Merge branch 'cli' into main

Author: kamurani

README.md

@@ -1,64 +1,84 @@
 # PyBS
 
-
 ## Installation 
 
+#### 1. Install `pybs` 
 `pip install pythonpbs` 
 
-## SSH Configuration 
+#### 2. SSH Configuration 
 
-OpenSSH 
+You will need to add the following to your `~/.ssh/config` file:  
 
+```
+# the host details of your login node:
+Host YOUR_LOGIN_SERVER_ALIAS
+  Hostname YOUR_LOGIN_SERVER_HOSTNAME
+  User YOUR_USERNAME
+```
+
+
+For better ssh performance, you can optionally add the following: 
 ```
 Host *
 	ControlMaster auto
 	ControlPath ~/.ssh/controlmasters/%r@%h:%p
 	ControlPersist yes
 
 ```
-Create directory 
+Then, create directory: 
 ```bash
 mkdir -p ~/.ssh/controlmasters
 ```
+To prevent disconnecting from timeouts, you can also add: 
+```
+# Send keepalive packets to prevent SSH disconnecting...
+Host *
+  ServerAliveInterval 60
+```
+
 
-## VScode
+#### 3. VS code setup
 
-To use the `launch` command, you will need to have `VS code` added to your `$PATH`. 
-#### Using command palette 
+To use the `code` command, you will need to have `VS code` added to your `$PATH`. 
+##### Using command palette 
 
 In VS code, open the **command palette** (`Cmd+Shift+P`), type "shell command",
 and run the `Shell Command: Install 'code' command in PATH` command.
-#### Manually configure the path 
+##### Manually configure the path 
 
-##### Zsh 
+###### Zsh 
 
 ```zsh
 cat << EOF >> ~/.zprofile
 # Add Visual Studio Code (code)
 export PATH="\$PATH:/Applications/Visual Studio Code.app/Contents/Resources/app/bin"
 EOF
 ```
-##### Bash
+###### Bash
 ```bash
 cat << EOF >> ~/.bash_profile
 # Add Visual Studio Code (code)
 export PATH="\$PATH:/Applications/Visual Studio Code.app/Contents/Resources/app/bin"
 EOF
 ```
 Restart your shell to register your changes.  You can check with `which code`.
-### Enable tab completion for Bash, Fish, or Zsh
+
+
+#### 4. Enable tab completions
+
+You can enable CLI tab completion for Bash, Fish, or Zsh. 
 
 
 > After modifying `.rc` files for your shell, you may have to restart the shell to enable completions. 
-#### Zsh
+##### Zsh
 
 ```zsh
 _PYBS_COMPLETE=zsh_source pybs > ~/.zsh/pybs-complete.zsh
 ```
 > NOTE: you may have to add `source ` to your `~/.zshrc` if this does not work.  
 
 
-#### Oh My Zsh 
+##### Oh My Zsh 
 
 ```zsh
 mkdir $ZSH_CUSTOM/plugins/pybs
@@ -72,7 +92,7 @@ plugins(
 	...
 )
 ```
-#### Bash 
+##### Bash 
 ```bash
 _PYBS_COMPLETE=bash_source pybs > ~/.pybs-complete.bash
 ```
@@ -84,3 +104,31 @@ Add the following to your `~/.bashrc`:
 ```fish
 _PYBS_COMPLETE=fish_source pybs > ~/.config/fish/completions/pybs.fish
 ```
+#### 5. Create job script 
+
+To use the `code` command to launch a VS code instance on a compute node, you will need to create a
+PBS-compatible job script with a `sleep infinity` command or similar to prevent early exiting of the
+job script.  
+
+##### Example job script 
+
+```bash
+#! /usr/bin/env bash
+
+#PBS -I 
+#PBS -l select=1:ncpus=6:ngpus=1:mem=46gb
+#PBS -l walltime=4:00:00
+#PBS -M YOUR_EMAIL_ADDRESS
+#PBS -m ae
+#PBS -j oe
+
+sleep infinity
+```
+
+
+Then, you can run `code` as follows: 
+
+```bash
+pybs code YOUR_SERVER_NAME '$HOME/path/to/notebook.ipynb' path/to/job_script.pbs 
+```
+

pybs/console/remote/code.py

@@ -21,6 +21,7 @@
 from pybs.console.tabcomplete import complete_remote_path, complete_hostname, complete_job_script
 from pybs.console.ui import CompactTimeColumn
 
+
 console = Console(
     theme=custom_theme,
     # stderr=True,
@@ -168,9 +169,6 @@ def code(
 
             console.print(syntax)
 
-
-
-
     # Expand path 
     with progress:
         task = progress.add_task(