Type in: - conda –version - also Close and Open up Git

Bash: conda –version

2.2 Conda Update

Open up Anaconda Navigator, it will update navigator automatically. If there are errors, might have to clean

ﬁrst.

There are diﬀerent channels/repositories from which packages could be installed: conda, conda-forge, for

example. Can change where to look for packages ﬁrst. Many packages are in multiple channels. Conda-forge

often have mroe recent packages.

# if there are bugs

# conda clean --packages

# use conda-forge as main channel, more updated packages

conda config --get channels

conda config --add channels conda-forge

conda config --get channels

# remove conda-forge from channels (do so for main env install)

conda config --remove channels conda-forge

# normal update

conda update --all

# install additional packages

# linux utilites

conda install -y m2-base

# stats and graphs

conda install -y statsmodels datashape seaborn

# various

conda install -c conda-forge -y interpolation awscli

# aws communicate

conda install -c anaconda -y boto3

2.3 Python Command Line Test

Fist test python under command line:

# windows

python "C:/Users/fan/PyFan/ProjectSupport/Testing/Numpy/Functions.py"

python "C:/Users/fan/PyFan/ProjectSupport/graph/subplot.py"

# linux

python ~/PyFan/ProjectSupport/Testing/Numpy/Functions.py

python ~/PyFan/ProjectSupport/graph/subplot.py

3 R Installation

R could be installed from Anaconda or directly on windows outside of the Anaconda directories. When

installing from within Anaconda, could create R environment that are isolated from the rest of the computer.

The R environment could be updated and deleted without disturbing dependencies in conda main or the rest

of the computer.

The computer could have multiple R installations. Several in diﬀerent conda R environment, and also several

under windows/linux primary main user R directories. Type which R/where R to see if you open up R from

command line at the moment, which directory’s R will be used. Inside Conda R environment, it will be a

diﬀerent R if there is a diﬀerent R version there.

3.1 Fully Uninstall r

If R was installed in R enviornments, just delete the environment. Otherwise, use system’s uninstaller. Before

that, from terminal/command-prompt, type R, and .libPaths() to ﬁnd paths. Do so inside conda main,

outside of conda main, inside diﬀerent environments, ﬁnd all paths. After uninstaller ﬁnishes, check in the

libPath folders to see if there are still stuﬀ there, delete all, delete the folders.

.libPath()

# C:/Users/fan/Documents/R/win-library/3.6

# C:/Program Files/R/R-3.6.1/library

For Linux and for unsintalling inside conda:

# Exit Conda

conda deactivate

# where is R installed outside of Conda

which R

# /usr/bin/R

# To remove all

sudo apt-get remove r-base

sudo apt-get remove r-base-core

# Inside Conda base

conda activate

# Conda r_env

conda activate r_env

# Where is it installed?

which R

# /home/wangfanbsg75/anaconda3/bin/R

conda uninstall r-base

3.2 Install R (outside of Conda)

Need to install R. Then need to install also an editor/IDE for R. Rstudio is the dominant R IDE. VSCode

and Atom also works well, especially VSCode as editors. Dramatically better experience for writing scripts

outside of Rstudio which feels unwieldy and slow especially compared to VSCode.

Overall plan:

1. download R

•

for debian: Johannes Ranke. For Linux/Debian installation, crucial to update the source.list to

include sources that have more recent versions of R. If not, will get very old R versions that is not

compatible with many packages.

•

add R to path for Windows. In Windows Path, add for example: C:/Program Files/R/R-

3.6.2/bin/x64/ and C:/Rtools/bin

2. download R-studio

3. Open R-studio and auto-detect R

4. Install additional packages (from commandline)

•

various R data-science packages have dependencies, and additional not-R programs might need to

be installed. Install them as needed, for example: libcurl4-openssl-dev and libssl-dev from command

prompt ﬁrst inside Debian.

3.2.1 Linux R Install

For linux/Debian, to Install latest R:

# Go to get latesdebian latest r sources.list

cat /etc/apt/sources.list

# Install this First (should already be installed)

sudo apt install dirmngr

# Debian R is maintained by Johannes Ranke, copied from https://cran.r-project.org/bin/linux/debian/:

apt-key adv --keyserver keys.gnupg.net --recv-key 'E19F5F87128899B192B1A2C2AD5F960A256A04AF'

# Add to source.list, for debian stretch (9)

# sudo su added for security issue as super-user

sudo su -c "sudo echo 'deb http://cloud.r-project.org/bin/linux/debian stretch-cran35/' >> /etc/apt/sources.list"

# if added wrong lines, delete 3rd line

sudo sed '3d' /etc/apt/sources.list

# Update and Install R, should say updated from cloud.r

sudo apt-get update

sudo apt-get install r-base r-base-dev

# Also install these, otherwise r-packages do not install

# libxml2 seems need for tidymodels

sudo apt-get install libcurl4-openssl-dev

sudo apt-get install libssl-dev

sudo apt-get install libxml2-dev

3.2.2 Install Packages for R

From command prompt, enter R by typeing R, and install packages:

# Can enter R from Command Prompt Conda ENV, much faster than from r-studio

# Install R-tools, RTOOLS is for WINDOWS

install.packages("installr")

library("installr")

install.Rtools()

# c:/Rtools/bin;

# c:/Rtools/mingw_32/bin;

# c:/Rtools/mingw_64/bin;

# main packagevps

# tidymodel installation on linux difficult

install.packages(c("tidyverse", "tidymodels", "tidyr"))

# development packages

install.packages(c("devtools", "IRkernel", "pkgdown", "roxygen2", "kableExtra"))

# other packages

install.packages(c("AER", "minpack.lm", "knitr", "matlab"))

# Install my package, need to prepare package to work for ubuntu

# if install does not work, load locally

devtools::install_github("fanwangecon/REconTools")

# Kernel

install.packages(c('repr', 'IRdisplay', 'evaluate', 'crayon', 'pbdZMQ', 'devtools', 'uuid', 'digest'))

IRkernel::installspec()

3.3 Install R (inside Conda)

Key packages are generally available in conda’s default channel (oﬃcial distribution) and also the more

frequently updated conda-forge channel. Prioritize conda-forge to get the latest packages. After adding

conda-forge to channels, that will be prioritized, so when creating a new environment, conda will install

ﬁrst from conda-forge if package exists there. Try the r_env generation line with and without ﬁrst adding

conda-forge to channel, and see that the packages installed will have diﬀerent versions, reﬂecting versions in

the default channel and in the conda-forge channels.

3.3.1 Set up Conda R environment

Create a Conda Environment called r_env, and update its channels.

• Location

: Installed environments are shown appear in the envs folder of C:/ProgramData/Anaconda3/envs/.

Can be easily deleted without disrupting the main base installation for conda. This is very important.

During installation, could easily run into problems, and need to re-install. Much better to only re-install

a folder. Note that when R is installed in envs, it will not show up under add or remove programs for

uninstallation from there, has to be uninstalled, deleted directly here.

• Use only in Env

: Note that if we installed r inside r_env, if we type r under the base environment,

we can not enter r. We can only enter r within r_env. With PATH properly set-up, this happens under

Conda Prompt, Windows Prompt, etc.

• Multiple Pythons

: With the above installation for R, one beneﬁt is that if R requires a diﬀerent

version of Python than what the base environment uses, the r_env could have a diﬀerent python version.

So type python in the base environment as well as inside the r_env. This also means potentially there

could be duplicated installations I think. Look at the python versions under conda list in the base and

in the r-environment.

• File Size

: Note that this creates a large installation folder, C:/ProgramData/Anaconda3/envs/r_env/,

without additional packages, is 1.3 GB in size

# outside of conda, install some depencies

sudo apt-get install libcurl4-openssl-dev

sudo apt-get install libssl-dev

sudo apt-get install libxml2-dev

# install key r packages within a r-environment

conda env remove -n r_env

# start empty environment

conda create -n r_env

# activate env and check, nothing yet

conda activate r_env

conda list

# check channel and add env specific channel

conda config --get channels

# to get latest r, use conda-forge, which has more recent Rs

# conda config --env --add channels conda-forge

# channels for base

conda config --get channels

# channels for cur env

conda config --get channels --env

# see all installed environments

conda env list

# activate an environment to use it, if in base, r does not exist, isolated in r_env

conda activate r_env

# see packages in environment

conda list

# to quit

conda deactivate

3.3.2 Install R and Some Packages in Conda

Either inside a R speciﬁc environment, or outside of it, now do additional installations for R and also R

packages.

During installation, the R programs might require downgrading other programs in the Conda environment

that Python for example also uses. That is why potentially it is safer to install in R environment. However,

when installing in R enviornment, certain packages could have issues if installer does not realize it is in an

environment with special folder structure, so installation could fail.

# install files

conda install -n r_env -c r r r-essentials r-tidyverse r-tidymodels -y

# trouble with igraph installation, install here from conda

# conda install -n r_env r-essentials r-base r-tidyr r-tidyverse r-devtools r-irkernel r-pkgdown r-roxygen2

conda install -n r_env -c r r-igraph

conda install -n r_env -c conda-forge igraph

conda install -n r_env -c r r-rstantools r-rstan r-rstanarm -y

3.4 Install Additional Packages inside the R

These are packages that I use, these should be installed inside the environment. Or they could be installed

later from inside r-studio. Installing inside r-studio is a lot better. tidymodel has installation issues sometimes.

In r_env, type in R, and then install from inside terminal’s R. For conda env, devtools will be installed and

will install packages inside envs/r_env/Lib/R.

# enter into env

# conda activate r_env

# enter R or type in rstudio

# sicne R is only install inside r_env, has to enter rstudio from r_env

# R

# rstudio

# main packagevps

# tidymodel installation on linux difficult

install.packages(c("rstantools", "rstan", "rstanarm"))

install.packages(c("tidyr", "tidyverse", "tidymodels"))

# tidymodels

# development packages

install.packages(c("devtools", "IRkernel", "pkgdown", "roxygen2", "kableExtra"))

# other packages

install.packages(c("AER", "minpack.lm", "knitr", "matlab"))

# Install my package, need to prepare package to work for ubuntu

# if install does not work, load locally

devtools::install_github("fanwangecon/REconTools")

# Kernel

install.packages(c('repr', 'IRdisplay', 'evaluate', 'crayon', 'pbdZMQ', 'devtools', 'uuid', 'digest'))

IRkernel::installspec()

3.5 R-Studio Set-up Download from Rstudio

Download R-studio, and install, as normal (not from conda, directly from rstudio website latest windows

version)

2. Open up anaconda prompt, enter r_env environment: activate r_env

3. cd into rstudio exe ﬁle folder: cd “C:/Program Files/RStudio/bin”

4. start r-studio from inside r_env: rstudio.exe

5. inside r-studio, check: .libPaths()

• “C:/ProgramData/Anaconda3/envs/r_env/Lib/R/library”

activate r_env

cd "C:/Program Files/RStudio/bin"

rstudio.exe

cd "C:/ProgramData/Anaconda3/envs/r_env/Lib/R/library"

"C:/Program Files/RStudio/bin/rstudio.exe"

For linux, note that rstudio oﬀers Ubuntu as well as Debian versions that can be installed with wget:

wget "https://download1.rstudio.org/desktop/bionic/amd64/rstudio-1.2.5033-amd64.deb"

sudo apt install ./rstudio-1.2.5033-amd64.deb

wget "https://download1.rstudio.org/desktop/debian9/x86_64/rstudio-1.2.5033-amd64.deb"

sudo apt install ./rstudio-1.2.5033-amd64.deb

conda install -c r rstudio

cd "C:/Program Files/RStudio/bin"

rstudio.exe

cd "C:/ProgramData/Anaconda3/envs/r_env/Lib/R/library"

"C:/Program Files/RStudio/bin/rstudio.exe"

Is RSTUDIO pointing to the R installation you want? Note you can open Rstudio from diﬀeren conda env

command line, that will use diﬀerent R installations. Or also set:

• export RSTUDIO_WHICH_R=/usr/bin/R

• export RSTUDIO_WHICH_R=/home/wangfanbsg75/anaconda3/bin/R

R-studio theme, VSCode theme for Rstudio works very well:

# admin rights

sudo rstudio --no-sandbox

remotes::install_github("anthonynorth/rscodeio")

rscodeio::install_theme()

3.6 R Tests

Test the following ﬁle to see if we can execute a R ﬁle. Do it inside r_env and inside a r session.

# A simple file with summary statistics using tidyverse

source('C:/Users/fan/R4Econ/summarize/dist/fst_hist_onevar.R')

# Another simple file with summary statistics using tidyverse

source('C:/Users/fan/R4Econ/support/tibble/fs_tib_basics.R')

# A file involving estimation

source('C:/Users/fan/R4Econ/optimization/cesloglin/fst_ces_plan_linlog.R')

# C:/Users/fan/R4Econ/summarize/dist/fst_hist_onevar.Rmd

# C:/Users/fan/R4Econ/support/tibble/fs_tib_basics.Rmd

# C:/Users/fan/R4Econ/optimization/cesloglin/fst_ces_plan_linlog.Rmd

4 Install Latex and PDF

Use a combination of overleaf and local compile. The goal is to have the same installation set-up for windows

as well as linux. And hopefully, locally compilable ﬁle also can be compiled on overleaf (only use packages

also available on overleaf).

There are several pieces of things to install:

1. latex compiler: pdﬂatex, etc

2. tex distributions: MikTex, texlive

• these folders, once various packages are installed, could be very large, many GB

3. latex packages from distributions

4. editor (gui): Atom, Sublime text, texStudio, etc

4.1 Uninstall

• uninstall MiKTeX: delete from programs, then delete remaining folder in Program Files.

• uninstall texlive: go to c:/texlive, delete the folder

4.2 Install

Install on Windows

• Install Texstudio

• Install texlive

Install on Ubuntu

install texlive and texstudio ubuntu/debian.

sudo apt-get update

sudo apt-get install texlive-full

sudo apt-get install texstudio

Test ﬁle compilations in TexStudio.

4.3 SumatraPDF

For windows, install SumatraPDF. Can easily modify colors.

Settings

Kindle Sepia modiﬁcations:

• Background color:

– Kindle Sepia: fbf0d9

– Kindle Sepia Light: ﬀf8e6

• Text color:

– Kindle Sepia: 5f4b32

– Kindle Sepia Darker: 503f2a

– Kindle Sepia Darkerer: 1e170f

FixedPageUI [

TextColor = #1e170f

BackgroundColor = #fff8e6

SelectionColor = #f5fc0c

WindowMargin = 2 4 2 4

PageSpacing = 4 4

]

4.4 Okular PDF

Linux: sudo apt-get install okular Windows: install okular from windows app store

4.4.1 Okular Shortcuts and Features

Settings:

• Background color:

–

background behind pdf: conﬁgure okular, general, use custom backgroun color, Gainsboro gray:

DCDCDC, kindle sepia: FBF0D9

–

pdf background itself: conﬁgure okular, accessbility, change color, change paper color, Light Kindle

Sepia: ﬀf8e6

Features:

• Okular 3 pages per row view: view, overview

•

Automatic Update when PDF updated elsewhere: this is one of the key reasons to use okular, when I

knit a Rmd ﬁle to PDF, the currently open Okular PDF ﬁle automatically updates and does not give

ﬁle is open error like Acrobat.

• Background color:

–

background behind pdf: conﬁgure okular, general, use custom backgroun color, Gainsboro gray:

DCDCDC, kindle sepia: FBF0D9

–

pdf background itself: conﬁgure okular, accessbility, change color, change paper color, Light Kindle

Sepia: ﬀf8e6

Shortcuts:

• Okular conﬁgure shortcuts: setting, conﬁgure shortcuts

• Okular if menu bar lost: Ctrl + m

• Okular comment pane: F6

• Okular close left pane: F7

• Okular full scrren: Ctrl + Shift + F

– unlike acrobat, pdf allows for multiple scrrens

4.5 Adobe PDF

PDF Adobe Acrobat Installation + go to adobe website, log in using fwan[email protected] + go to my account,

choose view and download my apps, choose acrobat & PDF, download Acrobat DC + UH account can only

be activated on two accounts at once, so need to kick other computers out temporarily potentially

5 Install Various Editors

Atom, VSCode, Notepad++, Sublime, etc. These are essential editors that allows for pleasant programming

and writing experiences. See here for fan instructions on vim installations.

All settings here JSON ﬁles here:

• windows: C:/Users/fan/AppData/Roaming/Code/User, can be modiﬁed here directly

5.1 VSCode Installation

VSCode is much more light-weight than Atom, much faster. On Windows, download here. VScode settings

easy to change for various extensions. Very very good Latex Editor, probably the best I have used.

For Linux:

# Debian Install

curl https://packages.microsoft.com/keys/microsoft.asc | gpg --dearmor > microsoft.gpg

sudo install -o root -g root -m 644 microsoft.gpg /usr/share/keyrings/microsoft-archive-keyring.gpg

sudo sh -c 'echo "deb [arch=amd64 signed-by=/usr/share/keyrings/microsoft-archive-keyring.gpg] https://packages.microsoft.com/repos/vscode stable main" > /etc/apt/sources.list.d/vscode.list'

sudo apt-get install apt-transport-https

sudo apt-get update

sudo apt-get install code # or code-insiders

# Change Font (https://wwFw.reddit.com/r/Crostini/comments/cesxr0/vscode_ui_and_fonts_too_small_heres_how_to_fix_it/)

# modify: /usr/share/applications/code.desktop

nvim /usr/share/applications/code.desktop

#replace this line: Exec=/usr/share/code/code --unity-launch %F

Exec=sommelier -X --scale=0.8 --dpi=160 /usr/share/code/code "--unity-launch %F"

#replace this line: Exec=/usr/share/code/code --new-window %F

Exec=sommelier -X --scale=0.8 --dpi=160 /usr/share/code/code "--new-window %F"

# Open File

# low density mode to see cleary

code

5.1.1 VSCode Extensions

Press Ctrl + P, paste the ext install commands below to install extensions. Extensions are in: %USERPRO-

FILE%/.vscode/extensions for windows. Can change code for extension there.

# [Microsoft Python Extension](https://marketplace.visualstudio.com/items?itemName=ms-python.python)

ext install ms-python.python

# [Latex Workshop](https://marketplace.visualstudio.com/items?itemName=James-Yu.latex-workshop)

ext install latex-workshop

# [R](https://marketplace.visualstudio.com/items?itemName=Ikuyadeu.r)

ext install ikuyadeu.r

5.1.2 VSCode Shortcuts and Features

Features:

open a ﬁle, if have workspace where the ﬁle is in, automatically expand tree and show where ﬁle is on

left pane.

Shortcuts :

• see all shortcuts: Ctrl + k, ctrl + s

• Zen model: Ctrl + k, z, this means press control k, then press z

– note that z mode can be adjusted by shiftin the bar on the left

• Open up Settings: Ctrl + ,

• Preview Markdown in VSCode: Ctrl + Shift + v

• Open up left pane: Ctrl + b

• Wrap Text: alt + z, switch between wrap or not to save screen space for example.

• Hide Console Pane (running code): Ctrl + j

personal bindings

• toggle minimap: Ctrl + k, ctrl + z

5.1.3 VSCode and R

VSCode works pretty well it seems with Rmd ﬁles. Rmd ﬁles are useful to work through algorithm, examples

in preparation for writing usable functions. Rstudio has been often very slow for me, and I generally feel like

can not stretch around and work in RStudio IDE.

In Atom, Hydrogen works, but really only works with very basic line by line testing.

Using VSCode with RMD ﬁles seems much quicker, and there is room to breath.

1. Install R following R installation instructions.

2. Then install extension R. Microsoft stopped supporting rmd in VSCode: R Tools for Visual Studio

3. properly set path (might have to call vscode from r env)

• r.rterm.linux: /home/wangfanbsg75/anaconda3/envs/r_env/bin/R

• r.rterm.windows: C:/Program Files/R/R-3.6.2/bin/x64/R.exe

– note R.exe at the end

4. Run:

• ctrl + enter to activate R terminal

• VSCode 2019 allows for Knit Rmd: Ctrl + Shift + K

• also can run code segment: select lines and ctrl + enter

5.1.4 VSCode and Latex

Download Latex Workshop.

Shortcuts

• compile: ctrl + alt + b

• sync: ctrl + alt + j

• live save

Settings

change background border pdf color (not pdf but border): ctrl + shift + x, LatexWorkshop, Set-

tings, Conﬁgure Extension Settings, Search for background, change color name. or enter: latex-

workshop.view.pdf.backgroundColor. use gainsboro gray: #DCDCDC, or lightgray #D3D3D3.

To take advantage of Okular (where background color can be none-white for example). Go

to settings, and: 1. Change: latex-workshop.view.pdf.viewer to external 2. Change: latex-

workshop.view.pdf.external.viewer.command to C:/Program Files/SumatraPDF/SumatraPDF.exe open up

C:/Users/fan/AppData/Roaming/Code/User/settings.json, and copy these in:

"latex-workshop.view.pdf.external.synctex.command": "C:/Program Files/SumatraPDF/SumatraPDF.exe",

"latex-workshop.view.pdf.external.synctex.args": [

"-forward-search",

"%TEX%",

"%LINE%",

"-reuse-instance",

"-inverse-search",

"code \"C:\\Users\\fan\\AppData\\Local\\Programs\\Microsoft VS Code\\resources\\app\\out\\cli.js\" -r -g \"%f:%l\"",

"%PDF%",

]

Features:

1. upon savings, rebuid ﬁle and update pdf (similar to overleaf)

2. hover oﬀers equation preview

Shortcuts:

1. preview: ctrl + alt + v

2. synctex location: ctrl + alt + j

5.1.5 VSCode settings.json

The settings.json ﬁle, %APPDATA%/Code/User/settings.json:

{

"r.rterm.windows": "C:/Program Files/R/R-3.6.2/bin/x64/R.exe",

"window.zoomLevel": 0,

"latex-workshop.view.pdf.viewer": "external",

"latex-workshop.view.pdf.external.synctex.command": "C:/Program Files/SumatraPDF/SumatraPDF.exe",

"latex-workshop.view.pdf.external.synctex.args": [

"-forward-search",

"%TEX%",

"%LINE%",

"-reuse-instance",

"-inverse-search",

"code \"C:\\Users\\fan\\AppData\\Local\\Programs\\Microsoft VS Code\\resources\\app\\out\\cli.js\" -r -g \"%f:%l\"",

"%PDF%",

"latex-workshop.view.pdf.external.viewer.command": "C:/Program Files/SumatraPDF/SumatraPDF.exe"

}

5.2 Atom Installation

Atom is slow but has clean look and nice git/github integration.

5.2.1 Atom Extensions

Terminal in windows or linux after installation: apm install hydrogen. apm is the atom package manager:

# Once atom is installed, can use apm to install packages

apm install hydrogen

# apm install project-manager

# r-related

# for me the best r-syntax highlighter I have found

apm install r-syntax

# latex-related

apm install language-latex

apm install latex

# Selection and Overview

apm install sublime-style-column-selection

apm install minimap

apm install highlight-selected

# vim distraction free editing

apm install vim-mode-plus

apm install ex-mode

apm install zen

# support

apm install date

# Inside Conda open up atom

atom

5.2.2 Atom Shortcuts and Features

Features:

# open multiple projects from atom at the same time, after repos synced

atom ~/fanwangecon.github.io ~/Pyfan ~/Teaching ~/Tex4Econ ~/R4Econ ~/M4Econ ~/Py4Econ

# open up any py from from within, try 1+1, does it work?

# also use script, try ctrl + shift + b, run whole file (not hydrogen)

Shortcuts :

• Git Pane: Ctrl + 9, Ctrl + 8

5.2.3 Atom and Python

Having installed Anaconda, now install Atom and Hydrogen to Test with Python. For both Jupyter as well

as Atom, always open from command prompt, open from Anaconda Prompt with admin rights.

Open up Jupyter Notebook, does the python kernel work? If does not, uninstall and re-install Anaconda.

# start jupyter lab, from prompt

jupyter lab

Try 1+1.

5.2.4 Atom and Latex

Install the following two packages in atom:

1. latex package on atom.

2. language-latex package on atom

In Atom Latex setting, note that on diﬀerent platforms, paths to texlive are diﬀerent:

• Path:

– Windows: C:/texlive/2019/bin/win32

– Chromebook Linux: /usr/bin/latex

• Which PDF viewer to use:

– download Okular and use Okular

# set TeX path

# C:/texlive/2019/bin/win32

# Latex, after installation

# see where texlive appears under root folder directories

sudo find / -name "texlive"

# see latex version, if texlive is used

latex -v

# see main exe directory

which latex

# /usr/bin/latex

5.2.5 Atom settings ﬁle

Atom keymap.cson ﬁle:

'atom-text-editor':

'ctrl-shift-j': 'pretty-json:prettify'

'alt-z':'date:date'

'alt-x':'date:time'

'alt-c':'date:datetime'

'body':

'ctrl-tab': 'pane:show-next-item'

'ctrl-shift-tab': 'pane:show-previous-item'

'.editor':

'ctrl-alt-z': 'atom-beautify:beautify-editor'

'ctrl-shift-r': 'hydrogen:restart-kernel'

'atom-text-editor:not([mini])':

'ctrl-*': 'highlight-selected:select-all'

'atom-text-editor, webview.markdown-preview-plus':

'ctrl-shift-X': 'markdown-preview-plus:toggle-render-latex'

# https://github.com/t9md/atom-vim-mode-plus/issues/130

'atom-text-editor.vim-mode-plus.insert-mode':

'j j': 'vim-mode-plus:activate-normal-mode'

5.3 Other Editors

5.3.1 Notepad++

Notepad++. Many old projects have xml folder structures for Notepad++.

•

Silently update ﬁle changes made in other editors: Settings, Preferences, MISC., File Status Auto

Detection, Update Silently.

5.3.2 Sublime

Sublime

there are some issues with atom. When a ﬁle is edited inside Vim, when changes are saved, a temp ﬁle is

created in atom. Sublime would, however, still show the ﬁle with the changes. This makes dual screen editing

very diﬃcult. Sublime text is used for this situation.

# Sublime Linux

wget -qO - https://download.sublimetext.com/sublimehq-pub.gpg | sudo apt-key add -

sudo apt-get install apt-transport-https

echo "deb https://download.sublimetext.com/ apt/stable/" | sudo tee /etc/apt/sources.list.d/sublime-text.list

sudo apt-get update

sudo apt-get install sublime-text

# launch from terminal

subl

Sublime Setup:

Put sublime path in windows path for example:

C:\Program Files\Sublime Text 3\

• r and rmd setup

5.3.3 PyCharm

pycharmjetbrains.com/pycharm/)

6 Other Programs to Install

6.1 Package Managers

To install packages in windows more easily:

• scoop

# in powershell

# enter cmd

# type powershell in cmd to enter powershell from cmd

powershell

# permission

set-executionpolicy remotesigned -scope currentuser

# install

iwr -useb get.scoop.sh | iex

6.2 Utilities

• 7-zip

• evernote

6.3 Security

• keepass

• Proton VPN: unlimited usage free version available.

• Express VPN