Virtual Environment Guide

environment/guide.md

+# Enhanced Virtual Environment Guide
+
+Guides for setting up development/research environments on the cluster (Made for Linux)
+
+## General Tips (New Section)
+
+- Always use version control (e.g., Git) alongside virtual environments
+- Document your project setup and dependencies
+- Regularly update your virtual environment and dependencies
+- Be consistent with naming conventions for your projects and environments
+
+## Python
+
+### How to create and use a virtual environment in Python
+
+#### Setup environment
+
+1. Ensure Python is installed:
+   ```
+   python3 --version
+   ```
+   If not installed, use your distribution's package manager to install Python 3.
+
+2. Create directory for project:
+   ```
+   mkdir Project
+   ```
+
+3. Navigate to directory:
+   ```
+   cd Project
+   ```
+
+4. Create a virtual environment:
+   ```
+   python3 -m venv research1
+   ```
+
+5. Ensure the environment is created:
+   ```
+   ls
+   ```
+   It should be listed as a directory in the results of running `ls`:
+   ```
+   research1
+   ```
+
+6. Activate the environment:
+   ```
+   source research1/bin/activate
+   ```
+   Your current line should be prefixed with the environment name:
+   ```
+   (research1) user@super-computer
+   ```
+
+7. Deactivate the environment (when you're done):
+   ```
+   deactivate
+   ```
+
+#### Installing packages
+
+(While virtual environment is activated)
+
+1. Upgrade pip to the latest version:
+   ```
+   pip install --upgrade pip
+   ```
+
+2. List installed packages:
+   ```
+   pip list
+   ```
+
+3. Install new package:
+   ```
+   pip install package_name
+   ```
+   For a specific version: `pip install package_name==1.0.0`
+
+4. List installed packages again to ensure the needed packages are installed:
+   ```
+   pip list
+   ```
+
+#### Saving dependencies
+
+(While virtual environment is activated)
+
+1. Save packages to a file:
+   ```
+   pip freeze > requirements.txt
+   ```
+
+2. Ensure the file was successfully created with package info:
+   ```
+   cat requirements.txt
+   ```
+
+3. Consider separating development and production dependencies:
+   ```
+   pip freeze > requirements-dev.txt
+   ```
+
+#### Using dependencies
+
+1. Install dependencies from requirements file:
+   ```
+   pip install -r requirements.txt
+   ```
+
+2. For development environments:
+   ```
+   pip install -r requirements-dev.txt
+   ```
+
+3. List installed packages to ensure dependencies are installed:
+   ```
+   pip list
+   ```
+
+#### Delete virtual environment
+
+1. Deactivate the environment if it's active:
+   ```
+   deactivate
+   ```
+
+2. Delete directory with virtual environment:
+   ```
+   rm -r research1
+   ```
+
+**Warning:**
+* Do not store source code inside virtual environment directories
+* All source code should be stored in main directory (project in this example)
+* Always use `.gitignore` to exclude the virtual environment directory from version control
+
+
+## R
+
+### How to create and use a virtual environment in R
+
+#### Setup environment
+
+1. Ensure R is installed:
+   ```
+   R --version
+   ```
+
+2. Create directory for project:
+   ```
+   mkdir Project
+   ```
+
+3. Navigate to directory:
+   ```
+   cd /Project
+   ```
+
+4. Create an R project:
+   ```R
+   R
+   > usethis::create_project(".")
+   ```
+
+5. Install renv for virtual environments:
+   ```R
+   > install.packages("renv")
+   ```
+
+6. Initialize renv:
+   ```R
+   > renv::init()
+   ```
+   This creates a project-specific library and .Rprofile
+
+#### Activate an environment
+
+```R
+> renv::activate()
+```
+
+#### Deactivate an environment
+
+```R
+> renv::deactivate()
+```
+
+#### Installing Packages
+
+(While virtual environment is activated)
+
+1. Install a package:
+   ```R
+   > install.packages("package")
+   ```
+
+2. Record the new package in the lockfile:
+   ```R
+   > renv::snapshot()
+   ```
+
+#### Using dependencies
+
+1. Save environment state to lock file:
+   ```R
+   > renv::snapshot()
+   ```
+
+2. Recreate another environment given the lock file:
+   ```R
+   > renv::restore()
+   ```
+
+3. Update all packages in the project:
+   ```R
+   > renv::update()
+   ```
+
+#### Delete virtual environment
+
+1. Exit R if you're in an R session
+
+2. Delete directory with virtual environment:
+   ```
+   rm -r renv
+   ```
+
+3. Remove .Rprofile and renv.lock files:
+   ```
+   rm .Rprofile renv.lock
+   ```
+
+## Julia
+
+### How to create and use a virtual environment in Julia
+
+#### Setup environment
+
+1. Check Julia version:
+   ```
+   julia -version
+   ```
+
+2. Create directory for project:
+   ```
+   mkdir Project
+   ```
+
+3. Navigate to directory:
+   ```
+   cd /Project
+   ```
+
+4. Start Julia and enter package manager mode:
+   ```
+   julia
+   julia> ]
+   ```
+
+5. Create a new environment and activate:
+   ```
+   (@v1.10) pkg> activate .
+   ```
+   This creates a new environment in the current directory.
+
+6. Create Project.toml and Manifest.toml files:
+   ```
+   (@v1.10) pkg> instantiate
+   ```
+
+#### Deactivate environment
+
+```
+(@v1.10) pkg> activate
+```
+
+#### Install packages
+
+(While virtual environment is activated)
+
+1. Install package:
+   ```
+   (@v1.10) pkg> add Package
+   ```
+
+2. Press backspace to exit package manager
+
+3. Ensure the new package is installed:
+   ```julia
+   julia> using Package
+   ```
+
+#### Using dependencies
+
+1. Enter package manager:
+   ```
+   julia> ]
+   ```
+
+2. Install dependencies from .toml files in the project directory:
+   ```
+   (@v1.10) pkg> instantiate
+   ```
+
+3. Update all packages:
+   ```
+   (@v1.10) pkg> update
+   ```
+
+#### Delete virtual environment
+
+Simply delete the Project.toml and Manifest.toml files from your project directory.
+
+## Node JS
+
+### How to create and use a virtual environment in Node JS
+
+#### Setup environment
+
+1. Check node version:
+   ```
+   node -v
+   ```
+
+2. Create directory for project:
+   ```
+   mkdir Project
+   ```
+
+3. Navigate to directory:
+   ```
+   cd /Project
+   ```
+
+4. Initialize the project:
+   ```
+   npm init -y
+   ```
+
+5. Create a .nvmrc file that specifies node version:
+   ```
+   node -v > .nvmrc
+   ```
+
+#### Install packages
+
+1. Install a package and save it to package.json:
+   ```
+   npm install package --save
+   ```
+
+2. Install a development dependency:
+   ```
+   npm install package --save-dev
+   ```
+
+#### Using dependencies
+
+1. Use .nvmrc for node version:
+   ```
+   nvm use
+   ```
+
+2. Install packages from package.json:
+   ```
+   npm install
+   ```
+
+3. Update all packages:
+   ```
+   npm update
+   ```
+
+#### Managing different Node.js versions
+
+1. Install a specific Node.js version:
+   ```
+   nvm install 14.17.0
+   ```
+
+2. Switch to a specific Node.js version:
+   ```
+   nvm use 14.17.0
+   ```
+
+#### Delete virtual environment
+
+In Node.js, the "virtual environment" is essentially your `node_modules` directory and `package.json` file. To remove:
+
+1. Delete the node_modules directory:
+   ```
+   rm -rf node_modules
+   ```
+
+2. Optionally, remove package.json and package-lock.json:
+   ```
+   rm package.json package-lock.json
+   ```
+
+Remember to keep your `package.json` if you want to reinstall your dependencies later.