Agenda

1. Python
2. R
3. Git
4. Others

Python

• Install.
  • Install python.
    • From the offical webisite.
    • Use homebrew.
  • Install python packages in terminal.
    • python3 -m pip install pacakge_name
  • Install jupyter notebook in terminal.
    • pip install notebook
  • Check python version in terminal.
    • python3 --version
  • Check python version in python/jupyter notebook.
    • import sys
    • sys.version
• Upgrade.
  • Update python in terminal.
    • conda update python3
• Calling.
  • Call jupyter notebook in terminal.
    • jupyter notebook
  • Call python in terminal.
    • python3

R

• Install.
  • Install R.
    • From CRAN.
  • Install RStudio.
    • From posit.
  • Install packages in R console.
    • install.packages("package_name")
  • Check R version in R console.
    • version
  • Check package status and version in R console.
    • packageStatus()
    • packageVersion("package_name")
• Upgrade.
  • Update R.
    • Reference.
    • Re-download and install R from CRAN.
    • Move all the package folders from your old R version to new R version.
      • Usually they are located at /Library/Frameworks/R.framework/Versions/x.xx/Resources/library
  • Update packages.
    • In R console, update.packages(checkBuilt = TRUE)
    • In RStudio, go to tools -> check for package updates.
• Git setup.
  • Reference.
  • Create a remote on github from the existing project.
    • Given your R project is already using git.
    • Given you use the usethis package AND you have configured a GitHub Personal Access Token (PAT) (see here for how to set it up).
    • In R console, usethis::use_github(host = "https://github.com/"). This will create a remote for your existing local git project.
  • Store git credentials.
    • In R console, gitcreds::gitcreds_set(url = "https://github.com/")
    • Switch between different remotes needs to reset the PAT.
  • Retrieve your credentials.
    • In R console, gitcreds::gitcreds_get(url = "https://github.com/")
• Fix data.table package single thread issue.
  • Reference 1.
  • Reference 2.
  • Reference 3. Recommend to use.
    • Under /Users/username, press cmd+shift+period to see hidden files, then under .R folder (case sensitive), create a Makevars file.
    • Add gcc (option 5) info in Makevars file is working on work computer.
    • Add libomp (option 1) info in Makevars file is working on personal computer.
  • Remove package.
    • In R console, remove.packages("data.table")
  • Install package from the source.
    • In R console.
      • install.packages("data.table", type = "source", repos = "https://Rdatatable.gitlab.io/data.table")
  • Check thread numbers.
    • In R console, data.table::getDTthreads()

Git

• Git setup.
  • In Visual studio code, click explore, then open a folder, this will be the work directory and then you can initiate a git project.
  • In Visual studio code, terminal -> new terminal, to open a command line window.
  • In the terminal, use git config --list to see the configuration.
  • In the terminal, use git init to initialize a project.
  • In the terminal, to staging a specific file: git add FILENAME, to add all files: git add ., to make a commit: git commit -m “commit message”.
• Create a remote.
  • First create a repo in GitHub.
  • Caching credentials. See here.
    • If use gitcreds::gitcreds_set(url = "https://github.com/") in R to update PAT, it seems that macOS keychain will also be updated.
  • Pushing to GitHub.
    • Add a remote, in terminal, run git remote add origin YOUR URL. (make sure to select the https one).
    • Git push, in terminal, run git push -u origin main (first time push), git push --all (push all the branches).

Others

• Markdown syntax.